Bio-ASN1-EntrezGene-1.73000755000765000024 013352317004 14766 5ustar00cjfieldsstaff000000000000Changes100644000765000024 1031413352317004 16361 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73Revision history for Bio-ASN1-Entrezgene 1.73 2018-09-24 21:31:26-05:00 America/Chicago * Fix regex warnings for Perl 5.28. * New module 'Bio::SeqIO::entrezgene' imported from the BioPerl distribution. This means Bio-ASN1-Entrezgene now "Enhances" BioPerl's Bio::SeqIO instead of being a hard dependency of BioPerl. 1.72 2016-09-02 06:49:48-05:00 America/Chicago * Full release (no changes from 1.71 beyond version) 1.71 2016-09-01 22:57:25-05:00 America/Chicago (TRIAL RELEASE) * Minor bump for impending BioPerl 1.7 release. * #2 : 'Unescaped left brace in regex is deprecated' with newer versions of perl fixed [fjossandon] 1.70 2013-09-14 14:39:54 America/Chicago * Bio::ASN1::EntrezGene is now able to parse EntrezGene-set in which case next_seq() will return the next set of sequences with each sequence as an element in the array ref instead of an array ref with a single element. version 1.10: Important update if you see segmentation fault when running the parser - so far I only saw it happen on Perl 5.8 (Perl 5.10 is fine) due to an exceedingly long (and invalid) URL in one Arabidopsis entry. It's due to Perl regex engine core dumps when matching the long string exhausted the stack. I changed the particular regex in EntrezGene.pm and Sequence.pm to solve the issue. The overall parsing runs 2-3% faster after the change. version 1.09: Added parser/indexer for NCBI's ASN.1-formatted sequence files (like Genbank records). Updated test, example scripts and documentation Minor fix on parse_entrez_gene_example.pl Added code to deal with CCDS xref and Hugo symbol (under gene properties! unlike before) in parse_entrez_gene_example.pl Updated parser & indexer file handle code to work with perl version 5.005_03 (previous code since 1.07 only works with 5.6 or higher). Commented out count_records call in testindex.t to allow successful test on 5.005_03-compatible bioperl versions. version 1.08: Split test script into two for better testing Minor change in documentation and test scripts NO change in parser/indexer code! version 1.07: Added indexing capability through a new module Added testing script for make test Added example script for indexing, reorganized examples scripts Fixed a bug in next_seq Reset line number after input_file() or fh() calls Added rawdata(), fh() functions and -file, -fh, fh to new() Updated documentation to reflect all changes version 1.06: integrated code from Util.pm into EntrezGene.pm. changed packaging to Perl standard changed next_seq() default option to 2, so now the call $parser->next_seq() is equivalent to the call $parser->next_seq(2) in version 1.05 updated documentation to reflect all changes version 1.05: added support to parse the NCBI 4/5/2005 download, which inexplicably added a useless space before ',' on all lines, broke some lines into two yet condensed others (brackets) to one line. This unfortunately slows down my parser because I have to use lookahead regexes to fix the parser for this weird new format. I also fixed a minor mistake in error reporting function version 1.04: added attempt at opening large file (2 GB) on Perl that does not support it; added 'file' option to new(); added file name in error reporting message; updated documentation version 1.03: added validating capability such that anything that does not conform to the current NCBI Entrez Gene ASN.1 format would raise error and stops program. Position of the offending data item would be reported. version 1.02: added input_file function that accepts filename input, and next_seq function that returns the next record version 1.01: unescaped double quote escapes in double quoted strings version 1.0: released LICENSE100644000765000024 4420513352317004 16101 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73This software is copyright (c) 2018 by Mingyi Liu, GPC Biotech AG, Altana Research Institute, Stefan Kirov . This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Terms of the Perl programming language system itself a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or b) the "Artistic License" --- The GNU General Public License, Version 1, February 1989 --- This software is Copyright (c) 2018 by Mingyi Liu, GPC Biotech AG, Altana Research Institute, Stefan Kirov . This is free software, licensed under: The GNU General Public License, Version 1, February 1989 GNU GENERAL PUBLIC LICENSE Version 1, February 1989 Copyright (C) 1989 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The license agreements of most software companies try to keep users at the mercy of those companies. 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The End dist.ini100644000765000024 44413352317004 16475 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73name = Bio-ASN1-EntrezGene version = 1.73 author = Mingyi Liu , Stefan Kirov license = Perl_5 copyright_holder = Mingyi Liu, GPC Biotech AG, Altana Research Institute, Stefan Kirov copyright_year = 2018 [@BioPerl] META.yml100644000765000024 2665113352317004 16352 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73--- abstract: 'Regular expression-based Perl Parser for NCBI Entrez Gene.' author: - 'Mingyi Liu , Stefan Kirov ' build_requires: Bio::Root::Test: '0' File::Spec: '0' IO::Handle: '0' IPC::Open3: '0' Test::More: '0' lib: '0' perl: '5.006' configure_requires: ExtUtils::MakeMaker: '0' dynamic_config: 0 generated_by: 'Dist::Zilla version 6.010, CPAN::Meta::Converter version 2.150010' license: perl meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html version: '1.4' name: Bio-ASN1-EntrezGene requires: Bio::Annotation::Comment: '0' Bio::Annotation::DBLink: '0' Bio::Annotation::OntologyTerm: '0' Bio::Annotation::Reference: '0' Bio::Annotation::SimpleValue: '0' Bio::Cluster::SequenceFamily: '0' Bio::Index::AbstractSeq: '0' Bio::Ontology::Term: '0' Bio::Seq: '0' Bio::SeqFeature::Gene::Exon: '0' Bio::SeqFeature::Gene::GeneStructure: '0' Bio::SeqFeature::Gene::Transcript: '0' Bio::SeqFeature::Generic: '0' Bio::SeqIO: '0' Bio::Species: '0' Carp: '0' Data::Dumper: '0' base: '0' parent: '0' strict: '0' utf8: '0' warnings: '0' resources: bugtracker: https://github.com/bioperl/bio-asn1-entrezgene/issues homepage: https://metacpan.org/release/Bio-ASN1-EntrezGene repository: git://github.com/bioperl/bio-asn1-entrezgene.git version: '1.73' x_Dist_Zilla: perl: version: '5.026000' plugins: - 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Changes LICENSE MANIFEST META.json META.yml Makefile.PL README.md dist.ini examples/indexer_test.pl examples/parse_entrez_gene_example.pl examples/parse_sequence_example.pl examples/regex_parser_test.pl lib/Bio/ASN1/EntrezGene.pm lib/Bio/ASN1/EntrezGene/Indexer.pm lib/Bio/ASN1/Sequence.pm lib/Bio/ASN1/Sequence/Indexer.pm lib/Bio/SeqIO/entrezgene.pm t/00-compile.t t/author-eol.t t/author-mojibake.t t/author-no-tabs.t t/author-pod-coverage.t t/author-pod-syntax.t t/data/entrezgene.dat t/data/entrezgene_bug3453.dat t/entrezgene.t t/input.asn t/input1.asn t/seq.asn t/testindexer.t t/testparser.t README.md100644000765000024 300613352317004 16325 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73[![Build Status](https://travis-ci.org/bioperl/Bio-ASN1-EntrezGene.svg?branch=master)](https://travis-ci.org/bioperl/Bio-ASN1-EntrezGene) [![Coverage Status](https://coveralls.io/repos/bioperl/Bio-ASN1-EntrezGene/badge.png?branch=master)](https://coveralls.io/r/bioperl/Bio-ASN1-EntrezGene?branch=master) Bio-ASN1-Entrezgene =================== This distribution includes: 1. XML parser-like parser for the ASN.1-formatted NCBI Entrez Gene files. 2. Indexer for Entrez Gene files. 3. XML parser-like parser for the ASN.1-formatted NCBI Sequence files. 4. Indexer for Sequence files. These modules have quite high performance and error reporting capabilities. Additionally, one could dump the data structure generated from extracted NCBI object records into XML extremely easily using XML::Simple's XMLout(). COPYRIGHT --------- Written by Dr. Mingyi Liu . Copyright (c) 2005 Mingyi Liu, GPC Biotech, Altana Research Institute. This program is free software - you can redistribute it and/or modify it under the same terms as Perl itself. INSTALLATION ------------ Bio::ASN1::EntrezGene package can be installed and tested as follows: dzill test # or dzil test --all dzil install DOCUMENTATION ------------- For documentation, among many other things, please refer to the POD ( plain old documentation) inside the module. It is highly recommended that you check the example scripts out (under the examples directory)! - - - This distribution is part of the [BioPerl](http://www.bioperl.org/) project. t000755000765000024 013352317004 15152 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73seq.asn100755000765000024 2515413352317004 16637 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/tSeq-entry ::= set { class nuc-prot , descr { title "Leishmania major polyadenylate-binding protein 1 (PAB1) gene, complete cds." , source { org { taxname "Leishmania major" , db { { db "taxon" , tag id 5664 } } , orgname { name binomial { genus "Leishmania" , species "major" } , mod { { subtype strain , subname "Friedlin" } } , lineage "Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania" , gcode 1 , mgcode 4 , div "INV" } } , subtype { { subtype chromosome , name "35" } , { subtype other , name "MHOM/IL/81" } } } , create-date std { year 1998 , month 10 , day 17 } , pub { pub { sub { authors { names std { { name name { last "Bates" , first "E" , initials "E.J." } } , { name name { last "Smith" , first "D" , initials "D.F." } } } , affil std { affil "Imperial College of Science, Technology and Medicine" , div "Biochemistry" , city "London" , country "UK" , street "Exhibition Road" , postal-code "SW7 2AZ" } } , medium email , date std { year 1998 , month 9 , day 18 } } } } , pub { pub { gen { cit "Unpublished" , authors { names std { { name name { last "Bates" , first "E" , initials "E.J." } } , { name name { last "Smith" , first "D" , initials "D.F." } } } } , title "Cloning and characterisation of a Leishmania major poly A-binding protein" } } } , pub { pub { sub { authors { names std { { name name { last "Bates" , first "E" , initials "E.J." } } , { name name { last "Smith" , first "D" , initials "D.F." } } } , affil std { affil "Imperial College of Science, Technology and Medicine" , div "Biochemistry" , city "London" , country "UK" , street "Exhibition Road" , postal-code 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genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "19" } } } , gene { locus "A1BG" , desc "alpha-1-B glycoprotein" , maploc "19q13.4" , db { { db "MIM" , tag id 138670 } } , syn { "A1B" , "ABG" , "GAB" , "HYST2477" , "DKFZp686F0970" } , locus-tag "HGNC:5" } , prot { name { "alpha 1B-glycoprotein" , "alpha-1B-glycoprotein" } } , summary "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins." , location { { display-str "19q13.4" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 1 , src-str2 "1" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000019" , version 8 , seqs { int { from 63548355 , to 63556668 , strand minus , id gi 42406306 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 63548355 , to 63550206 , strand minus , id gi 42406306 } , int { from 63550530 , to 63550817 , strand minus , id gi 42406306 } , int { from 63553547 , to 63553828 , strand minus , id gi 42406306 } , int { from 63554568 , to 63554864 , strand minus , id gi 42406306 } , int { from 63555460 , to 63555732 , strand minus , id gi 42406306 } , int { from 63556105 , to 63556374 , strand minus , id gi 42406306 } , int { from 63556469 , to 63556504 , strand minus , id gi 42406306 } , int { from 63556581 , to 63556668 , strand minus , id gi 42406306 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 63550199 , to 63550206 , strand minus , id gi 42406306 } , { from 63550530 , to 63550817 , strand minus , id gi 42406306 } , { from 63553547 , to 63553828 , strand minus , id gi 42406306 } , { from 63554568 , to 63554864 , strand minus , id gi 42406306 } , { from 63555460 , to 63555732 , strand minus , id gi 42406306 } , { from 63556105 , to 63556374 , strand minus , id gi 42406306 } , { from 63556469 , to 63556504 , strand minus , id gi 42406306 } , { from 63556581 , to 63556614 , strand minus , id gi 42406306 } } } , seqs { whole gi 21071030 } } } } } } , { type genomic , heading "Reference" , accession "NT_011109" , version 15 , seqs { int { from 31124733 , to 31133046 , strand minus , id gi 29800594 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 31124733 , to 31126584 , strand minus , id gi 29800594 } , int { from 31126908 , to 31127195 , strand minus , id gi 29800594 } , int { from 31129925 , to 31130206 , strand minus , id gi 29800594 } , int { from 31130946 , to 31131242 , strand minus , id gi 29800594 } , int { from 31131838 , to 31132110 , strand minus , id gi 29800594 } , int { from 31132483 , to 31132752 , strand minus , id gi 29800594 } , int { from 31132847 , to 31132882 , strand minus , id gi 29800594 } , int { from 31132959 , to 31133046 , strand minus , id gi 29800594 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 31126577 , to 31126584 , strand minus , id gi 29800594 } , { from 31126908 , to 31127195 , strand minus , id gi 29800594 } , { from 31129925 , to 31130206 , strand minus , id gi 29800594 } , { from 31130946 , to 31131242 , strand minus , id gi 29800594 } , { from 31131838 , to 31132110 , strand minus , id gi 29800594 } , { from 31132483 , to 31132752 , strand minus , id gi 29800594 } , { from 31132847 , to 31132882 , strand minus , id gi 29800594 } , { from 31132959 , to 31132992 , strand minus , id gi 29800594 } } } , seqs { whole gi 21071030 } } } } } } , { type genomic , heading "Reference" , accession "NT_086907" , version 1 , seqs { int { from 8163589 , to 8172398 , strand minus , id gi 51475048 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 8163589 , to 8165440 , strand minus , id gi 51475048 } , int { from 8165763 , to 8166050 , strand minus , id gi 51475048 } , int { from 8169274 , to 8169555 , strand minus , id gi 51475048 } , int { from 8170297 , to 8170593 , strand minus , id gi 51475048 } , int { from 8171190 , to 8171462 , strand minus , id gi 51475048 } , int { from 8171835 , to 8172104 , strand minus , id gi 51475048 } , int { from 8172199 , to 8172234 , strand minus , id gi 51475048 } , int { from 8172311 , to 8172398 , strand minus , id gi 51475048 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 8165433 , to 8165440 , strand minus , id gi 51475048 } , { from 8165763 , to 8166050 , strand minus , id gi 51475048 } , { from 8169274 , to 8169555 , strand minus , id gi 51475048 } , { from 8170297 , to 8170593 , strand minus , id gi 51475048 } , { from 8171190 , to 8171462 , strand minus , id gi 51475048 } , { from 8171835 , to 8172104 , strand minus , id gi 51475048 } , { from 8172199 , to 8172234 , strand minus , id gi 51475048 } , { from 8172311 , to 8172344 , strand minus , id gi 51475048 } } } , seqs { whole gi 21071030 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A1BG" , version 0 } , { type property , label "Official Full Name" , text "alpha-1-B glycoprotein" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 3458201 } , source { { src { db "GO" , tag id 5554 } , anchor "molecular_function unknown" , post-text "evidence: ND" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 4 } , anchor "biological_process unknown" , post-text "evidence: ND" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 3458201 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: IDA" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 11167 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=19& MAPS=genes-r-org/rat-chr/human%3A19,genes-r-org/mouse-chr/human%3A19,genes-r-o rg/human-chr19&query=e%3A1[id]+AND+gene[obj_type]&QSTR=a1bg&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 5 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15461460 , pmid 15221005 , pmid 14702039 , pmid 12477932 , pmid 8889549 , pmid 3458201 , pmid 2591067 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 89991 } , anchor "SHGC-67307" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH80032" , version 0 } , { type other , label "Alternate name" , text "RH86145" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 152074 } , anchor "D11S2921" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "GDB:461809" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 155756 } , anchor "D10S16" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "D10S23" , version 0 } , { type other , label "Alternate name" , text "GDB:193809" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_130786" , version 2 , source { { src { db "Nucleotide" , tag id 21071029 } , anchor "NM_130786" } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Product" , accession "NP_570602" , version 2 , source { { src { db "Protein" , tag id 21071030 } , anchor "NP_570602" , post-text "alpha 1B-glycoprotein" } } , seqs { whole gi 21071030 } , comment { { type other , heading "Consensus CDS (CCDS)" , version 0 , source { { src { db "CCDS" , tag str "CCDS12976.1" } , anchor "CCDS12976.1" } } } , { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 21071030 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 365 } , anchor "smart00408: IGc2; Immunoglobulin C-2 Type" } } , comment { { type other , text "Location: 223 - 282 Blast Score: 103" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AF414429,AK055885,AK056201" } , anchor "AF414429,AK055885,AK056201" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC010642" , version 5 , source { { src { db "Nucleotide" , tag id 9929687 } , anchor "AC010642" } } , seqs { int { from 41119 , to 43581 , strand plus , id gi 9929687 } } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AB073611" , version 1 , source { { src { db "Nucleotide" , tag id 51555784 } , anchor "AB073611" } } , seqs { whole gi 51555784 } , products { { type peptide , accession "BAD38648" , version 1 , source { { src { db "Protein" , tag id 51555785 } , anchor "BAD38648" } } , seqs { whole gi 51555785 } } } } , { type mRNA , heading "mRNA" , accession "AF414429" , version 1 , source { { src { db "Nucleotide" , tag id 15778555 } , anchor "AF414429" } } , seqs { whole gi 15778555 } , products { { type peptide , accession "AAL07469" , version 1 , source { { src { db "Protein" , tag id 15778556 } , anchor "AAL07469" } } , seqs { whole gi 15778556 } } } } , { type mRNA , heading "mRNA" , accession "AK055885" , version 1 , source { { src { db "Nucleotide" , tag id 16550723 } , anchor "AK055885" } } , seqs { whole gi 16550723 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK056201" , version 1 , source { { src { db "Nucleotide" , tag id 16551539 } , anchor "AK056201" } } , seqs { whole gi 16551539 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC035719" , version 1 , source { { src { db "Nucleotide" , tag id 23273475 } , anchor "BC035719" } } , seqs { whole gi 23273475 } , products { { type peptide , accession "AAH35719" , version 1 , source { { src { db "Protein" , tag id 23273476 } , anchor "AAH35719" } } , seqs { whole gi 23273476 } } } } , { type mRNA , heading "mRNA" , accession "BX537419" , version 1 , source { { src { db "Nucleotide" , tag id 31873339 } , anchor "BX537419" } } , seqs { whole gi 31873339 } , products { { type peptide , accession "CAD97661" , version 1 , source { { src { db "Protein" , tag id 31873340 } , anchor "CAD97661" } } , seqs { whole gi 31873340 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P04217" , version 0 , source { { src { db "Protein" , tag id 46577680 } , anchor "P04217" } } , seqs { whole gi 46577680 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "1" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_011109.15&gene=A1BG&lid=1&from=31124734&to=31133047" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "1" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_011109.15&gene=A1BG&lid=1" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.529161" } } , source { { src { db "UniGene" , tag str "Hs.529161" } , anchor "Hs.529161" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=52 9161" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "138670" } , anchor "138670" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "1" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 1[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 1 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=1" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:119638" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AK055 885" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= AK055885" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC035719" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC035719" } } } } } , { type generif , text "A1BG-cysteine-rich secretory protein 3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3" , version 0 , refs { pmid 15461460 } , create-date str "Nov 6 2004 10:01AM" , update-date str "Nov 6 2004 3:27PM" } } , unique-keys { { db "LocusID" , tag id 1 } , { db "MIM" , tag id 138670 } } , xtra-index-terms { "LOC1" } } Entrezgene ::= { track-info { geneid 2 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 3 , hour 13 , minute 27 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "12" } } } , gene { locus "A2M" , desc "alpha-2-macroglobulin" , maploc "12p13.3-p12.3" , db { { db "MIM" , tag id 103950 } } , syn { "FWP007" , "S863-7" , "DKFZp779B086" } , locus-tag "HGNC:7" } , prot { name { "alpha-2-macroglobulin" } } , summary "Alpha-2-macroglobulin is a protease inhibitor and cytokine transporter. It inhibits many proteases, including trypsin, thrombin and collagenase. A2M is implicated in Alzheimer disease (AD) due to its ability to mediate the clearance and degradation of A-beta, the major component of beta-amyloid deposits." , location { { display-str "12p13.3-p12.3" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 2 , src-str2 "2" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000012" , version 9 , seqs { int { from 9111576 , to 9159755 , strand minus , id gi 51511728 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 9111576 , to 9111701 , strand minus , id gi 51511728 } , int { from 9112045 , to 9112086 , strand minus , id gi 51511728 } , int { from 9112602 , to 9112704 , strand minus , id gi 51511728 } , int { from 9113607 , to 9113675 , strand minus , id gi 51511728 } , int { from 9114350 , to 9114440 , strand minus , id gi 51511728 } , int { from 9116221 , to 9116348 , strand minus , id gi 51511728 } , int { from 9116515 , to 9116733 , strand minus , id gi 51511728 } , int { from 9118422 , to 9118645 , strand minus , id gi 51511728 } , int { from 9120618 , to 9120798 , strand minus , id gi 51511728 } , int { from 9121208 , to 9121282 , strand minus , id gi 51511728 } , int { from 9121563 , to 9121719 , strand minus , id gi 51511728 } , int { from 9123106 , to 9123193 , strand minus , id gi 51511728 } , int { from 9123501 , to 9123677 , strand minus , id gi 51511728 } , int { from 9123956 , to 9124039 , strand minus , id gi 51511728 } , int { from 9133062 , to 9133113 , strand minus , id gi 51511728 } , int { from 9133764 , to 9133885 , strand minus , id gi 51511728 } , int { from 9134218 , to 9134344 , strand minus , id gi 51511728 } , int { from 9135063 , to 9135291 , strand minus , id gi 51511728 } , int { from 9137327 , to 9137441 , strand minus , id gi 51511728 } , int { from 9138835 , to 9138946 , strand minus , id gi 51511728 } , int { from 9139401 , to 9139562 , strand minus , id gi 51511728 } , int { from 9142469 , to 9142618 , strand minus , id gi 51511728 } , int { from 9143243 , to 9143385 , strand minus , id gi 51511728 } , int { from 9145006 , to 9145069 , strand minus , id gi 51511728 } , int { from 9145309 , to 9145536 , strand minus , id gi 51511728 } , int { from 9148101 , to 9148262 , strand minus , id gi 51511728 } , int { from 9150098 , to 9150207 , strand minus , id gi 51511728 } , int { from 9150353 , to 9150467 , strand minus , id gi 51511728 } , int { from 9151386 , to 9151506 , strand minus , id gi 51511728 } , int { from 9153183 , to 9153267 , strand minus , id gi 51511728 } , int { from 9153729 , to 9153897 , strand minus , id gi 51511728 } , int { from 9154176 , to 9154196 , strand minus , id gi 51511728 } , int { from 9156021 , to 9156073 , strand minus , id gi 51511728 } , int { from 9156239 , to 9156398 , strand minus , id gi 51511728 } , int { from 9157222 , to 9157405 , strand minus , id gi 51511728 } , int { from 9159626 , to 9159755 , strand minus , id gi 51511728 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 9111685 , to 9111701 , strand minus , id gi 51511728 } , { from 9112045 , to 9112086 , strand minus , id gi 51511728 } , { from 9112602 , to 9112704 , strand minus , id gi 51511728 } , { from 9113607 , to 9113675 , strand minus , id gi 51511728 } , { from 9114350 , to 9114440 , strand minus , id gi 51511728 } , { from 9116221 , to 9116348 , strand minus , id gi 51511728 } , { from 9116515 , to 9116733 , strand minus , id gi 51511728 } , { from 9118422 , to 9118645 , strand minus , id gi 51511728 } , { from 9120618 , to 9120798 , strand minus , id gi 51511728 } , { from 9121208 , to 9121282 , strand minus , id gi 51511728 } , { from 9121563 , to 9121719 , strand minus , id gi 51511728 } , { from 9123106 , to 9123193 , strand minus , id gi 51511728 } , { from 9123501 , to 9123677 , strand minus , id gi 51511728 } , { from 9123956 , to 9124039 , strand minus , id gi 51511728 } , { from 9133062 , to 9133113 , strand minus , id gi 51511728 } , { from 9133764 , to 9133885 , strand minus , id gi 51511728 } , { from 9134218 , to 9134344 , strand minus , id gi 51511728 } , { from 9135063 , to 9135291 , strand minus , id gi 51511728 } , { from 9137327 , to 9137441 , strand minus , id gi 51511728 } , { from 9138835 , to 9138946 , strand minus , id gi 51511728 } , { from 9139401 , to 9139562 , strand minus , id gi 51511728 } , { from 9142469 , to 9142618 , strand minus , id gi 51511728 } , { from 9143243 , to 9143385 , strand minus , id gi 51511728 } , { from 9145006 , to 9145069 , strand minus , id gi 51511728 } , { from 9145309 , to 9145536 , strand minus , id gi 51511728 } , { from 9148101 , to 9148262 , strand minus , id gi 51511728 } , { from 9150098 , to 9150207 , strand minus , id gi 51511728 } , { from 9150353 , to 9150467 , strand minus , id gi 51511728 } , { from 9151386 , to 9151506 , strand minus , id gi 51511728 } , { from 9153183 , to 9153267 , strand minus , id gi 51511728 } , { from 9153729 , to 9153897 , strand minus , id gi 51511728 } , { from 9154176 , to 9154196 , strand minus , id gi 51511728 } , { from 9156021 , to 9156073 , strand minus , id gi 51511728 } , { from 9156239 , to 9156398 , strand minus , id gi 51511728 } , { from 9157222 , to 9157405 , strand minus , id gi 51511728 } , { from 9159626 , to 9159711 , strand minus , id gi 51511728 } } } , seqs { whole gi 4557225 } } } } } } , { type genomic , heading "Reference" , accession "NT_009714" , version 16 , seqs { int { from 1979283 , to 2027462 , strand minus , id gi 37543832 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 1979283 , to 1979408 , strand minus , id gi 37543832 } , int { from 1979752 , to 1979793 , strand minus , id gi 37543832 } , int { from 1980309 , to 1980411 , strand minus , id gi 37543832 } , int { from 1981314 , to 1981382 , strand minus , id gi 37543832 } , int { from 1982057 , to 1982147 , strand minus , id gi 37543832 } , int { from 1983928 , to 1984055 , strand minus , id gi 37543832 } , int { from 1984222 , to 1984440 , strand minus , id gi 37543832 } , int { from 1986129 , to 1986352 , strand minus , id gi 37543832 } , int { from 1988325 , to 1988505 , strand minus , id gi 37543832 } , int { from 1988915 , to 1988989 , strand minus , id gi 37543832 } , int { from 1989270 , to 1989426 , strand minus , id gi 37543832 } , int { from 1990813 , to 1990900 , strand minus , id gi 37543832 } , int { from 1991208 , to 1991384 , strand minus , id gi 37543832 } , int { from 1991663 , to 1991746 , strand minus , id gi 37543832 } , int { from 2000769 , to 2000820 , strand minus , id gi 37543832 } , int { from 2001471 , to 2001592 , strand minus , id gi 37543832 } , int { from 2001925 , to 2002051 , strand minus , id gi 37543832 } , int { from 2002770 , to 2002998 , strand minus , id gi 37543832 } , int { from 2005034 , to 2005148 , strand minus , id gi 37543832 } , int { from 2006542 , to 2006653 , strand minus , id gi 37543832 } , int { from 2007108 , to 2007269 , strand minus , id gi 37543832 } , int { from 2010176 , to 2010325 , strand minus , id gi 37543832 } , int { from 2010950 , to 2011092 , strand minus , id gi 37543832 } , int { from 2012713 , to 2012776 , strand minus , id gi 37543832 } , int { from 2013016 , to 2013243 , strand minus , id gi 37543832 } , int { from 2015808 , to 2015969 , strand minus , id gi 37543832 } , int { from 2017805 , to 2017914 , strand minus , id gi 37543832 } , int { from 2018060 , to 2018174 , strand minus , id gi 37543832 } , int { from 2019093 , to 2019213 , strand minus , id gi 37543832 } , int { from 2020890 , to 2020974 , strand minus , id gi 37543832 } , int { from 2021436 , to 2021604 , strand minus , id gi 37543832 } , int { from 2021883 , to 2021903 , strand minus , id gi 37543832 } , int { from 2023728 , to 2023780 , strand minus , id gi 37543832 } , int { from 2023946 , to 2024105 , strand minus , id gi 37543832 } , int { from 2024929 , to 2025112 , strand minus , id gi 37543832 } , int { from 2027333 , to 2027462 , strand minus , id gi 37543832 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 1979392 , to 1979408 , strand minus , id gi 37543832 } , { from 1979752 , to 1979793 , strand minus , id gi 37543832 } , { from 1980309 , to 1980411 , strand minus , id gi 37543832 } , { from 1981314 , to 1981382 , strand minus , id gi 37543832 } , { from 1982057 , to 1982147 , strand minus , id gi 37543832 } , { from 1983928 , to 1984055 , strand minus , id gi 37543832 } , { from 1984222 , to 1984440 , strand minus , id gi 37543832 } , { from 1986129 , to 1986352 , strand minus , id gi 37543832 } , { from 1988325 , to 1988505 , strand minus , id gi 37543832 } , { from 1988915 , to 1988989 , strand minus , id gi 37543832 } , { from 1989270 , to 1989426 , strand minus , id gi 37543832 } , { from 1990813 , to 1990900 , strand minus , id gi 37543832 } , { from 1991208 , to 1991384 , strand minus , id gi 37543832 } , { from 1991663 , to 1991746 , strand minus , id gi 37543832 } , { from 2000769 , to 2000820 , strand minus , id gi 37543832 } , { from 2001471 , to 2001592 , strand minus , id gi 37543832 } , { from 2001925 , to 2002051 , strand minus , id gi 37543832 } , { from 2002770 , to 2002998 , strand minus , id gi 37543832 } , { from 2005034 , to 2005148 , strand minus , id gi 37543832 } , { from 2006542 , to 2006653 , strand minus , id gi 37543832 } , { from 2007108 , to 2007269 , strand minus , id gi 37543832 } , { from 2010176 , to 2010325 , strand minus , id gi 37543832 } , { from 2010950 , to 2011092 , strand minus , id gi 37543832 } , { from 2012713 , to 2012776 , strand minus , id gi 37543832 } , { from 2013016 , to 2013243 , strand minus , id gi 37543832 } , { from 2015808 , to 2015969 , strand minus , id gi 37543832 } , { from 2017805 , to 2017914 , strand minus , id gi 37543832 } , { from 2018060 , to 2018174 , strand minus , id gi 37543832 } , { from 2019093 , to 2019213 , strand minus , id gi 37543832 } , { from 2020890 , to 2020974 , strand minus , id gi 37543832 } , { from 2021436 , to 2021604 , strand minus , id gi 37543832 } , { from 2021883 , to 2021903 , strand minus , id gi 37543832 } , { from 2023728 , to 2023780 , strand minus , id gi 37543832 } , { from 2023946 , to 2024105 , strand minus , id gi 37543832 } , { from 2024929 , to 2025112 , strand minus , id gi 37543832 } , { from 2027333 , to 2027418 , strand minus , id gi 37543832 } } } , seqs { whole gi 4557225 } } } } } } , { type genomic , heading "Reference" , accession "NT_086792" , version 1 , seqs { int { from 4173171 , to 4221277 , strand minus , id gi 51471135 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 4173171 , to 4173296 , strand minus , id gi 51471135 } , int { from 4173640 , to 4173681 , strand minus , id gi 51471135 } , int { from 4174197 , to 4174299 , strand minus , id gi 51471135 } , int { from 4175201 , to 4175269 , strand minus , id gi 51471135 } , int { from 4175944 , to 4176034 , strand minus , id gi 51471135 } , int { from 4177816 , to 4177943 , strand minus , id gi 51471135 } , int { from 4178110 , to 4178328 , strand minus , id gi 51471135 } , int { from 4180017 , to 4180240 , strand minus , id gi 51471135 } , int { from 4182213 , to 4182393 , strand minus , id gi 51471135 } , int { from 4182803 , to 4182877 , strand minus , id gi 51471135 } , int { from 4183158 , to 4183314 , strand minus , id gi 51471135 } , int { from 4184702 , to 4184789 , strand minus , id gi 51471135 } , int { from 4185097 , to 4185273 , strand minus , id gi 51471135 } , int { from 4185552 , to 4185635 , strand minus , id gi 51471135 } , int { from 4194661 , to 4194712 , strand minus , id gi 51471135 } , int { from 4195363 , to 4195484 , strand minus , id gi 51471135 } , int { from 4195817 , to 4195943 , strand minus , id gi 51471135 } , int { from 4196662 , to 4196890 , strand minus , id gi 51471135 } , int { from 4198926 , to 4199040 , strand minus , id gi 51471135 } , int { from 4200364 , to 4200475 , strand minus , id gi 51471135 } , int { from 4200930 , to 4201091 , strand minus , id gi 51471135 } , int { from 4203997 , to 4204146 , strand minus , id gi 51471135 } , int { from 4204771 , to 4204913 , strand minus , id gi 51471135 } , int { from 4206534 , to 4206597 , strand minus , id gi 51471135 } , int { from 4206837 , to 4207064 , strand minus , id gi 51471135 } , int { from 4209629 , to 4209790 , strand minus , id gi 51471135 } , int { from 4211627 , to 4211736 , strand minus , id gi 51471135 } , int { from 4211882 , to 4211996 , strand minus , id gi 51471135 } , int { from 4212916 , to 4213036 , strand minus , id gi 51471135 } , int { from 4214705 , to 4214789 , strand minus , id gi 51471135 } , int { from 4215251 , to 4215419 , strand minus , id gi 51471135 } , int { from 4215698 , to 4215718 , strand minus , id gi 51471135 } , int { from 4217543 , to 4217595 , strand minus , id gi 51471135 } , int { from 4217761 , to 4217920 , strand minus , id gi 51471135 } , int { from 4218744 , to 4218927 , strand minus , id gi 51471135 } , int { from 4221148 , to 4221277 , strand minus , id gi 51471135 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 4173280 , to 4173296 , strand minus , id gi 51471135 } , { from 4173640 , to 4173681 , strand minus , id gi 51471135 } , { from 4174197 , to 4174299 , strand minus , id gi 51471135 } , { from 4175201 , to 4175269 , strand minus , id gi 51471135 } , { from 4175944 , to 4176034 , strand minus , id gi 51471135 } , { from 4177816 , to 4177943 , strand minus , id gi 51471135 } , { from 4178110 , to 4178328 , strand minus , id gi 51471135 } , { from 4180017 , to 4180240 , strand minus , id gi 51471135 } , { from 4182213 , to 4182393 , strand minus , id gi 51471135 } , { from 4182803 , to 4182877 , strand minus , id gi 51471135 } , { from 4183158 , to 4183314 , strand minus , id gi 51471135 } , { from 4184702 , to 4184789 , strand minus , id gi 51471135 } , { from 4185097 , to 4185273 , strand minus , id gi 51471135 } , { from 4185552 , to 4185635 , strand minus , id gi 51471135 } , { from 4194661 , to 4194712 , strand minus , id gi 51471135 } , { from 4195363 , to 4195484 , strand minus , id gi 51471135 } , { from 4195817 , to 4195943 , strand minus , id gi 51471135 } , { from 4196662 , to 4196890 , strand minus , id gi 51471135 } , { from 4198926 , to 4199040 , strand minus , id gi 51471135 } , { from 4200364 , to 4200475 , strand minus , id gi 51471135 } , { from 4200930 , to 4201091 , strand minus , id gi 51471135 } , { from 4203997 , to 4204146 , strand minus , id gi 51471135 } , { from 4204771 , to 4204913 , strand minus , id gi 51471135 } , { from 4206534 , to 4206597 , strand minus , id gi 51471135 } , { from 4206837 , to 4207064 , strand minus , id gi 51471135 } , { from 4209629 , to 4209790 , strand minus , id gi 51471135 } , { from 4211627 , to 4211736 , strand minus , id gi 51471135 } , { from 4211882 , to 4211996 , strand minus , id gi 51471135 } , { from 4212916 , to 4213036 , strand minus , id gi 51471135 } , { from 4214705 , to 4214789 , strand minus , id gi 51471135 } , { from 4215251 , to 4215419 , strand minus , id gi 51471135 } , { from 4215698 , to 4215718 , strand minus , id gi 51471135 } , { from 4217543 , to 4217595 , strand minus , id gi 51471135 } , { from 4217761 , to 4217920 , strand minus , id gi 51471135 } , { from 4218744 , to 4218927 , strand minus , id gi 51471135 } , { from 4221148 , to 4221233 , strand minus , id gi 51471135 } } } , seqs { whole gi 4557225 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A2M" , version 0 } , { type property , label "Official Full Name" , text "alpha-2-macroglobulin" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 11435418 } , source { { src { db "GO" , tag id 19899 } , anchor "enzyme binding" , post-text "evidence: IPI" } } } , { type comment , version 0 , refs { pmid 9714181 } , source { { src { db "GO" , tag id 19966 } , anchor "interleukin-1 binding" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 10880251 } , source { { src { db "GO" , tag id 19959 } , anchor "interleukin-8 binding" , post-text "evidence: IPI" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 8320 } , anchor "protein carrier activity" , post-text "evidence: NR" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 4867 } , anchor "serine-type endopeptidase inhibitor activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 9714181 } , source { { src { db "GO" , tag id 43120 } , anchor "tumor necrosis factor binding" , post-text "evidence: IDA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 17114 } , anchor "wide-spectrum protease inhibitor activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 6886 } , anchor "intracellular protein transport" , post-text "evidence: NR" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 51260 } , anchor "protein homooligomerization" , post-text "evidence: NAS" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 14718574 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: NAS" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 37248 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=12& MAPS=genes-r-org/rat-chr/human%3A12,genes-r-org/mouse-chr/human%3A12,genes-r-o rg/human-chr12&query=e%3A2[id]+AND+gene[obj_type]&QSTR=a2m&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 7 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15511627 , pmid 15023809 , pmid 14760718 , pmid 14718574 , pmid 14715656 , pmid 14678766 , pmid 14675603 , pmid 14637088 , pmid 14506912 , pmid 12966032 , pmid 12755687 , pmid 12755614 , pmid 12631277 , pmid 12477932 , pmid 12221172 , pmid 12175343 , pmid 12062545 , pmid 12042276 , pmid 12015318 , pmid 11916201 , pmid 11910179 , pmid 11901360 , pmid 11823454 , pmid 11811950 , pmid 11435418 , pmid 11100124 , pmid 10880251 , pmid 9714181 , pmid 2581245 , pmid 2408344 , pmid 1707161 , pmid 1370808 , pmid 1281457 } } , { type comment , heading "Phenotypes" , version 0 , comment { { type phenotype , text "Alzheimer disease, susceptibility to" , version 0 , source { { src { db "MIM" , tag id 103950 } , anchor "MIM: 103950" } } } , { type phenotype , text "Emphysema due to alpha-2-macroglobulin deficiency" , version 0 , source { { src { db "MIM" , tag id 103950 } , anchor "MIM: 103950" } } } } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 25036 } , anchor "RH1601" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH44109" , version 0 } , { type other , label "Alternate name" , text "stSG1293" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 40245 } , anchor "SGC31674" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "EST130345" , version 0 } , { type other , label "Alternate name" , text "RH52474" , version 0 } , { type other , label "Alternate name" , text "WI-219" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 46849 } , anchor "RH11157" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH44108" , version 0 } , { type other , label "Alternate name" , text "stSG1290R" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 95143 } , anchor "G44356" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "WIAF-1430-STS" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 147540 } , anchor "NoName" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 151442 } , anchor "NoName" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_000014" , version 3 , source { { src { db "Nucleotide" , tag id 6226959 } , anchor "NM_000014" } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Product" , accession "NP_000005" , version 1 , source { { src { db "Protein" , tag id 4557225 } , anchor "NP_000005" , post-text "alpha-2-macroglobulin precursor" } } , seqs { whole gi 4557225 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 4557225 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5952 } , anchor "pfam00207: A2M; Alpha-2-macroglobulin family" } } , comment { { type other , text "Location: 725 - 1463 Blast Score: 2329" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 25832 } , anchor "pfam01835: A2M_N; Alpha-2-macroglobulin family N-terminal region" } } , comment { { type other , text "Location: 21 - 628 Blast Score: 1960" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "M11313" } , anchor "M11313" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AF349032" , version 1 , source { { src { db "Nucleotide" , tag id 13661813 } , anchor "AF349032" } } , seqs { whole gi 13661813 } , products { { type peptide , accession "AAK38109" , version 1 , source { { src { db "Protein" , tag id 13661814 } , anchor "AAK38109" } } , seqs { whole gi 13661814 } } } } , { type genomic , heading "Genomic" , accession "AF349033" , version 1 , source { { src { db "Nucleotide" , tag id 13661815 } , anchor "AF349033" } } , seqs { whole gi 13661815 } , products { { type peptide , accession "AAK38110" , version 1 , source { { src { db "Protein" , tag id 13661816 } , anchor "AAK38110" } } , seqs { whole gi 13661816 } } } } , { type genomic , heading "Genomic" , accession "X68728" , version 1 , source { { src { db "Nucleotide" , tag id 450521 } , anchor "X68728" } } , seqs { whole gi 450521 } , products { { type peptide , accession "CAA48670" , version 1 , source { { src { db "Protein" , tag id 825615 } , anchor "CAA48670" } } , seqs { whole gi 825615 } } } } , { type genomic , heading "Genomic" , accession "Z11711" , version 1 , source { { src { db "Nucleotide" , tag id 24760 } , anchor "Z11711" } } , seqs { whole gi 24760 } , products { { type peptide , accession "CAA77774" , version 1 , source { { src { db "Protein" , tag id 24761 } , anchor "CAA77774" } } , seqs { whole gi 24761 } } } } , { type mRNA , heading "mRNA" , accession "AB209614" , version 1 , source { { src { db "Nucleotide" , tag id 62088807 } , anchor "AB209614" } } , seqs { whole gi 62088807 } , products { { type peptide , accession "BAD92851" , version 1 , source { { src { db "Protein" , tag id 62088808 } , anchor "BAD92851" } } , seqs { whole gi 62088808 } } } } , { type mRNA , heading "mRNA" , accession "AF109189" , version 1 , source { { src { db "Nucleotide" , tag id 33337723 } , anchor "AF109189" } } , seqs { whole gi 33337723 } , products { { type peptide , accession "AAQ13498" , version 1 , source { { src { db "Protein" , tag id 33337724 } , anchor "AAQ13498" } } , seqs { whole gi 33337724 } } } } , { type mRNA , heading "mRNA" , accession "AY591530" , version 1 , source { { src { db "Nucleotide" , tag id 46812314 } , anchor "AY591530" } } , seqs { whole gi 46812314 } , products { { type peptide , accession "AAT02228" , version 1 , source { { src { db "Protein" , tag id 46812315 } , anchor "AAT02228" } } , seqs { whole gi 46812315 } } } } , { type mRNA , heading "mRNA" , accession "BC026246" , version 1 , source { { src { db "Nucleotide" , tag id 45708660 } , anchor "BC026246" } } , seqs { whole gi 45708660 } , products { { type peptide , accession "AAH26246" , version 1 , source { { src { db "Protein" , tag id 45708661 } , anchor "AAH26246" } } , seqs { whole gi 45708661 } } } } , { type mRNA , heading "mRNA" , accession "BC040071" , version 1 , source { { src { db "Nucleotide" , tag id 25303945 } , anchor "BC040071" } } , seqs { whole gi 25303945 } , products { { type peptide , accession "AAH40071" , version 1 , source { { src { db "Protein" , tag id 25303946 } , anchor "AAH40071" } } , seqs { whole gi 25303946 } } } } , { type mRNA , heading "mRNA" , accession "BX647329" , version 1 , source { { src { db "Nucleotide" , tag id 34366357 } , anchor "BX647329" } } , seqs { whole gi 34366357 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "CR749334" , version 1 , source { { src { db "Nucleotide" , tag id 51476395 } , anchor "CR749334" } } , seqs { whole gi 51476395 } , products { { type peptide , accession "CAH18188" , version 1 , source { { src { db "Protein" , tag id 51476396 } , anchor "CAH18188" } } , seqs { whole gi 51476396 } } } } , { type mRNA , heading "mRNA" , accession "M11313" , version 1 , source { { src { db "Nucleotide" , tag id 177869 } , anchor "M11313" } } , seqs { whole gi 177869 } , products { { type peptide , accession "AAA51551" , version 1 , source { { src { db "Protein" , tag id 177870 } , anchor "AAA51551" } } , seqs { whole gi 177870 } } } } , { type mRNA , heading "mRNA" , accession "M36501" , version 1 , source { { src { db "Nucleotide" , tag id 177871 } , anchor "M36501" } } , seqs { whole gi 177871 } , products { { type peptide , accession "AAA51552" , version 1 , source { { src { db "Protein" , tag id 177872 } , anchor "AAA51552" } } , seqs { whole gi 177872 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P01023" , version 0 , source { { src { db "Protein" , tag id 112911 } , anchor "P01023" } } , seqs { whole gi 112911 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "2" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_009714.16&gene=A2M&lid=2&from=1979284&to=2027463" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "2" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_009714.16&gene=A2M&lid=2" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.212838" } } , source { { src { db "UniGene" , tag str "Hs.212838" } , anchor "Hs.212838" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=21 2838" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "103950" } , anchor "103950" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "2" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 2[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 2 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=2" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:119639" } } } } , { type comment , version 0 , source { { src { db "HGMD" , tag str "" } , url "http://www.uwcm.ac.uk/uwcm/mg/search/119639.html" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=CR749 334" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= CR749334" } } } , { type comment , version 0 , source { { src { db "KEGG" , tag str "" } , url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:2" } } } , { type comment , text "PharmGKB" , version 0 , source { { src { db "PharmGKB" , tag str "PA24357" } , anchor "PA24357" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC040071" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC040071" } } } } } , { type comment , heading "Pathways" , version 0 , comment { { type comment , text "KEGG pathway: Alzheimer's disease" , version 0 , source { { src { db "05010" , tag str "05010" } , anchor "05010" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+2" } } } , { type comment , text "KEGG pathway: Coagulation cascade" , version 0 , source { { src { db "04610" , tag str "04610" } , anchor "04610" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } , { type comment , text "KEGG pathway: Complement and coagulation cascades" , version 0 , source { { src { db "04610" , tag str "04610" } , anchor "04610" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } , { type comment , text "Reactome: Hemostasis" , version 0 , source { { anchor "49292" , url "http://www.reactome.org/cgi-bin/link?SOURCE=UniProt&ID=P010 23" } } } } } , { type generif , text "an important involvement of alpha2M in regulation of increased proteolytic activity occurring in multiple sclerosis disease" , version 0 , refs { pmid 15511627 } , create-date str "Dec 18 2004 10:01AM" , update-date str "Dec 18 2004 1:19PM" } , { type generif , text "alpha2-macroglobulin inhibits human pepsin and gastricsin" , version 0 , refs { pmid 14506912 } , create-date str "Oct 7 2003 12:00AM" , update-date str "Jul 7 2004 1:36PM" } , { type generif , text "There is a significant genetic association of the 5 bp deletion and two novel polymorphisms in alpha-2-macroglobulin alpha-2-macroglobulin precursor with AD" , version 0 , refs { pmid 12966032 } , create-date str "Jun 27 2004 5:41PM" , update-date str "Jun 27 2004 6:18PM" } , { type generif , text "Alpha2-macroglobulin is a substrate and an endogenous inhibitor for ADAMTS-4 and ADAMTS-5" , version 0 , refs { pmid 14715656 } , create-date str "Jun 14 2004 4:41PM" , update-date str "Jun 14 2004 5:44PM" } , { type generif , text "A2M-D allele played a weak Alzheimer disease protective role, and APOE-E4 and A2M-G alleles might act synergistically in Alzheimer disease risk for mainland Han Chinese." , version 0 , refs { pmid 14675603 } , create-date str "Feb 17 2004 12:00AM" , update-date str "Apr 13 2004 1:35PM" } , { type generif , text "Plasma from patients homozygous for the intronic deletion (DD) showed normal alpha(2)M subunit size, conformation, and proteinase inhibitory activity. Plasma alpha(2)M from two DD patients showed markedly increased TGF-beta1 binding." , version 0 , refs { pmid 14678766 } , create-date str "Jan 20 2004 12:00AM" , update-date str "Mar 7 2004 7:01AM" } , { type generif , text "The presence of MPO-G/G and A2M-Val/Val genotypes synergistically increased the risk of AD (OR, 25.5; 95% CI, 4.65-139.75)." , version 0 , refs { pmid 15023809 } , create-date str "Mar 25 2004 12:00AM" , update-date str "Apr 18 2004 7:02AM" } , { type generif , text "alpha2-M deletion polymorphism is probably not associated with functional deficiencies important in Alzheimer's disease pathology" , version 0 , refs { pmid 14637088 } , create-date str "Dec 31 2003 12:00AM" , update-date str "Jan 11 2004 7:02AM" } , { type generif , text "FGF-2 and this protein interact at specific binding sites, involving different FGF-2 sequences." , version 0 , refs { pmid 12755687 } , create-date str "Sep 7 2003 12:00AM" , update-date str "Sep 28 2003 7:01AM" } , { type generif , text "alpha(2)M-derived peptides target the receptor-binding sequence in TGF-beta" , version 0 , refs { pmid 12755614 } , create-date str "Jun 25 2003 12:00AM" , update-date str "Jul 6 2003 7:01AM" } , { type generif , text "These results suggest the possible involvement of cathepsin E in disruption of the structural and functional integrity of alpha 2-macroglobulin in the endolysosome system." , version 0 , refs { pmid 12631277 } , create-date str "May 8 2003 12:00AM" , update-date str "May 11 2003 7:01AM" } , { type generif , text "Alpha 2-macroglobulin enhances prothrombin activation and thrombin potential by inhibiting the anticoagulant protein C/protein S system in cord and adult plasma." , version 0 , refs { pmid 12062545 } , create-date str "Feb 6 2003 12:00AM" , update-date str "Aug 17 2003 7:01AM" } , { type generif , text "relationship between serum VEGF levels, alpha(2)M levels and the development of OHSS in hyperstimulated subjects undergoing IVF" , version 0 , refs { pmid 12042276 } , create-date str "Dec 16 2002 12:00AM" , update-date str "Feb 2 2003 7:00AM" } , { type generif , text "Genetic association of alpha2-macroglobulin polymorphisms with Alzheimer's disease" , version 0 , refs { pmid 12221172 } , create-date str "Sep 27 2002 12:00AM" , update-date str "Oct 7 2002 8:10AM" } , { type generif , text "Genetic association of argyrophilic grain disease with polymorphisms in alpha-2 macroglobulin." , version 0 , refs { pmid 12175343 } , create-date str "Sep 24 2002 12:00AM" , update-date str "Oct 7 2002 8:10AM" } , { type generif , text "The three-dimensional structure of the dimer reveals its structural organization in the tetrameric native and chymotrypsin alpha 2-macroglobulin complexes." , version 0 , refs { pmid 12015318 } , create-date str "Sep 5 2002 12:00AM" , update-date str "Sep 23 2002 6:27AM" } , { type generif , text "has an important role in the AD-specific neurodegenerative process but its exon 24 Val-1000-Ile polymorphism is not likely to be associated with late-onset sporadic AD in the Hungarian population" , version 0 , refs { pmid 11901360 } , create-date str "Aug 6 2002 12:00AM" , update-date str "Aug 28 2002 6:15PM" } , { type generif , text "REVIEW: binds and neutralizes alfimeprase, which has direct proteolytic activity against the fibrinogen Aalpha chain" , version 0 , refs { pmid 11910179 } , create-date str "Jun 12 2002 12:00AM" , update-date str "Sep 7 2003 7:01AM" } , { type generif , text "distinct binding sites mediate interaction with beta-amyloid peptide and growth factors" , version 0 , refs { pmid 11823454 } , create-date str "May 4 2002 12:00AM" , update-date str "May 18 2002 6:08AM" } , { type generif , text "Differential binding to ldl receptor related protein" , version 0 , refs { pmid 11811950 } , create-date str "Feb 14 2002 12:00AM" , update-date str "Mar 4 2002 7:46AM" } , { type generif , heading "HIV-1 protein interactions" , version 0 , comment { { type generif , text "Binding of HIV-1 Tat to LRP inhibits neuronal binding, uptake and degradation of physiological ligands for LRP, including alpha2-macroglobulin, apolipoprotein E4, amyloid precursor and amyloid beta-protein" , version 0 , refs { pmid 11100124 } , comment { { type comment , label "Tat" , accession "NP_057853" , version 1 , source { { src { db "GeneID" , tag id 155871 } } } } , { type comment , accession "NP_000005" , version 1 } } , create-date str "May 11 2004 12:48PM" , update-date str "May 11 2004 1:10PM" } } } } , unique-keys { { db "LocusID" , tag id 2 } , { db "MIM" , tag id 103950 } } , xtra-index-terms { "LOC2" } , xtra-properties { { tag "PROP" , value "phenotype" } } } Makefile.PL100644000765000024 504213352317004 17022 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.010. use strict; use warnings; use 5.006; use ExtUtils::MakeMaker; my %WriteMakefileArgs = ( "ABSTRACT" => "Regular expression-based Perl Parser for NCBI Entrez Gene.", "AUTHOR" => "Mingyi Liu , Stefan Kirov ", "CONFIGURE_REQUIRES" => { "ExtUtils::MakeMaker" => 0 }, "DISTNAME" => "Bio-ASN1-EntrezGene", "LICENSE" => "perl", "MIN_PERL_VERSION" => "5.006", "NAME" => "Bio::ASN1::EntrezGene", "PREREQ_PM" => { "Bio::Annotation::Comment" => 0, "Bio::Annotation::DBLink" => 0, "Bio::Annotation::OntologyTerm" => 0, "Bio::Annotation::Reference" => 0, "Bio::Annotation::SimpleValue" => 0, "Bio::Cluster::SequenceFamily" => 0, "Bio::Index::AbstractSeq" => 0, "Bio::Ontology::Term" => 0, "Bio::Seq" => 0, "Bio::SeqFeature::Gene::Exon" => 0, "Bio::SeqFeature::Gene::GeneStructure" => 0, "Bio::SeqFeature::Gene::Transcript" => 0, "Bio::SeqFeature::Generic" => 0, "Bio::SeqIO" => 0, "Bio::Species" => 0, "Carp" => 0, "Data::Dumper" => 0, "base" => 0, "parent" => 0, "strict" => 0, "utf8" => 0, "warnings" => 0 }, "TEST_REQUIRES" => { "Bio::Root::Test" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "lib" => 0 }, "VERSION" => "1.73", "test" => { "TESTS" => "t/*.t" } ); my %FallbackPrereqs = ( "Bio::Annotation::Comment" => 0, "Bio::Annotation::DBLink" => 0, "Bio::Annotation::OntologyTerm" => 0, "Bio::Annotation::Reference" => 0, "Bio::Annotation::SimpleValue" => 0, "Bio::Cluster::SequenceFamily" => 0, "Bio::Index::AbstractSeq" => 0, "Bio::Ontology::Term" => 0, "Bio::Root::Test" => 0, "Bio::Seq" => 0, "Bio::SeqFeature::Gene::Exon" => 0, "Bio::SeqFeature::Gene::GeneStructure" => 0, "Bio::SeqFeature::Gene::Transcript" => 0, "Bio::SeqFeature::Generic" => 0, "Bio::SeqIO" => 0, "Bio::Species" => 0, "Carp" => 0, "Data::Dumper" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "base" => 0, "lib" => 0, "parent" => 0, "strict" => 0, "utf8" => 0, "warnings" => 0 ); unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) { delete $WriteMakefileArgs{TEST_REQUIRES}; delete $WriteMakefileArgs{BUILD_REQUIRES}; $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs; } delete $WriteMakefileArgs{CONFIGURE_REQUIRES} unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; WriteMakefile(%WriteMakefileArgs); input1.asn100755000765000024 2034413352317004 17263 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/tEntrezgene ::= { track-info { geneid 3 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type pseudo , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "12" } } } , gene { locus "A2MP" , desc "alpha-2-macroglobulin pseudogene" , maploc "12p13.3-p12.3" , locus-tag "HGNC:8" } , location { { display-str "12p13.3-p12.3" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 3 , src-str2 "3" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000012" , version 9 , seqs { int { from 9275468 , to 9278174 , strand minus , id gi 51511728 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NT_009714" , version 16 , seqs { int { from 2143175 , to 2145881 , strand minus , id gi 37543832 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NT_086792" , version 1 , seqs { int { from 4337316 , to 4340022 , strand minus , id gi 51471135 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NG_001067" , version 1 , seqs { int { from 176 , to 2880 , strand plus , id gi 20270626 , fuzz-from lim lt , fuzz-to lim gt } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A2MP" , version 0 } , { type property , label "Official Full Name" , text "alpha-2-macroglobulin pseudogene" , version 0 } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 8 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 2478422 } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , comment { { type genomic , heading "Reference" , accession "NG_001067" , version 1 , source { { src { db "Nucleotide" , tag id 20270626 } , anchor "NG_001067" } } , seqs { int { from 1 , to 3003 , strand plus , id gi 20270626 } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "M24415" , version 1 , source { { src { db "Nucleotide" , tag id 187575 } , anchor "M24415" } } , seqs { int { from 177 , to 2881 , strand plus , id gi 187575 } } , products { { type peptide , text "None" , version 0 } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "3" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_009714.16&gene=A2MP&lid=3&from=2143176&to=2145882" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "3" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_009714.16&gene=A2MP&lid=3" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 3 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=3" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:128103" } } } } } } } , unique-keys { { db "LocusID" , tag id 3 } } , xtra-index-terms { "LOC3" } } Entrezgene ::= { track-info { geneid 4 , status discontinued , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "1" } } } , gene { desc "adenovirus-12 chromosome modification site 1C" , maploc "1q42-q43" , syn { "A12M1" } } , prot { name { "adenovirus-12 chromosome modification site 1C" , "Adenovirus-12 chromosome modification site-1q1" } } , location { { display-str "1q42-q43" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 4 , src-str2 "4" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , comments { { type comment , heading "RefSeq Status" , label "WITHDRAWN" , version 0 } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118950" } } } } } } } , unique-keys { { db "LocusID" , tag id 4 } } , xtra-index-terms { "LOC4" } } entrezgene.t100644000765000024 4504413352317004 17674 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 1427, -requires_module => 'Bio::ASN1::EntrezGene'); use_ok('Bio::SeqIO::entrezgene'); } my @species=('Homo sapiens','Mus musculus', 'Caenorhabditis elegans'); my @pubmed=qw(15461460 15221005 14702039 12477932 8889549 3610142 3458201 2591067); my %pmed=(1=>8, 2=>55, 3=>1, 4=>0, 5=>0, 6=>0, 7=>0, 8=>1, 9=>32, 10=>58, 11=>1, 12=>76, 13=>7, 14=>5, 15=>13, 9996=>0, 11286=>0, 11287=>5, 11288=>0, 11289=>0, 11293=>0, 11294=>0, 11295=>0, 11296=>0, 11297=>0, 11298=>3, 11299=>0, 11300=>0, 11301=>0, 11302=>9, 11303=>54, 11304=>11, 11305=>3, 11306=>9, 171590=>0, 171591=>0, 171592=>0, 171593=>0, 171594=>0); my %asym=(1=>['A1B', 'ABG', 'GAB', 'HYST2477', 'DKFZp686F0970'], 2=>['FWP007','S863-7','DKFZp779B086'], 4=>['A12M1'], 5=>['A12M2'],6=>['A12M3'],7=>['A12M4'], 9=>['AAC1'],10=>['AAC2'],11=>['NATP'], 12=>['ACT','AACT','MGC88254'],13=>['DAC'],15=>['SNAT','AA-NAT'], 14=>[''], 11287=>['A1m','A2m','MAM'], 11298=>['Nat4','SNAT','Nat-2'], 11302=>['AATYK','mKIAA0641'],11303=>['Abc1'], 11304=>['RmP','Abcr','Abc10','D430003I15Rik'], 11305=>['Abc2','mKIAA1062','D2H0S1474E'], 11306=>['Abc7'], 171590=>['Y74C9A.3','CELK05052'], 171591=>['Y74C9A.2','CELK01753'], 171592=>['Y74C9A.4a','Y74C9A.4b','CELK08126'], 171593=>['Y74C9A.5','CELK09643'], 171594=>['Y48G1C.4','CELK05819']); my @ids=qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 9996 11286 11287 11288 11289 11293 11294 11295 11296 11297 11298 11299 11300 11301 11302 11303 11304 11305 11306 171590 171591 171592 171593 171594); my @loop_counts = ([1,1,1,1,5,1,12,1,1,1,14,8,16], [1,1,1,1,3,1,40,1,1,1,14,31], [1,1,1,1,0,1,4,1,10,5], [1,1,0,1,1,1,1,7,0], [1,1,0,1,1,1,1,7,0], [1,1,0,1,1,1,1,7,0], [1,1,0,1,1,1,1,7,0], [1,0,1,1,0,1,4,1,1,1,13,0], [1,1,1,1,1,1,33,1,1,1,14,41], [1,1,1,1,1,1,51,1,1,1,14,51], [1,0,1,1,1,1,1,1,10,1], [1,1,1,1,3,1,28,1,1,1,14,33], [1,1,1,1,1,1,17,1,1,1,14,10], [1,1,1,1,0,1,11,1,1,1,13,20], [1,1,1,1,2,1,16,1,1,1,14,23], [1,0,0,0,0,0,0,2,0], [1,0,0,0,0,0,0,3,0], [1,1,1,1,3,1,10,1,13,10], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,2,0], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,2,0], [1,0,0,0,0,0,0,2,0], [1,1,1,1,3,1,9,1,13,5,16], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,3,0], [1,0,0,0,0,0,0,2,0], [1,1,1,1,2,1,10,1,12,19], [1,1,1,1,1,1,50,1,13,14], [1,1,1,1,4,1,9,1,13,12], [1,1,1,1,3,1,9,1,13,8,8], [1,1,1,1,1,1,11,1,13,12], [1,1,0,1,2,0,0,1,1,1,1,9,4], [1,1,0,1,2,0,0,1,1,1,1,9,4], [1,1,0,1,3,0,0,1,1,1,1,9,8], [1,1,0,1,2,0,0,1,1,1,1,9,4], [1,1,0,1,2,0,0,1,1,1,1,9,4]); my $fs='!'; my @revkeys=('Entrez Gene Status','RefSeq status','Official Full Name','chromosome','cyto','Reference','dblink', 'ALIAS_SYMBOL','OntologyTerm','Index terms','Official Symbol','cM','Property'); ok my $eio=Bio::SeqIO->new(-file=>test_input_file('entrezgene.dat'), -format=>'entrezgene', -debug=>'on',-service_record=>'yes'); my ($seq,$struct,$uncapt); my $num_of_seqs = 0; while (1) { my $seq; ($seq,$struct,$uncapt)=$eio->next_seq; last unless ($seq); my @lc = @{$loop_counts[$num_of_seqs]}; $num_of_seqs++; #T0: GENERAL TESTS ok $seq; is ref($struct),'Bio::Cluster::SequenceFamily'; my $acc=$seq->accession_number; #T1: ORGANISM my $org=$seq->species->binomial; is grep(/\b$org\b/,@species),1; #T2: SUMMARY test ok $seq->desc if ($acc eq '1')||($acc eq '2')||($acc eq '11304'); ok !defined $seq->desc if ($acc eq '171592')||($acc eq '11306'); #Are we supposed to have this in our test? ok grep(/\b$acc\b/,@ids); my $ann=$seq->annotation(); my $tcount; #T3: ENTREZGENE STATUS TESTS my @egstatus=$ann->get_Annotations('Entrez Gene Status'); my $loop_count = 0; foreach my $status (@egstatus) { $loop_count++; STATUS: { if ($acc==1) {is $status->value,'live'; last STATUS;} if ($acc==2) {is $status->value,'live'; last STATUS;} if ($acc==4) {is $status->value,'discontinued'; last STATUS;} if ($acc==6) {is $status->value,'discontinued'; last STATUS;} if ($acc==11288) {is $status->value,'secondary'; last STATUS;} if ($acc==11293) {is $status->value,'secondary'; last STATUS;} if ($acc==171594) {is $status->value,'live'; last STATUS;} } } is $loop_count, shift @lc, "correct number of loops for T3"; $loop_count = 0; #T4: REFSEQ STATUS TESTS my @refstatus=$ann->get_Annotations('RefSeq status'); foreach my $status (@refstatus) { $loop_count++; STATUS: { if ($acc==1) {is $status->value,'REVIEWED'; last STATUS;} if ($acc==2) {is $status->value,'REVIEWED'; last STATUS;} if ($acc==3) {is $status->value,'PROVISIONAL'; last STATUS;} if ($acc==4) {is $status->value,'WITHDRAWN'; last STATUS;} if ($acc==9) {is $status->value,'VALIDATED'; last STATUS;} if ($acc==11300) {is $status->value,''; last STATUS;} if ($acc==11306) {is $status->value,'MODEL'; last STATUS;} if ($acc==11293) {is $status->value,'secondary'; last STATUS;} if ($acc==171594) {is $status->value,'Reviewed'; last STATUS;} } } is $loop_count, shift @lc, "correct number of loops for T4"; $loop_count = 0; #T5: GENE NAME TESTS my @ofname=$ann->get_Annotations('Official Full Name'); foreach my $name (@ofname) { $loop_count++; STATUS: { if ($acc==10) {is $name->value,'N-acetyltransferase 2 (arylamine N-acetyltransferase)'; last STATUS;} if ($acc==13) {is $name->value,'arylacetamide deacetylase (esterase)'; last STATUS;} if ($acc==14) {is $name->value,'angio-associated, migratory cell protein'; last STATUS;} if ($acc==11287) {is $name->value,'pregnancy zone protein'; last STATUS;} if ($acc==11298) {is $name->value,'arylalkylamine N-acetyltransferase'; last STATUS;} if ($acc==11304) {is $name->value,'ATP-binding cassette, sub-family A (ABC1), member 4'; last STATUS;} if ($acc==11306) {is $name->value,'ATP-binding cassette, sub-family B (MDR/TAP), member 7'; last STATUS;} } } is $loop_count, shift @lc, "correct number of loops for T5"; $loop_count = 0; #T6: CHROMOSOME TESTS my @chr=$ann->get_Annotations('chromosome'); foreach my $chr (@chr) { $loop_count++; STATUS: { if ($acc==5) {is $chr->value,1; last STATUS;} if ($acc==6) {is $chr->value,1; last STATUS;} if ($acc==7) {is $chr->value,17; last STATUS;} if ($acc==11306) {is $chr->value,'X'; last STATUS;} if ($acc==11304) {is $chr->value,3; last STATUS;} if ($acc==171590) {is $chr->value,'I'; last STATUS;} if ($acc==171592) {is $chr->value,'I'; last STATUS;} } } is $loop_count, shift @lc, "correct number of loops for T6"; $loop_count = 0; #T7: GENE SYMBOL ALIAS TESTS my @sym=$ann->get_Annotations('ALIAS_SYMBOL'); foreach my $sym (@sym) { $loop_count++; my $val = $sym->display_text; next if (($val eq '')||!defined($val)); is grep(/\b$val\b/,@{$asym{$acc}}),1; } is $loop_count, shift @lc, "correct number of loops for T7"; $loop_count = 0; #T8: CYTO LOCATION TESTS my @map=$ann->get_Annotations('cyto'); foreach my $map (@map) { $loop_count++; STATUS: { if ($acc==10) {is $map->value,'8p22'; last STATUS;} if ($acc==11) {is $map->value,'8p22'; last STATUS;} if ($acc==13) {is $map->value,'3q21.3-q25.2'; last STATUS;} if ($acc==11306) {is $map->value,'X C-D'; last STATUS;} if ($acc==11305) {is $map->value,'2 A2-B'; last STATUS;} if ($acc==11304) {is $map->value,'3 G1'; last STATUS;} if ($acc==11303) {is $map->value,'4 A5-B3'; last STATUS;} } } is $loop_count, shift @lc, "correct number of loops for T8"; $loop_count = 0; #T9: REFERENCE NUMBER TEST my @refs=$ann->get_Annotations('Reference'); my $refs=$#refs+1||0; is $pmed{$acc},$refs; my @dblinks=$ann->get_Annotations('dblink'); my @keys=$ann->get_all_annotation_keys; #T10: GENERIF AND OTHER DBLINK TESTS my @url=qw(HGMD Ensembl KEGG Homologene);#Only validate the URL foreach my $dblink (@dblinks) { $loop_count++; my $dbname=$dblink->database||''; DB: { if ( $dbname eq 'generif') {#Should have ID and text ok $dblink->primary_id; ok $dblink->comment->text; last DB; } if ($acc==2) { if (($dbname eq 'MIM')&&($dblink->authority)&&($dblink->authority eq 'phenotype')) { ok $dblink->optional_id; last DB; } if ($dbname eq 'Evidence viewer') { ok $dblink->url; #We may even validate the urls? is $dblink->primary_id,2; last DB; } if ($dbname eq 'Model maker') { ok $dblink->url; #We may even validate the urls? is $dblink->primary_id,2; last DB; } if ($dbname eq 'AceView') { ok $dblink->url; #We may even validate the urls? is $dblink->primary_id,2; last DB; } if (grep(/$dbname/,@url)) { ok $dblink->url; #We may even validate the urls? last DB; } if ($dbname eq 'GDB') { is $dblink->primary_id,'GDB:119639'; #We may even validate the urls? last DB; } if ($dbname eq 'UniGene') { ok $dblink->url; #We may even validate the urls? is $dblink->primary_id,'Hs.212838'; last DB; } if ($dbname eq 'PharmGKB') { is $dblink->primary_id,'PA24357'; last DB; } if ($dbname eq 'MGC') { ok $dblink->url; #We may even validate the urls? is $dblink->primary_id,'BC040071'; last DB; } } } } is $loop_count, shift @lc, "correct number of loops for T10"; $loop_count = 0; #T11: SOME EXTERNAL DATABASE IDS TESTS foreach my $key (@keys) { $loop_count++; next if grep(/\b$key\b/, @revkeys); my @all=$ann->get_Annotations($key); #Checking xref to some databases- OMIM, Wormbase and HGNC, others later my $loop_count_internal = 0; foreach my $pid (@all) { $loop_count_internal++; DBID: { if (($acc==8)&&($key eq 'MIM')) {is $pid->value,'108985'; last DBID;} if (($acc==9)&&($key eq 'HGNC')) {is $pid->value,'7645'; last DBID;} if (($acc==11298)&&($key eq 'MGI')) {is $pid->value,'1328365'; last DBID;} if (($acc==171593)&&($key eq 'AceView/WormGenes')) {is $pid->value,'1A502'; last DBID;} if (($acc==171594)&&($key eq 'WormBase')) {is $pid->value,'Y48G1C.4'; last DBID;} } } is $loop_count_internal, shift @lc, "correct number of loops for T11a"; } is $loop_count, shift @lc, "correct number of loops for T11"; $loop_count = 0; #T12: REFERENCE RECORD TEST if ($acc==1) { foreach my $ref (@refs) { $loop_count++; my $pmed=$ref->medline; is grep(/\b$pmed\b/,@pubmed),1; } is $loop_count, shift @lc, "correct number of loops for T12"; $loop_count = 0; } #T13/14: STS Markers and Gene Ontology my @syn=('MGI:707739','MPC786'); my @evid=qw(IEA TAS ISS); my (%pmeds,%go); $go{11305}=['5524', '16887', '5215', '8203', '6810', '16021' ,'5765']; $go{11298}=['8080', '8415', '4060', '16740']; $pmeds{11305}=['12466851']; my @types=qw(Function Component Process); if (($acc==11305)||($acc==11298)) { #Let's check just this two... foreach my $ot ($ann->get_Annotations('OntologyTerm')) { $loop_count++; if (($ot->term->authority)&&($ot->term->authority eq 'STS marker')) { if ($acc==11305) { is $ot->name,'AI413825'; is $ot->term->namespace,'UniSTS'; is $ot->identifier,158928; } else { is $ot->name,'D11Mit102'; is $ot->term->namespace,'UniSTS'; is $ot->identifier,126289; foreach my $syn ($ot->get_synonyms) { is grep(/\b$syn\b/,@syn),1; } } next; } my $evid=$ot->comment; $evid=~s/evidence: //i; my $type=$ot->ontology->name; my @ref=$ot->term->get_references; my $id=$ot->identifier; my $thispmed=$ref[0]->medline if (@ref); is grep(/\b$type\b/,@types),1; is grep(/\b$id\b/,@{$go{$acc}}),1; is grep(/\b$thispmed\b/,@{$pmeds{$acc}}),1 if ($thispmed); ok $ot->name; } is $loop_count, shift @lc, "correct number of loops for T13/14"; $loop_count = 0; } #T15/16/17: GENOMIC LOCATION TESTS/SEQUENCE TYPES TESTS/CONSERVED DOMAINS TESTS my @gffs=("SEQ\tentrezgene\tgene location\t63548355\t63556668\t.\t+\t.", "SEQ\tentrezgene\tgenestructure\t63548355\t63556668\t.\t+\t.", "SEQ\tentrezgene\tgene location\t31124733\t31133046\t.\t+\t.", "SEQ\tentrezgene\tgenestructure\t31124733\t31133046\t.\t+\t.", "SEQ\tentrezgene\tgene location\t8163589\t8172398\t.\t+\t.", "SEQ\tentrezgene\tgenestructure\t8163589\t8172398\t.\t+\t."); my @contigs=$struct->get_members; my @auth=('mrna','genomic','product','mrna sequence','protein','peptide');#Known types.... foreach my $contig (@contigs) { $loop_count++; my $stype=$contig->authority; is grep(/^$stype$/i,@auth),1; if ($acc==1) {#Do just 1? if (($contig->authority eq 'genomic')||($contig->authority eq 'Genomic')) { foreach my $sf ($contig->get_SeqFeatures) { $sf->source_tag('entrezgene'); my $gff=$sf->gff_string; $gff=~s/[\t\s]+$//g; foreach my $gffstr (@gffs) { if ($gffstr eq $gff) { ok(1); last; } } } } if ($contig->authority eq 'Product') { is $contig->id,'NP_570602'; is $contig->accession_number,21071030; foreach my $sf ($contig->get_SeqFeatures) { foreach my $dblink ($sf->annotation->get_Annotations('dblink')) { my $key=$dblink->{_anchor}?$dblink->{_anchor}:$dblink->optional_id; my $db=$dblink->database; next unless (($db =~/cdd/i)||($sf->primary_tag=~ /conserved/i)); my $desc; if ($key =~ /:/) { ($key,$desc)=split(/:/,$key); } $desc=~s/^\s+//;#THIS SHOULD GO IN entrezgene.pm!!! is $desc,'IGc2; Immunoglobulin C-2 Type'; is $key,'smart00408'; is $sf->score,103; is $db,'CDD'; is $sf->start,223; is $sf->end,282; } } } } } cmp_ok( $loop_count,'>=', shift @lc, "correct number of loops for T15"); $loop_count = 0; } is $num_of_seqs, 39, 'looped through correct number of sequences'; #, -locuslink=>'convert'); #See if we can convert to locuslink #T18: BACKCOMPATIBILITY TESTS my @llsp =('OFFICIAL_GENE_NAME','CHR','MAP','OFFICIAL_SYMBOL'); ok my $eio_b=Bio::SeqIO->new(-file=>test_input_file('entrezgene.dat'),-format=>'entrezgene', -debug=>'on',-service_record=>'yes',-locuslink=>'convert'); my $loop_count = 0; while (my $seq=$eio_b->next_seq) { $loop_count++; ok $seq; my $acc=$seq->accession_number; is grep(/\b$acc\b/,@ids),1; my $ann=$seq->annotation; last if ($acc==4);#3 is enough? and 4 does not have gene name, so.... foreach my $key (@llsp) { my @vals=$ann->get_Annotations($key); ok @vals; } } is $loop_count, 4, "correct number of loops for T18"; # Test for Bug #3453 ok my $eio_c = Bio::SeqIO->new(-format => 'entrezgene', -file => test_input_file('entrezgene_bug3453.dat') ); my $entry = 0; while ( my ( $gene, $genestructure, $uncaptured ) = $eio_c->next_seq ) { $entry++; if ($entry == 1) { is $gene->accession_number, 3581; is scalar @{ $uncaptured }, 55; } elsif ($entry == 2) { is $gene->accession_number, 56111; is scalar @{ $uncaptured }, 32; } } testparser.t100755000765000024 274213352317004 17703 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t#!/usr/bin/env perl use strict; use warnings; use File::Spec; use Test::More tests => 10; my ($nogene, $noseq); BEGIN { diag("\n\nTest parsers (Bio::ASN1::EntrezGene, Bio::ASN1::Sequence),\nparsing and method call:\n"); use_ok('Bio::ASN1::EntrezGene') || $nogene++; use_ok('Bio::ASN1::Sequence') || $noseq++; } diag("\n\nFirst testing gene parser:\n"); if(!$nogene) { my $parser = Bio::ASN1::EntrezGene->new(file => File::Spec->catfile('t','input.asn')); isa_ok($parser, 'Bio::ASN1::EntrezGene'); my $value = $parser->next_seq; isa_ok($value, 'ARRAY'); like($value->[0]{'track-info'}[0]{geneid}, qr/^\d+$/, 'correct geneid format'); my $raw = $parser->rawdata; like($raw, qr/^Entrezgene ::=/, 'rawdata() call'); } else { diag("\nThere's some problem with the installation of Bio::ASN1::EntrezGene!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now"); } diag("\n\nNow testing sequence parser:\n"); if(!$noseq) { my $parser = Bio::ASN1::Sequence->new(file => File::Spec->catfile('t','seq.asn')); isa_ok($parser, 'Bio::ASN1::Sequence'); my $value = $parser->next_seq; isa_ok($value, 'ARRAY'); like($value->[0]{'seq-set'}[0]{seq}[0]{id}[0]{genbank}[0]{accession}, qr/^[A-Za-z0-9.]+$/, 'genbank id format test'); my $raw = $parser->rawdata; like($raw, qr/^Seq-entry ::= set/, 'rawdata() call'); } else { diag("\nThere's some problem with the installation of Bio::ASN1::Sequence!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now"); } 00-compile.t100644000765000024 305113352317004 17343 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/tuse 5.006; use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::Compile 2.057 use Test::More; plan tests => 5 + ($ENV{AUTHOR_TESTING} ? 1 : 0); my @module_files = ( 'Bio/ASN1/EntrezGene.pm', 'Bio/ASN1/EntrezGene/Indexer.pm', 'Bio/ASN1/Sequence.pm', 'Bio/ASN1/Sequence/Indexer.pm', 'Bio/SeqIO/entrezgene.pm' ); # no fake home requested my @switches = ( -d 'blib' ? '-Mblib' : '-Ilib', ); use File::Spec; use IPC::Open3; use IO::Handle; open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!"; my @warnings; for my $lib (@module_files) { # see L my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-e', "require q[$lib]")) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]"); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$lib loaded ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; if (@_warnings) { warn @_warnings; push @warnings, @_warnings; } } is(scalar(@warnings), 0, 'no warnings found') or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) ) if $ENV{AUTHOR_TESTING}; author-eol.t100644000765000024 146213352317004 17561 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::EOL 0.19 use Test::More 0.88; use Test::EOL; my @files = ( 'lib/Bio/ASN1/EntrezGene.pm', 'lib/Bio/ASN1/EntrezGene/Indexer.pm', 'lib/Bio/ASN1/Sequence.pm', 'lib/Bio/ASN1/Sequence/Indexer.pm', 'lib/Bio/SeqIO/entrezgene.pm', 't/00-compile.t', 't/author-eol.t', 't/author-mojibake.t', 't/author-no-tabs.t', 't/author-pod-coverage.t', 't/author-pod-syntax.t', 't/entrezgene.t', 't/input.asn', 't/input1.asn', 't/seq.asn', 't/testindexer.t', 't/testparser.t' ); eol_unix_ok($_, { trailing_whitespace => 1 }) foreach @files; done_testing; testindexer.t100755000765000024 666313352317004 20053 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t#!/usr/bin/env perl use strict; use warnings; use File::Spec; use Test::More tests => 6; sub check_dependency { my $class = shift; eval "require $class; 1"; if ($@) { return; } 1; } my ( $noindex, $noabseq, $nogene, $noseq, $noseqindex ); BEGIN { note( "\n\nTest indexers (Bio::ASN1::EntrezGene::Indexer, Bio::ASN1::Sequence::Indexer)\nIndexing and retrieval:\n" ); check_dependency('Bio::ASN1::EntrezGene') || $nogene++; check_dependency('Bio::Index::AbstractSeq') || $noabseq++; check_dependency('Bio::ASN1::EntrezGene::Indexer') || $noindex++; check_dependency('Bio::ASN1::Sequence') || $noseq++; check_dependency('Bio::ASN1::Sequence::Indexer') || $noseqindex++; } note("\n\nFirst testing gene indexer:\n"); SKIP: { if ( !$nogene ) { skip( "BioPerl not installed, skipping", 3 ) if $noabseq; # test indexer if ( !$noabseq ) { if ( !$noindex ) { my $inx = Bio::ASN1::EntrezGene::Indexer->new( -filename => File::Spec->catfile('t','testgene.idx'), -write_flag => 'WRITE' ); isa_ok( $inx, 'Bio::ASN1::EntrezGene::Indexer' ); $inx->make_index( File::Spec->catfile('t','input.asn'), File::Spec->catfile('t','input1.asn' )); # cmp_ok($inx->count_records, '==', 4, 'total number of indexed gene records'); my $value = $inx->fetch_hash(3); isa_ok( $value, 'ARRAY' ); cmp_ok( $value->[0]{'track-info'}[0]{geneid}, '==', 3, 'correct gene record retrieved' ); } else { diag( "\nThere's some problem with the installation of Bio::ASN1::EntrezGene::Indexer!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now" ); } } } else { diag( "\nThere's some problem with the installation of Bio::ASN1::EntrezGene!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now" ); } } note("\n\nNow testing sequence indexer:\n"); SKIP: { if ( !$noseq ) { skip( "BioPerl not installed, skipping", 3 ) if $noabseq; # test indexer if ( !$noabseq ) { if ( !$noseqindex ) { my $inx = Bio::ASN1::Sequence::Indexer->new( -filename => File::Spec->catfile('t','testseq.idx'), -write_flag => 'WRITE' ); isa_ok( $inx, 'Bio::ASN1::Sequence::Indexer' ); $inx->make_index(File::Spec->catfile('t','seq.asn')); # cmp_ok($inx->count_records, '==', 2, 'total number of sequence ids in index'); my $value = $inx->fetch_hash('AF093062'); isa_ok( $value, 'ARRAY' ); cmp_ok( $value->[0]{'seq-set'}[0]{seq}[0]{id}[0]{genbank}[0] {accession}, 'eq', 'AF093062', 'correct sequence record retrieved' ); } else { diag( "\nThere's some problem with the installation of Bio::ASN1::Sequence::Indexer!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now" ); } } } else { diag( "\nThere's some problem with the installation of Bio::ASN1::Sequence!\nTry install again using:\n\tperl Makefile.PL\n\tmake\nQuitting now" ); } } author-no-tabs.t100644000765000024 143013352317004 20340 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::NoTabs 0.15 use Test::More 0.88; use Test::NoTabs; my @files = ( 'lib/Bio/ASN1/EntrezGene.pm', 'lib/Bio/ASN1/EntrezGene/Indexer.pm', 'lib/Bio/ASN1/Sequence.pm', 'lib/Bio/ASN1/Sequence/Indexer.pm', 'lib/Bio/SeqIO/entrezgene.pm', 't/00-compile.t', 't/author-eol.t', 't/author-mojibake.t', 't/author-no-tabs.t', 't/author-pod-coverage.t', 't/author-pod-syntax.t', 't/entrezgene.t', 't/input.asn', 't/input1.asn', 't/seq.asn', 't/testindexer.t', 't/testparser.t' ); notabs_ok($_) foreach @files; done_testing; author-mojibake.t100644000765000024 35313352317004 20541 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings qw(all); use Test::More; use Test::Mojibake; all_files_encoding_ok(); data000755000765000024 013352317004 16063 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/tentrezgene.dat100644000765000024 265314213352317004 21160 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t/dataEntrezgene ::= { track-info { geneid 1 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 14 , hour 13 , minute 15 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "19" } } } , gene { locus "A1BG" , desc "alpha-1-B glycoprotein" , maploc "19q13.4" , db { { db "MIM" , tag id 138670 } } , syn { "A1B" , "ABG" , "GAB" , "HYST2477" , "DKFZp686F0970" } , locus-tag "HGNC:5" } , prot { name { "alpha 1B-glycoprotein" , "alpha-1B-glycoprotein" } } , summary "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins." , location { { display-str "19q13.4" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 1 , src-str2 "1" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000019" , version 8 , seqs { int { from 63548355 , to 63556668 , strand minus , id gi 42406306 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 63548355 , to 63550206 , strand minus , id gi 42406306 } , int { from 63550530 , to 63550817 , strand minus , id gi 42406306 } , int { from 63553547 , to 63553828 , strand minus , id gi 42406306 } , int { from 63554568 , to 63554864 , strand minus , id gi 42406306 } , int { from 63555460 , to 63555732 , strand minus , id gi 42406306 } , int { from 63556105 , to 63556374 , strand minus , id gi 42406306 } , int { from 63556469 , to 63556504 , strand minus , id gi 42406306 } , int { from 63556581 , to 63556668 , strand minus , id gi 42406306 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 63550199 , to 63550206 , strand minus , id gi 42406306 } , { from 63550530 , to 63550817 , strand minus , id gi 42406306 } , { from 63553547 , to 63553828 , strand minus , id gi 42406306 } , { from 63554568 , to 63554864 , strand minus , id gi 42406306 } , { from 63555460 , to 63555732 , strand minus , id gi 42406306 } , { from 63556105 , to 63556374 , strand minus , id gi 42406306 } , { from 63556469 , to 63556504 , strand minus , id gi 42406306 } , { from 63556581 , to 63556614 , strand minus , id gi 42406306 } } } , seqs { whole gi 21071030 } } } } } } , { type genomic , heading "Reference" , accession "NT_011109" , version 15 , seqs { int { from 31124733 , to 31133046 , strand minus , id gi 29800594 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 31124733 , to 31126584 , strand minus , id gi 29800594 } , int { from 31126908 , to 31127195 , strand minus , id gi 29800594 } , int { from 31129925 , to 31130206 , strand minus , id gi 29800594 } , int { from 31130946 , to 31131242 , strand minus , id gi 29800594 } , int { from 31131838 , to 31132110 , strand minus , id gi 29800594 } , int { from 31132483 , to 31132752 , strand minus , id gi 29800594 } , int { from 31132847 , to 31132882 , strand minus , id gi 29800594 } , int { from 31132959 , to 31133046 , strand minus , id gi 29800594 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 31126577 , to 31126584 , strand minus , id gi 29800594 } , { from 31126908 , to 31127195 , strand minus , id gi 29800594 } , { from 31129925 , to 31130206 , strand minus , id gi 29800594 } , { from 31130946 , to 31131242 , strand minus , id gi 29800594 } , { from 31131838 , to 31132110 , strand minus , id gi 29800594 } , { from 31132483 , to 31132752 , strand minus , id gi 29800594 } , { from 31132847 , to 31132882 , strand minus , id gi 29800594 } , { from 31132959 , to 31132992 , strand minus , id gi 29800594 } } } , seqs { whole gi 21071030 } } } } } } , { type genomic , heading "Reference" , accession "NT_086907" , version 1 , seqs { int { from 8163589 , to 8172398 , strand minus , id gi 51475048 } } , products { { type mRNA , heading "Reference" , accession "NM_130786" , version 2 , genomic-coords { mix { int { from 8163589 , to 8165440 , strand minus , id gi 51475048 } , int { from 8165763 , to 8166050 , strand minus , id gi 51475048 } , int { from 8169274 , to 8169555 , strand minus , id gi 51475048 } , int { from 8170297 , to 8170593 , strand minus , id gi 51475048 } , int { from 8171190 , to 8171462 , strand minus , id gi 51475048 } , int { from 8171835 , to 8172104 , strand minus , id gi 51475048 } , int { from 8172199 , to 8172234 , strand minus , id gi 51475048 } , int { from 8172311 , to 8172398 , strand minus , id gi 51475048 } } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Reference" , accession "NP_570602" , version 2 , genomic-coords { packed-int { { from 8165433 , to 8165440 , strand minus , id gi 51475048 } , { from 8165763 , to 8166050 , strand minus , id gi 51475048 } , { from 8169274 , to 8169555 , strand minus , id gi 51475048 } , { from 8170297 , to 8170593 , strand minus , id gi 51475048 } , { from 8171190 , to 8171462 , strand minus , id gi 51475048 } , { from 8171835 , to 8172104 , strand minus , id gi 51475048 } , { from 8172199 , to 8172234 , strand minus , id gi 51475048 } , { from 8172311 , to 8172344 , strand minus , id gi 51475048 } } } , seqs { whole gi 21071030 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A1BG" , version 0 } , { type property , label "Official Full Name" , text "alpha-1-B glycoprotein" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 3458201 } , source { { src { db "GO" , tag id 5554 } , anchor "molecular_function unknown" , post-text "evidence: ND" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 4 } , anchor "biological_process unknown" , post-text "evidence: ND" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 3458201 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: IDA" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 11167 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=19& MAPS=genes-r-org/rat-chr/human%3A19,genes-r-org/mouse-chr/human%3A19,genes-r-o rg/human-chr19&query=e%3A1[id]+AND+gene[obj_type]&QSTR=a1bg&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 5 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15461460 , pmid 15221005 , pmid 14702039 , pmid 12477932 , pmid 8889549 , pmid 3610142 , pmid 3458201 , pmid 2591067 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 89991 } , anchor "SHGC-67307" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH80032" , version 0 } , { type other , label "Alternate name" , text "RH86145" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 152074 } , anchor "D11S2921" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "GDB:461809" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 155756 } , anchor "D10S16" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "D10S23" , version 0 } , { type other , label "Alternate name" , text "GDB:193809" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_130786" , version 2 , source { { src { db "Nucleotide" , tag id 21071029 } , anchor "NM_130786" } } , seqs { whole gi 21071029 } , products { { type peptide , heading "Product" , accession "NP_570602" , version 2 , source { { src { db "Protein" , tag id 21071030 } , anchor "NP_570602" , post-text "alpha 1B-glycoprotein" } } , seqs { whole gi 21071030 } , comment { { type other , heading "Consensus CDS (CCDS)" , version 0 , source { { src { db "CCDS" , tag str "CCDS12976.1" } , anchor "CCDS12976.1" } } } , { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 21071030 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 365 } , anchor "smart00408: IGc2; Immunoglobulin C-2 Type" } } , comment { { type other , text "Location: 223 - 282 Blast Score: 103" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AF414429,AK055885,AK056201" } , anchor "AF414429,AK055885,AK056201" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC010642" , version 5 , source { { src { db "Nucleotide" , tag id 9929687 } , anchor "AC010642" } } , seqs { int { from 41119 , to 43581 , strand plus , id gi 9929687 } } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AB073611" , version 1 , source { { src { db "Nucleotide" , tag id 51555784 } , anchor "AB073611" } } , seqs { whole gi 51555784 } , products { { type peptide , accession "BAD38648" , version 1 , source { { src { db "Protein" , tag id 51555785 } , anchor "BAD38648" } } , seqs { whole gi 51555785 } } } } , { type mRNA , heading "mRNA" , accession "AF414429" , version 1 , source { { src { db "Nucleotide" , tag id 15778555 } , anchor "AF414429" } } , seqs { whole gi 15778555 } , products { { type peptide , accession "AAL07469" , version 1 , source { { src { db "Protein" , tag id 15778556 } , anchor "AAL07469" } } , seqs { whole gi 15778556 } } } } , { type mRNA , heading "mRNA" , accession "AK055885" , version 1 , source { { src { db "Nucleotide" , tag id 16550723 } , anchor "AK055885" } } , seqs { whole gi 16550723 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK056201" , version 1 , source { { src { db "Nucleotide" , tag id 16551539 } , anchor "AK056201" } } , seqs { whole gi 16551539 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC035719" , version 1 , source { { src { db "Nucleotide" , tag id 23273475 } , anchor "BC035719" } } , seqs { whole gi 23273475 } , products { { type peptide , accession "AAH35719" , version 1 , source { { src { db "Protein" , tag id 23273476 } , anchor "AAH35719" } } , seqs { whole gi 23273476 } } } } , { type mRNA , heading "mRNA" , accession "BX537419" , version 1 , source { { src { db "Nucleotide" , tag id 31873339 } , anchor "BX537419" } } , seqs { whole gi 31873339 } , products { { type peptide , accession "CAD97661" , version 1 , source { { src { db "Protein" , tag id 31873340 } , anchor "CAD97661" } } , seqs { whole gi 31873340 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P04217" , version 0 , source { { src { db "Protein" , tag id 46577680 } , anchor "P04217" } } , seqs { whole gi 46577680 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "1" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_011109.15&gene=A1BG&lid=1&from=31124734&to=31133047" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "1" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_011109.15&gene=A1BG&lid=1" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.529161" } } , source { { src { db "UniGene" , tag str "Hs.529161" } , anchor "Hs.529161" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=52 9161" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "138670" } , anchor "138670" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "1" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 1[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 1 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=1" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:119638" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AK055 885" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= AK055885" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC035719" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC035719" } } } } } , { type generif , text "A1BG-cysteine-rich secretory protein 3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3" , version 0 , refs { pmid 15461460 } , create-date str "Nov 6 2004 10:01AM" , update-date str "Nov 6 2004 3:27PM" } } , unique-keys { { db "LocusID" , tag id 1 } , { db "MIM" , tag id 138670 } } , xtra-index-terms { "LOC1" } } Entrezgene ::= { track-info { geneid 2 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 14 , hour 13 , minute 15 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "12" } } } , gene { locus "A2M" , desc "alpha-2-macroglobulin" , maploc "12p13.3-p12.3" , db { { db "MIM" , tag id 103950 } } , syn { "FWP007" , "S863-7" , "DKFZp779B086" } , locus-tag "HGNC:7" } , prot { name { "alpha-2-macroglobulin" } } , summary "Alpha-2-macroglobulin is a protease inhibitor and cytokine transporter. It inhibits many proteases, including trypsin, thrombin and collagenase. A2M is implicated in Alzheimer disease (AD) due to its ability to mediate the clearance and degradation of A-beta, the major component of beta-amyloid deposits." , location { { display-str "12p13.3-p12.3" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 2 , src-str2 "2" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000012" , version 9 , seqs { int { from 9111576 , to 9159755 , strand minus , id gi 51511728 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 9111576 , to 9111701 , strand minus , id gi 51511728 } , int { from 9112045 , to 9112086 , strand minus , id gi 51511728 } , int { from 9112602 , to 9112704 , strand minus , id gi 51511728 } , int { from 9113607 , to 9113675 , strand minus , id gi 51511728 } , int { from 9114350 , to 9114440 , strand minus , id gi 51511728 } , int { from 9116221 , to 9116348 , strand minus , id gi 51511728 } , int { from 9116515 , to 9116733 , strand minus , id gi 51511728 } , int { from 9118422 , to 9118645 , strand minus , id gi 51511728 } , int { from 9120618 , to 9120798 , strand minus , id gi 51511728 } , int { from 9121208 , to 9121282 , strand minus , id gi 51511728 } , int { from 9121563 , to 9121719 , strand minus , id gi 51511728 } , int { from 9123106 , to 9123193 , strand minus , id gi 51511728 } , int { from 9123501 , to 9123677 , strand minus , id gi 51511728 } , int { from 9123956 , to 9124039 , strand minus , id gi 51511728 } , int { from 9133062 , to 9133113 , strand minus , id gi 51511728 } , int { from 9133764 , to 9133885 , strand minus , id gi 51511728 } , int { from 9134218 , to 9134344 , strand minus , id gi 51511728 } , int { from 9135063 , to 9135291 , strand minus , id gi 51511728 } , int { from 9137327 , to 9137441 , strand minus , id gi 51511728 } , int { from 9138835 , to 9138946 , strand minus , id gi 51511728 } , int { from 9139401 , to 9139562 , strand minus , id gi 51511728 } , int { from 9142469 , to 9142618 , strand minus , id gi 51511728 } , int { from 9143243 , to 9143385 , strand minus , id gi 51511728 } , int { from 9145006 , to 9145069 , strand minus , id gi 51511728 } , int { from 9145309 , to 9145536 , strand minus , id gi 51511728 } , int { from 9148101 , to 9148262 , strand minus , id gi 51511728 } , int { from 9150098 , to 9150207 , strand minus , id gi 51511728 } , int { from 9150353 , to 9150467 , strand minus , id gi 51511728 } , int { from 9151386 , to 9151506 , strand minus , id gi 51511728 } , int { from 9153183 , to 9153267 , strand minus , id gi 51511728 } , int { from 9153729 , to 9153897 , strand minus , id gi 51511728 } , int { from 9154176 , to 9154196 , strand minus , id gi 51511728 } , int { from 9156021 , to 9156073 , strand minus , id gi 51511728 } , int { from 9156239 , to 9156398 , strand minus , id gi 51511728 } , int { from 9157222 , to 9157405 , strand minus , id gi 51511728 } , int { from 9159626 , to 9159755 , strand minus , id gi 51511728 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 9111685 , to 9111701 , strand minus , id gi 51511728 } , { from 9112045 , to 9112086 , strand minus , id gi 51511728 } , { from 9112602 , to 9112704 , strand minus , id gi 51511728 } , { from 9113607 , to 9113675 , strand minus , id gi 51511728 } , { from 9114350 , to 9114440 , strand minus , id gi 51511728 } , { from 9116221 , to 9116348 , strand minus , id gi 51511728 } , { from 9116515 , to 9116733 , strand minus , id gi 51511728 } , { from 9118422 , to 9118645 , strand minus , id gi 51511728 } , { from 9120618 , to 9120798 , strand minus , id gi 51511728 } , { from 9121208 , to 9121282 , strand minus , id gi 51511728 } , { from 9121563 , to 9121719 , strand minus , id gi 51511728 } , { from 9123106 , to 9123193 , strand minus , id gi 51511728 } , { from 9123501 , to 9123677 , strand minus , id gi 51511728 } , { from 9123956 , to 9124039 , strand minus , id gi 51511728 } , { from 9133062 , to 9133113 , strand minus , id gi 51511728 } , { from 9133764 , to 9133885 , strand minus , id gi 51511728 } , { from 9134218 , to 9134344 , strand minus , id gi 51511728 } , { from 9135063 , to 9135291 , strand minus , id gi 51511728 } , { from 9137327 , to 9137441 , strand minus , id gi 51511728 } , { from 9138835 , to 9138946 , strand minus , id gi 51511728 } , { from 9139401 , to 9139562 , strand minus , id gi 51511728 } , { from 9142469 , to 9142618 , strand minus , id gi 51511728 } , { from 9143243 , to 9143385 , strand minus , id gi 51511728 } , { from 9145006 , to 9145069 , strand minus , id gi 51511728 } , { from 9145309 , to 9145536 , strand minus , id gi 51511728 } , { from 9148101 , to 9148262 , strand minus , id gi 51511728 } , { from 9150098 , to 9150207 , strand minus , id gi 51511728 } , { from 9150353 , to 9150467 , strand minus , id gi 51511728 } , { from 9151386 , to 9151506 , strand minus , id gi 51511728 } , { from 9153183 , to 9153267 , strand minus , id gi 51511728 } , { from 9153729 , to 9153897 , strand minus , id gi 51511728 } , { from 9154176 , to 9154196 , strand minus , id gi 51511728 } , { from 9156021 , to 9156073 , strand minus , id gi 51511728 } , { from 9156239 , to 9156398 , strand minus , id gi 51511728 } , { from 9157222 , to 9157405 , strand minus , id gi 51511728 } , { from 9159626 , to 9159711 , strand minus , id gi 51511728 } } } , seqs { whole gi 4557225 } } } } } } , { type genomic , heading "Reference" , accession "NT_009714" , version 16 , seqs { int { from 1979283 , to 2027462 , strand minus , id gi 37543832 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 1979283 , to 1979408 , strand minus , id gi 37543832 } , int { from 1979752 , to 1979793 , strand minus , id gi 37543832 } , int { from 1980309 , to 1980411 , strand minus , id gi 37543832 } , int { from 1981314 , to 1981382 , strand minus , id gi 37543832 } , int { from 1982057 , to 1982147 , strand minus , id gi 37543832 } , int { from 1983928 , to 1984055 , strand minus , id gi 37543832 } , int { from 1984222 , to 1984440 , strand minus , id gi 37543832 } , int { from 1986129 , to 1986352 , strand minus , id gi 37543832 } , int { from 1988325 , to 1988505 , strand minus , id gi 37543832 } , int { from 1988915 , to 1988989 , strand minus , id gi 37543832 } , int { from 1989270 , to 1989426 , strand minus , id gi 37543832 } , int { from 1990813 , to 1990900 , strand minus , id gi 37543832 } , int { from 1991208 , to 1991384 , strand minus , id gi 37543832 } , int { from 1991663 , to 1991746 , strand minus , id gi 37543832 } , int { from 2000769 , to 2000820 , strand minus , id gi 37543832 } , int { from 2001471 , to 2001592 , strand minus , id gi 37543832 } , int { from 2001925 , to 2002051 , strand minus , id gi 37543832 } , int { from 2002770 , to 2002998 , strand minus , id gi 37543832 } , int { from 2005034 , to 2005148 , strand minus , id gi 37543832 } , int { from 2006542 , to 2006653 , strand minus , id gi 37543832 } , int { from 2007108 , to 2007269 , strand minus , id gi 37543832 } , int { from 2010176 , to 2010325 , strand minus , id gi 37543832 } , int { from 2010950 , to 2011092 , strand minus , id gi 37543832 } , int { from 2012713 , to 2012776 , strand minus , id gi 37543832 } , int { from 2013016 , to 2013243 , strand minus , id gi 37543832 } , int { from 2015808 , to 2015969 , strand minus , id gi 37543832 } , int { from 2017805 , to 2017914 , strand minus , id gi 37543832 } , int { from 2018060 , to 2018174 , strand minus , id gi 37543832 } , int { from 2019093 , to 2019213 , strand minus , id gi 37543832 } , int { from 2020890 , to 2020974 , strand minus , id gi 37543832 } , int { from 2021436 , to 2021604 , strand minus , id gi 37543832 } , int { from 2021883 , to 2021903 , strand minus , id gi 37543832 } , int { from 2023728 , to 2023780 , strand minus , id gi 37543832 } , int { from 2023946 , to 2024105 , strand minus , id gi 37543832 } , int { from 2024929 , to 2025112 , strand minus , id gi 37543832 } , int { from 2027333 , to 2027462 , strand minus , id gi 37543832 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 1979392 , to 1979408 , strand minus , id gi 37543832 } , { from 1979752 , to 1979793 , strand minus , id gi 37543832 } , { from 1980309 , to 1980411 , strand minus , id gi 37543832 } , { from 1981314 , to 1981382 , strand minus , id gi 37543832 } , { from 1982057 , to 1982147 , strand minus , id gi 37543832 } , { from 1983928 , to 1984055 , strand minus , id gi 37543832 } , { from 1984222 , to 1984440 , strand minus , id gi 37543832 } , { from 1986129 , to 1986352 , strand minus , id gi 37543832 } , { from 1988325 , to 1988505 , strand minus , id gi 37543832 } , { from 1988915 , to 1988989 , strand minus , id gi 37543832 } , { from 1989270 , to 1989426 , strand minus , id gi 37543832 } , { from 1990813 , to 1990900 , strand minus , id gi 37543832 } , { from 1991208 , to 1991384 , strand minus , id gi 37543832 } , { from 1991663 , to 1991746 , strand minus , id gi 37543832 } , { from 2000769 , to 2000820 , strand minus , id gi 37543832 } , { from 2001471 , to 2001592 , strand minus , id gi 37543832 } , { from 2001925 , to 2002051 , strand minus , id gi 37543832 } , { from 2002770 , to 2002998 , strand minus , id gi 37543832 } , { from 2005034 , to 2005148 , strand minus , id gi 37543832 } , { from 2006542 , to 2006653 , strand minus , id gi 37543832 } , { from 2007108 , to 2007269 , strand minus , id gi 37543832 } , { from 2010176 , to 2010325 , strand minus , id gi 37543832 } , { from 2010950 , to 2011092 , strand minus , id gi 37543832 } , { from 2012713 , to 2012776 , strand minus , id gi 37543832 } , { from 2013016 , to 2013243 , strand minus , id gi 37543832 } , { from 2015808 , to 2015969 , strand minus , id gi 37543832 } , { from 2017805 , to 2017914 , strand minus , id gi 37543832 } , { from 2018060 , to 2018174 , strand minus , id gi 37543832 } , { from 2019093 , to 2019213 , strand minus , id gi 37543832 } , { from 2020890 , to 2020974 , strand minus , id gi 37543832 } , { from 2021436 , to 2021604 , strand minus , id gi 37543832 } , { from 2021883 , to 2021903 , strand minus , id gi 37543832 } , { from 2023728 , to 2023780 , strand minus , id gi 37543832 } , { from 2023946 , to 2024105 , strand minus , id gi 37543832 } , { from 2024929 , to 2025112 , strand minus , id gi 37543832 } , { from 2027333 , to 2027418 , strand minus , id gi 37543832 } } } , seqs { whole gi 4557225 } } } } } } , { type genomic , heading "Reference" , accession "NT_086792" , version 1 , seqs { int { from 4173171 , to 4221277 , strand minus , id gi 51471135 } } , products { { type mRNA , heading "Reference" , accession "NM_000014" , version 3 , genomic-coords { mix { int { from 4173171 , to 4173296 , strand minus , id gi 51471135 } , int { from 4173640 , to 4173681 , strand minus , id gi 51471135 } , int { from 4174197 , to 4174299 , strand minus , id gi 51471135 } , int { from 4175201 , to 4175269 , strand minus , id gi 51471135 } , int { from 4175944 , to 4176034 , strand minus , id gi 51471135 } , int { from 4177816 , to 4177943 , strand minus , id gi 51471135 } , int { from 4178110 , to 4178328 , strand minus , id gi 51471135 } , int { from 4180017 , to 4180240 , strand minus , id gi 51471135 } , int { from 4182213 , to 4182393 , strand minus , id gi 51471135 } , int { from 4182803 , to 4182877 , strand minus , id gi 51471135 } , int { from 4183158 , to 4183314 , strand minus , id gi 51471135 } , int { from 4184702 , to 4184789 , strand minus , id gi 51471135 } , int { from 4185097 , to 4185273 , strand minus , id gi 51471135 } , int { from 4185552 , to 4185635 , strand minus , id gi 51471135 } , int { from 4194661 , to 4194712 , strand minus , id gi 51471135 } , int { from 4195363 , to 4195484 , strand minus , id gi 51471135 } , int { from 4195817 , to 4195943 , strand minus , id gi 51471135 } , int { from 4196662 , to 4196890 , strand minus , id gi 51471135 } , int { from 4198926 , to 4199040 , strand minus , id gi 51471135 } , int { from 4200364 , to 4200475 , strand minus , id gi 51471135 } , int { from 4200930 , to 4201091 , strand minus , id gi 51471135 } , int { from 4203997 , to 4204146 , strand minus , id gi 51471135 } , int { from 4204771 , to 4204913 , strand minus , id gi 51471135 } , int { from 4206534 , to 4206597 , strand minus , id gi 51471135 } , int { from 4206837 , to 4207064 , strand minus , id gi 51471135 } , int { from 4209629 , to 4209790 , strand minus , id gi 51471135 } , int { from 4211627 , to 4211736 , strand minus , id gi 51471135 } , int { from 4211882 , to 4211996 , strand minus , id gi 51471135 } , int { from 4212916 , to 4213036 , strand minus , id gi 51471135 } , int { from 4214705 , to 4214789 , strand minus , id gi 51471135 } , int { from 4215251 , to 4215419 , strand minus , id gi 51471135 } , int { from 4215698 , to 4215718 , strand minus , id gi 51471135 } , int { from 4217543 , to 4217595 , strand minus , id gi 51471135 } , int { from 4217761 , to 4217920 , strand minus , id gi 51471135 } , int { from 4218744 , to 4218927 , strand minus , id gi 51471135 } , int { from 4221148 , to 4221277 , strand minus , id gi 51471135 } } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_000005" , version 1 , genomic-coords { packed-int { { from 4173280 , to 4173296 , strand minus , id gi 51471135 } , { from 4173640 , to 4173681 , strand minus , id gi 51471135 } , { from 4174197 , to 4174299 , strand minus , id gi 51471135 } , { from 4175201 , to 4175269 , strand minus , id gi 51471135 } , { from 4175944 , to 4176034 , strand minus , id gi 51471135 } , { from 4177816 , to 4177943 , strand minus , id gi 51471135 } , { from 4178110 , to 4178328 , strand minus , id gi 51471135 } , { from 4180017 , to 4180240 , strand minus , id gi 51471135 } , { from 4182213 , to 4182393 , strand minus , id gi 51471135 } , { from 4182803 , to 4182877 , strand minus , id gi 51471135 } , { from 4183158 , to 4183314 , strand minus , id gi 51471135 } , { from 4184702 , to 4184789 , strand minus , id gi 51471135 } , { from 4185097 , to 4185273 , strand minus , id gi 51471135 } , { from 4185552 , to 4185635 , strand minus , id gi 51471135 } , { from 4194661 , to 4194712 , strand minus , id gi 51471135 } , { from 4195363 , to 4195484 , strand minus , id gi 51471135 } , { from 4195817 , to 4195943 , strand minus , id gi 51471135 } , { from 4196662 , to 4196890 , strand minus , id gi 51471135 } , { from 4198926 , to 4199040 , strand minus , id gi 51471135 } , { from 4200364 , to 4200475 , strand minus , id gi 51471135 } , { from 4200930 , to 4201091 , strand minus , id gi 51471135 } , { from 4203997 , to 4204146 , strand minus , id gi 51471135 } , { from 4204771 , to 4204913 , strand minus , id gi 51471135 } , { from 4206534 , to 4206597 , strand minus , id gi 51471135 } , { from 4206837 , to 4207064 , strand minus , id gi 51471135 } , { from 4209629 , to 4209790 , strand minus , id gi 51471135 } , { from 4211627 , to 4211736 , strand minus , id gi 51471135 } , { from 4211882 , to 4211996 , strand minus , id gi 51471135 } , { from 4212916 , to 4213036 , strand minus , id gi 51471135 } , { from 4214705 , to 4214789 , strand minus , id gi 51471135 } , { from 4215251 , to 4215419 , strand minus , id gi 51471135 } , { from 4215698 , to 4215718 , strand minus , id gi 51471135 } , { from 4217543 , to 4217595 , strand minus , id gi 51471135 } , { from 4217761 , to 4217920 , strand minus , id gi 51471135 } , { from 4218744 , to 4218927 , strand minus , id gi 51471135 } , { from 4221148 , to 4221233 , strand minus , id gi 51471135 } } } , seqs { whole gi 4557225 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A2M" , version 0 } , { type property , label "Official Full Name" , text "alpha-2-macroglobulin" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 11435418 } , source { { src { db "GO" , tag id 19899 } , anchor "enzyme binding" , post-text "evidence: IPI" } } } , { type comment , version 0 , refs { pmid 9714181 } , source { { src { db "GO" , tag id 19966 } , anchor "interleukin-1 binding" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 10880251 } , source { { src { db "GO" , tag id 19959 } , anchor "interleukin-8 binding" , post-text "evidence: IPI" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 8320 } , anchor "protein carrier activity" , post-text "evidence: NR" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 4867 } , anchor "serine-type endopeptidase inhibitor activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 9714181 } , source { { src { db "GO" , tag id 43120 } , anchor "tumor necrosis factor binding" , post-text "evidence: IDA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 17114 } , anchor "wide-spectrum protease inhibitor activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 6886 } , anchor "intracellular protein transport" , post-text "evidence: NR" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 51260 } , anchor "protein homooligomerization" , post-text "evidence: NAS" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 14718574 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: NAS" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 37248 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=12& MAPS=genes-r-org/rat-chr/human%3A12,genes-r-org/mouse-chr/human%3A12,genes-r-o rg/human-chr12&query=e%3A2[id]+AND+gene[obj_type]&QSTR=a2m&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 7 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15511627 , pmid 15023809 , pmid 14760718 , pmid 14718574 , pmid 14715656 , pmid 14678766 , pmid 14675603 , pmid 14637088 , pmid 14506912 , pmid 12966032 , pmid 12755687 , pmid 12755614 , pmid 12631277 , pmid 12477932 , pmid 12221172 , pmid 12194978 , pmid 12175343 , pmid 12062545 , pmid 12042276 , pmid 12015318 , pmid 11916201 , pmid 11910179 , pmid 11901360 , pmid 11823454 , pmid 11811950 , pmid 11435418 , pmid 11162584 , pmid 11100124 , pmid 11023837 , pmid 10880251 , pmid 10731476 , pmid 10714547 , pmid 10652313 , pmid 10373500 , pmid 9831625 , pmid 9724081 , pmid 9714181 , pmid 8583572 , pmid 7680268 , pmid 7533769 , pmid 7533162 , pmid 7519849 , pmid 6191979 , pmid 6153632 , pmid 3289986 , pmid 2581245 , pmid 2476070 , pmid 2460294 , pmid 2459995 , pmid 2408344 , pmid 1707161 , pmid 1697852 , pmid 1370808 , pmid 1281457 , pmid 89758 } } , { type comment , heading "Phenotypes" , version 0 , comment { { type phenotype , text "Alzheimer disease, susceptibility to" , version 0 , source { { src { db "MIM" , tag id 103950 } , anchor "MIM: 103950" } } } , { type phenotype , text "Emphysema due to alpha-2-macroglobulin deficiency" , version 0 , source { { src { db "MIM" , tag id 103950 } , anchor "MIM: 103950" } } } } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 25036 } , anchor "RH1601" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH44109" , version 0 } , { type other , label "Alternate name" , text "stSG1293" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 40245 } , anchor "SGC31674" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "EST130345" , version 0 } , { type other , label "Alternate name" , text "RH52474" , version 0 } , { type other , label "Alternate name" , text "WI-219" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 46849 } , anchor "RH11157" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH44108" , version 0 } , { type other , label "Alternate name" , text "stSG1290R" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 95143 } , anchor "G44356" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "WIAF-1430-STS" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 147540 } , anchor "NoName" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 151442 } , anchor "NoName" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_000014" , version 3 , source { { src { db "Nucleotide" , tag id 6226959 } , anchor "NM_000014" } } , seqs { whole gi 6226959 } , products { { type peptide , heading "Product" , accession "NP_000005" , version 1 , source { { src { db "Protein" , tag id 4557225 } , anchor "NP_000005" , post-text "alpha-2-macroglobulin precursor" } } , seqs { whole gi 4557225 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 4557225 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5952 } , anchor "pfam00207: A2M; Alpha-2-macroglobulin family" } } , comment { { type other , text "Location: 725 - 1463 Blast Score: 2322" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 25832 } , anchor "pfam01835: A2M_N; Alpha-2-macroglobulin family N-terminal region" } } , comment { { type other , text "Location: 21 - 628 Blast Score: 1948" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "M11313" } , anchor "M11313" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AF349032" , version 1 , source { { src { db "Nucleotide" , tag id 13661813 } , anchor "AF349032" } } , seqs { whole gi 13661813 } , products { { type peptide , accession "AAK38109" , version 1 , source { { src { db "Protein" , tag id 13661814 } , anchor "AAK38109" } } , seqs { whole gi 13661814 } } } } , { type genomic , heading "Genomic" , accession "AF349033" , version 1 , source { { src { db "Nucleotide" , tag id 13661815 } , anchor "AF349033" } } , seqs { whole gi 13661815 } , products { { type peptide , accession "AAK38110" , version 1 , source { { src { db "Protein" , tag id 13661816 } , anchor "AAK38110" } } , seqs { whole gi 13661816 } } } } , { type genomic , heading "Genomic" , accession "X68728" , version 1 , source { { src { db "Nucleotide" , tag id 450521 } , anchor "X68728" } } , seqs { whole gi 450521 } , products { { type peptide , accession "CAA48670" , version 1 , source { { src { db "Protein" , tag id 825615 } , anchor "CAA48670" } } , seqs { whole gi 825615 } } } } , { type genomic , heading "Genomic" , accession "Z11711" , version 1 , source { { src { db "Nucleotide" , tag id 24760 } , anchor "Z11711" } } , seqs { whole gi 24760 } , products { { type peptide , accession "CAA77774" , version 1 , source { { src { db "Protein" , tag id 24761 } , anchor "CAA77774" } } , seqs { whole gi 24761 } } } } , { type mRNA , heading "mRNA" , accession "AB209614" , version 1 , source { { src { db "Nucleotide" , tag id 62088807 } , anchor "AB209614" } } , seqs { whole gi 62088807 } , products { { type peptide , accession "BAD92851" , version 1 , source { { src { db "Protein" , tag id 62088808 } , anchor "BAD92851" } } , seqs { whole gi 62088808 } } } } , { type mRNA , heading "mRNA" , accession "AF109189" , version 1 , source { { src { db "Nucleotide" , tag id 33337723 } , anchor "AF109189" } } , seqs { whole gi 33337723 } , products { { type peptide , accession "AAQ13498" , version 1 , source { { src { db "Protein" , tag id 33337724 } , anchor "AAQ13498" } } , seqs { whole gi 33337724 } } } } , { type mRNA , heading "mRNA" , accession "AY591530" , version 1 , source { { src { db "Nucleotide" , tag id 46812314 } , anchor "AY591530" } } , seqs { whole gi 46812314 } , products { { type peptide , accession "AAT02228" , version 1 , source { { src { db "Protein" , tag id 46812315 } , anchor "AAT02228" } } , seqs { whole gi 46812315 } } } } , { type mRNA , heading "mRNA" , accession "BC026246" , version 1 , source { { src { db "Nucleotide" , tag id 45708660 } , anchor "BC026246" } } , seqs { whole gi 45708660 } , products { { type peptide , accession "AAH26246" , version 1 , source { { src { db "Protein" , tag id 45708661 } , anchor "AAH26246" } } , seqs { whole gi 45708661 } } } } , { type mRNA , heading "mRNA" , accession "BC040071" , version 1 , source { { src { db "Nucleotide" , tag id 25303945 } , anchor "BC040071" } } , seqs { whole gi 25303945 } , products { { type peptide , accession "AAH40071" , version 1 , source { { src { db "Protein" , tag id 25303946 } , anchor "AAH40071" } } , seqs { whole gi 25303946 } } } } , { type mRNA , heading "mRNA" , accession "BX647329" , version 1 , source { { src { db "Nucleotide" , tag id 34366357 } , anchor "BX647329" } } , seqs { whole gi 34366357 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "CR749334" , version 1 , source { { src { db "Nucleotide" , tag id 51476395 } , anchor "CR749334" } } , seqs { whole gi 51476395 } , products { { type peptide , accession "CAH18188" , version 1 , source { { src { db "Protein" , tag id 51476396 } , anchor "CAH18188" } } , seqs { whole gi 51476396 } } } } , { type mRNA , heading "mRNA" , accession "M11313" , version 1 , source { { src { db "Nucleotide" , tag id 177869 } , anchor "M11313" } } , seqs { whole gi 177869 } , products { { type peptide , accession "AAA51551" , version 1 , source { { src { db "Protein" , tag id 177870 } , anchor "AAA51551" } } , seqs { whole gi 177870 } } } } , { type mRNA , heading "mRNA" , accession "M36501" , version 1 , source { { src { db "Nucleotide" , tag id 177871 } , anchor "M36501" } } , seqs { whole gi 177871 } , products { { type peptide , accession "AAA51552" , version 1 , source { { src { db "Protein" , tag id 177872 } , anchor "AAA51552" } } , seqs { whole gi 177872 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P01023" , version 0 , source { { src { db "Protein" , tag id 112911 } , anchor "P01023" } } , seqs { whole gi 112911 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "2" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_009714.16&gene=A2M&lid=2&from=1979284&to=2027463" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "2" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_009714.16&gene=A2M&lid=2" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.212838" } } , source { { src { db "UniGene" , tag str "Hs.212838" } , anchor "Hs.212838" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=21 2838" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "103950" } , anchor "103950" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "2" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 2[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 2 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=2" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:119639" } } } } , { type comment , version 0 , source { { src { db "HGMD" , tag str "" } , url "http://www.uwcm.ac.uk/uwcm/mg/search/119639.html" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=CR749 334" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= CR749334" } } } , { type comment , version 0 , source { { src { db "KEGG" , tag str "" } , url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:2" } } } , { type comment , text "PharmGKB" , version 0 , source { { src { db "PharmGKB" , tag str "PA24357" } , anchor "PA24357" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC040071" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC040071" } } } } } , { type comment , heading "Pathways" , version 0 , comment { { type comment , text "KEGG pathway: Alzheimer's disease" , version 0 , source { { src { db "05010" , tag str "05010" } , anchor "05010" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+2" } } } , { type comment , text "KEGG pathway: Coagulation cascade" , version 0 , source { { src { db "04610" , tag str "04610" } , anchor "04610" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } , { type comment , text "KEGG pathway: Complement and coagulation cascades" , version 0 , source { { src { db "04610" , tag str "04610" } , anchor "04610" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } , { type comment , text "Reactome: Hemostasis" , version 0 , source { { anchor "49292" , url "http://www.reactome.org/cgi-bin/link?SOURCE=UniProt&ID=P010 23" } } } } } , { type generif , text "an important involvement of alpha2M in regulation of increased proteolytic activity occurring in multiple sclerosis disease" , version 0 , refs { pmid 15511627 } , create-date str "Dec 18 2004 10:01AM" , update-date str "Dec 18 2004 1:19PM" } , { type generif , text "alpha2-macroglobulin inhibits human pepsin and gastricsin" , version 0 , refs { pmid 14506912 } , create-date str "Oct 7 2003 12:00AM" , update-date str "Jul 7 2004 1:36PM" } , { type generif , text "There is a significant genetic association of the 5 bp deletion and two novel polymorphisms in alpha-2-macroglobulin alpha-2-macroglobulin precursor with AD" , version 0 , refs { pmid 12966032 } , create-date str "Jun 27 2004 5:41PM" , update-date str "Jun 27 2004 6:18PM" } , { type generif , text "Alpha2-macroglobulin is a substrate and an endogenous inhibitor for ADAMTS-4 and ADAMTS-5" , version 0 , refs { pmid 14715656 } , create-date str "Jun 14 2004 4:41PM" , update-date str "Jun 14 2004 5:44PM" } , { type generif , text "A2M-D allele played a weak Alzheimer disease protective role, and APOE-E4 and A2M-G alleles might act synergistically in Alzheimer disease risk for mainland Han Chinese." , version 0 , refs { pmid 14675603 } , create-date str "Feb 17 2004 12:00AM" , update-date str "Apr 13 2004 1:35PM" } , { type generif , text "Plasma from patients homozygous for the intronic deletion (DD) showed normal alpha(2)M subunit size, conformation, and proteinase inhibitory activity. Plasma alpha(2)M from two DD patients showed markedly increased TGF-beta1 binding." , version 0 , refs { pmid 14678766 } , create-date str "Jan 20 2004 12:00AM" , update-date str "Mar 7 2004 7:01AM" } , { type generif , text "The presence of MPO-G/G and A2M-Val/Val genotypes synergistically increased the risk of AD (OR, 25.5; 95% CI, 4.65-139.75)." , version 0 , refs { pmid 15023809 } , create-date str "Mar 25 2004 12:00AM" , update-date str "Apr 18 2004 7:02AM" } , { type generif , text "alpha2-M deletion polymorphism is probably not associated with functional deficiencies important in Alzheimer's disease pathology" , version 0 , refs { pmid 14637088 } , create-date str "Dec 31 2003 12:00AM" , update-date str "Jan 11 2004 7:02AM" } , { type generif , text "FGF-2 and this protein interact at specific binding sites, involving different FGF-2 sequences." , version 0 , refs { pmid 12755687 } , create-date str "Sep 7 2003 12:00AM" , update-date str "Sep 28 2003 7:01AM" } , { type generif , text "alpha(2)M-derived peptides target the receptor-binding sequence in TGF-beta" , version 0 , refs { pmid 12755614 } , create-date str "Jun 25 2003 12:00AM" , update-date str "Jul 6 2003 7:01AM" } , { type generif , text "These results suggest the possible involvement of cathepsin E in disruption of the structural and functional integrity of alpha 2-macroglobulin in the endolysosome system." , version 0 , refs { pmid 12631277 } , create-date str "May 8 2003 12:00AM" , update-date str "May 11 2003 7:01AM" } , { type generif , text "Alpha 2-macroglobulin enhances prothrombin activation and thrombin potential by inhibiting the anticoagulant protein C/protein S system in cord and adult plasma." , version 0 , refs { pmid 12062545 } , create-date str "Feb 6 2003 12:00AM" , update-date str "Aug 17 2003 7:01AM" } , { type generif , text "relationship between serum VEGF levels, alpha(2)M levels and the development of OHSS in hyperstimulated subjects undergoing IVF" , version 0 , refs { pmid 12042276 } , create-date str "Dec 16 2002 12:00AM" , update-date str "Feb 2 2003 7:00AM" } , { type generif , text "Genetic association of alpha2-macroglobulin polymorphisms with Alzheimer's disease" , version 0 , refs { pmid 12221172 } , create-date str "Sep 27 2002 12:00AM" , update-date str "Oct 7 2002 8:10AM" } , { type generif , text "Genetic association of argyrophilic grain disease with polymorphisms in alpha-2 macroglobulin." , version 0 , refs { pmid 12175343 } , create-date str "Sep 24 2002 12:00AM" , update-date str "Oct 7 2002 8:10AM" } , { type generif , text "The three-dimensional structure of the dimer reveals its structural organization in the tetrameric native and chymotrypsin alpha 2-macroglobulin complexes." , version 0 , refs { pmid 12015318 } , create-date str "Sep 5 2002 12:00AM" , update-date str "Sep 23 2002 6:27AM" } , { type generif , text "has an important role in the AD-specific neurodegenerative process but its exon 24 Val-1000-Ile polymorphism is not likely to be associated with late-onset sporadic AD in the Hungarian population" , version 0 , refs { pmid 11901360 } , create-date str "Aug 6 2002 12:00AM" , update-date str "Aug 28 2002 6:15PM" } , { type generif , text "REVIEW: binds and neutralizes alfimeprase, which has direct proteolytic activity against the fibrinogen Aalpha chain" , version 0 , refs { pmid 11910179 } , create-date str "Jun 12 2002 12:00AM" , update-date str "Sep 7 2003 7:01AM" } , { type generif , text "distinct binding sites mediate interaction with beta-amyloid peptide and growth factors" , version 0 , refs { pmid 11823454 } , create-date str "May 4 2002 12:00AM" , update-date str "May 18 2002 6:08AM" } , { type generif , text "Differential binding to ldl receptor related protein" , version 0 , refs { pmid 11811950 } , create-date str "Feb 14 2002 12:00AM" , update-date str "Mar 4 2002 7:46AM" } , { type generif , heading "HIV-1 protein interactions" , version 0 , comment { { type generif , text "Binding of HIV-1 Tat to LRP inhibits neuronal binding, uptake and degradation of physiological ligands for LRP, including alpha2-macroglobulin, apolipoprotein E4, amyloid precursor and amyloid beta-protein" , version 0 , refs { pmid 11100124 } , comment { { type comment , label "Tat" , accession "NP_057853" , version 1 , source { { src { db "GeneID" , tag id 155871 } } } } , { type comment , accession "NP_000005" , version 1 } } , create-date str "May 11 2004 12:48PM" , update-date str "May 11 2004 1:10PM" } } } } , unique-keys { { db "LocusID" , tag id 2 } , { db "MIM" , tag id 103950 } } , xtra-index-terms { "LOC2" } , xtra-properties { { tag "PROP" , value "phenotype" } } } Entrezgene ::= { track-info { geneid 3 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type pseudo , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "12" } } } , gene { locus "A2MP" , desc "alpha-2-macroglobulin pseudogene" , maploc "12p13.3-p12.3" , locus-tag "HGNC:8" } , location { { display-str "12p13.3-p12.3" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 3 , src-str2 "3" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000012" , version 9 , seqs { int { from 9275468 , to 9278174 , strand minus , id gi 51511728 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NT_009714" , version 16 , seqs { int { from 2143175 , to 2145881 , strand minus , id gi 37543832 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NT_086792" , version 1 , seqs { int { from 4337316 , to 4340022 , strand minus , id gi 51471135 , fuzz-from lim lt , fuzz-to lim gt } } } , { type genomic , heading "Reference" , accession "NG_001067" , version 1 , seqs { int { from 176 , to 2880 , strand plus , id gi 20270626 , fuzz-from lim lt , fuzz-to lim gt } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "A2MP" , version 0 } , { type property , label "Official Full Name" , text "alpha-2-macroglobulin pseudogene" , version 0 } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 8 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 2478422 } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , comment { { type genomic , heading "Reference" , accession "NG_001067" , version 1 , source { { src { db "Nucleotide" , tag id 20270626 } , anchor "NG_001067" } } , seqs { int { from 1 , to 3003 , strand plus , id gi 20270626 } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "M24415" , version 1 , source { { src { db "Nucleotide" , tag id 187575 } , anchor "M24415" } } , seqs { int { from 177 , to 2881 , strand plus , id gi 187575 } } , products { { type peptide , text "None" , version 0 } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "3" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_009714.16&gene=A2MP&lid=3&from=2143176&to=2145882" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "3" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_009714.16&gene=A2MP&lid=3" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 3 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=3" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:128103" } } } } } } } , unique-keys { { db "LocusID" , tag id 3 } } , xtra-index-terms { "LOC3" } } Entrezgene ::= { track-info { geneid 4 , status discontinued , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "1" } } } , gene { desc "adenovirus-12 chromosome modification site 1C" , maploc "1q42-q43" , syn { "A12M1" } } , prot { name { "adenovirus-12 chromosome modification site 1C" , "Adenovirus-12 chromosome modification site-1q1" } } , location { { display-str "1q42-q43" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 4 , src-str2 "4" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , comments { { type comment , heading "RefSeq Status" , label "WITHDRAWN" , version 0 } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118950" } } } } } } } , unique-keys { { db "LocusID" , tag id 4 } } , xtra-index-terms { "LOC4" } } Entrezgene ::= { track-info { geneid 5 , status discontinued , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "1" } } } , gene { desc "adenovirus-12 chromosome modification site 1A" , maploc "1p36" , syn { "A12M2" } } , prot { name { "adenovirus-12 chromosome modification site 1A" , "Adenovirus-12 chromosome modification site-1p" } } , location { { display-str "1p36" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 5 , src-str2 "5" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , comments { { type comment , heading "RefSeq Status" , label "WITHDRAWN" , version 0 } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118951" } } } } } } } , unique-keys { { db "LocusID" , tag id 5 } } , xtra-index-terms { "LOC5" } } Entrezgene ::= { track-info { geneid 6 , status discontinued , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "1" } } } , gene { desc "adenovirus-12 chromosome modification site 1B" , maploc "1q21" , syn { "A12M3" } } , prot { name { "adenovirus-12 chromosome modification site 1B" , "Adenovirus-12 chromosome modification site-1q2" } } , location { { display-str "1q21" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 6 , src-str2 "6" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , comments { { type comment , heading "RefSeq Status" , label "WITHDRAWN" , version 0 } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118952" } } } } } } } , unique-keys { { db "LocusID" , tag id 6 } } , xtra-index-terms { "LOC6" } } Entrezgene ::= { track-info { geneid 7 , status discontinued , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "17" } } } , gene { desc "adenovirus-12 chromosome modification site 17" , maploc "17q21-q22" , syn { "A12M4" } } , prot { name { "adenovirus-12 chromosome modification site 17" } } , location { { display-str "17q21-q22" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 7 , src-str2 "7" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , comments { { type comment , heading "RefSeq Status" , label "WITHDRAWN" , version 0 } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118953" } } } } } } } , unique-keys { { db "LocusID" , tag id 7 } } , xtra-index-terms { "LOC7" } } Entrezgene ::= { track-info { geneid 8 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 3 , day 16 , hour 16 , minute 24 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "11" } } } , gene { locus "AA" , desc "atrophia areata, peripapillary chorioretinal degeneration" , maploc "11p15" , db { { db "MIM" , tag id 108985 } } , locus-tag "HGNC:11" } , location { { display-str "11p15" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 8 , src-str2 "8" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "AA" , version 0 } , { type property , label "Official Full Name" , text "atrophia areata, peripapillary chorioretinal degeneration" , version 0 } } } , { type property , label "Property" , text "phenotype only" , version 0 } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 11 } } } } , { type comment , version 0 , refs { pmid 7795606 } } , { type comment , heading "Phenotypes" , version 0 , comment { { type phenotype , text "Atrophia areata" , version 0 , source { { src { db "MIM" , tag id 108985 } , anchor "MIM: 108985" } } } , { type phenotype , label "AA" , text "atrophia areata, peripapillary chorioretinal degeneration" , version 0 , source { { src { db "HGNC" , tag id 11 } , anchor "HGNC:11" } } } } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 31863 } , anchor "D11S902" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "072YD3" , version 0 } , { type other , label "Alternate name" , text "AFM072yd3" , version 0 } , { type other , label "Alternate name" , text "GDB:187919" , version 0 } , { type other , label "Alternate name" , text "HS072YD3" , version 0 } , { type other , label "Alternate name" , text "RH15041" , version 0 } , { type other , label "Alternate name" , text "RH3044" , version 0 } , { type other , label "Alternate name" , text "RH51860" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 31863 } , anchor "D11S902 (flanking)" } } , comment { { type other , label "Alternate name" , text "072YD3" , version 0 } , { type other , label "Alternate name" , text "AFM072yd3" , version 0 } , { type other , label "Alternate name" , text "GDB:187919" , version 0 } , { type other , label "Alternate name" , text "HS072YD3" , version 0 } , { type other , label "Alternate name" , text "RH15041" , version 0 } , { type other , label "Alternate name" , text "RH3044" , version 0 } , { type other , label "Alternate name" , text "RH51860" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 67612 } , anchor "D11S1323" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "AFM248xf9" , version 0 } , { type other , label "Alternate name" , text "RH31202" , version 0 } , { type other , label "Alternate name" , text "RH73986" , version 0 } , { type other , label "Alternate name" , text "SHGC-2070" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 67612 } , anchor "D11S1323 (flanking)" } } , comment { { type other , label "Alternate name" , text "AFM248xf9" , version 0 } , { type other , label "Alternate name" , text "RH31202" , version 0 } , { type other , label "Alternate name" , text "RH73986" , version 0 } , { type other , label "Alternate name" , text "SHGC-2070" , version 0 } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "108985" } , anchor "108985" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:568984" } } } } } } } , unique-keys { { db "LocusID" , tag id 8 } , { db "MIM" , tag id 108985 } } , xtra-index-terms { "LOC8" } , xtra-properties { { tag "PROP" , value "phenotype" } , { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 9 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 15 , hour 9 , minute 40 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "8" } } } , gene { locus "NAT1" , desc "N-acetyltransferase 1 (arylamine N-acetyltransferase)" , maploc "8p23.1-p21.3" , db { { db "MIM" , tag id 108345 } } , syn { "AAC1" } , locus-tag "HGNC:7645" } , prot { name { "N-acetyltransferase 1" , "arylamine N-acetyltransferase 1" , "arylamide acetylase 1 (N-acetyltransferase 1)" } } , location { { display-str "8p23.1-p21.3" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 9 , src-str2 "9" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000008" , version 9 , seqs { int { from 18111894 , to 18125099 , strand plus , id gi 51511724 } } , products { { type mRNA , heading "Reference" , accession "NM_000662" , version 4 , genomic-coords { mix { int { from 18111894 , to 18111968 , strand plus , id gi 51511724 } , int { from 18121199 , to 18121277 , strand plus , id gi 51511724 } , int { from 18123830 , to 18125099 , strand plus , id gi 51511724 } } } , seqs { whole gi 42741670 } , products { { type peptide , heading "Reference" , accession "NP_000653" , version 3 , genomic-coords { int { from 18123836 , to 18124708 , strand plus , id gi 51511724 } } , seqs { whole gi 42741671 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_030737" , version 9 , seqs { int { from 5912542 , to 5925747 , strand plus , id gi 51466871 } } , products { { type mRNA , heading "Reference" , accession "NM_000662" , version 4 , genomic-coords { mix { int { from 5912542 , to 5912616 , strand plus , id gi 51466871 } , int { from 5921847 , to 5921925 , strand plus , id gi 51466871 } , int { from 5924478 , to 5925747 , strand plus , id gi 51466871 } } } , seqs { whole gi 42741670 } , products { { type peptide , heading "Reference" , accession "NP_000653" , version 3 , genomic-coords { int { from 5924484 , to 5925356 , strand plus , id gi 51466871 } } , seqs { whole gi 42741671 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_086740" , version 1 , seqs { int { from 5593338 , to 5606579 , strand plus , id gi 51467159 } } , products { { type mRNA , heading "Reference" , accession "NM_000662" , version 4 , genomic-coords { mix { int { from 5593338 , to 5593412 , strand plus , id gi 51467159 } , int { from 5602680 , to 5602758 , strand plus , id gi 51467159 } , int { from 5605310 , to 5606579 , strand plus , id gi 51467159 } } } , seqs { whole gi 42741670 } , products { { type peptide , heading "Reference" , accession "NP_000653" , version 3 , genomic-coords { int { from 5605316 , to 5606188 , strand plus , id gi 51467159 } } , seqs { whole gi 42741671 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "NAT1" , version 0 } , { type property , label "Official Full Name" , text "N-acetyltransferase 1 (arylamine N-acetyltransferase)" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 16407 } , anchor "acetyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 10908296 } , source { { src { db "GO" , tag id 4060 } , anchor "arylamine N-acetyltransferase activity" , post-text "evidence: TAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16740 } , anchor "transferase activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8152 } , anchor "metabolism" , post-text "evidence: IEA" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 37329 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&M APS=genes-r-org/rat-chr/human%3A8,genes-r-org/mouse-chr/human%3A8,genes-r-org/ human-chr8&query=e%3A9[id]+AND+gene[obj_type]&QSTR=nat1&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 7645 } } } } , { type comment , heading "RefSeq Status" , label "VALIDATED" , version 0 } , { type comment , version 0 , refs { pmid 15487985 , pmid 15320760 , pmid 15226672 , pmid 15039438 , pmid 14705222 , pmid 14672957 , pmid 14608357 , pmid 14517345 , pmid 12946272 , pmid 12902152 , pmid 12888564 , pmid 12860276 , pmid 12832400 , pmid 12692115 , pmid 12682333 , pmid 12485520 , pmid 12477932 , pmid 12355549 , pmid 12052143 , pmid 12037388 , pmid 11955677 , pmid 11955676 , pmid 11927838 , pmid 11470991 , pmid 10908296 , pmid 10862520 , pmid 10767335 , pmid 9168895 , pmid 8110178 , pmid 7773298 , pmid 2340091 , pmid 1968463 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 24445 } , anchor "STS-R79401" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH40594" , version 0 } , { type other , label "Alternate name" , text "sts-R79401" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 57372 } , anchor "STS-D90041" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH75822" , version 0 } , { type other , label "Alternate name" , text "sts-D90041" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 63787 } , anchor "RH70671" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "U52007" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 271536 } , anchor "PMC165273P2" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_000662" , version 4 , source { { src { db "Nucleotide" , tag id 42741670 } , anchor "NM_000662" } } , seqs { whole gi 42741670 } , products { { type peptide , heading "Product" , accession "NP_000653" , version 3 , source { { src { db "Protein" , tag id 42741671 } , anchor "NP_000653" , post-text "N-acetyltransferase 1" } } , seqs { whole gi 42741671 } , comment { { type other , heading "Consensus CDS (CCDS)" , version 0 , source { { src { db "CCDS" , tag str "CCDS6007.1" } , anchor "CCDS6007.1" } } } , { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 42741671 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 1353 } , anchor "pfam00797: Acetyltransf_2; N-acetyltransferase" } } , comment { { type other , text "Location: 20 - 280 Blast Score: 1195" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AV754344,BC047666,BQ024509" } , anchor "AV754344,BC047666,BQ024509" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AF008204" , version 1 , source { { src { db "Nucleotide" , tag id 2618821 } , anchor "AF008204" } } , seqs { whole gi 2618821 } , products { { type peptide , accession "AAB84384" , version 1 , source { { src { db "Protein" , tag id 2258431 } , anchor "AAB84384" } } , seqs { whole gi 2258431 } } } } , { type genomic , heading "Genomic" , accession "AF032677" , version 1 , source { { src { db "Nucleotide" , tag id 2641552 } , anchor "AF032677" } } , seqs { whole gi 2641552 } , products { { type peptide , accession "AAB86878" , version 1 , source { { src { db "Protein" , tag id 2641553 } , anchor "AAB86878" } } , seqs { whole gi 2641553 } } } } , { type genomic , heading "Genomic" , accession "AF032678" , version 1 , source { { src { db "Nucleotide" , tag id 2641554 } , anchor "AF032678" } } , seqs { whole gi 2641554 } , products { { type peptide , accession "AAB86879" , version 1 , source { { src { db "Protein" , tag id 2641555 } , anchor "AAB86879" } } , seqs { whole gi 2641555 } } } } , { type genomic , heading "Genomic" , accession "AF067408" , version 1 , source { { src { db "Nucleotide" , tag id 3265061 } , anchor "AF067408" } } , seqs { whole gi 3265061 } , products { { type peptide , accession "AAC24707" , version 1 , source { { src { db "Protein" , tag id 3265062 } , anchor "AAC24707" } } , seqs { whole gi 3265062 } } } } , { type genomic , heading "Genomic" , accession "AF071552" , version 1 , source { { src { db "Nucleotide" , tag id 3265151 } , anchor "AF071552" } } , seqs { whole gi 3265151 } , products { { type peptide , accession "AAC24712" , version 1 , source { { src { db "Protein" , tag id 3265152 } , anchor "AAC24712" } } , seqs { whole gi 3265152 } } } } , { type genomic , heading "Genomic" , accession "AF082903" , version 1 , source { { src { db "Nucleotide" , tag id 3435297 } , anchor "AF082903" } } , seqs { whole gi 3435297 } , products { { type peptide , accession "AAD13343" , version 1 , source { { src { db "Protein" , tag id 3435298 } , anchor "AAD13343" } } , seqs { whole gi 3435298 } } } } , { type genomic , heading "Genomic" , accession "AF082904" , version 1 , source { { src { db "Nucleotide" , tag id 3435299 } , anchor "AF082904" } } , seqs { whole gi 3435299 } , products { { type peptide , accession "AAC32388" , version 1 , source { { src { db "Protein" , tag id 3435300 } , anchor "AAC32388" } } , seqs { whole gi 3435300 } } } } , { type genomic , heading "Genomic" , accession "AF308866" , version 1 , source { { src { db "Nucleotide" , tag id 10834832 } , anchor "AF308866" } } , seqs { whole gi 10834832 } , products { { type peptide , accession "AAG23842" , version 1 , source { { src { db "Protein" , tag id 10834833 } , anchor "AAG23842" } } , seqs { whole gi 10834833 } } } } , { type genomic , heading "Genomic" , accession "AJ278017" , version 1 , source { { src { db "Nucleotide" , tag id 9663144 } , anchor "AJ278017" } } , seqs { whole gi 9663144 } , products { { type peptide , accession "CAC01128" , version 1 , source { { src { db "Protein" , tag id 9663145 } , anchor "CAC01128" } } , seqs { whole gi 9663145 } } } } , { type genomic , heading "Genomic" , accession "AJ307007" , version 1 , source { { src { db "Nucleotide" , tag id 14018355 } , anchor "AJ307007" } } , seqs { whole gi 14018355 } , products { { type peptide , accession "CAC38345" , version 1 , source { { src { db "Protein" , tag id 14018356 } , anchor "CAC38345" } } , seqs { whole gi 14018356 } } } } , { type genomic , heading "Genomic" , accession "AY338489" , version 1 , source { { src { db "Nucleotide" , tag id 32815075 } , anchor "AY338489" } } , seqs { whole gi 32815075 } , products { { type peptide , accession "AAP88036" , version 1 , source { { src { db "Protein" , tag id 32815076 } , anchor "AAP88036" } } , seqs { whole gi 32815076 } } } } , { type genomic , heading "Genomic" , accession "AY376850" , version 1 , source { { src { db "Nucleotide" , tag id 34555772 } , anchor "AY376850" } } , seqs { whole gi 34555772 } , products { { type peptide , accession "AAQ74989" , version 1 , source { { src { db "Protein" , tag id 34555773 } , anchor "AAQ74989" } } , seqs { whole gi 34555773 } } } } , { type genomic , heading "Genomic" , accession "U80835" , version 1 , source { { src { db "Nucleotide" , tag id 2245375 } , anchor "U80835" } } , seqs { whole gi 2245375 } , products { { type peptide , accession "AAB62398" , version 1 , source { { src { db "Protein" , tag id 2245376 } , anchor "AAB62398" } } , seqs { whole gi 2245376 } } } } , { type genomic , heading "Genomic" , accession "X17059" , version 1 , source { { src { db "Nucleotide" , tag id 34993 } , anchor "X17059" } } , seqs { whole gi 34993 } , products { { type peptide , accession "CAA34905" , version 1 , source { { src { db "Protein" , tag id 34994 } , anchor "CAA34905" } } , seqs { whole gi 34994 } } } } , { type mRNA , heading "mRNA" , accession "AV754344" , version 1 , source { { src { db "Nucleotide" , tag id 10912192 } , anchor "AV754344" } } , seqs { whole gi 10912192 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC013732" , version 1 , source { { src { db "Nucleotide" , tag id 16975545 } , anchor "BC013732" } } , seqs { whole gi 16975545 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC047666" , version 1 , source { { src { db "Nucleotide" , tag id 28838335 } , anchor "BC047666" } } , seqs { whole gi 28838335 } , products { { type peptide , accession "AAH47666" , version 1 , source { { src { db "Protein" , tag id 28838336 } , anchor "AAH47666" } } , seqs { whole gi 28838336 } } } } , { type mRNA , heading "mRNA" , accession "BQ024509" , version 1 , source { { src { db "Nucleotide" , tag id 19759788 } , anchor "BQ024509" } } , seqs { whole gi 19759788 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BX647521" , version 1 , source { { src { db "Nucleotide" , tag id 34366678 } , anchor "BX647521" } } , seqs { whole gi 34366678 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "D90041" , version 1 , source { { src { db "Nucleotide" , tag id 219413 } , anchor "D90041" } } , seqs { whole gi 219413 } , products { { type peptide , accession "BAA14095" , version 1 , source { { src { db "Protein" , tag id 219414 } , anchor "BAA14095" } } , seqs { whole gi 219414 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P18440" , version 0 , source { { src { db "Protein" , tag id 114234 } , anchor "P18440" } } , seqs { whole gi 114234 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "9" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_030737.9&gene=NAT1&lid=9&from=5912543&to=5925748" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "9" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_030737.9&gene=NAT1&lid=9" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.155956" } } , source { { src { db "UniGene" , tag str "Hs.155956" } , anchor "Hs.155956" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=15 5956" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "108345" } , anchor "108345" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "9" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 9[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 9 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=9" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:125364" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=BC013 732" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= BC013732" } } } , { type comment , text "PharmGKB" , version 0 , source { { src { db "PharmGKB" , tag str "PA17" } , anchor "PA17" } } } , { type comment , text "Arylamine N-Acetyltransferase Nomenclature" , version 0 , source { { src { db "Arylamine N-Acetyltransferase Nomenclature" , tag str "Arylamine N-Acetyltransferase Nomenclature" } , anchor "Arylamine N-Acetyltransferase Nomenclature" , url "http://www.louisville.edu/medschool/pharmacology/NAT.html" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC047666" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC047666" } } } } } , { type generif , text "In breast, NAT1 mRNA is transcribed from a strong promoter located 11.8 kb upstream of the translated exon, and the mature spliced mRNA includes at least one additional non-coding exon." , version 0 , refs { pmid 15226672 } , create-date str "Mar 26 2005 10:01AM" , update-date str "Mar 26 2005 1:53PM" } , { type generif , text "Polymorphism at the NAT1 locus has been associated with the existence of at least 26 allelic variants, generating phenotypic variations in terms NAT-1 catalytic activity. This genetic variation affects the acetylator status of individuals." , version 0 , refs { pmid 15320760 } , create-date str "Dec 18 2004 10:01AM" , update-date str "Mar 17 2005 6:52AM" } , { type generif , text "NAT1 exists in the cell in either a stable acetylated state or an unstable non-acetylated state and mutations in the NAT1 gene that prevent protein acetylation produce a slow acetylator phenotype" , version 0 , refs { pmid 15039438 } , create-date str "Jul 6 2004 11:50AM" , update-date str "Jul 6 2004 12:11PM" } , { type generif , text "Analysis of the effect of active NAT-1 overexpression in a normal luminal epithelial-derived cell line demonstrated enhanced growth properties and etoposide resistance relative to control cells." , version 0 , refs { pmid 14517345 } , create-date str "Jun 23 2004 4:43PM" , update-date str "Jun 23 2004 5:16PM" } , { type generif , text "cellular generation of peroxynitrite may contribute to carcinogenesis and tumor progression by weakening key cellular defense enzymes such as arylamine N-acetyltransferase 1 (NAT1)" , version 0 , refs { pmid 14672957 } , create-date str "Mar 24 2004 12:00AM" , update-date str "May 9 2004 7:01AM" } , { type generif , text "although there is little overall association between NAT genotypes and risk of developing systemic lupus erythematosus, the interaction between NAT1 and NAT2 and specific exposures such as hair dyes may be important." , version 0 , refs { pmid 14705222 } , create-date str "Apr 16 2004 12:00AM" , update-date str "May 2 2004 7:01AM" } , { type generif , text "A putative RUNX1 binding site variant of NAT9 is associated with susceptibility to psoriasis" , version 0 , refs { pmid 14608357 } , create-date str "Dec 18 2003 12:00AM" , update-date str "Jan 11 2004 7:03AM" } , { type generif , text "Identification of minimal promoter sequences for transcription factor binding sites in the human N-acetyltransferase Type I gene. that binds" , version 0 , refs { pmid 12946272 } , create-date str "Nov 24 2003 12:00AM" , update-date str "Dec 7 2003 7:02AM" } , { type generif , text "Oxidative stress and cellular redox status may regulate NAT1 activity and have important consequences with regard to drug biotransformation and cancer risk." , version 0 , refs { pmid 12832400 } , create-date str "Oct 7 2003 12:00AM" , update-date str "Nov 16 2003 7:02AM" } , { type generif , text "Variation in capacity for acetylation of 4ABP and PABA resulting from human NAT1 transgene is insufficient to affect 4ABP genotoxicity in mouse liver." , version 0 , refs { pmid 12902152 } , create-date str "Sep 6 2003 12:00AM" , update-date str "Sep 14 2003 7:01AM" } , { type generif , text "It is unlikely that the NAT1*10 or NAT2 rapid/intermediate genotypes are related to stomach cancer risk." , version 0 , refs { pmid 12692115 } , create-date str "Sep 4 2003 12:00AM" , update-date str "Sep 28 2003 7:01AM" } , { type generif , text "genetic polymorphisms of NAT1 and NAT2 have no independent effect on breast cancer risk, but they modulate breast cancer risk in the presence of GSTM1 and GSTT1 null genotypes." , version 0 , refs { pmid 12860276 } , create-date str "Aug 18 2003 12:00AM" , update-date str "Aug 24 2003 7:01AM" } , { type generif , text "NAT1 * 10 has increased risk of sporadic colorectal adenocarcinoma and significantly related to the later stage tumors, is not significantly related to the tumor location" , version 0 , refs { pmid 12485520 } , create-date str "Jun 25 2003 12:00AM" , update-date str "Jul 13 2003 7:01AM" } , { type generif , text "Single nucleotide polymorphisms of NAT1 and NAT2, and acetylation haplotype were not associated with increased risk for Parkinson disease" , version 0 , refs { pmid 12682333 } , create-date str "Apr 11 2003 12:00AM" , update-date str "Apr 27 2003 7:01AM" } , { type generif , text "NAT1 polymorphism (NAT1*10) indicates increased susceptibility to prostate cancer" , version 0 , refs { pmid 12355549 } , create-date str "Oct 31 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "susceptibility gene for multifactorial adverse effects and xenobiotic-related diseases (review)" , version 0 , refs { pmid 12052143 } , create-date str "Sep 12 2002 12:00AM" , update-date str "Sep 16 2002 5:48AM" } , { type generif , text "NAT1 genotype acts as a modifier of diisothionate exposure-associated asthma risk" , version 0 , refs { pmid 11927838 } , create-date str "Aug 30 2002 12:00AM" , update-date str "Sep 16 2002 5:48AM" } , { type generif , text "NAT1 polymorphisms may be correlated with an increased risk of larynx cancer" , version 0 , refs { pmid 12037388 } , create-date str "Aug 19 2002 12:00AM" , update-date str "Aug 28 2002 6:15PM" } , { type generif , text "paclitaxel affected human leukemia HL-60 cells arylamine N-acetyltransferase (NAT) activity and DNA-2-aminofluorene adduct formation." , version 0 , refs { pmid 11955677 } , create-date str "Jun 19 2002 12:00AM" , update-date str "Jun 24 2002 6:31AM" } , { type generif , text "paclitaxel is an uncompetitive inhibitor to arylamine N-acetyltransferase (NAT) enzyme" , version 0 , refs { pmid 11955676 } , create-date str "Jun 19 2002 12:00AM" , update-date str "Jun 24 2002 6:31AM" } } , unique-keys { { db "LocusID" , tag id 9 } , { db "MIM" , tag id 108345 } } , xtra-index-terms { "LOC9" } } Entrezgene ::= { track-info { geneid 10 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 17 , hour 11 , minute 9 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "8" } } } , gene { locus "NAT2" , desc "N-acetyltransferase 2 (arylamine N-acetyltransferase)" , maploc "8p22" , db { { db "MIM" , tag id 243400 } } , syn { "AAC2" } , locus-tag "HGNC:7646" } , prot { name { "arylamide acetylase 2" , "Arylamine N-acetyltransferase-2" , "arylamide acetylase 2 (N-acetyltransferase 2, isoniazid inactivation)" } } , summary "The intronless NAT2 gene encodes N-acetyltransferase 2 (arylamine N-acetyltransferase 2). This enzyme functions to both activate and deactivate arylamine and hydrazine drugs and carcinogens. Polymorphisms in this gene are reponsible for the N-acetylation polymorphism in which human populations segregate into rapid,intermediate, and slow acetylator phenotypes. Polymorphisms in NAT2 are also associated with higher incidences of cancer and drug toxicity.A second arylamine N-acetyltransferase gene (NAT1) is located near NAT2." , location { { display-str "8p22" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 10 , src-str2 "10" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000008" , version 9 , seqs { int { from 18293034 , to 18302961 , strand plus , id gi 51511724 } } , products { { type mRNA , heading "Reference" , accession "NM_000015" , version 1 , genomic-coords { mix { int { from 18293034 , to 18293134 , strand plus , id gi 51511724 } , int { from 18301787 , to 18302961 , strand plus , id gi 51511724 } } } , seqs { whole gi 4557782 } , products { { type peptide , heading "Reference" , accession "NP_000006" , version 1 , genomic-coords { int { from 18301793 , to 18302665 , strand plus , id gi 51511724 } } , seqs { whole gi 4557783 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_030737" , version 9 , seqs { int { from 6093682 , to 6103609 , strand plus , id gi 51466871 } } , products { { type mRNA , heading "Reference" , accession "NM_000015" , version 1 , genomic-coords { mix { int { from 6093682 , to 6093782 , strand plus , id gi 51466871 } , int { from 6102435 , to 6103609 , strand plus , id gi 51466871 } } } , seqs { whole gi 4557782 } , products { { type peptide , heading "Reference" , accession "NP_000006" , version 1 , genomic-coords { int { from 6102441 , to 6103313 , strand plus , id gi 51466871 } } , seqs { whole gi 4557783 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_086740" , version 1 , seqs { int { from 5773920 , to 5783845 , strand plus , id gi 51467159 } } , products { { type mRNA , heading "Reference" , accession "NM_000015" , version 1 , genomic-coords { mix { int { from 5773920 , to 5774020 , strand plus , id gi 51467159 } , int { from 5782671 , to 5783845 , strand plus , id gi 51467159 } } } , seqs { whole gi 4557782 } , products { { type peptide , heading "Reference" , accession "NP_000006" , version 1 , genomic-coords { int { from 5782677 , to 5783549 , strand plus , id gi 51467159 } } , seqs { whole gi 4557783 } , comment { { type property , label "EC" , text "2.3.1.5" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.5" } } } } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "NAT2" , version 0 } , { type property , label "Official Full Name" , text "N-acetyltransferase 2 (arylamine N-acetyltransferase)" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 16407 } , anchor "acetyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 2340091 } , source { { src { db "GO" , tag id 4060 } , anchor "arylamine N-acetyltransferase activity" , post-text "evidence: TAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16740 } , anchor "transferase activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8152 } , anchor "metabolism" , post-text "evidence: IEA" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 32047 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&M APS=genes-r-org/rat-chr/human%3A8,genes-r-org/mouse-chr/human%3A8,genes-r-org/ human-chr8&query=e%3A10[id]+AND+gene[obj_type]&QSTR=nat2&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 7646 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15671210 , pmid 15637738 , pmid 15609332 , pmid 15588473 , pmid 15225898 , pmid 15162844 , pmid 15005011 , pmid 14747882 , pmid 14705222 , pmid 14648207 , pmid 14618622 , pmid 14528063 , pmid 12884528 , pmid 12877350 , pmid 12860276 , pmid 12835615 , pmid 12773763 , pmid 12760253 , pmid 12724621 , pmid 12692115 , pmid 12682333 , pmid 12654968 , pmid 12622714 , pmid 12611196 , pmid 12477932 , pmid 12474054 , pmid 12469231 , pmid 12465141 , pmid 12430181 , pmid 12397635 , pmid 12360107 , pmid 12355549 , pmid 12235453 , pmid 12222688 , pmid 12163321 , pmid 12037388 , pmid 12016157 , pmid 12015038 , pmid 11915035 , pmid 11872636 , pmid 11846845 , pmid 11470991 , pmid 9202751 , pmid 8460648 , pmid 8110178 , pmid 8102597 , pmid 7915226 , pmid 7902079 , pmid 7773298 , pmid 2734109 , pmid 2340091 , pmid 2068113 , pmid 1996083 , pmid 1968463 , pmid 1676262 , pmid 1441598 , pmid 1381364 , pmid 1306121 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 17088 } , anchor "G06461" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "WI-7224" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 44576 } , anchor "WIAF-2120" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH11442" , version 0 } , { type other , label "Alternate name" , text "RH20" , version 0 } , { type other , label "Alternate name" , text "WIAF-2120-STS" , version 0 } , { type other , label "Alternate name" , text "gdb:4559542" , version 0 } , { type other , label "Alternate name" , text "stSG40" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 137181 } , anchor "G59899" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "SHGC-130680" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 155563 } , anchor "GDB:187676" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 156422 } , anchor "GDB:310612" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 156423 } , anchor "GDB:310613" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 157141 } , anchor "GDB:386004" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 272646 } , anchor "PMC310725P3" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_000015" , version 1 , source { { src { db "Nucleotide" , tag id 4557782 } , anchor "NM_000015" } } , seqs { whole gi 4557782 } , products { { type peptide , heading "Product" , accession "NP_000006" , version 1 , source { { src { db "Protein" , tag id 4557783 } , anchor "NP_000006" , post-text "arylamide acetylase 2" } } , seqs { whole gi 4557783 } , comment { { type other , heading "Consensus CDS (CCDS)" , version 0 , source { { src { db "CCDS" , tag str "CCDS6008.1" } , anchor "CCDS6008.1" } } } , { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 4557783 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 1353 } , anchor "pfam00797: Acetyltransf_2; N-acetyltransferase" } } , comment { { type other , text "Location: 20 - 280 Blast Score: 1005" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "D90042" } , anchor "D90042" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AF042740" , version 1 , source { { src { db "Nucleotide" , tag id 2801806 } , anchor "AF042740" } } , seqs { whole gi 2801806 } , products { { type peptide , accession "AAC03773" , version 1 , source { { src { db "Protein" , tag id 2801807 } , anchor "AAC03773" } } , seqs { whole gi 2801807 } } } } , { type genomic , heading "Genomic" , accession "AF055874" , version 1 , source { { src { db "Nucleotide" , tag id 3063613 } , anchor "AF055874" } } , seqs { whole gi 3063613 } , products { { type peptide , accession "AAC14117" , version 1 , source { { src { db "Protein" , tag id 3063614 } , anchor "AAC14117" } } , seqs { whole gi 3063614 } } } } , { type genomic , heading "Genomic" , accession "AF055875" , version 1 , source { { src { db "Nucleotide" , tag id 3063615 } , anchor "AF055875" } } , seqs { whole gi 3063615 } , products { { type peptide , accession "AAC14118" , version 1 , source { { src { db "Protein" , tag id 3063616 } , anchor "AAC14118" } } , seqs { whole gi 3063616 } } } } , { type genomic , heading "Genomic" , accession "AF320309" , version 1 , source { { src { db "Nucleotide" , tag id 11321494 } , anchor "AF320309" } } , seqs { whole gi 11321494 } , products { { type peptide , accession "AAG34181" , version 1 , source { { src { db "Protein" , tag id 11321495 } , anchor "AAG34181" } } , seqs { whole gi 11321495 } } } } , { type genomic , heading "Genomic" , accession "AF348074" , version 1 , source { { src { db "Nucleotide" , tag id 14009675 } , anchor "AF348074" } } , seqs { whole gi 14009675 } , products { { type peptide , accession "AAK51710" , version 1 , source { { src { db "Protein" , tag id 14009676 } , anchor "AAK51710" } } , seqs { whole gi 14009676 } } } } , { type genomic , heading "Genomic" , accession "AF348075" , version 1 , source { { src { db "Nucleotide" , tag id 14009677 } , anchor "AF348075" } } , seqs { whole gi 14009677 } , products { { type peptide , accession "AAK51711" , version 1 , source { { src { db "Protein" , tag id 14009678 } , anchor "AAK51711" } } , seqs { whole gi 14009678 } } } } , { type genomic , heading "Genomic" , accession "AY230251" , version 1 , source { { src { db "Nucleotide" , tag id 29423785 } , anchor "AY230251" } } , seqs { whole gi 29423785 } , products { { type peptide , accession "AAO73561" , version 1 , source { { src { db "Protein" , tag id 29423786 } , anchor "AAO73561" } } , seqs { whole gi 29423786 } } } } , { type genomic , heading "Genomic" , accession "AY230252" , version 1 , source { { src { db "Nucleotide" , tag id 29423789 } , anchor "AY230252" } } , seqs { whole gi 29423789 } , products { { type peptide , accession "AAO73562" , version 1 , source { { src { db "Protein" , tag id 29423790 } , anchor "AAO73562" } } , seqs { whole gi 29423790 } } } } , { type genomic , heading "Genomic" , accession "AY331807" , version 1 , source { { src { db "Nucleotide" , tag id 32402490 } , anchor "AY331807" } } , seqs { whole gi 32402490 } , products { { type peptide , accession "AAP81164" , version 1 , source { { src { db "Protein" , tag id 32402491 } , anchor "AAP81164" } } , seqs { whole gi 32402491 } } } } , { type genomic , heading "Genomic" , accession "D10870" , version 1 , source { { src { db "Nucleotide" , tag id 219871 } , anchor "D10870" } } , seqs { whole gi 219871 } , products { { type peptide , accession "BAA01640" , version 1 , source { { src { db "Protein" , tag id 219872 } , anchor "BAA01640" } } , seqs { whole gi 219872 } } } } , { type genomic , heading "Genomic" , accession "D10871" , version 1 , source { { src { db "Nucleotide" , tag id 219874 } , anchor "D10871" } } , seqs { whole gi 219874 } , products { { type peptide , accession "BAA01641" , version 1 , source { { src { db "Protein" , tag id 219875 } , anchor "BAA01641" } } , seqs { whole gi 219875 } } } } , { type genomic , heading "Genomic" , accession "D10872" , version 1 , source { { src { db "Nucleotide" , tag id 219877 } , anchor "D10872" } } , seqs { whole gi 219877 } , products { { type peptide , accession "BAA01642" , version 1 , source { { src { db "Protein" , tag id 219878 } , anchor "BAA01642" } } , seqs { whole gi 219878 } } } } , { type genomic , heading "Genomic" , accession "M75163" , version 1 , source { { src { db "Nucleotide" , tag id 189075 } , anchor "M75163" } } , seqs { whole gi 189075 } , products { { type peptide , accession "AAA59906" , version 1 , source { { src { db "Protein" , tag id 553602 } , anchor "AAA59906" } } , seqs { whole gi 553602 } } } } , { type genomic , heading "Genomic" , accession "M75164" , version 1 , source { { src { db "Nucleotide" , tag id 189072 } , anchor "M75164" } } , seqs { whole gi 189072 } , products { { type peptide , accession "AAA59905" , version 1 , source { { src { db "Protein" , tag id 553601 } , anchor "AAA59905" } } , seqs { whole gi 553601 } } } } , { type genomic , heading "Genomic" , accession "U23052" , version 1 , source { { src { db "Nucleotide" , tag id 747646 } , anchor "U23052" } } , seqs { whole gi 747646 } , products { { type peptide , accession "AAA64584" , version 1 , source { { src { db "Protein" , tag id 727413 } , anchor "AAA64584" } } , seqs { whole gi 727413 } } } } , { type genomic , heading "Genomic" , accession "U23434" , version 1 , source { { src { db "Nucleotide" , tag id 727456 } , anchor "U23434" } } , seqs { whole gi 727456 } , products { { type peptide , accession "AAA64585" , version 1 , source { { src { db "Protein" , tag id 727457 } , anchor "AAA64585" } } , seqs { whole gi 727457 } } } } , { type genomic , heading "Genomic" , accession "U53473" , version 1 , source { { src { db "Nucleotide" , tag id 1297331 } , anchor "U53473" } } , seqs { whole gi 1297331 } , products { { type peptide , accession "AAA98976" , version 1 , source { { src { db "Protein" , tag id 1297332 } , anchor "AAA98976" } } , seqs { whole gi 1297332 } } } } , { type genomic , heading "Genomic" , accession "X14672" , version 1 , source { { src { db "Nucleotide" , tag id 28227 } , anchor "X14672" } } , seqs { whole gi 28227 } , products { { type peptide , accession "CAA32802" , version 1 , source { { src { db "Protein" , tag id 28228 } , anchor "CAA32802" } } , seqs { whole gi 28228 } } } } , { type mRNA , heading "mRNA" , accession "BC015878" , version 1 , source { { src { db "Nucleotide" , tag id 16198419 } , anchor "BC015878" } } , seqs { whole gi 16198419 } , products { { type peptide , accession "AAH15878" , version 1 , source { { src { db "Protein" , tag id 16198420 } , anchor "AAH15878" } } , seqs { whole gi 16198420 } } } } , { type mRNA , heading "mRNA" , accession "BC067218" , version 1 , source { { src { db "Nucleotide" , tag id 45501306 } , anchor "BC067218" } } , seqs { whole gi 45501306 } , products { { type peptide , accession "AAH67218" , version 1 , source { { src { db "Protein" , tag id 45501307 } , anchor "AAH67218" } } , seqs { whole gi 45501307 } } } } , { type mRNA , heading "mRNA" , accession "CR407631" , version 1 , source { { src { db "Nucleotide" , tag id 47115198 } , anchor "CR407631" } } , seqs { whole gi 47115198 } , products { { type peptide , accession "CAG28559" , version 1 , source { { src { db "Protein" , tag id 47115199 } , anchor "CAG28559" } } , seqs { whole gi 47115199 } } } } , { type mRNA , heading "mRNA" , accession "D90040" , version 1 , source { { src { db "Nucleotide" , tag id 219411 } , anchor "D90040" } } , seqs { whole gi 219411 } , products { { type peptide , accession "BAA14094" , version 1 , source { { src { db "Protein" , tag id 219412 } , anchor "BAA14094" } } , seqs { whole gi 219412 } } } } , { type mRNA , heading "mRNA" , accession "D90042" , version 1 , source { { src { db "Nucleotide" , tag id 219415 } , anchor "D90042" } } , seqs { whole gi 219415 } , products { { type peptide , accession "BAA14096" , version 1 , source { { src { db "Protein" , tag id 219416 } , anchor "BAA14096" } } , seqs { whole gi 219416 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P11245" , version 0 , source { { src { db "Protein" , tag id 114238 } , anchor "P11245" } } , seqs { whole gi 114238 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "10" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_030737.9&gene=NAT2&lid=10&from=6093683&to=6103610" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "10" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_030737.9&gene=NAT2&lid=10" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.2" } } , source { { src { db "UniGene" , tag str "Hs.2" } , anchor "Hs.2" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=2" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "243400" } , anchor "243400" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 10 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=10" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:125365" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=BC067 218" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= BC067218" } } } , { type comment , text "PharmGKB" , version 0 , source { { src { db "PharmGKB" , tag str "PA18" } , anchor "PA18" } } } , { type comment , text "Arylamine N-Acetyltransferase Nomenclature" , version 0 , source { { src { db "Arylamine N-Acetyltransferase Nomenclature" , tag str "Arylamine N-Acetyltransferase Nomenclature" } , anchor "Arylamine N-Acetyltransferase Nomenclature" , url "http://www.louisville.edu/medschool/pharmacology/NAT.html" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC015878,BC067218" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC015878 ,BC067218" } } } } } , { type generif , text "there is no association between endometriosis and NAT2 in South Indian women" , version 0 , refs { pmid 15588473 } , create-date str "Mar 19 2005 10:01AM" , update-date str "Mar 19 2005 11:47AM" } , { type generif , text "Risks for colorectal cancer are significantly associated with the genetic polymorphisms of GSTT1 deletion, NAT2-rapid acetylator phenotype and genotye and NAT2-rapid acetylator phenotype." , version 0 , refs { pmid 15637738 } , create-date str "Mar 7 2005 7:07PM" , update-date str "Mar 8 2005 12:10AM" } , { type generif , text "Cigarette smoking is associated with increased risk of breast cancer in women with the NAT2 slow acetylator genotype." , version 0 , refs { pmid 15225898 } , create-date str "Nov 13 2004 10:01AM" , update-date str "Nov 13 2004 10:50AM" } , { type generif , text "N-acetyltransferase 2 polymorphism does not play an important role in breast cancer risk of Turkish women by altering the capacity in deactivation of environmental carcinogens" , version 0 , refs { pmid 15162844 } , create-date str "Oct 4 2004 10:33AM" , update-date str "Oct 4 2004 11:19AM" } , { type generif , text "NAT2 slow acetylator genotypes might modulate the effect of carcinogenic arylamines contained in tobacco smoke." , version 0 , refs { pmid 14648207 } , create-date str "Sep 27 2004 4:34PM" , update-date str "Sep 27 2004 5:11PM" } , { type generif , text "Arylamine N-acetyltransferase 2 is a genetically polymorphic phase II enzyme with a role in the metabolism of many xenobiotics." , version 0 , refs { pmid 14747882 } , create-date str "Aug 2 2004 1:09PM" , update-date str "Aug 2 2004 1:38PM" } , { type generif , text "although there is little overall association between NAT genotypes and risk of developing systemic lupus erythematosus, the interaction between NAT1 and NAT2 and specific exposures such as hair dyes may be important" , version 0 , refs { pmid 14705222 } , create-date str "Apr 16 2004 12:00AM" , update-date str "May 2 2004 7:01AM" } , { type generif , text "The NAT2 acetylator genotype may modify esophageal cancer risk in humans from exposure to barbecued/grilled meat." , version 0 , refs { pmid 12773763 } , create-date str "Feb 13 2004 12:00AM" , update-date str "Feb 22 2004 7:01AM" } , { type generif , text "N-acetyltransferase 2 polymorphism does not differ between patients suffering from atopic dermatitis and healthy subjects" , version 0 , refs { pmid 14528063 } , create-date str "Feb 5 2004 12:00AM" , update-date str "Feb 15 2004 6:33PM" } , { type generif , text "Genetic NAT2 polymorphism may play a role in lifestyle factors-related hepato- carcinogenesis, particulary critical in smoking related hepatocarcinogenesis." , version 0 , refs { pmid 12877350 } , create-date str "Feb 4 2004 12:00AM" , update-date str "Feb 15 2004 6:32PM" } , { type generif , text "Slow acetylation activity is associated with age-related cataract formation." , version 0 , refs { pmid 12724621 } , create-date str "Jan 6 2004 12:00AM" , update-date str "Feb 22 2004 7:01AM" } , { type generif , text "A significant association between Parkinson disease & the slow acetylator genotype for N-acetyltransferase 2 in Hong Kong Chinesed provides evidence for a possible functional relationship between NAT2 slow acetylator genotype & PD in both racial groups." , version 0 , refs { pmid 12654968 } , create-date str "Dec 23 2003 12:00AM" , update-date str "Jan 18 2004 7:01AM" } , { type generif , text "RFLP of the gene coding for N-acetyltransferase 2 (NAT2) was typed in populations of the Volga-Ural region (Bashkirs, Tatars, Chuvashes, Udmurts, and Russians) and in patients with chronic obstructive pulmonary disease (COPD) and in healthy individuals" , version 0 , refs { pmid 12884528 } , create-date str "Dec 18 2003 12:00AM" , update-date str "Jan 25 2004 7:01AM" } , { type generif , text "We conclude that smoking increases risk of colorectal adenomas and that SULT1A1 and NAT2 only modestly modify this association." , version 0 , refs { pmid 14618622 } , create-date str "Dec 11 2003 12:00AM" , update-date str "Dec 21 2003 7:01AM" } , { type generif , text "In human, NAT2 polymorphism may be a genetic risk factor for joint destruction." , version 0 , refs { pmid 15005011 } , create-date str "May 7 2004 12:00AM" , update-date str "May 16 2004 7:01AM" } , { type generif , text "It is unlikely that the NAT1*10 or NAT2 rapid/intermediate genotypes are related to stomach cancer risk." , version 0 , refs { pmid 12692115 } , create-date str "Sep 4 2003 12:00AM" , update-date str "Sep 28 2003 7:01AM" } , { type generif , text "genetic polymorphisms of NAT1 and NAT2 have no independent effect on breast cancer risk, but they modulate breast cancer risk in the presence of GSTM1 and GSTT1 null genotypes." , version 0 , refs { pmid 12860276 } , create-date str "Aug 18 2003 12:00AM" , update-date str "Aug 24 2003 7:01AM" } , { type generif , text "NAT2 slow acetylator genotype plays an important role in determining the risk of developing prostate cancer in Japanese men and is also associated with more clinically advanced and pathologically aggressive disease." , version 0 , refs { pmid 12622714 } , create-date str "Aug 9 2003 12:00AM" , update-date str "Aug 24 2003 7:01AM" } , { type generif , text "Polymorphism of Nat2 encoding phase 2 xenobiotic detoxication enzyme was studied." , version 0 , refs { pmid 12760253 } , create-date str "Jun 26 2003 12:00AM" , update-date str "Aug 10 2003 7:01AM" } , { type generif , text "This enzyme is polymorphic in various ethnic populations of South India." , version 0 , refs { pmid 12469231 } , create-date str "May 24 2003 12:00AM" , update-date str "Jul 27 2003 7:01AM" } , { type generif , text "Maternal NAT2 acetylator status seems not to be an important factor in the etiology of orofacial clefts." , version 0 , refs { pmid 12397635 } , create-date str "May 7 2003 12:00AM" , update-date str "Jun 1 2003 7:01AM" } , { type generif , text "Genotyping the NAT2 gene and estimating diplotype configuration before administration of SSZ may reduce the frequency of adverse effects in Japanese patients with RA." , version 0 , refs { pmid 12465141 } , create-date str "May 2 2003 12:00AM" , update-date str "May 11 2003 7:01AM" } , { type generif , text "Single nucleotide polymorphisms of NAT1 and NAT2, and acetylation haplotype were not associated with increased risk for Parkinson disease" , version 0 , refs { pmid 12682333 } , create-date str "Apr 11 2003 12:00AM" , update-date str "Apr 27 2003 7:01AM" } , { type generif , text "lack of association between polymorphism of this gene and systemic lupus erythematosus" , version 0 , refs { pmid 12360107 } , create-date str "Apr 9 2003 12:00AM" , update-date str "Apr 27 2003 7:01AM" } , { type generif , text "Polymorphic N-acetyltransferase (NAT2) is involved in the metabolism of several compounds relevant in pharmacology or toxicology, with diverse clinical consequences--review" , version 0 , refs { pmid 12611196 } , create-date str "Mar 24 2003 12:00AM" , update-date str "Mar 31 2003 6:30AM" } , { type generif , text "N-acetyltransferase 2*19 possessing the C190T (R64W) single nucleotide polymorphisms encodes a slow acetylator phenotype for both N- and O-acetylation, due to a reduction in the amount and stability of the NAT2 19 allozyme" , version 0 , refs { pmid 12222688 } , create-date str "Mar 10 2003 12:00AM" , update-date str "Apr 13 2003 7:01AM" } , { type generif , text "NAT2 slow acetylation and GSTM1 null genotypes may increase postmenopausal breast cancer risk in long-term smoking women." , version 0 , refs { pmid 12835615 } , create-date str "Mar 7 2004 12:00AM" , update-date str "Apr 18 2004 7:02AM" } , { type generif , text "A slow acetylator genotype of this enzyme is associated with an increased risk of advanced cervical cancer." , version 0 , refs { pmid 12474054 } , create-date str "Feb 27 2003 12:00AM" , update-date str "Apr 13 2003 7:01AM" } , { type generif , text "Women with the GSTT1 null genotype were found to have a significant 3.15-fold increased risk of breast cancer (95% CI = 1.7-5.8), while GSTM1 and NAT2 genotypes were not associated with breast cancer risk." , version 0 , refs { pmid 12430181 } , create-date str "Nov 25 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "NAT2 slow genotype with NAT1 polymorphism indicates increased susceptibility to prostate cancer" , version 0 , refs { pmid 12355549 } , create-date str "Oct 31 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "NAT2 slow acetylation genotype may be a risk factor of individual susceptibility to rheumatoid arthritis." , version 0 , refs { pmid 12235453 } , create-date str "Oct 7 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "NAT2 acetylator status can influence susceptibility to breast cancer after exposure to tobacco smoke carcinogens; effect appears to be differential for active and passive smoke exposure" , version 0 , refs { pmid 12163321 } , create-date str "Sep 7 2002 12:00AM" , update-date str "Sep 16 2002 5:48AM" } , { type generif , text "NAT2 polymorphisms may be correlated with an increased risk of larynx cancer" , version 0 , refs { pmid 12037388 } , create-date str "Aug 19 2002 12:00AM" , update-date str "Aug 28 2002 6:15PM" } , { type generif , text "The combined effect of N-acetyltransferase 2 (NAT2) slow genotype and exposure to smoking is observed during the development of laryngeal cancer." , version 0 , refs { pmid 12015038 } , create-date str "Aug 9 2002 12:00AM" , update-date str "Sep 16 2002 5:48AM" } , { type generif , text "urinary excretion of N(2)-(beta-1-glucos-iduronyl)-2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]p yridine relationship to activity levels of NAT2" , version 0 , refs { pmid 12016157 } , create-date str "Jun 12 2002 12:00AM" , update-date str "Jun 24 2002 6:31AM" } , { type generif , text "Polymorphism of the N-acetyltransferase 2 gene as a susceptibility risk factor for antituberculosis drug-induced hepatitis." , version 0 , refs { pmid 11915035 } , create-date str "Apr 15 2002 12:00AM" , update-date str "Apr 28 2002 6:17PM" } , { type generif , text "Association between bone loss in periodontal disease and polymorphism of N-acetyltransferase (NAT2)" , version 0 , refs { pmid 11846845 } , create-date str "Apr 9 2002 12:00AM" , update-date str "May 14 2002 5:48AM" } , { type generif , text "we investigated the relationship between the levels of aromatic DNA adducts in breast tissues and polymorphisms of the drug-metabolizing genes CYP1A1, NAT2, and GSTM1 in 166 women having breast cancer" , version 0 , refs { pmid 11872636 } , create-date str "Apr 2 2002 12:00AM" , update-date str "Apr 8 2002 3:24PM" } } , unique-keys { { db "LocusID" , tag id 10 } , { db "MIM" , tag id 243400 } } , xtra-index-terms { "LOC10" } } Entrezgene ::= { track-info { geneid 11 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 3 , day 5 , hour 11 , minute 30 , second 0 } } , type pseudo , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "8" } } } , gene { locus "AACP" , desc "arylamide acetylase pseudogene" , maploc "8p22" , syn { "NATP" } , locus-tag "HGNC:15" } , location { { display-str "8p22" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 11 , src-str2 "11" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "AACP" , version 0 } , { type property , label "Official Full Name" , text "arylamide acetylase pseudogene" , version 0 } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 15 } } } } , { type comment , version 0 , refs { pmid 2340091 } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "X17060" , version 1 , source { { src { db "Nucleotide" , tag id 34995 } , anchor "X17060" } } , seqs { whole gi 34995 } , products { { type peptide , text "None" , version 0 } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:132838" } } } } } } } , unique-keys { { db "LocusID" , tag id 11 } } , xtra-index-terms { "LOC11" } } Entrezgene ::= { track-info { geneid 12 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 14 , hour 13 , minute 15 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "14" } } } , gene { locus "SERPINA3" , desc "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3" , maploc "14q32.1" , db { { db "MIM" , tag id 107280 } } , syn { "ACT" , "AACT" , "MGC88254" } , locus-tag "HGNC:16" } , prot { name { "serine (or cysteine) proteinase inhibitor, clade A, member 3" , "antichymotrypsin" , "alpha-1-antichymotrypsin" , "serine (or cysteine) proteinase inhibitor, clade A, member 3" } } , summary "The protein encoded by this gene is a plasma protease inhibitor and member of the serine protease inhibitor class. Polymorphisms in this protein appear to be tissue specific and influence protease targeting. Variation in this protein's sequence have been implicated in Alzheimer's disease, and deficiency of this protein has been associated with liver disease. Mutations have been identified in patients with Parkinson disease and chronic obstructive pulmonary disease." , location { { display-str "14q32.1" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 12 , src-str2 "12" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000014" , version 7 , seqs { int { from 94150523 , to 94160143 , strand plus , id gi 51511730 } } , products { { type mRNA , heading "Reference" , accession "NM_001085" , version 2 , genomic-coords { mix { int { from 94150523 , to 94151173 , strand plus , id gi 51511730 } , int { from 94155284 , to 94155557 , strand plus , id gi 51511730 } , int { from 94158430 , to 94158580 , strand plus , id gi 51511730 } , int { from 94159700 , to 94160143 , strand plus , id gi 51511730 } } } , seqs { whole gi 9665246 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_001076" , version 1 , genomic-coords { packed-int { { from 94150531 , to 94151173 , strand plus , id gi 51511730 } , { from 94155284 , to 94155557 , strand plus , id gi 51511730 } , { from 94158430 , to 94158580 , strand plus , id gi 51511730 } , { from 94159700 , to 94159935 , strand plus , id gi 51511730 } } } , seqs { whole gi 4501843 } } } } } } , { type genomic , heading "Reference" , accession "NT_026437" , version 11 , seqs { int { from 76080523 , to 76090143 , strand plus , id gi 51493278 } } , products { { type mRNA , heading "Reference" , accession "NM_001085" , version 2 , genomic-coords { mix { int { from 76080523 , to 76081173 , strand plus , id gi 51493278 } , int { from 76085284 , to 76085557 , strand plus , id gi 51493278 } , int { from 76088430 , to 76088580 , strand plus , id gi 51493278 } , int { from 76089700 , to 76090143 , strand plus , id gi 51493278 } } } , seqs { whole gi 9665246 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_001076" , version 1 , genomic-coords { packed-int { { from 76080531 , to 76081173 , strand plus , id gi 51493278 } , { from 76085284 , to 76085557 , strand plus , id gi 51493278 } , { from 76088430 , to 76088580 , strand plus , id gi 51493278 } , { from 76089700 , to 76089935 , strand plus , id gi 51493278 } } } , seqs { whole gi 4501843 } } } } } } , { type genomic , heading "Reference" , accession "NT_086807" , version 1 , seqs { int { from 23153523 , to 23163143 , strand plus , id gi 51472322 } } , products { { type mRNA , heading "Reference" , accession "NM_001085" , version 2 , genomic-coords { mix { int { from 23153523 , to 23154173 , strand plus , id gi 51472322 } , int { from 23158284 , to 23158557 , strand plus , id gi 51472322 } , int { from 23161430 , to 23161580 , strand plus , id gi 51472322 } , int { from 23162700 , to 23163143 , strand plus , id gi 51472322 } } } , seqs { whole gi 9665246 } , products { { type peptide , heading "Reference" , label "precursor" , accession "NP_001076" , version 1 , genomic-coords { packed-int { { from 23153531 , to 23154173 , strand plus , id gi 51472322 } , { from 23158284 , to 23158557 , strand plus , id gi 51472322 } , { from 23161430 , to 23161580 , strand plus , id gi 51472322 } , { from 23162700 , to 23162935 , strand plus , id gi 51472322 } } } , seqs { whole gi 4501843 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "SERPINA3" , version 0 } , { type property , label "Official Full Name" , text "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 9880565 } , source { { src { db "GO" , tag id 3677 } , anchor "DNA binding" , post-text "evidence: IC" } } } , { type comment , version 0 , refs { pmid 9880565 } , source { { src { db "GO" , tag id 30569 } , anchor "chymotrypsin inhibitor activity" , post-text "evidence: NAS" } } } , { type comment , version 0 , refs { pmid 12709365 } , source { { src { db "GO" , tag id 5515 } , anchor "protein binding" , post-text "evidence: IPI" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 4867 } , anchor "serine-type endopeptidase inhibitor activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 6953 } , anchor "acute-phase response" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 12475184 } , source { { src { db "GO" , tag id 6954 } , anchor "inflammatory response" , post-text "evidence: NAS" } } } , { type comment , version 0 , refs { pmid 11835318 } , source { { src { db "GO" , tag id 19216 } , anchor "regulation of lipid metabolism" , post-text "evidence: NAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 6810 } , anchor "transport" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 9880565 , pmid 14718574 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: NAS" } } } , { type comment , version 0 , refs { pmid 9880565 } , source { { src { db "GO" , tag id 5622 } , anchor "intracellular" , post-text "evidence: NAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 5634 } , anchor "nucleus" , post-text "evidence: IEA" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 40658 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=14& MAPS=genes-r-org/rat-chr/human%3A14,genes-r-org/mouse-chr/human%3A14,genes-r-o rg/human-chr14&query=e%3A12[id]+AND+gene[obj_type]&QSTR=serpina3&cmd=focus&fil l=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 16 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15546506 , pmid 15542006 , pmid 15530656 , pmid 15014966 , pmid 14718574 , pmid 14702039 , pmid 14668352 , pmid 12709365 , pmid 12600202 , pmid 12477932 , pmid 12475184 , pmid 12324297 , pmid 12023832 , pmid 11992569 , pmid 11959399 , pmid 11936240 , pmid 11835318 , pmid 11798857 , pmid 11735417 , pmid 11692021 , pmid 11317942 , pmid 11289720 , pmid 11274154 , pmid 11096092 , pmid 10829039 , pmid 10759471 , pmid 10660528 , pmid 10512690 , pmid 10228625 , pmid 10048303 , pmid 9880565 , pmid 9824262 , pmid 9698370 , pmid 9635374 , pmid 9580375 , pmid 9428387 , pmid 9261179 , pmid 9042371 , pmid 8849841 , pmid 8739078 , pmid 8732755 , pmid 8718849 , pmid 8376411 , pmid 8365378 , pmid 8267879 , pmid 8244391 , pmid 8226889 , pmid 8216224 , pmid 8011628 , pmid 7966721 , pmid 7924407 , pmid 7873202 , pmid 7759598 , pmid 7588564 , pmid 7528097 , pmid 6762318 , pmid 6687683 , pmid 6606438 , pmid 6556193 , pmid 6547997 , pmid 3637050 , pmid 3492865 , pmid 3490907 , pmid 3485824 , pmid 3260956 , pmid 3257719 , pmid 3028924 , pmid 2945424 , pmid 2456771 , pmid 2435303 , pmid 2432851 , pmid 2404007 , pmid 2190106 , pmid 1618300 , pmid 1351206 , pmid 1311327 } } , { type comment , heading "Phenotypes" , version 0 , comment { { type phenotype , text "Alpha-1-antichymotrypsin deficiency" , version 0 , source { { src { db "MIM" , tag id 107280 } , anchor "MIM: 107280" } } } , { type phenotype , text "Cerebrovascular disease, occlusive" , version 0 , source { { src { db "MIM" , tag id 107280 } , anchor "MIM: 107280" } } } } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 32177 } , anchor "RH1625" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH77711" , version 0 } , { type other , label "Alternate name" , text "stSG1393" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 37467 } , anchor "SHGC-32982" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "EST128561" , version 0 } , { type other , label "Alternate name" , text "RH32590" , version 0 } , { type other , label "Alternate name" , text "RH53830" , version 0 } , { type other , label "Alternate name" , text "SGC32982" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 64155 } , anchor "D14S845" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "GDB:588356" , version 0 } , { type other , label "Alternate name" , text "RH53900" , version 0 } , { type other , label "Alternate name" , text "UTR-04554" , version 0 } , { type other , label "Alternate name" , text "WI-7103" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 66238 } , anchor "G31126" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "SHGC-19718" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 74665 } , anchor "RH78280" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "stSG41027" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 86678 } , anchor "RH91507" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "stSG44830" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 272387 } , anchor "PMC27764P1" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_001085" , version 3 , source { { src { db "Nucleotide" , tag id 50659079 } , anchor "NM_001085" } } , seqs { whole gi 50659079 } , products { { type peptide , heading "Product" , accession "NP_001076" , version 2 , source { { src { db "Protein" , tag id 50659080 } , anchor "NP_001076" , post-text "serine (or cysteine) proteinase inhibitor, clade A, member 3 precursor" } } , seqs { whole gi 50659080 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 50659080 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 28234 } , anchor "cd02056: alpha-1-antitrypsin_like; alpha-1-antitrypsin_like" } } , comment { { type other , text "Location: 52 - 417 Blast Score: 1367" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "BC003559,BG565041" } , anchor "BC003559,BG565041" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "X00947" , version 1 , source { { src { db "Nucleotide" , tag id 28331 } , anchor "X00947" } } , seqs { whole gi 28331 } , products { { type peptide , accession "CAA25459" , version 1 , source { { src { db "Protein" , tag id 28332 } , anchor "CAA25459" } } , seqs { whole gi 28332 } } } } , { type genomic , heading "Genomic" , accession "X68733" , version 1 , source { { src { db "Nucleotide" , tag id 439137 } , anchor "X68733" } } , seqs { whole gi 439137 } , products { { type peptide , accession "CAA48671" , version 1 , source { { src { db "Protein" , tag id 1340142 } , anchor "CAA48671" } } , seqs { whole gi 1340142 } } } } , { type mRNA , heading "mRNA" , accession "AB209060" , version 1 , source { { src { db "Nucleotide" , tag id 62087699 } , anchor "AB209060" } } , seqs { whole gi 62087699 } , products { { type peptide , accession "BAD92297" , version 1 , source { { src { db "Protein" , tag id 62087700 } , anchor "BAD92297" } } , seqs { whole gi 62087700 } } } } , { type mRNA , heading "mRNA" , accession "AF089747" , version 1 , source { { src { db "Nucleotide" , tag id 4165889 } , anchor "AF089747" } } , seqs { whole gi 4165889 } , products { { type peptide , accession "AAD08810" , version 1 , source { { src { db "Protein" , tag id 4165890 } , anchor "AAD08810" } } , seqs { whole gi 4165890 } } } } , { type mRNA , heading "mRNA" , accession "AK093049" , version 1 , source { { src { db "Nucleotide" , tag id 21751790 } , anchor "AK093049" } } , seqs { whole gi 21751790 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK096120" , version 1 , source { { src { db "Nucleotide" , tag id 21755531 } , anchor "AK096120" } } , seqs { whole gi 21755531 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK123091" , version 1 , source { { src { db "Nucleotide" , tag id 34528556 } , anchor "AK123091" } } , seqs { whole gi 34528556 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC003559" , version 1 , source { { src { db "Nucleotide" , tag id 13097704 } , anchor "BC003559" } } , seqs { whole gi 13097704 } , products { { type peptide , accession "AAH03559" , version 1 , source { { src { db "Protein" , tag id 13097705 } , anchor "AAH03559" } } , seqs { whole gi 13097705 } } } } , { type mRNA , heading "mRNA" , accession "BC010530" , version 1 , source { { src { db "Nucleotide" , tag id 14714765 } , anchor "BC010530" } } , seqs { whole gi 14714765 } , products { { type peptide , accession "AAH10530" , version 1 , source { { src { db "Protein" , tag id 14714766 } , anchor "AAH10530" } } , seqs { whole gi 14714766 } } } } , { type mRNA , heading "mRNA" , accession "BC013189" , version 1 , source { { src { db "Nucleotide" , tag id 15341984 } , anchor "BC013189" } } , seqs { whole gi 15341984 } , products { { type peptide , accession "AAH13189" , version 1 , source { { src { db "Protein" , tag id 15341985 } , anchor "AAH13189" } } , seqs { whole gi 15341985 } } } } , { type mRNA , heading "mRNA" , accession "BC034554" , version 1 , source { { src { db "Nucleotide" , tag id 21961492 } , anchor "BC034554" } } , seqs { whole gi 21961492 } , products { { type peptide , accession "AAH34554" , version 1 , source { { src { db "Protein" , tag id 21961493 } , anchor "AAH34554" } } , seqs { whole gi 21961493 } } } } , { type mRNA , heading "mRNA" , accession "BC070265" , version 1 , source { { src { db "Nucleotide" , tag id 47124537 } , anchor "BC070265" } } , seqs { whole gi 47124537 } , products { { type peptide , accession "AAH70265" , version 1 , source { { src { db "Protein" , tag id 47124538 } , anchor "AAH70265" } } , seqs { whole gi 47124538 } } } } , { type mRNA , heading "mRNA" , accession "BG565041" , version 1 , source { { src { db "Nucleotide" , tag id 13572694 } , anchor "BG565041" } } , seqs { whole gi 13572694 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "J05176" , version 1 , source { { src { db "Nucleotide" , tag id 177932 } , anchor "J05176" } } , seqs { whole gi 177932 } , products { { type peptide , accession "AAA51560" , version 1 , source { { src { db "Protein" , tag id 177933 } , anchor "AAA51560" } } , seqs { whole gi 177933 } } } } , { type mRNA , heading "mRNA" , accession "K01500" , version 1 , source { { src { db "Nucleotide" , tag id 177808 } , anchor "K01500" } } , seqs { whole gi 177808 } , products { { type peptide , accession "AAA51543" , version 1 , source { { src { db "Protein" , tag id 177809 } , anchor "AAA51543" } } , seqs { whole gi 177809 } } } } , { type mRNA , heading "mRNA" , accession "M18906" , version 1 , source { { src { db "Nucleotide" , tag id 177928 } , anchor "M18906" } } , seqs { whole gi 177928 } , products { { type peptide , accession "AAA51559" , version 1 , source { { src { db "Protein" , tag id 177931 } , anchor "AAA51559" } } , seqs { whole gi 177931 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P01011" , version 0 , source { { src { db "Protein" , tag id 112874 } , anchor "P01011" } } , seqs { whole gi 112874 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "12" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_026437.11&gene=SERPINA3&lid=12&from=76080524&to=76090144" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "12" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_026437.11&gene=SERPINA3&lid=12" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.534293" } } , source { { src { db "UniGene" , tag str "Hs.534293" } , anchor "Hs.534293" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=53 4293" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "107280" } , anchor "107280" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "12" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 12[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 12 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=12" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:118955" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AK093 049" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= AK093049" } } } , { type comment , version 0 , source { { src { db "KEGG" , tag str "" } , url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:12" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC003559,BC010530,BC034554" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC003559 ,BC010530,BC034554" } } } } } , { type comment , heading "Pathways" , version 0 , comment { { type comment , text "KEGG pathway: Alzheimer's disease" , version 0 , source { { src { db "05010" , tag str "05010" } , anchor "05010" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+12" } } } } } , { type generif , text "overexpression of ACT by astrocytes could thus contribute to increased beta-amyloid fibril formation in Alzheimer's disease" , version 0 , refs { pmid 15530656 } , create-date str "Jan 29 2005 10:01AM" , update-date str "Jan 29 2005 1:54PM" } , { type generif , text "Multivariate analysis showed that ACT mRNA level, but not STC2 mRNA level, in HR-positive patients, was a significant prognostic factor (P = 0.042), which was independent of tumor size and lymph node metastases." , version 0 , refs { pmid 15546506 } , create-date str "Jan 15 2005 10:01AM" , update-date str "Jan 15 2005 4:35PM" } , { type generif , text "Alpha1-antichymotrypsin-AA may confer a modest protection against developing early-onset Parkinson disease in women" , version 0 , refs { pmid 15542006 } , create-date str "Jan 15 2005 10:01AM" , update-date str "Jan 15 2005 1:01PM" } , { type generif , text "Polymeric AACT specifically seeds the polymerization of native protein by a serpin-dependent process that occurs under physiological conditions and may be important in the deposition of AACT in plaques in patients with Alzheimer's disease." , version 0 , refs { pmid 12600202 } , create-date str "May 26 2003 12:00AM" , update-date str "Jun 1 2003 7:01AM" } , { type generif , text "alpha(1)-antichymotrypsin polymorphism: a risk factor for hemorrhagic stroke in normotensive subjects." , version 0 , refs { pmid 11692021 } , create-date str "Mar 5 2003 12:00AM" , update-date str "Mar 23 2003 7:01AM" } , { type generif , text "alpha(1)-antitrypsin and antichymotrypsin are produced by the mammary gland and are present in milk in relatively high amounts in early lactation" , version 0 , refs { pmid 12324297 } , create-date str "Oct 11 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "Gene regulation of the serine proteinase inhibitors alpha1-antitrypsin and alpha1-antichymotrypsin." , version 0 , refs { pmid 12023832 } , create-date str "Oct 9 2002 12:00AM" , update-date str "Feb 2 2003 7:01AM" } , { type generif , text "data suggested that the ApoE epsilon2/epsilon4 genotype might be a susceptibility variant of moderate effect for sporadic idiopathic Parkinson disease in our samples, whereas the ACT gene signal peptide polymorphism might not" , version 0 , refs { pmid 11992569 } , create-date str "Sep 26 2002 12:00AM" , update-date str "Oct 7 2002 8:10AM" } , { type generif , text "no association seen between alpha 1-antichymotrypsin and time to psychosis in Alzheimer's disease" , version 0 , refs { pmid 11936240 } , create-date str "Aug 28 2002 12:00AM" , update-date str "Sep 16 2002 5:48AM" } , { type generif , text "significantly higher in plasma of Alzheimer patients compared to controls" , version 0 , refs { pmid 11959399 } , create-date str "Jul 22 2002 12:00AM" , update-date str "Jul 29 2002 6:27PM" } , { type generif , text "A25G and G39A substitutions in the AACT gene are probably one of the risk factors to Alzheimer's disease (AD) in Han Chinese." , version 0 , refs { pmid 11798857 } , create-date str "Apr 7 2002 12:00AM" , update-date str "Apr 13 2002 5:25PM" } , { type generif , heading "Interactions" , version 0 , comment { { type generif , text "Alpha-1 ACT interacts with and inhibits cathepsin G." , version 0 , refs { pmid 15131125 } , source { { src { db "BIND" , tag id 149291 } , anchor "BIND" } } , comment { { type comment , label "SERPINA3" , accession "NP_001076" , version 1 } , { type comment , label "CTSG" , accession "NP_001902" , version 1 , source { { src { db "GeneID" , tag id 1511 } } } } } , create-date str "2005-01-21 20:10 EDT" , update-date str "2005-01-21 20:19 EDT" } , { type generif , text "LRP interacts with alpha-1-ACT." , version 0 , refs { pmid 15131125 } , source { { src { db "BIND" , tag id 149296 } , anchor "BIND" } } , comment { { type comment , label "SERPINA3" , accession "NP_001076" , version 1 } , { type comment , label "LRP1" , accession "NP_002323" , version 1 , source { { src { db "GeneID" , tag id 4035 } } } } } , create-date str "2005-01-21 20:10 EDT" , update-date str "2005-01-21 20:19 EDT" } } } } , unique-keys { { db "LocusID" , tag id 12 } , { db "MIM" , tag id 107280 } } , xtra-index-terms { "LOC12" } , xtra-properties { { tag "PROP" , value "phenotype" } } } Entrezgene ::= { track-info { geneid 13 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 3 , day 5 , hour 11 , minute 30 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "3" } } } , gene { locus "AADAC" , desc "arylacetamide deacetylase (esterase)" , maploc "3q21.3-q25.2" , db { { db "MIM" , tag id 600338 } } , syn { "DAC" } , locus-tag "HGNC:17" } , prot { name { "arylacetamide deacetylase" } } , summary "Microsomal arylacetamide deacetylase competes against the activity of cytosolic arylamine N-acetyltransferase, which catalyzes one of the initial biotransformation pathways for arylamine and heterocyclic amine carcinogens" , location { { display-str "3q21.3-q25.2" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 13 , src-str2 "13" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000003" , version 9 , seqs { int { from 153014563 , to 153028971 , strand plus , id gi 51511463 } } , products { { type mRNA , heading "Reference" , accession "NM_001086" , version 1 , genomic-coords { mix { int { from 153014563 , to 153014785 , strand plus , id gi 51511463 } , int { from 153017851 , to 153018073 , strand plus , id gi 51511463 } , int { from 153020868 , to 153020937 , strand plus , id gi 51511463 } , int { from 153025148 , to 153025319 , strand plus , id gi 51511463 } , int { from 153028061 , to 153028971 , strand plus , id gi 51511463 } } } , seqs { whole gi 4557226 } , products { { type peptide , heading "Reference" , accession "NP_001077" , version 1 , genomic-coords { packed-int { { from 153014648 , to 153014785 , strand plus , id gi 51511463 } , { from 153017851 , to 153018073 , strand plus , id gi 51511463 } , { from 153020868 , to 153020937 , strand plus , id gi 51511463 } , { from 153025148 , to 153025319 , strand plus , id gi 51511463 } , { from 153028061 , to 153028657 , strand plus , id gi 51511463 } } } , seqs { whole gi 4557227 } , comment { { type property , label "EC" , text "3.1.1.-" , version 0 , xtra-properties { { tag "EC" , value "3.1.1.-" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_005612" , version 14 , seqs { int { from 58027019 , to 58041427 , strand plus , id gi 37550867 } } , products { { type mRNA , heading "Reference" , accession "NM_001086" , version 1 , genomic-coords { mix { int { from 58027019 , to 58027241 , strand plus , id gi 37550867 } , int { from 58030307 , to 58030529 , strand plus , id gi 37550867 } , int { from 58033324 , to 58033393 , strand plus , id gi 37550867 } , int { from 58037604 , to 58037775 , strand plus , id gi 37550867 } , int { from 58040517 , to 58041427 , strand plus , id gi 37550867 } } } , seqs { whole gi 4557226 } , products { { type peptide , heading "Reference" , accession "NP_001077" , version 1 , genomic-coords { packed-int { { from 58027104 , to 58027241 , strand plus , id gi 37550867 } , { from 58030307 , to 58030529 , strand plus , id gi 37550867 } , { from 58033324 , to 58033393 , strand plus , id gi 37550867 } , { from 58037604 , to 58037775 , strand plus , id gi 37550867 } , { from 58040517 , to 58041113 , strand plus , id gi 37550867 } } } , seqs { whole gi 4557227 } , comment { { type property , label "EC" , text "3.1.1.-" , version 0 , xtra-properties { { tag "EC" , value "3.1.1.-" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_086641" , version 1 , seqs { int { from 24339789 , to 24354221 , strand plus , id gi 51464125 } } , products { { type mRNA , heading "Reference" , accession "NM_001086" , version 1 , genomic-coords { mix { int { from 24339789 , to 24340011 , strand plus , id gi 51464125 } , int { from 24343078 , to 24343300 , strand plus , id gi 51464125 } , int { from 24346094 , to 24346163 , strand plus , id gi 51464125 } , int { from 24350369 , to 24350540 , strand plus , id gi 51464125 } , int { from 24353311 , to 24354221 , strand plus , id gi 51464125 } } } , seqs { whole gi 4557226 } , products { { type peptide , heading "Reference" , accession "NP_001077" , version 1 , genomic-coords { packed-int { { from 24339874 , to 24340011 , strand plus , id gi 51464125 } , { from 24343078 , to 24343300 , strand plus , id gi 51464125 } , { from 24346094 , to 24346163 , strand plus , id gi 51464125 } , { from 24350369 , to 24350540 , strand plus , id gi 51464125 } , { from 24353311 , to 24353907 , strand plus , id gi 51464125 } } } , seqs { whole gi 4557227 } , comment { { type property , label "EC" , text "3.1.1.-" , version 0 , xtra-properties { { tag "EC" , value "3.1.1.-" } } } } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "AADAC" , version 0 } , { type property , label "Official Full Name" , text "arylacetamide deacetylase (esterase)" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 9665742 } , source { { src { db "GO" , tag id 19213 } , anchor "deacetylase activity" , post-text "evidence: IDA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8152 } , anchor "metabolism" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 10318829 , pmid 15152005 } , source { { src { db "GO" , tag id 5789 } , anchor "endoplasmic reticulum membrane" , post-text "evidence: IDA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16021 } , anchor "integral to membrane" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 8063807 } , source { { src { db "GO" , tag id 5792 } , anchor "microsome" , post-text "evidence: TAS" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 37436 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=3&M APS=genes-r-org/rat-chr/human%3A3,genes-r-org/mouse-chr/human%3A3,genes-r-org/ human-chr3&query=e%3A13[id]+AND+gene[obj_type]&QSTR=aadac&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 17 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15152005 , pmid 12721789 , pmid 12477932 , pmid 10318829 , pmid 9665742 , pmid 9299245 , pmid 8063807 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 13170 } , anchor "STS-L32179" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "RH41545" , version 0 } , { type other , label "Alternate name" , text "sts-L32179" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 18863 } , anchor "D3S4189" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "SHGC-9733" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 24707 } , anchor "RH36344" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "stSG13141" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 136046 } , anchor "RH124029" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "SHGC-105511" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_001086" , version 1 , source { { src { db "Nucleotide" , tag id 4557226 } , anchor "NM_001086" } } , seqs { whole gi 4557226 } , products { { type peptide , heading "Product" , accession "NP_001077" , version 1 , source { { src { db "Protein" , tag id 4557227 } , anchor "NP_001077" , post-text "arylacetamide deacetylase" } } , seqs { whole gi 4557227 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 4557227 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 10527 } , anchor "COG0657: Aes; Esterase/lipase [Lipid metabolism]" } } , comment { { type other , text "Location: 33 - 399 Blast Score: 380" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 16555 } , anchor "cd00312: Esterase_lipase; Esterases and lipases (includes fungal lipases, cholinesterases, etc" } } , comment { { type other , text "Location: 91 - 203 Blast Score: 144" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "L32179" } , anchor "L32179" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "BC020706" , version 1 , source { { src { db "Nucleotide" , tag id 18088402 } , anchor "BC020706" } } , seqs { whole gi 18088402 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC032309" , version 1 , source { { src { db "Nucleotide" , tag id 21595550 } , anchor "BC032309" } } , seqs { whole gi 21595550 } , products { { type peptide , accession "AAH32309" , version 1 , source { { src { db "Protein" , tag id 21595551 } , anchor "AAH32309" } } , seqs { whole gi 21595551 } } } } , { type mRNA , heading "mRNA" , accession "L32179" , version 1 , source { { src { db "Nucleotide" , tag id 537513 } , anchor "L32179" } } , seqs { whole gi 537513 } , products { { type peptide , accession "AAA35551" , version 1 , source { { src { db "Protein" , tag id 537514 } , anchor "AAA35551" } } , seqs { whole gi 537514 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P22760" , version 0 , source { { src { db "Protein" , tag id 57015294 } , anchor "P22760" } } , seqs { whole gi 57015294 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "13" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_005612.14&gene=AADAC&lid=13&from=58027020&to=58041428" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "13" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_005612.14&gene=AADAC&lid=13" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.506908" } } , source { { src { db "UniGene" , tag str "Hs.506908" } , anchor "Hs.506908" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=50 6908" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "600338" } , anchor "600338" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "13" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 13[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 13 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=13" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:392587" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=BC032 309" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= BC032309" } } } , { type comment , version 0 , source { { src { db "KEGG" , tag str "" } , url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:13" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC032309" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC032309" } } } } } , { type comment , heading "Pathways" , version 0 , comment { { type comment , text "KEGG pathway: Butanoate metabolism" , version 0 , source { { src { db "00650" , tag str "00650" } , anchor "00650" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00650+13" } } } , { type comment , text "KEGG pathway: Alkaloid biosynthesis II" , version 0 , source { { src { db "00960" , tag str "00960" } , anchor "00960" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00960+13" } } } , { type comment , text "KEGG pathway: 2,4-Dichlorobenzoate degradation" , version 0 , source { { src { db "00623" , tag str "00623" } , anchor "00623" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00623+13" } } } , { type comment , text "KEGG pathway: Pentose and glucuronate interconversions" , version 0 , source { { src { db "00040" , tag str "00040" } , anchor "00040" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00040+13" } } } , { type comment , text "KEGG pathway: Glycosylphosphatidylinositol(GPI)-anchor biosynthesis" , version 0 , source { { src { db "00563" , tag str "00563" } , anchor "00563" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00563+13" } } } } } } , unique-keys { { db "LocusID" , tag id 13 } , { db "MIM" , tag id 600338 } } , xtra-index-terms { "LOC13" } } Entrezgene ::= { track-info { geneid 14 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 14 , hour 13 , minute 15 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "2" } } } , gene { locus "AAMP" , desc "angio-associated, migratory cell protein" , maploc "2q35" , db { { db "MIM" , tag id 603488 } } , locus-tag "HGNC:18" } , prot { name { "angio-associated, migratory cell protein" } } , summary "The gene product is an immunoglobulin-type protein. It is found to be expressed strongly in endothelial cells, cytotrophoblasts, and poorly differentiated colon adenocarcinoma cells found in lymphatics. The protein contains a heparin-binding domain and mediates heparin-sensitive cell adhesion." , location { { display-str "2q35" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 14 , src-str2 "14" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000002" , version 9 , seqs { int { from 218954357 , to 218960364 , strand minus , id gi 51511462 } } , products { { type mRNA , heading "Reference" , accession "NM_001087" , version 1 , genomic-coords { mix { int { from 218954357 , to 218954835 , strand minus , id gi 51511462 } , int { from 218955247 , to 218955401 , strand minus , id gi 51511462 } , int { from 218955598 , to 218955688 , strand minus , id gi 51511462 } , int { from 218955806 , to 218955909 , strand minus , id gi 51511462 } , int { from 218956058 , to 218956173 , strand minus , id gi 51511462 } , int { from 218956291 , to 218956374 , strand minus , id gi 51511462 } , int { from 218956670 , to 218956814 , strand minus , id gi 51511462 } , int { from 218957074 , to 218957213 , strand minus , id gi 51511462 } , int { from 218957721 , to 218957840 , strand minus , id gi 51511462 } , int { from 218959609 , to 218959761 , strand minus , id gi 51511462 } , int { from 218960193 , to 218960364 , strand minus , id gi 51511462 } } } , seqs { whole gi 4557228 } , products { { type peptide , heading "Reference" , accession "NP_001078" , version 1 , genomic-coords { packed-int { { from 218954760 , to 218954835 , strand minus , id gi 51511462 } , { from 218955247 , to 218955401 , strand minus , id gi 51511462 } , { from 218955598 , to 218955688 , strand minus , id gi 51511462 } , { from 218955806 , to 218955909 , strand minus , id gi 51511462 } , { from 218956058 , to 218956173 , strand minus , id gi 51511462 } , { from 218956291 , to 218956374 , strand minus , id gi 51511462 } , { from 218956670 , to 218956814 , strand minus , id gi 51511462 } , { from 218957074 , to 218957213 , strand minus , id gi 51511462 } , { from 218957721 , to 218957840 , strand minus , id gi 51511462 } , { from 218959609 , to 218959761 , strand minus , id gi 51511462 } , { from 218960193 , to 218960364 , strand minus , id gi 51511462 } } } , seqs { whole gi 4557229 } } } } } } , { type genomic , heading "Reference" , accession "NT_005403" , version 15 , seqs { int { from 69338267 , to 69344274 , strand minus , id gi 51461028 } } , products { { type mRNA , heading "Reference" , accession "NM_001087" , version 1 , genomic-coords { mix { int { from 69338267 , to 69338745 , strand minus , id gi 51461028 } , int { from 69339157 , to 69339311 , strand minus , id gi 51461028 } , int { from 69339508 , to 69339598 , strand minus , id gi 51461028 } , int { from 69339716 , to 69339819 , strand minus , id gi 51461028 } , int { from 69339968 , to 69340083 , strand minus , id gi 51461028 } , int { from 69340201 , to 69340284 , strand minus , id gi 51461028 } , int { from 69340580 , to 69340724 , strand minus , id gi 51461028 } , int { from 69340984 , to 69341123 , strand minus , id gi 51461028 } , int { from 69341631 , to 69341750 , strand minus , id gi 51461028 } , int { from 69343519 , to 69343671 , strand minus , id gi 51461028 } , int { from 69344103 , to 69344274 , strand minus , id gi 51461028 } } } , seqs { whole gi 4557228 } , products { { type peptide , heading "Reference" , accession "NP_001078" , version 1 , genomic-coords { packed-int { { from 69338670 , to 69338745 , strand minus , id gi 51461028 } , { from 69339157 , to 69339311 , strand minus , id gi 51461028 } , { from 69339508 , to 69339598 , strand minus , id gi 51461028 } , { from 69339716 , to 69339819 , strand minus , id gi 51461028 } , { from 69339968 , to 69340083 , strand minus , id gi 51461028 } , { from 69340201 , to 69340284 , strand minus , id gi 51461028 } , { from 69340580 , to 69340724 , strand minus , id gi 51461028 } , { from 69340984 , to 69341123 , strand minus , id gi 51461028 } , { from 69341631 , to 69341750 , strand minus , id gi 51461028 } , { from 69343519 , to 69343671 , strand minus , id gi 51461028 } , { from 69344103 , to 69344274 , strand minus , id gi 51461028 } } } , seqs { whole gi 4557229 } } } } } } , { type genomic , heading "Reference" , accession "NT_086634" , version 1 , seqs { int { from 23772483 , to 23778490 , strand minus , id gi 51463854 } } , products { { type mRNA , heading "Reference" , accession "NM_001087" , version 1 , genomic-coords { mix { int { from 23772483 , to 23772961 , strand minus , id gi 51463854 } , int { from 23773373 , to 23773527 , strand minus , id gi 51463854 } , int { from 23773724 , to 23773814 , strand minus , id gi 51463854 } , int { from 23773932 , to 23774035 , strand minus , id gi 51463854 } , int { from 23774184 , to 23774299 , strand minus , id gi 51463854 } , int { from 23774417 , to 23774500 , strand minus , id gi 51463854 } , int { from 23774796 , to 23774940 , strand minus , id gi 51463854 } , int { from 23775200 , to 23775339 , strand minus , id gi 51463854 } , int { from 23775847 , to 23775966 , strand minus , id gi 51463854 } , int { from 23777735 , to 23777887 , strand minus , id gi 51463854 } , int { from 23778319 , to 23778490 , strand minus , id gi 51463854 } } } , seqs { whole gi 4557228 } , products { { type peptide , heading "Reference" , accession "NP_001078" , version 1 , genomic-coords { packed-int { { from 23772886 , to 23772961 , strand minus , id gi 51463854 } , { from 23773373 , to 23773527 , strand minus , id gi 51463854 } , { from 23773724 , to 23773814 , strand minus , id gi 51463854 } , { from 23773932 , to 23774035 , strand minus , id gi 51463854 } , { from 23774184 , to 23774299 , strand minus , id gi 51463854 } , { from 23774417 , to 23774500 , strand minus , id gi 51463854 } , { from 23774796 , to 23774940 , strand minus , id gi 51463854 } , { from 23775200 , to 23775339 , strand minus , id gi 51463854 } , { from 23775847 , to 23775966 , strand minus , id gi 51463854 } , { from 23777735 , to 23777887 , strand minus , id gi 51463854 } , { from 23778319 , to 23778490 , strand minus , id gi 51463854 } } } , seqs { whole gi 4557229 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "AAMP" , version 0 } , { type property , label "Official Full Name" , text "angio-associated, migratory cell protein" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 7743515 } , source { { src { db "GO" , tag id 8201 } , anchor "heparin binding" , post-text "evidence: TAS" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 6928 } , anchor "cell motility" , post-text "evidence: NR" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 846 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=2&M APS=genes-r-org/rat-chr/human%3A2,genes-r-org/mouse-chr/human%3A2,genes-r-org/ human-chr2&query=e%3A14[id]+AND+gene[obj_type]&QSTR=aamp&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 18 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 12477932 , pmid 11969303 , pmid 10329261 , pmid 8660919 , pmid 7743515 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 52581 } , anchor "SGC31591" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "CM4.18" , version 0 } , { type other , label "Alternate name" , text "GC" , version 0 } , { type other , label "Alternate name" , text "RH23156" , version 0 } , { type other , label "Alternate name" , text "STS4-18" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_001087" , version 2 , source { { src { db "Nucleotide" , tag id 55743074 } , anchor "NM_001087" } } , seqs { whole gi 55743074 } , products { { type peptide , heading "Product" , accession "NP_001078" , version 2 , source { { src { db "Protein" , tag id 55743075 } , anchor "NP_001078" , post-text "angio-associated, migratory cell protein" } } , seqs { whole gi 55743075 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 55743075 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5398 } , anchor "cd00200: WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly" } } , comment { { type other , text "Location: 86 - 386 Blast Score: 457" , version 0 } , { type other , text "Location: 325 - 430 Blast Score: 176" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "BG534787,CN277005,M95627" } , anchor "BG534787,CN277005,M95627" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "AB209790" , version 1 , source { { src { db "Nucleotide" , tag id 62089165 } , anchor "AB209790" } } , seqs { whole gi 62089165 } , products { { type peptide , accession "BAD93027" , version 1 , source { { src { db "Protein" , tag id 62089166 } , anchor "BAD93027" } } , seqs { whole gi 62089166 } } } } , { type mRNA , heading "mRNA" , accession "AK131047" , version 1 , source { { src { db "Nucleotide" , tag id 34528300 } , anchor "AK131047" } } , seqs { whole gi 34528300 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC008809" , version 2 , source { { src { db "Nucleotide" , tag id 39644831 } , anchor "BC008809" } } , seqs { whole gi 39644831 } , products { { type peptide , accession "AAH08809" , version 2 , source { { src { db "Protein" , tag id 39644832 } , anchor "AAH08809" } } , seqs { whole gi 39644832 } } } } , { type mRNA , heading "mRNA" , accession "BC014122" , version 2 , source { { src { db "Nucleotide" , tag id 33874729 } , anchor "BC014122" } } , seqs { whole gi 33874729 } , products { { type peptide , accession "AAH14122" , version 1 , source { { src { db "Protein" , tag id 33874730 } , anchor "AAH14122" } } , seqs { whole gi 33874730 } } } } , { type mRNA , heading "mRNA" , accession "BC020244" , version 1 , source { { src { db "Nucleotide" , tag id 18044383 } , anchor "BC020244" } } , seqs { whole gi 18044383 } , products { { type peptide , accession "AAH20244" , version 1 , source { { src { db "Protein" , tag id 18044384 } , anchor "AAH20244" } } , seqs { whole gi 18044384 } } } } , { type mRNA , heading "mRNA" , accession "BC039866" , version 1 , source { { src { db "Nucleotide" , tag id 25123215 } , anchor "BC039866" } } , seqs { whole gi 25123215 } , products { { type peptide , accession "AAH39866" , version 1 , source { { src { db "Protein" , tag id 56200511 } , anchor "AAH39866" } } , seqs { whole gi 56200511 } } } } , { type mRNA , heading "mRNA" , accession "CR456755" , version 1 , source { { src { db "Nucleotide" , tag id 48145626 } , anchor "CR456755" } } , seqs { whole gi 48145626 } , products { { type peptide , accession "CAG33036" , version 1 , source { { src { db "Protein" , tag id 48145627 } , anchor "CAG33036" } } , seqs { whole gi 48145627 } } } } , { type mRNA , heading "mRNA" , accession "M95627" , version 1 , source { { src { db "Nucleotide" , tag id 870802 } , anchor "M95627" } } , seqs { whole gi 870802 } , products { { type peptide , accession "AAA68889" , version 1 , source { { src { db "Protein" , tag id 870803 } , anchor "AAA68889" } } , seqs { whole gi 870803 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "Q13685" , version 0 , source { { src { db "Protein" , tag id 3121739 } , anchor "Q13685" } } , seqs { whole gi 3121739 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "14" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_005403.15&gene=AAMP&lid=14&from=69338268&to=69344275" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "14" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_005403.15&gene=AAMP&lid=14" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.83347" } } , source { { src { db "UniGene" , tag str "Hs.83347" } , anchor "Hs.83347" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=83 347" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "603488" } , anchor "603488" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "14" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 14[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 14 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=14" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:4573993" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AB209 790" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= AB209790" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC014122" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC014122" } } } } } } , unique-keys { { db "LocusID" , tag id 14 } , { db "MIM" , tag id 603488 } } , xtra-index-terms { "LOC14" } } Entrezgene ::= { track-info { geneid 15 , status live , create-date std { year 2003 , month 8 , day 28 , hour 20 , minute 30 , second 0 } , update-date std { year 2005 , month 4 , day 14 , hour 13 , minute 15 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Homo sapiens" , common "human" , db { { db "taxon" , tag id 9606 } } , syn { "man" } , orgname { name binomial { genus "Homo" , species "sapiens" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo" , gcode 1 , mgcode 2 , div "PRI" } } , subtype { { subtype chromosome , name "17" } } } , gene { locus "AANAT" , desc "arylalkylamine N-acetyltransferase" , maploc "17q25" , db { { db "MIM" , tag id 600950 } } , syn { "SNAT" , "AA-NAT" } , locus-tag "HGNC:19" } , prot { name { "arylalkylamine N-acetyltransferase" , "serotonin N-acetyltransferase" } } , summary "Arylalkylamine N-acetyltransferase belongs to the superfamily of acetyltransferases. It is the penultimate enzyme in melatonin synthesis and controls the night/day rhythm in melatonin production in the vertebrate pineal gland. Melatonin is essential for seasonal reproduction, modulates the function of the circadian clock in the suprachiasmatic nucleus, and influences activity and sleep. This enzyme is rapidly inactivated when animals are exposed to light at night. This protein is 80% identical to sheep and rat AA-NAT. Arylalkylamine N-acetyltransferase may contribute a multifactorial genetic diseases such as altered behavior in sleep/wake cycle." , location { { display-str "17q25" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 15 , src-str2 "15" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000017" , version 9 , seqs { int { from 71975245 , to 71977793 , strand plus , id gi 51511734 } } , products { { type mRNA , heading "Reference" , accession "NM_001088" , version 1 , genomic-coords { mix { int { from 71975245 , to 71975403 , strand plus , id gi 51511734 } , int { from 71976348 , to 71976585 , strand plus , id gi 51511734 } , int { from 71976849 , to 71977003 , strand plus , id gi 51511734 } , int { from 71977341 , to 71977793 , strand plus , id gi 51511734 } } } , seqs { whole gi 4501844 } , products { { type peptide , heading "Reference" , accession "NP_001079" , version 1 , genomic-coords { packed-int { { from 71976423 , to 71976585 , strand plus , id gi 51511734 } , { from 71976849 , to 71977003 , strand plus , id gi 51511734 } , { from 71977341 , to 71977646 , strand plus , id gi 51511734 } } } , seqs { whole gi 4501845 } , comment { { type property , label "EC" , text "2.3.1.87" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.87" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_010641" , version 15 , seqs { int { from 8389922 , to 8392470 , strand plus , id gi 51474120 } } , products { { type mRNA , heading "Reference" , accession "NM_001088" , version 1 , genomic-coords { mix { int { from 8389922 , to 8390080 , strand plus , id gi 51474120 } , int { from 8391025 , to 8391262 , strand plus , id gi 51474120 } , int { from 8391526 , to 8391680 , strand plus , id gi 51474120 } , int { from 8392018 , to 8392470 , strand plus , id gi 51474120 } } } , seqs { whole gi 4501844 } , products { { type peptide , heading "Reference" , accession "NP_001079" , version 1 , genomic-coords { packed-int { { from 8391100 , to 8391262 , strand plus , id gi 51474120 } , { from 8391526 , to 8391680 , strand plus , id gi 51474120 } , { from 8392018 , to 8392323 , strand plus , id gi 51474120 } } } , seqs { whole gi 4501845 } , comment { { type property , label "EC" , text "2.3.1.87" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.87" } } } } } } } } } , { type genomic , heading "Reference" , accession "NT_086886" , version 1 , seqs { int { from 11539555 , to 11542103 , strand plus , id gi 51474508 } } , products { { type mRNA , heading "Reference" , accession "NM_001088" , version 1 , genomic-coords { mix { int { from 11539555 , to 11539713 , strand plus , id gi 51474508 } , int { from 11540658 , to 11540895 , strand plus , id gi 51474508 } , int { from 11541159 , to 11541313 , strand plus , id gi 51474508 } , int { from 11541651 , to 11542103 , strand plus , id gi 51474508 } } } , seqs { whole gi 4501844 } , products { { type peptide , heading "Reference" , accession "NP_001079" , version 1 , genomic-coords { packed-int { { from 11540733 , to 11540895 , strand plus , id gi 51474508 } , { from 11541159 , to 11541313 , strand plus , id gi 51474508 } , { from 11541651 , to 11541956 , strand plus , id gi 51474508 } } } , seqs { whole gi 4501845 } , comment { { type property , label "EC" , text "2.3.1.87" , version 0 , xtra-properties { { tag "EC" , value "2.3.1.87" } } } } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "HUGO Gene Nomenclature Committee" } } , properties { { type property , label "Official Symbol" , text "AANAT" , version 0 } , { type property , label "Official Full Name" , text "arylalkylamine N-acetyltransferase" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "GOA" , url "http://www.ebi.ac.uk/GOA/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8415 } , anchor "acyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 8661026 } , source { { src { db "GO" , tag id 4059 } , anchor "aralkylamine N-acetyltransferase activity" , post-text "evidence: TAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16740 } , anchor "transferase activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , refs { pmid 8661026 } , source { { src { db "GO" , tag id 7623 } , anchor "circadian rhythm" , post-text "evidence: TAS" } } } } } } } } , homology { { type comment , heading "Mouse, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 31013 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=17& MAPS=genes-r-org/rat-chr/human%3A17,genes-r-org/mouse-chr/human%3A17,genes-r-o rg/human-chr17&query=e%3A15[id]+AND+gene[obj_type]&QSTR=aanat&cmd=focus&fill=1 0" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "HGNC" , tag id 19 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15332344 , pmid 12736803 , pmid 12552951 , pmid 12477932 , pmid 12039872 , pmid 11934439 , pmid 11427721 , pmid 11336675 , pmid 11313340 , pmid 9238858 , pmid 8661026 , pmid 7502081 , pmid 2181999 } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_001088" , version 1 , source { { src { db "Nucleotide" , tag id 4501844 } , anchor "NM_001088" } } , seqs { whole gi 4501844 } , products { { type peptide , heading "Product" , accession "NP_001079" , version 1 , source { { src { db "Protein" , tag id 4501845 } , anchor "NP_001079" , post-text "arylalkylamine N-acetyltransferase" } } , seqs { whole gi 4501845 } , comment { { type other , heading "Consensus CDS (CCDS)" , version 0 , source { { src { db "CCDS" , tag str "CCDS11745.1" } , anchor "CCDS11745.1" } } } , { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 4501845 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 25558 } , anchor "pfam00583: Acetyltransf_1; Acetyltransferase (GNAT) family" } } , comment { { type other , text "Location: 82 - 174 Blast Score: 94" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "U40347" } , anchor "U40347" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AB023793" , version 1 , source { { src { db "Nucleotide" , tag id 12248880 } , anchor "AB023793" } } , seqs { whole gi 12248880 } , products { { type peptide , accession "BAB20312" , version 1 , source { { src { db "Protein" , tag id 12248881 } , anchor "BAB20312" } } , seqs { whole gi 12248881 } } } } , { type genomic , heading "Genomic" , accession "AB023794" , version 1 , source { { src { db "Nucleotide" , tag id 12248882 } , anchor "AB023794" } } , seqs { whole gi 12248882 } , products { { type peptide , accession "BAB20313" , version 1 , source { { src { db "Protein" , tag id 12248883 } , anchor "BAB20313" } } , seqs { whole gi 12248883 } } } } , { type genomic , heading "Genomic" , accession "AB023795" , version 1 , source { { src { db "Nucleotide" , tag id 12248884 } , anchor "AB023795" } } , seqs { whole gi 12248884 } , products { { type peptide , accession "BAB20314" , version 1 , source { { src { db "Protein" , tag id 12248885 } , anchor "BAB20314" } } , seqs { whole gi 12248885 } } } } , { type genomic , heading "Genomic" , accession "AB023796" , version 1 , source { { src { db "Nucleotide" , tag id 12248886 } , anchor "AB023796" } } , seqs { whole gi 12248886 } , products { { type peptide , accession "BAB20315" , version 1 , source { { src { db "Protein" , tag id 12248887 } , anchor "BAB20315" } } , seqs { whole gi 12248887 } } } } , { type genomic , heading "Genomic" , accession "AB023797" , version 1 , source { { src { db "Nucleotide" , tag id 12248888 } , anchor "AB023797" } } , seqs { whole gi 12248888 } , products { { type peptide , accession "BAB20316" , version 1 , source { { src { db "Protein" , tag id 12248889 } , anchor "BAB20316" } } , seqs { whole gi 12248889 } } } } , { type genomic , heading "Genomic" , accession "AF360979" , version 1 , source { { src { db "Nucleotide" , tag id 13936890 } , anchor "AF360979" } } , seqs { whole gi 13936890 } , products { { type peptide , accession "AAK49981" , version 1 , source { { src { db "Protein" , tag id 13936891 } , anchor "AAK49981" } } , seqs { whole gi 13936891 } } } } , { type genomic , heading "Genomic" , accession "U40391" , version 1 , source { { src { db "Nucleotide" , tag id 1389593 } , anchor "U40391" } } , seqs { whole gi 1389593 } , products { { type peptide , accession "AAC50555" , version 1 , source { { src { db "Protein" , tag id 1389594 } , anchor "AAC50555" } } , seqs { whole gi 1389594 } } } } , { type mRNA , heading "mRNA" , accession "BC069434" , version 1 , source { { src { db "Nucleotide" , tag id 46854803 } , anchor "BC069434" } } , seqs { whole gi 46854803 } , products { { type peptide , accession "AAH69434" , version 1 , source { { src { db "Protein" , tag id 46854804 } , anchor "AAH69434" } } , seqs { whole gi 46854804 } } } } , { type mRNA , heading "mRNA" , accession "U40347" , version 1 , source { { src { db "Nucleotide" , tag id 1389591 } , anchor "U40347" } } , seqs { whole gi 1389591 } , products { { type peptide , accession "AAC50554" , version 1 , source { { src { db "Protein" , tag id 1389592 } , anchor "AAC50554" } } , seqs { whole gi 1389592 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "Q16613" , version 0 , source { { src { db "Protein" , tag id 11387096 } , anchor "Q16613" } } , seqs { whole gi 11387096 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "15" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_010641.15&gene=AANAT&lid=15&from=8389923&to=8392471" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "15" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96 06&contig=NT_010641.15&gene=AANAT&lid=15" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Hs.431417" } } , source { { src { db "UniGene" , tag str "Hs.431417" } , anchor "Hs.431417" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=43 1417" } } } , { type comment , text "MIM" , version 0 , source { { src { db "MIM" , tag str "600950" } , anchor "600950" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "15" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 15[loc]&TAXID=9606" } } } , { type comment , version 0 , source { { src { db "AceView" , tag id 15 } , anchor "AceView" , url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l ocusid&org=9606&l=15" } } } , { type comment , version 0 , source { { src { db "GDB" , tag str "GDB:700076" } } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=U4034 7" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= U40347" } } } , { type comment , version 0 , source { { src { db "KEGG" , tag str "" } , url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:15" } } } , { type comment , text "PharmGKB" , version 0 , source { { src { db "PharmGKB" , tag str "PA24366" } , anchor "PA24366" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC069434" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC069434" } } } } } , { type comment , heading "Pathways" , version 0 , comment { { type comment , text "KEGG pathway: Tryptophan metabolism" , version 0 , source { { src { db "00380" , tag str "00380" } , anchor "00380" , url "http://www.genome.jp/dbget-bin/show_pathway?hsa00380+15" } } } } } , { type generif , text "Data suggest that the -263G/C single nucleotide polymorphism of arylalkylamine-N-acetyl-transferase (AA-NAT) may be an important determinant of the late/short sleep pattern." , version 0 , refs { pmid 15332344 } , create-date str "Sep 27 2004 4:34PM" , update-date str "Sep 27 2004 7:00PM" } , { type generif , text "There is a significant increase in AANAT allele positivity at the single nucleotide polymorphism (alanine 129--> threonine) at between patients with DSPS & controls. AA-NAT could be a susceptibility gene for DSPS." , version 0 , refs { pmid 12736803 } , create-date str "Jul 10 2003 12:00AM" , update-date str "May 30 2004 7:11AM" } } , unique-keys { { db "LocusID" , tag id 15 } , { db "MIM" , tag id 600950 } } , xtra-index-terms { "LOC15" } } Entrezgene ::= { track-info { geneid 9996 , status secondary , current-id { { db "LocusID" , tag id 320632 } , { db "GeneID" , tag id 320632 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 9996 , src-str2 "9996" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , unique-keys { { db "LocusID" , tag id 9996 } } , xtra-index-terms { "LOC320632" } } Entrezgene ::= { track-info { geneid 11286 , status secondary , current-id { { db "LocusID" , tag id 50518 } , { db "GeneID" , tag id 50518 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11286 , src-str2 "11286" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11286 } } , xtra-index-terms { "LOC50518" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11287 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 4 , day 19 , hour 12 , minute 12 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "6" } } } , gene { locus "Pzp" , desc "pregnancy zone protein" , maploc "6 62.0 cM" , syn { "A1m" , "A2m" , "MAM" } , locus-tag "MGI:87854" } , prot { name { "pregnancy zone protein" , "alpha 1 macroglobulin" } } , location { { display-str "6 F1-G3" , method map-type cyto } , { display-str "6 62.0 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11287 , src-str2 "11287" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000072" , version 1 , seqs { int { from 129138521 , to 129181660 , strand minus , id gi 51863714 } } , products { { type mRNA , heading "Reference" , accession "NM_007376" , version 1 , genomic-coords { mix { int { from 129138521 , to 129138673 , strand minus , id gi 51863714 } , int { from 129139811 , to 129139852 , strand minus , id gi 51863714 } , int { from 129140505 , to 129140607 , strand minus , id gi 51863714 } , int { from 129141065 , to 129141133 , strand minus , id gi 51863714 } , int { from 129141840 , to 129141930 , strand minus , id gi 51863714 } , int { from 129142350 , to 129142480 , strand minus , id gi 51863714 } , int { from 129142828 , to 129143046 , strand minus , id gi 51863714 } , int { from 129143853 , to 129144094 , strand minus , id gi 51863714 } , int { from 129144629 , to 129144806 , strand minus , id gi 51863714 } , int { from 129144966 , to 129145040 , strand minus , id gi 51863714 } , int { from 129145470 , to 129145626 , strand minus , id gi 51863714 } , int { from 129146112 , to 129146202 , strand minus , id gi 51863714 } , int { from 129146443 , to 129146619 , strand minus , id gi 51863714 } , int { from 129147104 , to 129147187 , strand minus , id gi 51863714 } , int { from 129149375 , to 129149426 , strand minus , id gi 51863714 } , int { from 129149655 , to 129149776 , strand minus , id gi 51863714 } , int { from 129150140 , to 129150266 , strand minus , id gi 51863714 } , int { from 129150847 , to 129151075 , strand minus , id gi 51863714 } , int { from 129151526 , to 129151700 , strand minus , id gi 51863714 } , int { from 129153906 , to 129153993 , strand minus , id gi 51863714 } , int { from 129157123 , to 129157287 , strand minus , id gi 51863714 } , int { from 129158420 , to 129158569 , strand minus , id gi 51863714 } , int { from 129161683 , to 129161825 , strand minus , id gi 51863714 } , int { from 129165292 , to 129165355 , strand minus , id gi 51863714 } , int { from 129167103 , to 129167330 , strand minus , id gi 51863714 } , int { from 129168683 , to 129168844 , strand minus , id gi 51863714 } , int { from 129171020 , to 129171129 , strand minus , id gi 51863714 } , int { from 129171763 , to 129171877 , strand minus , id gi 51863714 } , int { from 129174339 , to 129174462 , strand minus , id gi 51863714 } , int { from 129176048 , to 129176132 , strand minus , id gi 51863714 } , int { from 129176963 , to 129177131 , strand minus , id gi 51863714 } , int { from 129177687 , to 129177707 , strand minus , id gi 51863714 } , int { from 129178724 , to 129178776 , strand minus , id gi 51863714 } , int { from 129178917 , to 129179070 , strand minus , id gi 51863714 } , int { from 129180062 , to 129180245 , strand minus , id gi 51863714 } , int { from 129181526 , to 129181660 , strand minus , id gi 51863714 } } } , seqs { whole gi 6680607 } , products { { type peptide , heading "Reference" , accession "NP_031402" , version 1 , genomic-coords { packed-int { { from 129138651 , to 129138673 , strand minus , id gi 51863714 } , { from 129139811 , to 129139852 , strand minus , id gi 51863714 } , { from 129140505 , to 129140607 , strand minus , id gi 51863714 } , { from 129141065 , to 129141133 , strand minus , id gi 51863714 } , { from 129141840 , to 129141930 , strand minus , id gi 51863714 } , { from 129142350 , to 129142480 , strand minus , id gi 51863714 } , { from 129142828 , to 129143046 , strand minus , id gi 51863714 } , { from 129143853 , to 129144094 , strand minus , id gi 51863714 } , { from 129144629 , to 129144806 , strand minus , id gi 51863714 } , { from 129144966 , to 129145040 , strand minus , id gi 51863714 } , { from 129145470 , to 129145626 , strand minus , id gi 51863714 } , { from 129146112 , to 129146202 , strand minus , id gi 51863714 } , { from 129146443 , to 129146619 , strand minus , id gi 51863714 } , { from 129147104 , to 129147187 , strand minus , id gi 51863714 } , { from 129149375 , to 129149426 , strand minus , id gi 51863714 } , { from 129149655 , to 129149776 , strand minus , id gi 51863714 } , { from 129150140 , to 129150266 , strand minus , id gi 51863714 } , { from 129150847 , to 129151075 , strand minus , id gi 51863714 } , { from 129151526 , to 129151700 , strand minus , id gi 51863714 } , { from 129153906 , to 129153993 , strand minus , id gi 51863714 } , { from 129157123 , to 129157287 , strand minus , id gi 51863714 } , { from 129158420 , to 129158569 , strand minus , id gi 51863714 } , { from 129161683 , to 129161825 , strand minus , id gi 51863714 } , { from 129165292 , to 129165355 , strand minus , id gi 51863714 } , { from 129167103 , to 129167330 , strand minus , id gi 51863714 } , { from 129168683 , to 129168844 , strand minus , id gi 51863714 } , { from 129171020 , to 129171129 , strand minus , id gi 51863714 } , { from 129171763 , to 129171877 , strand minus , id gi 51863714 } , { from 129174339 , to 129174462 , strand minus , id gi 51863714 } , { from 129176048 , to 129176132 , strand minus , id gi 51863714 } , { from 129176963 , to 129177131 , strand minus , id gi 51863714 } , { from 129177687 , to 129177707 , strand minus , id gi 51863714 } , { from 129178724 , to 129178776 , strand minus , id gi 51863714 } , { from 129178917 , to 129179070 , strand minus , id gi 51863714 } , { from 129180062 , to 129180245 , strand minus , id gi 51863714 } , { from 129181526 , to 129181611 , strand minus , id gi 51863714 } } } , seqs { whole gi 6680608 } } } } } } , { type genomic , heading "Reference" , accession "NT_039356" , version 3 , seqs { int { from 3999237 , to 4042376 , strand minus , id gi 51712708 } } , products { { type mRNA , heading "Reference" , accession "NM_007376" , version 1 , genomic-coords { mix { int { from 3999237 , to 3999389 , strand minus , id gi 51712708 } , int { from 4000527 , to 4000568 , strand minus , id gi 51712708 } , int { from 4001221 , to 4001323 , strand minus , id gi 51712708 } , int { from 4001781 , to 4001849 , strand minus , id gi 51712708 } , int { from 4002556 , to 4002646 , strand minus , id gi 51712708 } , int { from 4003066 , to 4003196 , strand minus , id gi 51712708 } , int { from 4003544 , to 4003762 , strand minus , id gi 51712708 } , int { from 4004569 , to 4004810 , strand minus , id gi 51712708 } , int { from 4005345 , to 4005522 , strand minus , id gi 51712708 } , int { from 4005682 , to 4005756 , strand minus , id gi 51712708 } , int { from 4006186 , to 4006342 , strand minus , id gi 51712708 } , int { from 4006828 , to 4006918 , strand minus , id gi 51712708 } , int { from 4007159 , to 4007335 , strand minus , id gi 51712708 } , int { from 4007820 , to 4007903 , strand minus , id gi 51712708 } , int { from 4010091 , to 4010142 , strand minus , id gi 51712708 } , int { from 4010371 , to 4010492 , strand minus , id gi 51712708 } , int { from 4010856 , to 4010982 , strand minus , id gi 51712708 } , int { from 4011563 , to 4011791 , strand minus , id gi 51712708 } , int { from 4012242 , to 4012416 , strand minus , id gi 51712708 } , int { from 4014622 , to 4014709 , strand minus , id gi 51712708 } , int { from 4017839 , to 4018003 , strand minus , id gi 51712708 } , int { from 4019136 , to 4019285 , strand minus , id gi 51712708 } , int { from 4022399 , to 4022541 , strand minus , id gi 51712708 } , int { from 4026008 , to 4026071 , strand minus , id gi 51712708 } , int { from 4027819 , to 4028046 , strand minus , id gi 51712708 } , int { from 4029399 , to 4029560 , strand minus , id gi 51712708 } , int { from 4031736 , to 4031845 , strand minus , id gi 51712708 } , int { from 4032479 , to 4032593 , strand minus , id gi 51712708 } , int { from 4035055 , to 4035178 , strand minus , id gi 51712708 } , int { from 4036764 , to 4036848 , strand minus , id gi 51712708 } , int { from 4037679 , to 4037847 , strand minus , id gi 51712708 } , int { from 4038403 , to 4038423 , strand minus , id gi 51712708 } , int { from 4039440 , to 4039492 , strand minus , id gi 51712708 } , int { from 4039633 , to 4039786 , strand minus , id gi 51712708 } , int { from 4040778 , to 4040961 , strand minus , id gi 51712708 } , int { from 4042242 , to 4042376 , strand minus , id gi 51712708 } } } , seqs { whole gi 6680607 } , products { { type peptide , heading "Reference" , accession "NP_031402" , version 1 , genomic-coords { packed-int { { from 3999367 , to 3999389 , strand minus , id gi 51712708 } , { from 4000527 , to 4000568 , strand minus , id gi 51712708 } , { from 4001221 , to 4001323 , strand minus , id gi 51712708 } , { from 4001781 , to 4001849 , strand minus , id gi 51712708 } , { from 4002556 , to 4002646 , strand minus , id gi 51712708 } , { from 4003066 , to 4003196 , strand minus , id gi 51712708 } , { from 4003544 , to 4003762 , strand minus , id gi 51712708 } , { from 4004569 , to 4004810 , strand minus , id gi 51712708 } , { from 4005345 , to 4005522 , strand minus , id gi 51712708 } , { from 4005682 , to 4005756 , strand minus , id gi 51712708 } , { from 4006186 , to 4006342 , strand minus , id gi 51712708 } , { from 4006828 , to 4006918 , strand minus , id gi 51712708 } , { from 4007159 , to 4007335 , strand minus , id gi 51712708 } , { from 4007820 , to 4007903 , strand minus , id gi 51712708 } , { from 4010091 , to 4010142 , strand minus , id gi 51712708 } , { from 4010371 , to 4010492 , strand minus , id gi 51712708 } , { from 4010856 , to 4010982 , strand minus , id gi 51712708 } , { from 4011563 , to 4011791 , strand minus , id gi 51712708 } , { from 4012242 , to 4012416 , strand minus , id gi 51712708 } , { from 4014622 , to 4014709 , strand minus , id gi 51712708 } , { from 4017839 , to 4018003 , strand minus , id gi 51712708 } , { from 4019136 , to 4019285 , strand minus , id gi 51712708 } , { from 4022399 , to 4022541 , strand minus , id gi 51712708 } , { from 4026008 , to 4026071 , strand minus , id gi 51712708 } , { from 4027819 , to 4028046 , strand minus , id gi 51712708 } , { from 4029399 , to 4029560 , strand minus , id gi 51712708 } , { from 4031736 , to 4031845 , strand minus , id gi 51712708 } , { from 4032479 , to 4032593 , strand minus , id gi 51712708 } , { from 4035055 , to 4035178 , strand minus , id gi 51712708 } , { from 4036764 , to 4036848 , strand minus , id gi 51712708 } , { from 4037679 , to 4037847 , strand minus , id gi 51712708 } , { from 4038403 , to 4038423 , strand minus , id gi 51712708 } , { from 4039440 , to 4039492 , strand minus , id gi 51712708 } , { from 4039633 , to 4039786 , strand minus , id gi 51712708 } , { from 4040778 , to 4040961 , strand minus , id gi 51712708 } , { from 4042242 , to 4042327 , strand minus , id gi 51712708 } } } , seqs { whole gi 6680608 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Pzp" , version 0 } , { type property , label "Official Full Name" , text "pregnancy zone protein" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , refs { pmid 5559967 } , source { { src { db "GO" , tag id 4866 } , anchor "endopeptidase inhibitor activity" , post-text "evidence: IDA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 4867 } , anchor "serine-type endopeptidase inhibitor activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 17114 } , anchor "wide-spectrum protease inhibitor activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 5559967 } , source { { src { db "GO" , tag id 5576 } , anchor "extracellular region" , post-text "evidence: TAS" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 5615 } , anchor "extracellular space" , post-text "evidence: TAS" } } } } } } } } , homology { { type comment , heading "Rat" , version 0 , source { { src { db "HomoloGene" , tag id 56378 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=6& MAPS=genes-r-org/rat-chr/mouse%3A6,genes-r-org/mouse-chr6&query=e%3A11287[id]+ AND+gene[obj_type]&QSTR=pzp&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 87854 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 12477932 , pmid 12466851 , pmid 7528166 , pmid 5559967 , pmid 1280217 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 140992 } , anchor "A2m" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "D6Uwa7" , version 0 } , { type other , label "Alternate name" , text "MGI:893149" , version 0 } , { type other , label "Alternate name" , text "Pzp" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 179416 } , anchor "AI838740" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "659717" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 179477 } , anchor "AI893533" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "681710" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_007376" , version 1 , source { { src { db "Nucleotide" , tag id 6680607 } , anchor "NM_007376" } } , seqs { whole gi 6680607 } , products { { type peptide , heading "Product" , accession "NP_031402" , version 1 , source { { src { db "Protein" , tag id 6680608 } , anchor "NP_031402" , post-text "pregnancy zone protein" } } , seqs { whole gi 6680608 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 6680608 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5952 } , anchor "pfam00207: A2M; Alpha-2-macroglobulin family" } } , comment { { type other , text "Location: 738 - 1482 Blast Score: 1820" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 25832 } , anchor "pfam01835: A2M_N; Alpha-2-macroglobulin family N-terminal region" } } , comment { { type other , text "Location: 22 - 622 Blast Score: 1231" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "M93264" } , anchor "M93264" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "U06977" , version 1 , source { { src { db "Nucleotide" , tag id 463883 } , anchor "U06977" } } , seqs { whole gi 463883 } , products { { type peptide , accession "AAA87890" , version 1 , source { { src { db "Protein" , tag id 463884 } , anchor "AAA87890" } } , seqs { whole gi 463884 } } } } , { type mRNA , heading "mRNA" , accession "BC057983" , version 1 , source { { src { db "Nucleotide" , tag id 34785995 } , anchor "BC057983" } } , seqs { whole gi 34785995 } , products { { type peptide , accession "AAH57983" , version 1 , source { { src { db "Protein" , tag id 34785996 } , anchor "AAH57983" } } , seqs { whole gi 34785996 } } } , comment { { type other , label "Strain" , text "FVB/N" , version 0 } } } , { type mRNA , heading "mRNA" , accession "M93264" , version 1 , source { { src { db "Nucleotide" , tag id 199085 } , anchor "M93264" } } , seqs { whole gi 199085 } , products { { type peptide , accession "AAA39508" , version 1 , source { { src { db "Protein" , tag id 199086 } , anchor "AAA39508" } } , seqs { whole gi 199086 } } } } , { type other , text "None" , version 0 , products { { type peptide , accession "Q61838" , version 0 , source { { src { db "Protein" , tag id 2492496 } , anchor "Q61838" } } , seqs { whole gi 2492496 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11287" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039356.3&gene=Pzp&lid=11287&from=3999238&to=4042377" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11287" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039356.3&gene=Pzp&lid=11287" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.260144" } } , source { { src { db "UniGene" , tag str "Mm.260144" } , anchor "Mm.260144" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=26 0144" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11287" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11287[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 87854 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:87854" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC057 983" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= BC057983" } } } , { type comment , text "Gene Expression Database (GXD) at MGI" , version 0 , source { { src { db "Gene Expression Database (GXD) at MGI" , tag str "MGI:87854" } , anchor "MGI:87854" , url "http://www.informatics.jax.org/searches/expression_report.c gi?id=MGI:87854" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC057983" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Mm&LIST=BC057983" } } } } } , { type comment , heading "Alleles" , version 0 , comment { { type comment , text "The following allele types are documented at Mouse Genome Informatics" , version 0 , source { { anchor "(MGI)" , url "http://www.informatics.jax.org/searches/allele_report.cgi?m arkerID=MGI:87854" } } } , { type comment , heading "Targeted (knock-out) (1)" , version 0 , refs { pmid 7544347 } } } } } , unique-keys { { db "LocusID" , tag id 11287 } , { db "MGI" , tag id 87854 } } , xtra-index-terms { "LOC11287" } } Entrezgene ::= { track-info { geneid 11288 , status secondary , current-id { { db "LocusID" , tag id 112131 } , { db "GeneID" , tag id 112131 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11288 , src-str2 "11288" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11288 } } , xtra-index-terms { "LOC112131" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11289 , status secondary , current-id { { db "LocusID" , tag id 107417 } , { db "GeneID" , tag id 107417 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11289 , src-str2 "11289" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , unique-keys { { db "LocusID" , tag id 11289 } } , xtra-index-terms { "LOC107417" } } Entrezgene ::= { track-info { geneid 11293 , status secondary , current-id { { db "LocusID" , tag id 112132 } , { db "GeneID" , tag id 112132 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11293 , src-str2 "11293" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11293 } } , xtra-index-terms { "LOC112132" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11294 , status secondary , current-id { { db "LocusID" , tag id 109413 } , { db "GeneID" , tag id 109413 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11294 , src-str2 "11294" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11294 } } , xtra-index-terms { "LOC109413" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11295 , status secondary , current-id { { db "LocusID" , tag id 109414 } , { db "GeneID" , tag id 109414 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11295 , src-str2 "11295" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11295 } } , xtra-index-terms { "LOC109414" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11296 , status secondary , current-id { { db "LocusID" , tag id 104236 } , { db "GeneID" , tag id 104236 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11296 , src-str2 "11296" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , unique-keys { { db "LocusID" , tag id 11296 } } , xtra-index-terms { "LOC104236" } } Entrezgene ::= { track-info { geneid 11297 , status secondary , current-id { { db "LocusID" , tag id 227290 } , { db "GeneID" , tag id 227290 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11297 , src-str2 "11297" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , unique-keys { { db "LocusID" , tag id 11297 } } , xtra-index-terms { "LOC227290" } } Entrezgene ::= { track-info { geneid 11298 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 3 , day 16 , hour 16 , minute 48 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "11" } } } , gene { locus "Aanat" , desc "arylalkylamine N-acetyltransferase" , maploc "11 70.0 cM" , syn { "Nat4" , "SNAT" , "Nat-2" } , locus-tag "MGI:1328365" } , prot { name { "arylalkylamine N-acetyltransferase" } } , location { { display-str "11 E2" , method map-type cyto } , { display-str "11 70.0 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11298 , src-str2 "11298" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000077" , version 1 , seqs { int { from 116264815 , to 116268672 , strand plus , id gi 51868608 } } , products { { type mRNA , heading "Reference" , accession "NM_009591" , version 1 , genomic-coords { mix { int { from 116264815 , to 116264902 , strand plus , id gi 51868608 } , int { from 116266704 , to 116266921 , strand plus , id gi 51868608 } , int { from 116267254 , to 116267408 , strand plus , id gi 51868608 } , int { from 116267917 , to 116268672 , strand plus , id gi 51868608 } } } , seqs { whole gi 6752937 } , products { { type peptide , heading "Reference" , accession "NP_033721" , version 1 , genomic-coords { packed-int { { from 116266765 , to 116266921 , strand plus , id gi 51868608 } , { from 116267254 , to 116267408 , strand plus , id gi 51868608 } , { from 116267917 , to 116268222 , strand plus , id gi 51868608 } } } , seqs { whole gi 6752938 } } } } } } , { type genomic , heading "Reference" , accession "NT_039521" , version 3 , seqs { int { from 27994169 , to 27998026 , strand plus , id gi 51766637 } } , products { { type mRNA , heading "Reference" , accession "NM_009591" , version 1 , genomic-coords { mix { int { from 27994169 , to 27994256 , strand plus , id gi 51766637 } , int { from 27996058 , to 27996275 , strand plus , id gi 51766637 } , int { from 27996608 , to 27996762 , strand plus , id gi 51766637 } , int { from 27997271 , to 27998026 , strand plus , id gi 51766637 } } } , seqs { whole gi 6752937 } , products { { type peptide , heading "Reference" , accession "NP_033721" , version 1 , genomic-coords { packed-int { { from 27996119 , to 27996275 , strand plus , id gi 51766637 } , { from 27996608 , to 27996762 , strand plus , id gi 51766637 } , { from 27997271 , to 27997576 , strand plus , id gi 51766637 } } } , seqs { whole gi 6752938 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Aanat" , version 0 } , { type property , label "Official Full Name" , text "arylalkylamine N-acetyltransferase" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8080 } , anchor "N-acetyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 8415 } , anchor "acyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 4060 } , anchor "arylamine N-acetyltransferase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16740 } , anchor "transferase activity" , post-text "evidence: IEA" } } } } } } } } , homology { { type comment , heading "Human, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 31013 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=11 &MAPS=genes-r-org/human-chr/mouse%3A11,genes-r-org/rat-chr/mouse%3A11,genes-r- org/mouse-chr11&query=e%3A11298[id]+AND+gene[obj_type]&QSTR=aanat&cmd=focus&fi ll=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 1328365 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 12138020 , pmid 9838107 , pmid 9708862 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 126289 } , anchor "D11Mit102" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "MGI:707739" , version 0 } , { type other , label "Alternate name" , text "MPC786" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_009591" , version 1 , source { { src { db "Nucleotide" , tag id 6752937 } , anchor "NM_009591" } } , seqs { whole gi 6752937 } , products { { type peptide , heading "Product" , accession "NP_033721" , version 1 , source { { src { db "Protein" , tag id 6752938 } , anchor "NP_033721" , post-text "arylalkylamine N-acetyltransferase" } } , seqs { whole gi 6752938 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 6752938 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 25558 } , anchor "pfam00583: Acetyltransf_1; Acetyltransferase (GNAT) family" } } , comment { { type other , text "Location: 80 - 172 Blast Score: 118" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AF004108" } , anchor "AF004108" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "U83462" , version 1 , source { { src { db "Nucleotide" , tag id 4159794 } , anchor "U83462" } } , seqs { whole gi 4159794 } , products { { type peptide , accession "AAD08637" , version 1 , source { { src { db "Protein" , tag id 4099097 } , anchor "AAD08637" } } , seqs { whole gi 4099097 } } } , comment { { type other , label "Strain" , text "129/Sv" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AB013358" , version 1 , source { { src { db "Nucleotide" , tag id 3298499 } , anchor "AB013358" } } , seqs { whole gi 3298499 } , products { { type peptide , accession "BAA31526" , version 1 , source { { src { db "Protein" , tag id 3298500 } , anchor "BAA31526" } } , seqs { whole gi 3298500 } } } , comment { { type other , label "Strain" , text "BALB/c" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AF004108" , version 1 , source { { src { db "Nucleotide" , tag id 4159890 } , anchor "AF004108" } } , seqs { whole gi 4159890 } , products { { type peptide , accession "AAD09408" , version 1 , source { { src { db "Protein" , tag id 4159891 } , anchor "AAD09408" } } , seqs { whole gi 4159891 } } } , comment { { type other , label "Strain" , text "C3H/He" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AF004109" , version 1 , source { { src { db "Nucleotide" , tag id 4159892 } , anchor "AF004109" } } , seqs { whole gi 4159892 } , products { { type peptide , accession "AAD09409" , version 1 , source { { src { db "Protein" , tag id 4159893 } , anchor "AAD09409" } } , seqs { whole gi 4159893 } } } , comment { { type other , label "Strain" , text "C3H/He" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AF004110" , version 1 , source { { src { db "Nucleotide" , tag id 4159894 } , anchor "AF004110" } } , seqs { whole gi 4159894 } , products { { type peptide , accession "AAD09410" , version 1 , source { { src { db "Protein" , tag id 4159895 } , anchor "AAD09410" } } , seqs { whole gi 4159895 } } } , comment { { type other , label "Strain" , text "C57BL/6" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AF004111" , version 1 , source { { src { db "Nucleotide" , tag id 4159896 } , anchor "AF004111" } } , seqs { whole gi 4159896 } , products { { type peptide , accession "AAD09411" , version 1 , source { { src { db "Protein" , tag id 4159897 } , anchor "AAD09411" } } , seqs { whole gi 4159897 } } } , comment { { type other , label "Strain" , text "C57BL/6" , version 0 } } } , { type other , text "None" , version 0 , products { { type peptide , accession "O88816" , version 0 , source { { src { db "Protein" , tag id 11387071 } , anchor "O88816" } } , seqs { whole gi 11387071 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11298" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039521.3&gene=Aanat&lid=11298&from=27994170&to=27998027" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11298" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039521.3&gene=Aanat&lid=11298" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.42233" } } , source { { src { db "UniGene" , tag str "Mm.42233" } , anchor "Mm.42233" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=42 233" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11298" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11298[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 1328365 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:1328365" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=AF004 110" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= AF004110" } } } } } , { type generif , text "AANAT expression and synthesis of N-acetylserotonin/melatonin could play a role in addictive properties of cocaine" , version 0 , refs { pmid 12138020 } , create-date str "Aug 19 2002 12:00AM" , update-date str "Aug 28 2002 6:19PM" } } , unique-keys { { db "LocusID" , tag id 11298 } , { db "MGI" , tag id 1328365 } } , xtra-index-terms { "LOC11298" } } Entrezgene ::= { track-info { geneid 11299 , status secondary , current-id { { db "LocusID" , tag id 20249 } , { db "GeneID" , tag id 20249 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11299 , src-str2 "11299" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11299 } } , xtra-index-terms { "LOC20249" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11300 , status secondary , current-id { { db "LocusID" , tag id 112133 } , { db "GeneID" , tag id 112133 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type unknown , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11300 , src-str2 "11300" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , properties { { type property , label "Property" , text "phenotype only" , version 0 } } , unique-keys { { db "LocusID" , tag id 11300 } } , xtra-index-terms { "LOC112133" } , xtra-properties { { tag "PROP" , value "phenotype only" } } } Entrezgene ::= { track-info { geneid 11301 , status secondary , current-id { { db "LocusID" , tag id 20700 } , { db "GeneID" , tag id 20700 } } , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 3 , day 9 , hour 17 , minute 35 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , gene { } , gene-source { src "LocusLink" , src-int 11301 , src-str2 "11301" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , version 0 } } , unique-keys { { db "LocusID" , tag id 11301 } } , xtra-index-terms { "LOC20700" } } Entrezgene ::= { track-info { geneid 11302 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 3 , day 26 , hour 10 , minute 32 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "11" } } } , gene { locus "Aatk" , desc "apoptosis-associated tyrosine kinase" , maploc "11 E2" , syn { "AATYK" , "mKIAA0641" } , locus-tag "MGI:1197518" } , prot { name { "apoptosis-associated tyrosine kinase" } } , location { { display-str "11 E2" , method map-type cyto } } , gene-source { src "LocusLink" , src-int 11302 , src-str2 "11302" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000077" , version 1 , seqs { int { from 119678449 , to 119692677 , strand minus , id gi 51868608 } } , products { { type mRNA , heading "Reference" , accession "NM_007377" , version 1 , genomic-coords { mix { int { from 119678449 , to 119679572 , strand minus , id gi 51868608 } , int { from 119680403 , to 119680603 , strand minus , id gi 51868608 } , int { from 119680735 , to 119680882 , strand minus , id gi 51868608 } , int { from 119680962 , to 119683554 , strand minus , id gi 51868608 } , int { from 119683851 , to 119684000 , strand minus , id gi 51868608 } , int { from 119684576 , to 119684697 , strand minus , id gi 51868608 } , int { from 119684778 , to 119684862 , strand minus , id gi 51868608 } , int { from 119686587 , to 119686720 , strand minus , id gi 51868608 } , int { from 119687234 , to 119687321 , strand minus , id gi 51868608 } , int { from 119687441 , to 119687559 , strand minus , id gi 51868608 } , int { from 119687856 , to 119687935 , strand minus , id gi 51868608 } , int { from 119689873 , to 119690020 , strand minus , id gi 51868608 } , int { from 119692530 , to 119692677 , strand minus , id gi 51868608 } } } , seqs { whole gi 6680609 } , products { { type peptide , heading "Reference" , accession "NP_031403" , version 1 , genomic-coords { packed-int { { from 119679532 , to 119679572 , strand minus , id gi 51868608 } , { from 119680403 , to 119680603 , strand minus , id gi 51868608 } , { from 119680735 , to 119680882 , strand minus , id gi 51868608 } , { from 119680962 , to 119683554 , strand minus , id gi 51868608 } , { from 119683851 , to 119684000 , strand minus , id gi 51868608 } , { from 119684576 , to 119684697 , strand minus , id gi 51868608 } , { from 119684778 , to 119684862 , strand minus , id gi 51868608 } , { from 119686587 , to 119686720 , strand minus , id gi 51868608 } , { from 119687234 , to 119687321 , strand minus , id gi 51868608 } , { from 119687441 , to 119687559 , strand minus , id gi 51868608 } , { from 119687856 , to 119687935 , strand minus , id gi 51868608 } , { from 119689873 , to 119690020 , strand minus , id gi 51868608 } , { from 119692530 , to 119692574 , strand minus , id gi 51868608 } } } , seqs { whole gi 6680610 } } } } } } , { type genomic , heading "Reference" , accession "NT_039521" , version 3 , seqs { int { from 31407803 , to 31422031 , strand minus , id gi 51766637 } } , products { { type mRNA , heading "Reference" , accession "NM_007377" , version 1 , genomic-coords { mix { int { from 31407803 , to 31408926 , strand minus , id gi 51766637 } , int { from 31409757 , to 31409957 , strand minus , id gi 51766637 } , int { from 31410089 , to 31410236 , strand minus , id gi 51766637 } , int { from 31410316 , to 31412908 , strand minus , id gi 51766637 } , int { from 31413205 , to 31413354 , strand minus , id gi 51766637 } , int { from 31413930 , to 31414051 , strand minus , id gi 51766637 } , int { from 31414132 , to 31414216 , strand minus , id gi 51766637 } , int { from 31415941 , to 31416074 , strand minus , id gi 51766637 } , int { from 31416588 , to 31416675 , strand minus , id gi 51766637 } , int { from 31416795 , to 31416913 , strand minus , id gi 51766637 } , int { from 31417210 , to 31417289 , strand minus , id gi 51766637 } , int { from 31419227 , to 31419374 , strand minus , id gi 51766637 } , int { from 31421884 , to 31422031 , strand minus , id gi 51766637 } } } , seqs { whole gi 6680609 } , products { { type peptide , heading "Reference" , accession "NP_031403" , version 1 , genomic-coords { packed-int { { from 31408886 , to 31408926 , strand minus , id gi 51766637 } , { from 31409757 , to 31409957 , strand minus , id gi 51766637 } , { from 31410089 , to 31410236 , strand minus , id gi 51766637 } , { from 31410316 , to 31412908 , strand minus , id gi 51766637 } , { from 31413205 , to 31413354 , strand minus , id gi 51766637 } , { from 31413930 , to 31414051 , strand minus , id gi 51766637 } , { from 31414132 , to 31414216 , strand minus , id gi 51766637 } , { from 31415941 , to 31416074 , strand minus , id gi 51766637 } , { from 31416588 , to 31416675 , strand minus , id gi 51766637 } , { from 31416795 , to 31416913 , strand minus , id gi 51766637 } , { from 31417210 , to 31417289 , strand minus , id gi 51766637 } , { from 31419227 , to 31419374 , strand minus , id gi 51766637 } , { from 31421884 , to 31421928 , strand minus , id gi 51766637 } } } , seqs { whole gi 6680610 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Aatk" , version 0 } , { type property , label "Official Full Name" , text "apoptosis-associated tyrosine kinase" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 5524 } , anchor "ATP binding" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16301 } , anchor "kinase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 4672 } , anchor "protein kinase activity" , post-text "evidence: ISS" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 4674 } , anchor "protein serine/threonine kinase activity" , post-text "evidence: ISS" } } } , { type comment , version 0 , refs { pmid 9444961 } , source { { src { db "GO" , tag id 4713 } , anchor "protein-tyrosine kinase activity" , post-text "evidence: ISS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16740 } , anchor "transferase activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , refs { pmid 9444961 } , source { { src { db "GO" , tag id 6915 } , anchor "apoptosis" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 6468 } , anchor "protein amino acid phosphorylation" , post-text "evidence: ISS" } } } } } } } } , homology { { type comment , heading "Rat" , version 0 , source { { src { db "HomoloGene" , tag id 7223 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=11 &MAPS=genes-r-org/rat-chr/mouse%3A11,genes-r-org/mouse-chr11&query=e%3A11302[i d]+AND+gene[obj_type]&QSTR=aatk&cmd=focus&fill=10" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 1197518 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 12670708 , pmid 12477932 , pmid 12466851 , pmid 11314039 , pmid 11217851 , pmid 11076861 , pmid 11042159 , pmid 10349636 , pmid 9444961 } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_007377" , version 2 , source { { src { db "Nucleotide" , tag id 52345410 } , anchor "NM_007377" } } , seqs { whole gi 52345410 } , products { { type peptide , heading "Product" , accession "NP_031403" , version 2 , source { { src { db "Protein" , tag id 52345411 } , anchor "NP_031403" , post-text "apoptosis-associated tyrosine kinase" } } , seqs { whole gi 52345411 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 52345411 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5392 } , anchor "cd00192: TyrKc; Tyrosine kinase, catalytic domain" } } , comment { { type other , text "Location: 75 - 348 Blast Score: 588" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "BC080846" } , anchor "BC080846" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "AB093253" , version 2 , source { { src { db "Nucleotide" , tag id 39104554 } , anchor "AB093253" } } , seqs { whole gi 39104554 } , products { { type peptide , accession "BAC41437" , version 2 , source { { src { db "Protein" , tag id 39104555 } , anchor "BAC41437" } } , seqs { whole gi 39104555 } } } } , { type mRNA , heading "mRNA" , accession "AF011908" , version 1 , source { { src { db "Nucleotide" , tag id 2459992 } , anchor "AF011908" } } , seqs { whole gi 2459992 } , products { { type peptide , accession "AAB71837" , version 1 , source { { src { db "Protein" , tag id 2459993 } , anchor "AAB71837" } } , seqs { whole gi 2459993 } } } } , { type mRNA , heading "mRNA" , accession "AK036705" , version 1 , source { { src { db "Nucleotide" , tag id 26331621 } , anchor "AK036705" } } , seqs { whole gi 26331621 } , products { { type peptide , accession "BAC29541" , version 1 , source { { src { db "Protein" , tag id 26331622 } , anchor "BAC29541" } } , seqs { whole gi 26331622 } } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK076214" , version 1 , source { { src { db "Nucleotide" , tag id 26096668 } , anchor "AK076214" } } , seqs { whole gi 26096668 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AY236858" , version 1 , source { { src { db "Nucleotide" , tag id 29824955 } , anchor "AY236858" } } , seqs { whole gi 29824955 } , products { { type peptide , accession "AAO92350" , version 1 , source { { src { db "Protein" , tag id 29824956 } , anchor "AAO92350" } } , seqs { whole gi 29824956 } } } } , { type mRNA , heading "mRNA" , accession "AY236859" , version 1 , source { { src { db "Nucleotide" , tag id 29824957 } , anchor "AY236859" } } , seqs { whole gi 29824957 } , products { { type peptide , accession "AAO92351" , version 1 , source { { src { db "Protein" , tag id 29824958 } , anchor "AAO92351" } } , seqs { whole gi 29824958 } } } , comment { { type other , label "Strain" , text "129/SvJ" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC042837" , version 1 , source { { src { db "Nucleotide" , tag id 27769340 } , anchor "BC042837" } } , seqs { whole gi 27769340 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC052323" , version 1 , source { { src { db "Nucleotide" , tag id 30410866 } , anchor "BC052323" } } , seqs { whole gi 30410866 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC080846" , version 1 , source { { src { db "Nucleotide" , tag id 51593713 } , anchor "BC080846" } } , seqs { whole gi 51593713 } , products { { type peptide , accession "AAH80846" , version 1 , source { { src { db "Protein" , tag id 51593714 } , anchor "AAH80846" } } , seqs { whole gi 51593714 } } } , comment { { type other , label "Strain" , text "C57BL/6" , version 0 } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11302" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039521.3&gene=Aatk&lid=11302&from=31407804&to=31422032" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11302" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039521.3&gene=Aatk&lid=11302" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.6826" } } , source { { src { db "UniGene" , tag str "Mm.6826" } , anchor "Mm.6826" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=68 26" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11302" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11302[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 1197518 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:1197518" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC052 323" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= BC052323" } } } , { type comment , version 0 , source { { src { db "MGC" , tag str "BC080846" } , anchor "MGC" , url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Mm&LIST=BC080846" } } } } } , { type generif , text "Expression of AATYK mRNA and protein increased during postnatal brain development. In immature granule cells, overexpression of AATYK promoted neurite outgrowth; a tyrosine kinase-defective mutant significantly inhibited it." , version 0 , refs { pmid 12670708 } , create-date str "Jun 17 2003 12:00AM" , update-date str "Aug 3 2003 7:06AM" } } , unique-keys { { db "LocusID" , tag id 11302 } , { db "MGI" , tag id 1197518 } } , xtra-index-terms { "LOC11302" } } Entrezgene ::= { track-info { geneid 11303 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 4 , day 19 , hour 12 , minute 12 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "4" } } } , gene { locus "Abca1" , desc "ATP-binding cassette, sub-family A (ABC1), member 1" , maploc "4 23.1 cM" , syn { "Abc1" } , locus-tag "MGI:99607" } , prot { name { "ATP-binding cassette 1, sub-family A, member 1" , "ATP-binding cassette 1" } } , summary "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. In humans, this protein functions as a cholesterol efflux pump in the cellular lipid removal pathway. Mutations in the human gene have been associated with Tangier's disease and familial high-density lipoprotein deficiency." , location { { display-str "4 A5-B3" , method map-type cyto } , { display-str "4 23.1 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11303 , src-str2 "11303" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000070" , version 1 , seqs { int { from 52275832 , to 52404936 , strand minus , id gi 51860768 } } , products { { type mRNA , heading "Reference" , accession "NM_013454" , version 2 , genomic-coords { mix { int { from 52275832 , to 52279127 , strand minus , id gi 51860768 } , int { from 52280381 , to 52280624 , strand minus , id gi 51860768 } , int { from 52281306 , to 52281398 , strand minus , id gi 51860768 } , int { from 52281917 , to 52282020 , strand minus , id gi 51860768 } , int { from 52283201 , to 52283335 , strand minus , id gi 51860768 } , int { from 52283663 , to 52283804 , strand minus , id gi 51860768 } , int { from 52285763 , to 52285869 , strand minus , id gi 51860768 } , int { from 52286583 , to 52286645 , strand minus , id gi 51860768 } , int { from 52287358 , to 52287478 , strand minus , id gi 51860768 } , int { from 52287708 , to 52287837 , strand minus , id gi 51860768 } , int { from 52289159 , to 52289282 , strand minus , id gi 51860768 } , int { from 52290819 , to 52290963 , strand minus , id gi 51860768 } , int { from 52291074 , to 52291189 , strand minus , id gi 51860768 } , int { from 52294000 , to 52294177 , strand minus , id gi 51860768 } , int { from 52295333 , to 52295502 , strand minus , id gi 51860768 } , int { from 52295979 , to 52296053 , strand minus , id gi 51860768 } , int { from 52304301 , to 52304406 , strand minus , id gi 51860768 } , int { from 52305377 , to 52305409 , strand minus , id gi 51860768 } , int { from 52306531 , to 52306625 , strand minus , id gi 51860768 } , int { from 52307434 , to 52307623 , strand minus , id gi 51860768 } , int { from 52310945 , to 52311043 , strand minus , id gi 51860768 } , int { from 52312075 , to 52312199 , strand minus , id gi 51860768 } , int { from 52313731 , to 52313879 , strand minus , id gi 51860768 } , int { from 52314836 , to 52314949 , strand minus , id gi 51860768 } , int { from 52315120 , to 52315168 , strand minus , id gi 51860768 } , int { from 52316867 , to 52317069 , strand minus , id gi 51860768 } , int { from 52317942 , to 52318014 , strand minus , id gi 51860768 } , int { from 52319264 , to 52319484 , strand minus , id gi 51860768 } , int { from 52320175 , to 52320312 , strand minus , id gi 51860768 } , int { from 52320491 , to 52320633 , strand minus , id gi 51860768 } , int { from 52321935 , to 52322066 , strand minus , id gi 51860768 } , int { from 52322987 , to 52323158 , strand minus , id gi 51860768 } , int { from 52324615 , to 52324728 , strand minus , id gi 51860768 } , int { from 52325810 , to 52326014 , strand minus , id gi 51860768 } , int { from 52326966 , to 52327187 , strand minus , id gi 51860768 } , int { from 52328761 , to 52328983 , strand minus , id gi 51860768 } , int { from 52329428 , to 52329604 , strand minus , id gi 51860768 } , int { from 52330140 , to 52330345 , strand minus , id gi 51860768 } , int { from 52331037 , to 52331234 , strand minus , id gi 51860768 } , int { from 52334843 , to 52334959 , strand minus , id gi 51860768 } , int { from 52335298 , to 52335437 , strand minus , id gi 51860768 } , int { from 52337773 , to 52338013 , strand minus , id gi 51860768 } , int { from 52340629 , to 52340721 , strand minus , id gi 51860768 } , int { from 52352050 , to 52352226 , strand minus , id gi 51860768 } , int { from 52354208 , to 52354329 , strand minus , id gi 51860768 } , int { from 52372641 , to 52372759 , strand minus , id gi 51860768 } , int { from 52373765 , to 52373906 , strand minus , id gi 51860768 } , int { from 52377966 , to 52378059 , strand minus , id gi 51860768 } , int { from 52388974 , to 52389139 , strand minus , id gi 51860768 } , int { from 52404720 , to 52404936 , strand minus , id gi 51860768 } } } , seqs { whole gi 34577068 } , products { { type peptide , heading "Reference" , accession "NP_038482" , version 2 , genomic-coords { packed-int { { from 52278987 , to 52279127 , strand minus , id gi 51860768 } , { from 52280381 , to 52280624 , strand minus , id gi 51860768 } , { from 52281306 , to 52281398 , strand minus , id gi 51860768 } , { from 52281917 , to 52282020 , strand minus , id gi 51860768 } , { from 52283201 , to 52283335 , strand minus , id gi 51860768 } , { from 52283663 , to 52283804 , strand minus , id gi 51860768 } , { from 52285763 , to 52285869 , strand minus , id gi 51860768 } , { from 52286583 , to 52286645 , strand minus , id gi 51860768 } , { from 52287358 , to 52287478 , strand minus , id gi 51860768 } , { from 52287708 , to 52287837 , strand minus , id gi 51860768 } , { from 52289159 , to 52289282 , strand minus , id gi 51860768 } , { from 52290819 , to 52290963 , strand minus , id gi 51860768 } , { from 52291074 , to 52291189 , strand minus , id gi 51860768 } , { from 52294000 , to 52294177 , strand minus , id gi 51860768 } , { from 52295333 , to 52295502 , strand minus , id gi 51860768 } , { from 52295979 , to 52296053 , strand minus , id gi 51860768 } , { from 52304301 , to 52304406 , strand minus , id gi 51860768 } , { from 52305377 , to 52305409 , strand minus , id gi 51860768 } , { from 52306531 , to 52306625 , strand minus , id gi 51860768 } , { from 52307434 , to 52307623 , strand minus , id gi 51860768 } , { from 52310945 , to 52311043 , strand minus , id gi 51860768 } , { from 52312075 , to 52312199 , strand minus , id gi 51860768 } , { from 52313731 , to 52313879 , strand minus , id gi 51860768 } , { from 52314836 , to 52314949 , strand minus , id gi 51860768 } , { from 52315120 , to 52315168 , strand minus , id gi 51860768 } , { from 52316867 , to 52317069 , strand minus , id gi 51860768 } , { from 52317942 , to 52318014 , strand minus , id gi 51860768 } , { from 52319264 , to 52319484 , strand minus , id gi 51860768 } , { from 52320175 , to 52320312 , strand minus , id gi 51860768 } , { from 52320491 , to 52320633 , strand minus , id gi 51860768 } , { from 52321935 , to 52322066 , strand minus , id gi 51860768 } , { from 52322987 , to 52323158 , strand minus , id gi 51860768 } , { from 52324615 , to 52324728 , strand minus , id gi 51860768 } , { from 52325810 , to 52326014 , strand minus , id gi 51860768 } , { from 52326966 , to 52327187 , strand minus , id gi 51860768 } , { from 52328761 , to 52328983 , strand minus , id gi 51860768 } , { from 52329428 , to 52329604 , strand minus , id gi 51860768 } , { from 52330140 , to 52330345 , strand minus , id gi 51860768 } , { from 52331037 , to 52331234 , strand minus , id gi 51860768 } , { from 52334843 , to 52334959 , strand minus , id gi 51860768 } , { from 52335298 , to 52335437 , strand minus , id gi 51860768 } , { from 52337773 , to 52338013 , strand minus , id gi 51860768 } , { from 52340629 , to 52340721 , strand minus , id gi 51860768 } , { from 52352050 , to 52352226 , strand minus , id gi 51860768 } , { from 52354208 , to 52354329 , strand minus , id gi 51860768 } , { from 52372641 , to 52372759 , strand minus , id gi 51860768 } , { from 52373765 , to 52373906 , strand minus , id gi 51860768 } , { from 52377966 , to 52378059 , strand minus , id gi 51860768 } , { from 52388974 , to 52389039 , strand minus , id gi 51860768 } } } , seqs { whole gi 34577069 } } } } } } , { type genomic , heading "Reference" , accession "NT_039260" , version 3 , seqs { int { from 26554540 , to 26683644 , strand minus , id gi 51709342 } } , products { { type mRNA , heading "Reference" , accession "NM_013454" , version 2 , genomic-coords { mix { int { from 26554540 , to 26557835 , strand minus , id gi 51709342 } , int { from 26559089 , to 26559332 , strand minus , id gi 51709342 } , int { from 26560014 , to 26560106 , strand minus , id gi 51709342 } , int { from 26560625 , to 26560728 , strand minus , id gi 51709342 } , int { from 26561909 , to 26562043 , strand minus , id gi 51709342 } , int { from 26562371 , to 26562512 , strand minus , id gi 51709342 } , int { from 26564471 , to 26564577 , strand minus , id gi 51709342 } , int { from 26565291 , to 26565353 , strand minus , id gi 51709342 } , int { from 26566066 , to 26566186 , strand minus , id gi 51709342 } , int { from 26566416 , to 26566545 , strand minus , id gi 51709342 } , int { from 26567867 , to 26567990 , strand minus , id gi 51709342 } , int { from 26569527 , to 26569671 , strand minus , id gi 51709342 } , int { from 26569782 , to 26569897 , strand minus , id gi 51709342 } , int { from 26572708 , to 26572885 , strand minus , id gi 51709342 } , int { from 26574041 , to 26574210 , strand minus , id gi 51709342 } , int { from 26574687 , to 26574761 , strand minus , id gi 51709342 } , int { from 26583009 , to 26583114 , strand minus , id gi 51709342 } , int { from 26584085 , to 26584117 , strand minus , id gi 51709342 } , int { from 26585239 , to 26585333 , strand minus , id gi 51709342 } , int { from 26586142 , to 26586331 , strand minus , id gi 51709342 } , int { from 26589653 , to 26589751 , strand minus , id gi 51709342 } , int { from 26590783 , to 26590907 , strand minus , id gi 51709342 } , int { from 26592439 , to 26592587 , strand minus , id gi 51709342 } , int { from 26593544 , to 26593657 , strand minus , id gi 51709342 } , int { from 26593828 , to 26593876 , strand minus , id gi 51709342 } , int { from 26595575 , to 26595777 , strand minus , id gi 51709342 } , int { from 26596650 , to 26596722 , strand minus , id gi 51709342 } , int { from 26597972 , to 26598192 , strand minus , id gi 51709342 } , int { from 26598883 , to 26599020 , strand minus , id gi 51709342 } , int { from 26599199 , to 26599341 , strand minus , id gi 51709342 } , int { from 26600643 , to 26600774 , strand minus , id gi 51709342 } , int { from 26601695 , to 26601866 , strand minus , id gi 51709342 } , int { from 26603323 , to 26603436 , strand minus , id gi 51709342 } , int { from 26604518 , to 26604722 , strand minus , id gi 51709342 } , int { from 26605674 , to 26605895 , strand minus , id gi 51709342 } , int { from 26607469 , to 26607691 , strand minus , id gi 51709342 } , int { from 26608136 , to 26608312 , strand minus , id gi 51709342 } , int { from 26608848 , to 26609053 , strand minus , id gi 51709342 } , int { from 26609745 , to 26609942 , strand minus , id gi 51709342 } , int { from 26613551 , to 26613667 , strand minus , id gi 51709342 } , int { from 26614006 , to 26614145 , strand minus , id gi 51709342 } , int { from 26616481 , to 26616721 , strand minus , id gi 51709342 } , int { from 26619337 , to 26619429 , strand minus , id gi 51709342 } , int { from 26630758 , to 26630934 , strand minus , id gi 51709342 } , int { from 26632916 , to 26633037 , strand minus , id gi 51709342 } , int { from 26651349 , to 26651467 , strand minus , id gi 51709342 } , int { from 26652473 , to 26652614 , strand minus , id gi 51709342 } , int { from 26656674 , to 26656767 , strand minus , id gi 51709342 } , int { from 26667682 , to 26667847 , strand minus , id gi 51709342 } , int { from 26683428 , to 26683644 , strand minus , id gi 51709342 } } } , seqs { whole gi 34577068 } , products { { type peptide , heading "Reference" , accession "NP_038482" , version 2 , genomic-coords { packed-int { { from 26557695 , to 26557835 , strand minus , id gi 51709342 } , { from 26559089 , to 26559332 , strand minus , id gi 51709342 } , { from 26560014 , to 26560106 , strand minus , id gi 51709342 } , { from 26560625 , to 26560728 , strand minus , id gi 51709342 } , { from 26561909 , to 26562043 , strand minus , id gi 51709342 } , { from 26562371 , to 26562512 , strand minus , id gi 51709342 } , { from 26564471 , to 26564577 , strand minus , id gi 51709342 } , { from 26565291 , to 26565353 , strand minus , id gi 51709342 } , { from 26566066 , to 26566186 , strand minus , id gi 51709342 } , { from 26566416 , to 26566545 , strand minus , id gi 51709342 } , { from 26567867 , to 26567990 , strand minus , id gi 51709342 } , { from 26569527 , to 26569671 , strand minus , id gi 51709342 } , { from 26569782 , to 26569897 , strand minus , id gi 51709342 } , { from 26572708 , to 26572885 , strand minus , id gi 51709342 } , { from 26574041 , to 26574210 , strand minus , id gi 51709342 } , { from 26574687 , to 26574761 , strand minus , id gi 51709342 } , { from 26583009 , to 26583114 , strand minus , id gi 51709342 } , { from 26584085 , to 26584117 , strand minus , id gi 51709342 } , { from 26585239 , to 26585333 , strand minus , id gi 51709342 } , { from 26586142 , to 26586331 , strand minus , id gi 51709342 } , { from 26589653 , to 26589751 , strand minus , id gi 51709342 } , { from 26590783 , to 26590907 , strand minus , id gi 51709342 } , { from 26592439 , to 26592587 , strand minus , id gi 51709342 } , { from 26593544 , to 26593657 , strand minus , id gi 51709342 } , { from 26593828 , to 26593876 , strand minus , id gi 51709342 } , { from 26595575 , to 26595777 , strand minus , id gi 51709342 } , { from 26596650 , to 26596722 , strand minus , id gi 51709342 } , { from 26597972 , to 26598192 , strand minus , id gi 51709342 } , { from 26598883 , to 26599020 , strand minus , id gi 51709342 } , { from 26599199 , to 26599341 , strand minus , id gi 51709342 } , { from 26600643 , to 26600774 , strand minus , id gi 51709342 } , { from 26601695 , to 26601866 , strand minus , id gi 51709342 } , { from 26603323 , to 26603436 , strand minus , id gi 51709342 } , { from 26604518 , to 26604722 , strand minus , id gi 51709342 } , { from 26605674 , to 26605895 , strand minus , id gi 51709342 } , { from 26607469 , to 26607691 , strand minus , id gi 51709342 } , { from 26608136 , to 26608312 , strand minus , id gi 51709342 } , { from 26608848 , to 26609053 , strand minus , id gi 51709342 } , { from 26609745 , to 26609942 , strand minus , id gi 51709342 } , { from 26613551 , to 26613667 , strand minus , id gi 51709342 } , { from 26614006 , to 26614145 , strand minus , id gi 51709342 } , { from 26616481 , to 26616721 , strand minus , id gi 51709342 } , { from 26619337 , to 26619429 , strand minus , id gi 51709342 } , { from 26630758 , to 26630934 , strand minus , id gi 51709342 } , { from 26632916 , to 26633037 , strand minus , id gi 51709342 } , { from 26651349 , to 26651467 , strand minus , id gi 51709342 } , { from 26652473 , to 26652614 , strand minus , id gi 51709342 } , { from 26656674 , to 26656767 , strand minus , id gi 51709342 } , { from 26667682 , to 26667747 , strand minus , id gi 51709342 } } } , seqs { whole gi 34577069 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Abca1" , version 0 } , { type property , label "Official Full Name" , text "ATP-binding cassette, sub-family A (ABC1), member 1" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 5524 } , anchor "ATP binding" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16887 } , anchor "ATPase activity" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , refs { pmid 11559713 } , source { { src { db "GO" , tag id 8203 } , anchor "cholesterol metabolism" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 11559713 } , source { { src { db "GO" , tag id 30301 } , anchor "cholesterol transport" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 12859204 } , source { { src { db "GO" , tag id 42158 } , anchor "lipoprotein biosynthesis" , post-text "evidence: IMP" } } } , { type comment , version 0 , refs { pmid 10878804 } , source { { src { db "GO" , tag id 6911 } , anchor "phagocytosis, engulfment" , post-text "evidence: IMP" } } } , { type comment , version 0 , refs { pmid 10878804 } , source { { src { db "GO" , tag id 45332 } , anchor "phospholipid translocation" , post-text "evidence: IMP" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 6810 } , anchor "transport" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 10878804 } , source { { src { db "GO" , tag id 5794 } , anchor "Golgi apparatus" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 16021 } , anchor "integral to membrane" , post-text "evidence: TAS" } } } , { type comment , version 0 , refs { pmid 10878804 } , source { { src { db "GO" , tag id 5887 } , anchor "integral to plasma membrane" , post-text "evidence: IDA" } } } , { type comment , version 0 , refs { pmid 10878804 } , source { { src { db "GO" , tag id 43231 } , anchor "intracellular membrane-bound organelle" , post-text "evidence: IDA" } } } } } } } } , homology { { type comment , heading "Human, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 21130 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=4& MAPS=genes-r-org/human-chr/mouse%3A4,genes-r-org/rat-chr/mouse%3A4,genes-r-org /mouse-chr4&query=e%3A11303[id]+AND+gene[obj_type]&QSTR=abca1&cmd=focus&fill=1 0" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 99607 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 15632021 , pmid 15269218 , pmid 15269217 , pmid 15163665 , pmid 15051721 , pmid 15033469 , pmid 15026428 , pmid 14993246 , pmid 14729855 , pmid 14726413 , pmid 14722086 , pmid 14703508 , pmid 14560020 , pmid 14559902 , pmid 12928428 , pmid 12897186 , pmid 12897148 , pmid 12859204 , pmid 12777468 , pmid 12754274 , pmid 12615679 , pmid 12586783 , pmid 12576511 , pmid 12551894 , pmid 12547832 , pmid 12511593 , pmid 12488454 , pmid 12487373 , pmid 12466851 , pmid 12384498 , pmid 12215451 , pmid 12196520 , pmid 12151852 , pmid 12105210 , pmid 12050168 , pmid 11972062 , pmid 11909955 , pmid 11896206 , pmid 11893753 , pmid 11752403 , pmid 11741998 , pmid 11559713 , pmid 11352567 , pmid 11217851 , pmid 11076861 , pmid 11042159 , pmid 10878804 , pmid 10760292 , pmid 10655069 , pmid 10581369 , pmid 10349636 , pmid 8889548 , pmid 8088782 , pmid 7774911 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 179001 } , anchor "X75926" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "3512" , version 0 } , { type other , label "Alternate name" , text "ND" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 271599 } , anchor "PMC16657P1" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 271951 } , anchor "PMC207565P1" , post-text "(e-PCR)" } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_013454" , version 2 , source { { src { db "Nucleotide" , tag id 34577068 } , anchor "NM_013454" } } , seqs { whole gi 34577068 } , products { { type peptide , heading "Product" , accession "NP_038482" , version 2 , source { { src { db "Protein" , tag id 34577069 } , anchor "NP_038482" , post-text "ATP-binding cassette 1, sub-family A, member 1" } } , seqs { whole gi 34577069 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 34577069 } , pre-text "(3)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5341 } , anchor "cd00267: ABC_ATPase; ABC (ATP-binding cassette) transporter nucleotide-binding domain" } } , comment { { type other , text "Location: 899 - 1114 Blast Score: 462" , version 0 } , { type other , text "Location: 1912 - 2121 Blast Score: 356" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 13428 } , anchor "COG4152: COG4152; ABC-type uncharacterized transport system, ATPase component [General function prediction only]" } } , comment { { type other , text "Location: 1912 - 2218 Blast Score: 360" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AK045442,BB657864,CA885568,X75926" } , anchor "AK045442,BB657864,CA885568,X75926" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AF287263" , version 1 , source { { src { db "Nucleotide" , tag id 11611824 } , anchor "AF287263" } } , seqs { whole gi 11611824 } , products { { type peptide , accession "AAG39073" , version 1 , source { { src { db "Protein" , tag id 11611825 } , anchor "AAG39073" } } , seqs { whole gi 11611825 } } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK019548" , version 1 , source { { src { db "Nucleotide" , tag id 12859824 } , anchor "AK019548" } } , seqs { whole gi 12859824 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK045442" , version 1 , source { { src { db "Nucleotide" , tag id 26090897 } , anchor "AK045442" } } , seqs { whole gi 26090897 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK051920" , version 1 , source { { src { db "Nucleotide" , tag id 26342297 } , anchor "AK051920" } } , seqs { whole gi 26342297 } , products { { type peptide , accession "BAC34811" , version 1 , source { { src { db "Protein" , tag id 26342298 } , anchor "BAC34811" } } , seqs { whole gi 26342298 } } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BB657864" , version 1 , source { { src { db "Nucleotide" , tag id 16491690 } , anchor "BB657864" } } , seqs { whole gi 16491690 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "CA885568" , version 1 , source { { src { db "Nucleotide" , tag id 27337117 } , anchor "CA885568" } } , seqs { whole gi 27337117 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "CD-1" , version 0 } } } , { type mRNA , heading "mRNA" , accession "X75926" , version 1 , source { { src { db "Nucleotide" , tag id 495256 } , anchor "X75926" } } , seqs { whole gi 495256 } , products { { type peptide , accession "CAA53530" , version 1 , source { { src { db "Protein" , tag id 495257 } , anchor "CAA53530" } } , seqs { whole gi 495257 } } } , comment { { type other , label "Strain" , text "DBA/2" , version 0 } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P41233" , version 0 , source { { src { db "Protein" , tag id 51338775 } , anchor "P41233" } } , seqs { whole gi 51338775 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11303" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039260.3&gene=Abca1&lid=11303&from=26554541&to=26683645" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11303" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039260.3&gene=Abca1&lid=11303" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.277376" } } , source { { src { db "UniGene" , tag str "Mm.277376" } , anchor "Mm.277376" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=27 7376" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11303" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11303[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 99607 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:99607" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=X7592 6" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= X75926" } } } , { type comment , text "Gene Expression Database (GXD) at MGI" , version 0 , source { { src { db "Gene Expression Database (GXD) at MGI" , tag str "MGI:99607" } , anchor "MGI:99607" , url "http://www.informatics.jax.org/searches/expression_report.c gi?id=MGI:99607" } } } , { type comment , text "Human ABC-Transporter Proteins" , version 0 , source { { src { db "Human ABC-Transporter Proteins" , tag str "Human ABC-Transporter Proteins" } , anchor "Human ABC-Transporter Proteins" , url "http://nutrigene.4t.com/humanabc.htm" } } } } } , { type generif , text "Gene deletion protects aginst cerebral malaria from Plasmodium berghei." , version 0 , refs { pmid 15632021 } , create-date str "Mar 7 2005 7:07PM" , update-date str "Mar 8 2005 3:26AM" } , { type generif , text "ABCA1-dependent cholesterol mobilization to apoA-I increased new cholesterol synthesis, indicating depletion of the regulatory pool of hepatocyte cholesterol during HDL formation" , version 0 , refs { pmid 14993246 } , create-date str "Mar 7 2005 7:07PM" , update-date str "Mar 8 2005 12:40AM" } , { type generif , text "a 21% decrease (P = 0.01) in fertility was observed between ABCA1(-/-) males compared with WT controls across their reproductive lifespans" , version 0 , refs { pmid 15026428 } , create-date str "Mar 7 2005 7:07PM" , update-date str "Mar 7 2005 9:28PM" } , { type generif , text "Verapamil increases ABCA1 expression through LXR-independent mechanism and thereby increases apoA-I-mediated cellular lipid release and production of HDL." , version 0 , refs { pmid 14726413 } , create-date str "Jan 8 2005 10:01AM" , update-date str "Jan 8 2005 2:49PM" } , { type generif , text "In murine macrophage cell line RAW264 cells, cAMP induced expression of ABCA1, release of cellular phospholipid and cholesterol by apoA-I, and reversible binding of apoA-I to the cell." , version 0 , refs { pmid 14729855 } , create-date str "Dec 4 2004 10:01AM" , update-date str "Dec 4 2004 2:26PM" } , { type generif , text "The time course and temperature dependence of ABCA1-mediated lipid efflux to apoA-I support a role for endocytosis in this process" , version 0 , refs { pmid 14703508 } , create-date str "Dec 4 2004 10:01AM" , update-date str "Dec 4 2004 11:09AM" } , { type generif , text "conclude that intact ATP binding cassette transporter A1 (ABCA1) function is necessary for proper maturation of dense bodies in platelets" , version 0 , refs { pmid 15163665 } , create-date str "Oct 30 2004 10:01AM" , update-date str "Oct 30 2004 10:58AM" } , { type generif , text "glial ABCA1 has a key role in apoE metabolism in the brain" , version 0 , refs { pmid 15269218 } , create-date str "Oct 30 2004 10:01AM" , update-date str "Oct 30 2004 10:43AM" } , { type generif , text "ABCA1 plays a critical role in central nervous system apoE metabolism" , version 0 , refs { pmid 15269217 } , create-date str "Oct 30 2004 10:01AM" , update-date str "Oct 30 2004 10:43AM" } , { type generif , text "PPAR alpha influences cholesterol absorption through modulating the ATP binding cassette transporter A1 activity in the intestine by a mechanism involving liver X receptor alpha" , version 0 , refs { pmid 12897186 } , create-date str "Aug 9 2004 1:01PM" , update-date str "Aug 9 2004 1:41PM" } , { type generif , text "When endotoxin or cytokines (tumor necrosis factor and interleukin-1) were incubated with J774 murine macrophages, the mRNA levels of ABCA1 were decreased." , version 0 , refs { pmid 12777468 } , create-date str "Jul 12 2004 11:39AM" , update-date str "Jul 12 2004 12:16PM" } , { type generif , text "ABCA1 is stabilized by a specific structural element possessing a linear array of acidic residues spanning two apoA-I amphipathic alpha-helices" , version 0 , refs { pmid 15051721 } , create-date str "Jul 12 2004 11:39AM" , update-date str "Jul 12 2004 11:52AM" } , { type generif , text "despite large induction of ABCA1 mRNA during differentiation, cholesterol efflux through the ABCA1 pathway remains limited in adipocytes and requires prolonged lipolysis" , version 0 , refs { pmid 12754274 } , create-date str "Jun 23 2004 4:43PM" , update-date str "Jun 23 2004 5:25PM" } , { type generif , text "ABCA1 turnover is modulated by alpha1-syntrophin" , version 0 , refs { pmid 14722086 } , create-date str "Jun 14 2004 4:41PM" , update-date str "Jun 14 2004 5:46PM" } , { type generif , text "Review. ABCA1-deficient mice are used to demonstrate the relation between ABCA1 expression, cellular lipid efflux, & HDL metabolism. The ABCA1-deficient mouse phenotype parallels that of human Tangier disease." , version 0 , refs { pmid 12615679 } , create-date str "Jan 25 2004 12:00AM" , update-date str "Feb 29 2004 7:03AM" } , { type generif , text "cellular ATP-binding cassette transporter A1 has a role in transporting cholesterol and phospholipids from cells to lipoprotein particles by a process involving PLTP interactions" , version 0 , refs { pmid 14559902 } , create-date str "Jan 20 2004 12:00AM" , update-date str "Feb 15 2004 6:35PM" } , { type generif , text "Results demonstrate that ABCA1 plays a key role in hepatic cholesterol efflux, inducing pathways that modulate cholesterol homeostasis in the liver, and establish the liver as a major source of plasma HDL-C." , version 0 , refs { pmid 12576511 } , create-date str "Jan 5 2004 12:00AM" , update-date str "Feb 29 2004 7:03AM" } , { type generif , text "ABCA1-mediated vesicle release involves lipid raft plasma membrane domains" , version 0 , refs { pmid 12928428 } , create-date str "Nov 30 2003 12:00AM" , update-date str "Jan 4 2004 7:03AM" } , { type generif , text "These studies indicate a direct role of retinoic acid receptor gamma/retinoid x receptor in induction of macrophage ABCA1." , version 0 , refs { pmid 14560020 } , create-date str "Nov 17 2003 12:00AM" , update-date str "Dec 7 2003 7:05AM" } , { type generif , text "As observed in knockout mice, ABCA1 is necessary for the adequate lipidation of apoAI, which enables the interaction with LCAT and subsequent maturation." , version 0 , refs { pmid 12859204 } , create-date str "Sep 30 2003 12:00AM" , update-date str "Oct 12 2003 7:03AM" } , { type generif , text "ABCA1 and SREBP1 are regulated by liver X receptor/corepressor complexes" , version 0 , refs { pmid 12897148 } , create-date str "Aug 25 2003 12:00AM" , update-date str "Aug 31 2003 7:04AM" } , { type generif , text "Estrogen's antiatherogenic effects may occur via ABCA1-mediated pathway, and circulating HDL levels may influence expression of ABCA1" , version 0 , refs { pmid 12487373 } , create-date str "Jun 3 2003 12:00AM" , update-date str "Jun 8 2003 7:28AM" } , { type generif , text "Hepatocyte expression of ABCA1 is central to the lipidation of newly synthesized apoA-I but also contributes to the lipidation of exogenous apoA-I." , version 0 , refs { pmid 12547832 } , create-date str "Apr 2 2003 12:00AM" , update-date str "May 11 2003 7:05AM" } , { type generif , text "Golgi is involved in ABCA1-mediated cholesterol efflux." , version 0 , refs { pmid 12551894 } , create-date str "Apr 1 2003 12:00AM" , update-date str "May 11 2003 7:05AM" } , { type generif , text "ATP-binding cassette transporter A1 (ABCA1)-mediated lipid efflux is promoted by central helices of ApoA-I; amino acid residues 220-231 of the wild-type ApoA-I are required for lipid efflux and high density lipoprotein formation" , version 0 , refs { pmid 12488454 } , create-date str "Mar 20 2003 12:00AM" , update-date str "Apr 13 2003 7:04AM" } , { type generif , text "annexin I is externalized from pituitary folliculo-stellate cells by an ABC transporter and the ATP binding cassette transporter A1 is a likely candidate" , version 0 , refs { pmid 12586783 } , create-date str "Mar 19 2003 12:00AM" , update-date str "Mar 31 2003 6:34AM" } , { type generif , text "ATP-binding-cassette transporter A1 gene expression in macrophages is downregulated by statins" , version 0 , refs { pmid 15033469 } , create-date str "Apr 26 2004 12:00AM" , update-date str "May 23 2004 7:05AM" } , { type generif , text "ABCA1 is regulated by PEST sequence-mediated calpain proteolysis that appears to be reversed by apolipoprotein-mediated phospholipid efflux" , version 0 , refs { pmid 12511593 } , create-date str "Feb 7 2003 12:00AM" , update-date str "Mar 9 2003 7:04AM" } , { type generif , text "REVIEW: ATP-binding cassette transporter A1 and cholesterol trafficking" , version 0 , refs { pmid 12151852 } , create-date str "Jan 24 2003 12:00AM" , update-date str "Feb 2 2003 7:50AM" } , { type generif , text "mediates cholesterol efflux and is defective in free cholesterol-loaded macrophages; mechanism involves enhanced degradation and full npc1 activity." , version 0 , refs { pmid 12215451 } , create-date str "Jan 16 2003 12:00AM" , update-date str "Feb 9 2003 7:14AM" } , { type generif , text "induction as a result of liver X receptor agonism increases secreted Abeta levels" , version 0 , refs { pmid 12384498 } , create-date str "Jan 9 2003 12:00AM" , update-date str "Feb 2 2003 7:50AM" } , { type generif , text "Increased hepatobiliary and fecal cholesterol excretion upon activation of the liver X receptor is independent of ABCA1." , version 0 , refs { pmid 12105210 } , create-date str "Nov 20 2002 12:00AM" , update-date str "Feb 2 2003 7:50AM" } , { type generif , text "A novel serine (Ser-2054) on the ABCA1 protein crucial for PKA phosphorylation and for regulation of ABCA1 transporter activity." , version 0 , refs { pmid 12196520 } , create-date str "Nov 16 2002 12:00AM" , update-date str "Feb 2 2003 7:50AM" } , { type generif , text "studies establish a novel binding site for apoA-I on the macrophage extracellular matrix that may function together with ABCA1 in promoting cholesterol efflux" , version 0 , refs { pmid 12050168 } , create-date str "Sep 27 2002 12:00AM" , update-date str "Feb 2 2003 7:49AM" } , { type generif , text "Role as a phosphatidylserine translocase" , version 0 , refs { pmid 11893753 } , create-date str "Jul 8 2002 12:00AM" , update-date str "Jul 22 2002 5:59AM" } , { type generif , text "Leukocyte ABCA1 controls susceptibility to atherosclerosis and macrophage recruitment into tissues" , version 0 , refs { pmid 11972062 } , create-date str "May 31 2002 12:00AM" , update-date str "Jun 15 2002 8:10AM" } , { type generif , text "Conditional disruption of the peroxisome proliferator-activated receptor gamma gene in mice results in lowered expression of ABCA1, ABCG1, and apoE in macrophages and reduced cholesterol efflux." , version 0 , refs { pmid 11909955 } , create-date str "Apr 16 2002 12:00AM" , update-date str "Apr 28 2002 6:21PM" } , { type generif , text "in the presence of apoE, overexpression of ABCA1 modulates HDL as well as apoB-containing lipoprotein metabolism and reduces atherosclerosis in vivo" , version 0 , refs { pmid 11752403 } , create-date str "Apr 2 2002 12:00AM" , update-date str "Apr 28 2002 6:21PM" } , { type generif , text "ABCA1 is expressed in a pattern consistent with its role in HDL-C metabolism" , version 0 , refs { pmid 11896206 } , create-date str "Mar 27 2002 12:00AM" , update-date str "Apr 8 2002 3:24PM" } , { type generif , text "unsaturated fatty acids reduce the macrophage ABCA1 content by enhancing its degradation rate" , version 0 , refs { pmid 11741998 } , create-date str "Mar 5 2002 12:00AM" , update-date str "Apr 1 2002 5:34AM" } , { type comment , heading "Alleles" , version 0 , comment { { type comment , text "The following allele types are documented at Mouse Genome Informatics" , version 0 , source { { anchor "(MGI)" , url "http://www.informatics.jax.org/searches/allele_report.cgi?m arkerID=MGI:99607" } } } , { type comment , heading "Targeted (knock-out) (2)" , version 0 , refs { pmid 10760292 , pmid 10980140 } } } } } , unique-keys { { db "LocusID" , tag id 11303 } , { db "MGI" , tag id 99607 } } , xtra-index-terms { "LOC11303" } } Entrezgene ::= { track-info { geneid 11304 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 4 , day 15 , hour 9 , minute 44 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "3" } } } , gene { locus "Abca4" , desc "ATP-binding cassette, sub-family A (ABC1), member 4" , maploc "3 61.8 cM" , syn { "RmP" , "Abcr" , "Abc10" , "D430003I15Rik" } , locus-tag "MGI:109424" } , prot { name { "ATP-binding cassette, sub-family A, member 4" , "Rim protein" , "ATP-binding cassette 10" } } , summary "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein was the first of the ABC transporters to be observed in photoreceptors and may play a role in the photoresponse. Mutations in the human gene are found in patients diagnosed with Stargardt disease and are associated with retinitis pigmentosa-19 and macular degeneration age-related 2." , location { { display-str "3 G1" , method map-type cyto } , { display-str "3 61.8 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11304 , src-str2 "11304" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000069" , version 1 , seqs { int { from 122426366 , to 122561663 , strand plus , id gi 51860767 } } , products { { type mRNA , heading "Reference" , accession "NM_007378" , version 1 , genomic-coords { mix { int { from 122426366 , to 122426518 , strand plus , id gi 51860767 } , int { from 122434867 , to 122434960 , strand plus , id gi 51860767 } , int { from 122436157 , to 122436298 , strand plus , id gi 51860767 } , int { from 122437283 , to 122437422 , strand plus , id gi 51860767 } , int { from 122444741 , to 122444868 , strand plus , id gi 51860767 } , int { from 122451134 , to 122451331 , strand plus , id gi 51860767 } , int { from 122462504 , to 122462593 , strand plus , id gi 51860767 } , int { from 122465447 , to 122465687 , strand plus , id gi 51860767 } , int { from 122467129 , to 122467268 , strand plus , id gi 51860767 } , int { from 122468154 , to 122468270 , strand plus , id gi 51860767 } , int { from 122468889 , to 122469086 , strand plus , id gi 51860767 } , int { from 122484278 , to 122484483 , strand plus , id gi 51860767 } , int { from 122485037 , to 122485213 , strand plus , id gi 51860767 } , int { from 122486910 , to 122487132 , strand plus , id gi 51860767 } , int { from 122492064 , to 122492285 , strand plus , id gi 51860767 } , int { from 122493968 , to 122494172 , strand plus , id gi 51860767 } , int { from 122498257 , to 122498322 , strand plus , id gi 51860767 } , int { from 122501632 , to 122501721 , strand plus , id gi 51860767 } , int { from 122503233 , to 122503407 , strand plus , id gi 51860767 } , int { from 122505161 , to 122505292 , strand plus , id gi 51860767 } , int { from 122507723 , to 122507862 , strand plus , id gi 51860767 } , int { from 122508424 , to 122508561 , strand plus , id gi 51860767 } , int { from 122509727 , to 122509920 , strand plus , id gi 51860767 } , int { from 122510918 , to 122511002 , strand plus , id gi 51860767 } , int { from 122514126 , to 122514331 , strand plus , id gi 51860767 } , int { from 122514655 , to 122514703 , strand plus , id gi 51860767 } , int { from 122516604 , to 122516866 , strand plus , id gi 51860767 } , int { from 122518583 , to 122518707 , strand plus , id gi 51860767 } , int { from 122519172 , to 122519270 , strand plus , id gi 51860767 } , int { from 122520026 , to 122520212 , strand plus , id gi 51860767 } , int { from 122523293 , to 122523387 , strand plus , id gi 51860767 } , int { from 122525002 , to 122525034 , strand plus , id gi 51860767 } , int { from 122528800 , to 122528905 , strand plus , id gi 51860767 } , int { from 122529033 , to 122529107 , strand plus , id gi 51860767 } , int { from 122529332 , to 122529501 , strand plus , id gi 51860767 } , int { from 122530477 , to 122530654 , strand plus , id gi 51860767 } , int { from 122536879 , to 122536994 , strand plus , id gi 51860767 } , int { from 122537940 , to 122538087 , strand plus , id gi 51860767 } , int { from 122539437 , to 122539560 , strand plus , id gi 51860767 } , int { from 122539916 , to 122540045 , strand plus , id gi 51860767 } , int { from 122543903 , to 122544023 , strand plus , id gi 51860767 } , int { from 122544463 , to 122544525 , strand plus , id gi 51860767 } , int { from 122545390 , to 122545496 , strand plus , id gi 51860767 } , int { from 122548250 , to 122548391 , strand plus , id gi 51860767 } , int { from 122551495 , to 122551629 , strand plus , id gi 51860767 } , int { from 122552344 , to 122552447 , strand plus , id gi 51860767 } , int { from 122552531 , to 122552623 , strand plus , id gi 51860767 } , int { from 122555381 , to 122555630 , strand plus , id gi 51860767 } , int { from 122557676 , to 122557762 , strand plus , id gi 51860767 } , int { from 122561316 , to 122561663 , strand plus , id gi 51860767 } } } , seqs { whole gi 6671494 } , products { { type peptide , heading "Reference" , accession "NP_031404" , version 1 , genomic-coords { packed-int { { from 122426453 , to 122426518 , strand plus , id gi 51860767 } , { from 122434867 , to 122434960 , strand plus , id gi 51860767 } , { from 122436157 , to 122436298 , strand plus , id gi 51860767 } , { from 122437283 , to 122437422 , strand plus , id gi 51860767 } , { from 122444741 , to 122444868 , strand plus , id gi 51860767 } , { from 122451134 , to 122451331 , strand plus , id gi 51860767 } , { from 122462504 , to 122462593 , strand plus , id gi 51860767 } , { from 122465447 , to 122465687 , strand plus , id gi 51860767 } , { from 122467129 , to 122467268 , strand plus , id gi 51860767 } , { from 122468154 , to 122468270 , strand plus , id gi 51860767 } , { from 122468889 , to 122469086 , strand plus , id gi 51860767 } , { from 122484278 , to 122484483 , strand plus , id gi 51860767 } , { from 122485037 , to 122485213 , strand plus , id gi 51860767 } , { from 122486910 , to 122487132 , strand plus , id gi 51860767 } , { from 122492064 , to 122492285 , strand plus , id gi 51860767 } , { from 122493968 , to 122494172 , strand plus , id gi 51860767 } , { from 122498257 , to 122498322 , strand plus , id gi 51860767 } , { from 122501632 , to 122501721 , strand plus , id gi 51860767 } , { from 122503233 , to 122503407 , strand plus , id gi 51860767 } , { from 122505161 , to 122505292 , strand plus , id gi 51860767 } , { from 122507723 , to 122507862 , strand plus , id gi 51860767 } , { from 122508424 , to 122508561 , strand plus , id gi 51860767 } , { from 122509727 , to 122509920 , strand plus , id gi 51860767 } , { from 122510918 , to 122511002 , strand plus , id gi 51860767 } , { from 122514126 , to 122514331 , strand plus , id gi 51860767 } , { from 122514655 , to 122514703 , strand plus , id gi 51860767 } , { from 122516604 , to 122516866 , strand plus , id gi 51860767 } , { from 122518583 , to 122518707 , strand plus , id gi 51860767 } , { from 122519172 , to 122519270 , strand plus , id gi 51860767 } , { from 122520026 , to 122520212 , strand plus , id gi 51860767 } , { from 122523293 , to 122523387 , strand plus , id gi 51860767 } , { from 122525002 , to 122525034 , strand plus , id gi 51860767 } , { from 122528800 , to 122528905 , strand plus , id gi 51860767 } , { from 122529033 , to 122529107 , strand plus , id gi 51860767 } , { from 122529332 , to 122529501 , strand plus , id gi 51860767 } , { from 122530477 , to 122530654 , strand plus , id gi 51860767 } , { from 122536879 , to 122536994 , strand plus , id gi 51860767 } , { from 122537940 , to 122538087 , strand plus , id gi 51860767 } , { from 122539437 , to 122539560 , strand plus , id gi 51860767 } , { from 122539916 , to 122540045 , strand plus , id gi 51860767 } , { from 122543903 , to 122544023 , strand plus , id gi 51860767 } , { from 122544463 , to 122544525 , strand plus , id gi 51860767 } , { from 122545390 , to 122545496 , strand plus , id gi 51860767 } , { from 122548250 , to 122548391 , strand plus , id gi 51860767 } , { from 122551495 , to 122551629 , strand plus , id gi 51860767 } , { from 122552344 , to 122552447 , strand plus , id gi 51860767 } , { from 122552531 , to 122552623 , strand plus , id gi 51860767 } , { from 122555381 , to 122555630 , strand plus , id gi 51860767 } , { from 122557676 , to 122557762 , strand plus , id gi 51860767 } , { from 122561316 , to 122561435 , strand plus , id gi 51860767 } } } , seqs { whole gi 6671495 } } } } } } , { type genomic , heading "Reference" , accession "NT_039240" , version 3 , seqs { int { from 8569036 , to 8704333 , strand plus , id gi 51708444 } } , products { { type mRNA , heading "Reference" , accession "NM_007378" , version 1 , genomic-coords { mix { int { from 8569036 , to 8569188 , strand plus , id gi 51708444 } , int { from 8577537 , to 8577630 , strand plus , id gi 51708444 } , int { from 8578827 , to 8578968 , strand plus , id gi 51708444 } , int { from 8579953 , to 8580092 , strand plus , id gi 51708444 } , int { from 8587411 , to 8587538 , strand plus , id gi 51708444 } , int { from 8593804 , to 8594001 , strand plus , id gi 51708444 } , int { from 8605174 , to 8605263 , strand plus , id gi 51708444 } , int { from 8608117 , to 8608357 , strand plus , id gi 51708444 } , int { from 8609799 , to 8609938 , strand plus , id gi 51708444 } , int { from 8610824 , to 8610940 , strand plus , id gi 51708444 } , int { from 8611559 , to 8611756 , strand plus , id gi 51708444 } , int { from 8626948 , to 8627153 , strand plus , id gi 51708444 } , int { from 8627707 , to 8627883 , strand plus , id gi 51708444 } , int { from 8629580 , to 8629802 , strand plus , id gi 51708444 } , int { from 8634734 , to 8634955 , strand plus , id gi 51708444 } , int { from 8636638 , to 8636842 , strand plus , id gi 51708444 } , int { from 8640927 , to 8640992 , strand plus , id gi 51708444 } , int { from 8644302 , to 8644391 , strand plus , id gi 51708444 } , int { from 8645903 , to 8646077 , strand plus , id gi 51708444 } , int { from 8647831 , to 8647962 , strand plus , id gi 51708444 } , int { from 8650393 , to 8650532 , strand plus , id gi 51708444 } , int { from 8651094 , to 8651231 , strand plus , id gi 51708444 } , int { from 8652397 , to 8652590 , strand plus , id gi 51708444 } , int { from 8653588 , to 8653672 , strand plus , id gi 51708444 } , int { from 8656796 , to 8657001 , strand plus , id gi 51708444 } , int { from 8657325 , to 8657373 , strand plus , id gi 51708444 } , int { from 8659274 , to 8659536 , strand plus , id gi 51708444 } , int { from 8661253 , to 8661377 , strand plus , id gi 51708444 } , int { from 8661842 , to 8661940 , strand plus , id gi 51708444 } , int { from 8662696 , to 8662882 , strand plus , id gi 51708444 } , int { from 8665963 , to 8666057 , strand plus , id gi 51708444 } , int { from 8667672 , to 8667704 , strand plus , id gi 51708444 } , int { from 8671470 , to 8671575 , strand plus , id gi 51708444 } , int { from 8671703 , to 8671777 , strand plus , id gi 51708444 } , int { from 8672002 , to 8672171 , strand plus , id gi 51708444 } , int { from 8673147 , to 8673324 , strand plus , id gi 51708444 } , int { from 8679549 , to 8679664 , strand plus , id gi 51708444 } , int { from 8680610 , to 8680757 , strand plus , id gi 51708444 } , int { from 8682107 , to 8682230 , strand plus , id gi 51708444 } , int { from 8682586 , to 8682715 , strand plus , id gi 51708444 } , int { from 8686573 , to 8686693 , strand plus , id gi 51708444 } , int { from 8687133 , to 8687195 , strand plus , id gi 51708444 } , int { from 8688060 , to 8688166 , strand plus , id gi 51708444 } , int { from 8690920 , to 8691061 , strand plus , id gi 51708444 } , int { from 8694165 , to 8694299 , strand plus , id gi 51708444 } , int { from 8695014 , to 8695117 , strand plus , id gi 51708444 } , int { from 8695201 , to 8695293 , strand plus , id gi 51708444 } , int { from 8698051 , to 8698300 , strand plus , id gi 51708444 } , int { from 8700346 , to 8700432 , strand plus , id gi 51708444 } , int { from 8703986 , to 8704333 , strand plus , id gi 51708444 } } } , seqs { whole gi 6671494 } , products { { type peptide , heading "Reference" , accession "NP_031404" , version 1 , genomic-coords { packed-int { { from 8569123 , to 8569188 , strand plus , id gi 51708444 } , { from 8577537 , to 8577630 , strand plus , id gi 51708444 } , { from 8578827 , to 8578968 , strand plus , id gi 51708444 } , { from 8579953 , to 8580092 , strand plus , id gi 51708444 } , { from 8587411 , to 8587538 , strand plus , id gi 51708444 } , { from 8593804 , to 8594001 , strand plus , id gi 51708444 } , { from 8605174 , to 8605263 , strand plus , id gi 51708444 } , { from 8608117 , to 8608357 , strand plus , id gi 51708444 } , { from 8609799 , to 8609938 , strand plus , id gi 51708444 } , { from 8610824 , to 8610940 , strand plus , id gi 51708444 } , { from 8611559 , to 8611756 , strand plus , id gi 51708444 } , { from 8626948 , to 8627153 , strand plus , id gi 51708444 } , { from 8627707 , to 8627883 , strand plus , id gi 51708444 } , { from 8629580 , to 8629802 , strand plus , id gi 51708444 } , { from 8634734 , to 8634955 , strand plus , id gi 51708444 } , { from 8636638 , to 8636842 , strand plus , id gi 51708444 } , { from 8640927 , to 8640992 , strand plus , id gi 51708444 } , { from 8644302 , to 8644391 , strand plus , id gi 51708444 } , { from 8645903 , to 8646077 , strand plus , id gi 51708444 } , { from 8647831 , to 8647962 , strand plus , id gi 51708444 } , { from 8650393 , to 8650532 , strand plus , id gi 51708444 } , { from 8651094 , to 8651231 , strand plus , id gi 51708444 } , { from 8652397 , to 8652590 , strand plus , id gi 51708444 } , { from 8653588 , to 8653672 , strand plus , id gi 51708444 } , { from 8656796 , to 8657001 , strand plus , id gi 51708444 } , { from 8657325 , to 8657373 , strand plus , id gi 51708444 } , { from 8659274 , to 8659536 , strand plus , id gi 51708444 } , { from 8661253 , to 8661377 , strand plus , id gi 51708444 } , { from 8661842 , to 8661940 , strand plus , id gi 51708444 } , { from 8662696 , to 8662882 , strand plus , id gi 51708444 } , { from 8665963 , to 8666057 , strand plus , id gi 51708444 } , { from 8667672 , to 8667704 , strand plus , id gi 51708444 } , { from 8671470 , to 8671575 , strand plus , id gi 51708444 } , { from 8671703 , to 8671777 , strand plus , id gi 51708444 } , { from 8672002 , to 8672171 , strand plus , id gi 51708444 } , { from 8673147 , to 8673324 , strand plus , id gi 51708444 } , { from 8679549 , to 8679664 , strand plus , id gi 51708444 } , { from 8680610 , to 8680757 , strand plus , id gi 51708444 } , { from 8682107 , to 8682230 , strand plus , id gi 51708444 } , { from 8682586 , to 8682715 , strand plus , id gi 51708444 } , { from 8686573 , to 8686693 , strand plus , id gi 51708444 } , { from 8687133 , to 8687195 , strand plus , id gi 51708444 } , { from 8688060 , to 8688166 , strand plus , id gi 51708444 } , { from 8690920 , to 8691061 , strand plus , id gi 51708444 } , { from 8694165 , to 8694299 , strand plus , id gi 51708444 } , { from 8695014 , to 8695117 , strand plus , id gi 51708444 } , { from 8695201 , to 8695293 , strand plus , id gi 51708444 } , { from 8698051 , to 8698300 , strand plus , id gi 51708444 } , { from 8700346 , to 8700432 , strand plus , id gi 51708444 } , { from 8703986 , to 8704105 , strand plus , id gi 51708444 } } } , seqs { whole gi 6671495 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Abca4" , version 0 } , { type property , label "Official Full Name" , text "ATP-binding cassette, sub-family A (ABC1), member 4" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 5524 } , anchor "ATP binding" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16887 } , anchor "ATPase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 9202155 } , source { { src { db "GO" , tag id 42626 } , anchor "ATPase activity, coupled to transmembrane movement of substances" , post-text "evidence: TAS" } } } , { type comment , version 0 , refs { pmid 10412977 } , source { { src { db "GO" , tag id 5548 } , anchor "phospholipid transporter activity" , post-text "evidence: IMP" } } } , { type comment , version 0 , refs { pmid 10412977 } , source { { src { db "GO" , tag id 4012 } , anchor "phospholipid-translocating ATPase activity" , post-text "evidence: IMP" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , refs { pmid 10412977 } , source { { src { db "GO" , tag id 6649 } , anchor "phospholipid transfer to membrane" , post-text "evidence: IMP" } } } , { type comment , version 0 , refs { pmid 11431429 } , source { { src { db "GO" , tag id 45494 } , anchor "photoreceptor maintenance" , post-text "evidence: IMP" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 7600 } , anchor "sensory perception" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 6810 } , anchor "transport" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 10412977 } , source { { src { db "GO" , tag id 7601 } , anchor "visual perception" , post-text "evidence: IMP" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 16021 } , anchor "integral to membrane" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 9202155 } , source { { src { db "GO" , tag id 5887 } , anchor "integral to plasma membrane" , post-text "evidence: TAS" } } } } } } } } , homology { { type comment , heading "Human, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 298 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=3& MAPS=genes-r-org/human-chr/mouse%3A3,genes-r-org/rat-chr/mouse%3A3,genes-r-org /mouse-chr3&query=e%3A11304[id]+AND+gene[obj_type]&QSTR=abca4&cmd=focus&fill=1 0" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 109424 } } } } , { type comment , heading "RefSeq Status" , label "REVIEWED" , version 0 } , { type comment , version 0 , refs { pmid 12477932 , pmid 12466851 , pmid 11431429 , pmid 11217851 , pmid 11076861 , pmid 11042159 , pmid 10852960 , pmid 10412977 , pmid 10349636 , pmid 9202155 , pmid 8889548 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 140994 } , anchor "Abca4" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "MGI:8523" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 159184 } , anchor "AF000149" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "192133" , version 0 } , { type other , label "Alternate name" , text "693384" , version 0 } , { type other , label "Alternate name" , text "ND" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_007378" , version 1 , source { { src { db "Nucleotide" , tag id 6671494 } , anchor "NM_007378" } } , seqs { whole gi 6671494 } , products { { type peptide , heading "Product" , accession "NP_031404" , version 1 , source { { src { db "Protein" , tag id 6671495 } , anchor "NP_031404" , post-text "ATP-binding cassette, sub-family A, member 4" } } , seqs { whole gi 6671495 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 6671495 } , pre-text "(3)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5341 } , anchor "cd00267: ABC_ATPase; ABC (ATP-binding cassette) transporter nucleotide-binding domain" } } , comment { { type other , text "Location: 931 - 1144 Blast Score: 454" , version 0 } , { type other , text "Location: 1937 - 2152 Blast Score: 353" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 13428 } , anchor "COG4152: COG4152; ABC-type uncharacterized transport system, ATPase component [General function prediction only]" } } , comment { { type other , text "Location: 1937 - 2253 Blast Score: 387" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "AF000149" } , anchor "AF000149" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "AF000149" , version 1 , source { { src { db "Nucleotide" , tag id 3243083 } , anchor "AF000149" } } , seqs { whole gi 3243083 } , products { { type peptide , accession "AAC23916" , version 1 , source { { src { db "Protein" , tag id 2547314 } , anchor "AAC23916" } } , seqs { whole gi 2547314 } } } , comment { { type other , label "Strain" , text "C57BL/6" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK053043" , version 1 , source { { src { db "Nucleotide" , tag id 26095532 } , anchor "AK053043" } } , seqs { whole gi 26095532 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK084860" , version 1 , source { { src { db "Nucleotide" , tag id 26102289 } , anchor "AK084860" } } , seqs { whole gi 26102289 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC043937" , version 1 , source { { src { db "Nucleotide" , tag id 27882179 } , anchor "BC043937" } } , seqs { whole gi 27882179 } , products { { type peptide , accession "AAH43937" , version 1 , source { { src { db "Protein" , tag id 27882180 } , anchor "AAH43937" } } , seqs { whole gi 27882180 } } } } , { type mRNA , heading "mRNA" , accession "BC057853" , version 1 , source { { src { db "Nucleotide" , tag id 34783941 } , anchor "BC057853" } } , seqs { whole gi 34783941 } , products { { type peptide , accession "AAH57853" , version 1 , source { { src { db "Protein" , tag id 34783942 } , anchor "AAH57853" } } , seqs { whole gi 34783942 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11304" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039240.3&gene=Abca4&lid=11304&from=8569037&to=8704334" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11304" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039240.3&gene=Abca4&lid=11304" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.3918" } } , source { { src { db "UniGene" , tag str "Mm.3918" } , anchor "Mm.3918" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=39 18" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11304" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11304[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 109424 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:109424" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC057 853" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= BC057853" } } } , { type comment , text "Human ABC-Transporter Proteins" , version 0 , source { { src { db "Human ABC-Transporter Proteins" , tag str "Human ABC-Transporter Proteins" } , anchor "Human ABC-Transporter Proteins" , url "http://nutrigene.4t.com/humanabc.htm" } } } } } , { type comment , heading "Alleles" , version 0 , comment { { type comment , text "The following allele types are documented at Mouse Genome Informatics" , version 0 , source { { anchor "(MGI)" , url "http://www.informatics.jax.org/searches/allele_report.cgi?m arkerID=MGI:109424" } } } , { type comment , heading "Targeted (knock-out) (1)" , version 0 , refs { pmid 10412977 } } } } } , unique-keys { { db "LocusID" , tag id 11304 } , { db "MGI" , tag id 109424 } } , xtra-index-terms { "LOC11304" } } Entrezgene ::= { track-info { geneid 11305 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 2 , day 17 , hour 12 , minute 54 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "2" } } } , gene { locus "Abca2" , desc "ATP-binding cassette, sub-family A (ABC1), member 2" , maploc "2 12.6 cM" , syn { "Abc2" , "mKIAA1062" , "D2H0S1474E" } , locus-tag "MGI:99606" } , prot { name { "ATP-binding cassette, sub-family A (ABC1), member 2" , "ATP-binding cassette 2" } } , location { { display-str "2 A2-B" , method map-type cyto } , { display-str "2 12.6 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11305 , src-str2 "11305" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000068" , version 1 , seqs { int { from 25388791 , to 25408220 , strand plus , id gi 51860766 } } , products { { type mRNA , heading "Reference" , accession "NM_007379" , version 1 , genomic-coords { mix { int { from 25388791 , to 25388856 , strand plus , id gi 51860766 } , int { from 25392017 , to 25392110 , strand plus , id gi 51860766 } , int { from 25393119 , to 25393230 , strand plus , id gi 51860766 } , int { from 25393315 , to 25393478 , strand plus , id gi 51860766 } , int { from 25393703 , to 25393830 , strand plus , id gi 51860766 } , int { from 25393985 , to 25394095 , strand plus , id gi 51860766 } , int { from 25394330 , to 25394548 , strand plus , id gi 51860766 } , int { from 25394911 , to 25395278 , strand plus , id gi 51860766 } , int { from 25395520 , to 25395679 , strand plus , id gi 51860766 } , int { from 25396389 , to 25396517 , strand plus , id gi 51860766 } , int { from 25396610 , to 25396774 , strand plus , id gi 51860766 } , int { from 25396851 , to 25396947 , strand plus , id gi 51860766 } , int { from 25397266 , to 25397439 , strand plus , id gi 51860766 } , int { from 25397509 , to 25397611 , strand plus , id gi 51860766 } , int { from 25397686 , to 25397800 , strand plus , id gi 51860766 } , int { from 25397914 , to 25398104 , strand plus , id gi 51860766 } , int { from 25398252 , to 25398402 , strand plus , id gi 51860766 } , int { from 25398479 , to 25398683 , strand plus , id gi 51860766 } , int { from 25398822 , to 25398986 , strand plus , id gi 51860766 } , int { from 25399088 , to 25399268 , strand plus , id gi 51860766 } , int { from 25399348 , to 25399560 , strand plus , id gi 51860766 } , int { from 25400546 , to 25400742 , strand plus , id gi 51860766 } , int { from 25400831 , to 25401013 , strand plus , id gi 51860766 } , int { from 25401209 , to 25401393 , strand plus , id gi 51860766 } , int { from 25401500 , to 25401620 , strand plus , id gi 51860766 } , int { from 25401896 , to 25402132 , strand plus , id gi 51860766 } , int { from 25402212 , to 25402418 , strand plus , id gi 51860766 } , int { from 25402671 , to 25402773 , strand plus , id gi 51860766 } , int { from 25402856 , to 25403175 , strand plus , id gi 51860766 } , int { from 25403250 , to 25403463 , strand plus , id gi 51860766 } , int { from 25403550 , to 25403655 , strand plus , id gi 51860766 } , int { from 25403747 , to 25403858 , strand plus , id gi 51860766 } , int { from 25403948 , to 25404008 , strand plus , id gi 51860766 } , int { from 25404091 , to 25404265 , strand plus , id gi 51860766 } , int { from 25404346 , to 25404461 , strand plus , id gi 51860766 } , int { from 25404543 , to 25404690 , strand plus , id gi 51860766 } , int { from 25404835 , to 25404958 , strand plus , id gi 51860766 } , int { from 25405093 , to 25405225 , strand plus , id gi 51860766 } , int { from 25405329 , to 25405446 , strand plus , id gi 51860766 } , int { from 25405571 , to 25405749 , strand plus , id gi 51860766 } , int { from 25405991 , to 25406132 , strand plus , id gi 51860766 } , int { from 25406232 , to 25406366 , strand plus , id gi 51860766 } , int { from 25406459 , to 25406562 , strand plus , id gi 51860766 } , int { from 25406636 , to 25406728 , strand plus , id gi 51860766 } , int { from 25406812 , to 25406914 , strand plus , id gi 51860766 } , int { from 25406999 , to 25407136 , strand plus , id gi 51860766 } , int { from 25407221 , to 25407421 , strand plus , id gi 51860766 } , int { from 25407862 , to 25408220 , strand plus , id gi 51860766 } } } , seqs { whole gi 11993938 } , products { { type peptide , heading "Reference" , accession "NP_031405" , version 1 , genomic-coords { packed-int { { from 25388791 , to 25388856 , strand plus , id gi 51860766 } , { from 25392017 , to 25392110 , strand plus , id gi 51860766 } , { from 25393119 , to 25393230 , strand plus , id gi 51860766 } , { from 25393315 , to 25393478 , strand plus , id gi 51860766 } , { from 25393703 , to 25393830 , strand plus , id gi 51860766 } , { from 25393985 , to 25394095 , strand plus , id gi 51860766 } , { from 25394330 , to 25394548 , strand plus , id gi 51860766 } , { from 25394911 , to 25395278 , strand plus , id gi 51860766 } , { from 25395520 , to 25395679 , strand plus , id gi 51860766 } , { from 25396389 , to 25396517 , strand plus , id gi 51860766 } , { from 25396610 , to 25396774 , strand plus , id gi 51860766 } , { from 25396851 , to 25396947 , strand plus , id gi 51860766 } , { from 25397266 , to 25397439 , strand plus , id gi 51860766 } , { from 25397509 , to 25397611 , strand plus , id gi 51860766 } , { from 25397686 , to 25397800 , strand plus , id gi 51860766 } , { from 25397914 , to 25398104 , strand plus , id gi 51860766 } , { from 25398252 , to 25398402 , strand plus , id gi 51860766 } , { from 25398479 , to 25398683 , strand plus , id gi 51860766 } , { from 25398822 , to 25398986 , strand plus , id gi 51860766 } , { from 25399088 , to 25399268 , strand plus , id gi 51860766 } , { from 25399348 , to 25399560 , strand plus , id gi 51860766 } , { from 25400546 , to 25400742 , strand plus , id gi 51860766 } , { from 25400831 , to 25401013 , strand plus , id gi 51860766 } , { from 25401209 , to 25401393 , strand plus , id gi 51860766 } , { from 25401500 , to 25401620 , strand plus , id gi 51860766 } , { from 25401896 , to 25402132 , strand plus , id gi 51860766 } , { from 25402212 , to 25402418 , strand plus , id gi 51860766 } , { from 25402671 , to 25402773 , strand plus , id gi 51860766 } , { from 25402856 , to 25403175 , strand plus , id gi 51860766 } , { from 25403250 , to 25403463 , strand plus , id gi 51860766 } , { from 25403550 , to 25403655 , strand plus , id gi 51860766 } , { from 25403747 , to 25403858 , strand plus , id gi 51860766 } , { from 25403948 , to 25404008 , strand plus , id gi 51860766 } , { from 25404091 , to 25404265 , strand plus , id gi 51860766 } , { from 25404346 , to 25404461 , strand plus , id gi 51860766 } , { from 25404543 , to 25404690 , strand plus , id gi 51860766 } , { from 25404835 , to 25404958 , strand plus , id gi 51860766 } , { from 25405093 , to 25405225 , strand plus , id gi 51860766 } , { from 25405329 , to 25405446 , strand plus , id gi 51860766 } , { from 25405571 , to 25405749 , strand plus , id gi 51860766 } , { from 25405991 , to 25406132 , strand plus , id gi 51860766 } , { from 25406232 , to 25406366 , strand plus , id gi 51860766 } , { from 25406459 , to 25406562 , strand plus , id gi 51860766 } , { from 25406636 , to 25406728 , strand plus , id gi 51860766 } , { from 25406812 , to 25406914 , strand plus , id gi 51860766 } , { from 25406999 , to 25407136 , strand plus , id gi 51860766 } , { from 25407221 , to 25407421 , strand plus , id gi 51860766 } , { from 25407862 , to 25407897 , strand plus , id gi 51860766 } } } , seqs { whole gi 11993939 } } } } } } , { type genomic , heading "Reference" , accession "NT_039206" , version 3 , seqs { int { from 2857415 , to 2876844 , strand plus , id gi 51706164 } } , products { { type mRNA , heading "Reference" , accession "NM_007379" , version 1 , genomic-coords { mix { int { from 2857415 , to 2857480 , strand plus , id gi 51706164 } , int { from 2860641 , to 2860734 , strand plus , id gi 51706164 } , int { from 2861743 , to 2861854 , strand plus , id gi 51706164 } , int { from 2861939 , to 2862102 , strand plus , id gi 51706164 } , int { from 2862327 , to 2862454 , strand plus , id gi 51706164 } , int { from 2862609 , to 2862719 , strand plus , id gi 51706164 } , int { from 2862954 , to 2863172 , strand plus , id gi 51706164 } , int { from 2863535 , to 2863902 , strand plus , id gi 51706164 } , int { from 2864144 , to 2864303 , strand plus , id gi 51706164 } , int { from 2865013 , to 2865141 , strand plus , id gi 51706164 } , int { from 2865234 , to 2865398 , strand plus , id gi 51706164 } , int { from 2865475 , to 2865571 , strand plus , id gi 51706164 } , int { from 2865890 , to 2866063 , strand plus , id gi 51706164 } , int { from 2866133 , to 2866235 , strand plus , id gi 51706164 } , int { from 2866310 , to 2866424 , strand plus , id gi 51706164 } , int { from 2866538 , to 2866728 , strand plus , id gi 51706164 } , int { from 2866876 , to 2867026 , strand plus , id gi 51706164 } , int { from 2867103 , to 2867307 , strand plus , id gi 51706164 } , int { from 2867446 , to 2867610 , strand plus , id gi 51706164 } , int { from 2867712 , to 2867892 , strand plus , id gi 51706164 } , int { from 2867972 , to 2868184 , strand plus , id gi 51706164 } , int { from 2869170 , to 2869366 , strand plus , id gi 51706164 } , int { from 2869455 , to 2869637 , strand plus , id gi 51706164 } , int { from 2869833 , to 2870017 , strand plus , id gi 51706164 } , int { from 2870124 , to 2870244 , strand plus , id gi 51706164 } , int { from 2870520 , to 2870756 , strand plus , id gi 51706164 } , int { from 2870836 , to 2871042 , strand plus , id gi 51706164 } , int { from 2871295 , to 2871397 , strand plus , id gi 51706164 } , int { from 2871480 , to 2871799 , strand plus , id gi 51706164 } , int { from 2871874 , to 2872087 , strand plus , id gi 51706164 } , int { from 2872174 , to 2872279 , strand plus , id gi 51706164 } , int { from 2872371 , to 2872482 , strand plus , id gi 51706164 } , int { from 2872572 , to 2872632 , strand plus , id gi 51706164 } , int { from 2872715 , to 2872889 , strand plus , id gi 51706164 } , int { from 2872970 , to 2873085 , strand plus , id gi 51706164 } , int { from 2873167 , to 2873314 , strand plus , id gi 51706164 } , int { from 2873459 , to 2873582 , strand plus , id gi 51706164 } , int { from 2873717 , to 2873849 , strand plus , id gi 51706164 } , int { from 2873953 , to 2874070 , strand plus , id gi 51706164 } , int { from 2874195 , to 2874373 , strand plus , id gi 51706164 } , int { from 2874615 , to 2874756 , strand plus , id gi 51706164 } , int { from 2874856 , to 2874990 , strand plus , id gi 51706164 } , int { from 2875083 , to 2875186 , strand plus , id gi 51706164 } , int { from 2875260 , to 2875352 , strand plus , id gi 51706164 } , int { from 2875436 , to 2875538 , strand plus , id gi 51706164 } , int { from 2875623 , to 2875760 , strand plus , id gi 51706164 } , int { from 2875845 , to 2876045 , strand plus , id gi 51706164 } , int { from 2876486 , to 2876844 , strand plus , id gi 51706164 } } } , seqs { whole gi 11993938 } , products { { type peptide , heading "Reference" , accession "NP_031405" , version 1 , genomic-coords { packed-int { { from 2857415 , to 2857480 , strand plus , id gi 51706164 } , { from 2860641 , to 2860734 , strand plus , id gi 51706164 } , { from 2861743 , to 2861854 , strand plus , id gi 51706164 } , { from 2861939 , to 2862102 , strand plus , id gi 51706164 } , { from 2862327 , to 2862454 , strand plus , id gi 51706164 } , { from 2862609 , to 2862719 , strand plus , id gi 51706164 } , { from 2862954 , to 2863172 , strand plus , id gi 51706164 } , { from 2863535 , to 2863902 , strand plus , id gi 51706164 } , { from 2864144 , to 2864303 , strand plus , id gi 51706164 } , { from 2865013 , to 2865141 , strand plus , id gi 51706164 } , { from 2865234 , to 2865398 , strand plus , id gi 51706164 } , { from 2865475 , to 2865571 , strand plus , id gi 51706164 } , { from 2865890 , to 2866063 , strand plus , id gi 51706164 } , { from 2866133 , to 2866235 , strand plus , id gi 51706164 } , { from 2866310 , to 2866424 , strand plus , id gi 51706164 } , { from 2866538 , to 2866728 , strand plus , id gi 51706164 } , { from 2866876 , to 2867026 , strand plus , id gi 51706164 } , { from 2867103 , to 2867307 , strand plus , id gi 51706164 } , { from 2867446 , to 2867610 , strand plus , id gi 51706164 } , { from 2867712 , to 2867892 , strand plus , id gi 51706164 } , { from 2867972 , to 2868184 , strand plus , id gi 51706164 } , { from 2869170 , to 2869366 , strand plus , id gi 51706164 } , { from 2869455 , to 2869637 , strand plus , id gi 51706164 } , { from 2869833 , to 2870017 , strand plus , id gi 51706164 } , { from 2870124 , to 2870244 , strand plus , id gi 51706164 } , { from 2870520 , to 2870756 , strand plus , id gi 51706164 } , { from 2870836 , to 2871042 , strand plus , id gi 51706164 } , { from 2871295 , to 2871397 , strand plus , id gi 51706164 } , { from 2871480 , to 2871799 , strand plus , id gi 51706164 } , { from 2871874 , to 2872087 , strand plus , id gi 51706164 } , { from 2872174 , to 2872279 , strand plus , id gi 51706164 } , { from 2872371 , to 2872482 , strand plus , id gi 51706164 } , { from 2872572 , to 2872632 , strand plus , id gi 51706164 } , { from 2872715 , to 2872889 , strand plus , id gi 51706164 } , { from 2872970 , to 2873085 , strand plus , id gi 51706164 } , { from 2873167 , to 2873314 , strand plus , id gi 51706164 } , { from 2873459 , to 2873582 , strand plus , id gi 51706164 } , { from 2873717 , to 2873849 , strand plus , id gi 51706164 } , { from 2873953 , to 2874070 , strand plus , id gi 51706164 } , { from 2874195 , to 2874373 , strand plus , id gi 51706164 } , { from 2874615 , to 2874756 , strand plus , id gi 51706164 } , { from 2874856 , to 2874990 , strand plus , id gi 51706164 } , { from 2875083 , to 2875186 , strand plus , id gi 51706164 } , { from 2875260 , to 2875352 , strand plus , id gi 51706164 } , { from 2875436 , to 2875538 , strand plus , id gi 51706164 } , { from 2875623 , to 2875760 , strand plus , id gi 51706164 } , { from 2875845 , to 2876045 , strand plus , id gi 51706164 } , { from 2876486 , to 2876521 , strand plus , id gi 51706164 } } } , seqs { whole gi 11993939 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Abca2" , version 0 } , { type property , label "Official Full Name" , text "ATP-binding cassette, sub-family A (ABC1), member 2" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 5524 } , anchor "ATP binding" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16887 } , anchor "ATPase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 5215 } , anchor "transporter activity" , post-text "evidence: ISS" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 8203 } , anchor "cholesterol metabolism" , post-text "evidence: ISS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 6810 } , anchor "transport" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , refs { pmid 12466851 } , source { { src { db "GO" , tag id 16021 } , anchor "integral to membrane" , post-text "evidence: TAS" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 5765 } , anchor "lysosomal membrane" , post-text "evidence: ISS" } } } } } } } } , homology { { type comment , heading "Human, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 55590 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=2& MAPS=genes-r-org/human-chr/mouse%3A2,genes-r-org/rat-chr/mouse%3A2,genes-r-org /mouse-chr2&query=e%3A11305[id]+AND+gene[obj_type]&QSTR=abca2&cmd=focus&fill=1 0" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 99606 } } } } , { type comment , heading "RefSeq Status" , label "PROVISIONAL" , version 0 } , { type comment , version 0 , refs { pmid 14621295 , pmid 12466851 , pmid 8088782 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 158928 } , anchor "AI413825" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "421529" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_007379" , version 1 , source { { src { db "Nucleotide" , tag id 11993938 } , anchor "NM_007379" } } , seqs { whole gi 11993938 } , products { { type peptide , heading "Product" , accession "NP_031405" , version 1 , source { { src { db "Protein" , tag id 11993939 } , anchor "NP_031405" , post-text "ATP-binding cassette, sub-family A (ABC1), member 2" } } , seqs { whole gi 11993939 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 11993939 } , pre-text "(2)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5341 } , anchor "cd00267: ABC_ATPase; ABC (ATP-binding cassette) transporter nucleotide-binding domain" } } , comment { { type other , text "Location: 1018 - 1205 Blast Score: 389" , version 0 } , { type other , text "Location: 2051 - 2269 Blast Score: 372" , version 0 } } } } } } } } , comment { { type other , heading "Source Sequence" , version 0 , source { { src { db "Nucleotide" , tag str "X75927" } , anchor "X75927" } } , comment { { type other , version 0 } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "AK129274" , version 1 , source { { src { db "Nucleotide" , tag id 37360211 } , anchor "AK129274" } } , seqs { whole gi 37360211 } , products { { type peptide , accession "BAC98084" , version 1 , source { { src { db "Protein" , tag id 37360212 } , anchor "BAC98084" } } , seqs { whole gi 37360212 } } } } , { type mRNA , heading "mRNA" , accession "X75927" , version 2 , source { { src { db "Nucleotide" , tag id 11990230 } , anchor "X75927" } } , seqs { whole gi 11990230 } , products { { type peptide , accession "CAA53531" , version 2 , source { { src { db "Protein" , tag id 11990231 } , anchor "CAA53531" } } , seqs { whole gi 11990231 } } } , comment { { type other , label "Strain" , text "DBA/2" , version 0 } } } , { type other , text "None" , version 0 , products { { type peptide , accession "P41234" , version 0 , source { { src { db "Protein" , tag id 14916951 } , anchor "P41234" } } , seqs { whole gi 14916951 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11305" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039206.3&gene=Abca2&lid=11305&from=2857416&to=2876845" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11305" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039206.3&gene=Abca2&lid=11305" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.2210" } } , source { { src { db "UniGene" , tag str "Mm.2210" } , anchor "Mm.2210" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=22 10" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11305" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11305[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 99606 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:99606" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=X7592 7" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= X75927" } } } , { type comment , text "Human ABC-Transporter Proteins" , version 0 , source { { src { db "Human ABC-Transporter Proteins" , tag str "Human ABC-Transporter Proteins" } , anchor "Human ABC-Transporter Proteins" , url "http://nutrigene.4t.com/humanabc.htm" } } } } } } , unique-keys { { db "LocusID" , tag id 11305 } , { db "MGI" , tag id 99606 } } , xtra-index-terms { "LOC11305" } } Entrezgene ::= { track-info { geneid 11306 , status live , create-date std { year 2003 , month 8 , day 28 , hour 21 , minute 39 , second 0 } , update-date std { year 2005 , month 4 , day 19 , hour 12 , minute 12 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , syn { "mouse" } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } , subtype { { subtype chromosome , name "X" } } } , gene { locus "Abcb7" , desc "ATP-binding cassette, sub-family B (MDR/TAP), member 7" , maploc "X 39.0 cM" , syn { "Abc7" } , locus-tag "MGI:109533" } , prot { name { "ATP-binding cassette, sub-family B (MDR/TAP), member 7" , "ATP-binding cassette 7" } } , location { { display-str "X C-D" , method map-type cyto } , { display-str "X 39.0 cM" , method map-type cM } } , gene-source { src "LocusLink" , src-int 11306 , src-str2 "11306" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , heading "Reference" , accession "NC_000086" , version 1 , seqs { int { from 95684235 , to 95817474 , strand minus , id gi 51869957 } } , products { { type mRNA , heading "Reference" , accession "XM_356348" , version 2 , genomic-coords { mix { int { from 95684235 , to 95687836 , strand minus , id gi 51869957 } , int { from 95694701 , to 95694808 , strand minus , id gi 51869957 } , int { from 95698046 , to 95698149 , strand minus , id gi 51869957 } , int { from 95699409 , to 95699580 , strand minus , id gi 51869957 } , int { from 95703347 , to 95703476 , strand minus , id gi 51869957 } , int { from 95703628 , to 95703791 , strand minus , id gi 51869957 } , int { from 95704349 , to 95704506 , strand minus , id gi 51869957 } , int { from 95705372 , to 95705546 , strand minus , id gi 51869957 } , int { from 95706530 , to 95706617 , strand minus , id gi 51869957 } , int { from 95706707 , to 95706795 , strand minus , id gi 51869957 } , int { from 95707710 , to 95707978 , strand minus , id gi 51869957 } , int { from 95708848 , to 95708980 , strand minus , id gi 51869957 } , int { from 95726912 , to 95727031 , strand minus , id gi 51869957 } , int { from 95746072 , to 95746158 , strand minus , id gi 51869957 } , int { from 95748503 , to 95748580 , strand minus , id gi 51869957 } , int { from 95817235 , to 95817474 , strand minus , id gi 51869957 } } } , seqs { whole gi 51772276 } , products { { type peptide , heading "Reference" , accession "XP_356348" , version 1 , genomic-coords { packed-int { { from 95687621 , to 95687836 , strand minus , id gi 51869957 } , { from 95694701 , to 95694808 , strand minus , id gi 51869957 } , { from 95698046 , to 95698149 , strand minus , id gi 51869957 } , { from 95699409 , to 95699580 , strand minus , id gi 51869957 } , { from 95703347 , to 95703476 , strand minus , id gi 51869957 } , { from 95703628 , to 95703791 , strand minus , id gi 51869957 } , { from 95704349 , to 95704506 , strand minus , id gi 51869957 } , { from 95705372 , to 95705546 , strand minus , id gi 51869957 } , { from 95706530 , to 95706617 , strand minus , id gi 51869957 } , { from 95706707 , to 95706795 , strand minus , id gi 51869957 } , { from 95707710 , to 95707978 , strand minus , id gi 51869957 } , { from 95708848 , to 95708980 , strand minus , id gi 51869957 } , { from 95726912 , to 95727031 , strand minus , id gi 51869957 } , { from 95746072 , to 95746158 , strand minus , id gi 51869957 } , { from 95748503 , to 95748580 , strand minus , id gi 51869957 } , { from 95817235 , to 95817474 , strand minus , id gi 51869957 } } } , seqs { whole gi 38086485 } } } } } } , { type genomic , heading "Reference" , accession "NT_039711" , version 3 , seqs { int { from 9312469 , to 9445708 , strand minus , id gi 51772331 } } , products { { type mRNA , heading "Reference" , accession "XM_356348" , version 2 , genomic-coords { mix { int { from 9312469 , to 9316070 , strand minus , id gi 51772331 } , int { from 9322935 , to 9323042 , strand minus , id gi 51772331 } , int { from 9326280 , to 9326383 , strand minus , id gi 51772331 } , int { from 9327643 , to 9327814 , strand minus , id gi 51772331 } , int { from 9331581 , to 9331710 , strand minus , id gi 51772331 } , int { from 9331862 , to 9332025 , strand minus , id gi 51772331 } , int { from 9332583 , to 9332740 , strand minus , id gi 51772331 } , int { from 9333606 , to 9333780 , strand minus , id gi 51772331 } , int { from 9334764 , to 9334851 , strand minus , id gi 51772331 } , int { from 9334941 , to 9335029 , strand minus , id gi 51772331 } , int { from 9335944 , to 9336212 , strand minus , id gi 51772331 } , int { from 9337082 , to 9337214 , strand minus , id gi 51772331 } , int { from 9355146 , to 9355265 , strand minus , id gi 51772331 } , int { from 9374306 , to 9374392 , strand minus , id gi 51772331 } , int { from 9376737 , to 9376814 , strand minus , id gi 51772331 } , int { from 9445469 , to 9445708 , strand minus , id gi 51772331 } } } , seqs { whole gi 51772276 } , products { { type peptide , heading "Reference" , accession "XP_356348" , version 1 , genomic-coords { packed-int { { from 9315855 , to 9316070 , strand minus , id gi 51772331 } , { from 9322935 , to 9323042 , strand minus , id gi 51772331 } , { from 9326280 , to 9326383 , strand minus , id gi 51772331 } , { from 9327643 , to 9327814 , strand minus , id gi 51772331 } , { from 9331581 , to 9331710 , strand minus , id gi 51772331 } , { from 9331862 , to 9332025 , strand minus , id gi 51772331 } , { from 9332583 , to 9332740 , strand minus , id gi 51772331 } , { from 9333606 , to 9333780 , strand minus , id gi 51772331 } , { from 9334764 , to 9334851 , strand minus , id gi 51772331 } , { from 9334941 , to 9335029 , strand minus , id gi 51772331 } , { from 9335944 , to 9336212 , strand minus , id gi 51772331 } , { from 9337082 , to 9337214 , strand minus , id gi 51772331 } , { from 9355146 , to 9355265 , strand minus , id gi 51772331 } , { from 9374306 , to 9374392 , strand minus , id gi 51772331 } , { from 9376737 , to 9376814 , strand minus , id gi 51772331 } , { from 9445469 , to 9445708 , strand minus , id gi 51772331 } } } , seqs { whole gi 38086485 } } } } } } } , properties { { type comment , label "Nomenclature" , version 0 , source { { anchor "Mouse Genome Informatics" } } , properties { { type property , label "Official Symbol" , text "Abcb7" , version 0 } , { type property , label "Official Full Name" , text "ATP-binding cassette, sub-family B (MDR/TAP), member 7" , version 0 } } } , { type comment , heading "GeneOntology" , version 0 , source { { pre-text "Provided by" , anchor "MGI" , url "http://www.informatics.jax.org/" } } , comment { { type comment , label "Function" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 5524 } , anchor "ATP binding" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16887 } , anchor "ATPase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 42626 } , anchor "ATPase activity, coupled to transmembrane movement of substances" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 17111 } , anchor "nucleoside-triphosphatase activity" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 166 } , anchor "nucleotide binding" , post-text "evidence: IEA" } } } } } , { type comment , label "Process" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 6810 } , anchor "transport" , post-text "evidence: IEA" } } } } } , { type comment , label "Component" , version 0 , comment { { type comment , version 0 , source { { src { db "GO" , tag id 19866 } , anchor "inner membrane" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16021 } , anchor "integral to membrane" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 16020 } , anchor "membrane" , post-text "evidence: IEA" } } } , { type comment , version 0 , source { { src { db "GO" , tag id 5739 } , anchor "mitochondrion" , post-text "evidence: IEA" } } } } } } } } , homology { { type comment , heading "Human, Rat" , version 0 , source { { src { db "HomoloGene" , tag id 3175 } , anchor "Map Viewer" , url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=X& MAPS=genes-r-org/human-chr/mouse%3AX,genes-r-org/rat-chr/mouse%3AX,genes-r-org /mouse-chrX&query=e%3A11306[id]+AND+gene[obj_type]&QSTR=abcb7&cmd=focus&fill=1 0" } } } } , comments { { type comment , heading "LocusTagLink" , version 0 , source { { src { db "MGI" , tag id 109533 } } } } , { type comment , heading "RefSeq Status" , label "MODEL" , version 0 } , { type comment , version 0 , refs { pmid 14651853 , pmid 12480705 , pmid 12477932 , pmid 11217851 , pmid 11076861 , pmid 11042159 , pmid 10922068 , pmid 10349636 , pmid 9143506 } } , { type comment , heading "Markers (Sequence Tagged Sites/STS)" , version 0 , comment { { type comment , version 0 , source { { src { db "UniSTS" , tag id 161105 } , anchor "RH124283" , post-text "(e-PCR)" } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 178992 } , anchor "AW537380" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "953972" , version 0 } } } , { type comment , version 0 , source { { src { db "UniSTS" , tag id 181314 } , anchor "AU019072" , post-text "(e-PCR)" } } , comment { { type other , label "Alternate name" , text "359130" , version 0 } } } } } , { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "XM_356348" , version 2 , source { { src { db "Nucleotide" , tag id 51772276 } , anchor "XM_356348" } } , seqs { whole gi 51772276 } , products { { type peptide , accession "XP_356348" , version 1 , source { { src { db "Protein" , tag id 38086485 } , anchor "XP_356348" } } , seqs { whole gi 38086485 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 38086485 } , pre-text "(3)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5341 } , anchor "cd00267: ABC_ATPase; ABC (ATP-binding cassette) transporter nucleotide-binding domain" } } , comment { { type other , text "Location: 496 - 714 Blast Score: 577" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 14387 } , anchor "COG5265: ATM1; ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]" } } , comment { { type other , text "Location: 234 - 729 Blast Score: 1506" , version 0 } } } , { type other , version 0 , source { { src { db "CDD" , tag id 25581 } , anchor "pfam00664: ABC_membrane; ABC transporter transmembrane region" } } , comment { { type other , text "Location: 164 - 435 Blast Score: 247" , version 0 } } } } } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type mRNA , heading "mRNA" , accession "AA517758" , version 1 , source { { src { db "Nucleotide" , tag id 2257282 } , anchor "AA517758" } } , seqs { whole gi 2257282 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J x DBA/2J F1" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK040069" , version 1 , source { { src { db "Nucleotide" , tag id 26087598 } , anchor "AK040069" } } , seqs { whole gi 26087598 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AK084853" , version 1 , source { { src { db "Nucleotide" , tag id 26102284 } , anchor "AK084853" } } , seqs { whole gi 26102284 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AU019072" , version 1 , source { { src { db "Nucleotide" , tag id 3374656 } , anchor "AU019072" } } , seqs { whole gi 3374656 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "AW537380" , version 1 , source { { src { db "Nucleotide" , tag id 7179797 } , anchor "AW537380" } } , seqs { whole gi 7179797 } , products { { type peptide , text "None" , version 0 } } , comment { { type other , label "Strain" , text "C57BL/6J" , version 0 } } } , { type mRNA , heading "mRNA" , accession "BC035534" , version 1 , source { { src { db "Nucleotide" , tag id 23243450 } , anchor "BC035534" } } , seqs { whole gi 23243450 } , products { { type peptide , text "None" , version 0 } } } , { type mRNA , heading "mRNA" , accession "U43892" , version 1 , source { { src { db "Nucleotide" , tag id 1167981 } , anchor "U43892" } } , seqs { whole gi 1167981 } , products { { type peptide , accession "AAC53152" , version 1 , source { { src { db "Protein" , tag id 1167982 } , anchor "AAC53152" } } , seqs { whole gi 1167982 } } } , comment { { type other , label "Strain" , text "DBA/2" , version 0 } } } , { type other , text "None" , version 0 , products { { type peptide , accession "Q61102" , version 0 , source { { src { db "Protein" , tag id 5902709 } , anchor "Q61102" } } , seqs { whole gi 5902709 } } } } } } , { type comment , heading "Additional Links" , version 0 , comment { { type comment , version 0 , source { { src { db "Evidence Viewer" , tag str "11306" } , anchor "Evidence Viewer" , url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont ig=NT_039711.3&gene=Abcb7&lid=11306&from=9312470&to=9445709" } } } , { type comment , version 0 , source { { src { db "ModelMaker" , tag str "11306" } , anchor "ModelMaker" , url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10 090&contig=NT_039711.3&gene=Abcb7&lid=11306" } } } , { type comment , text "UniGene" , version 0 , xtra-properties { { tag "UNIGENE" , value "Mm.262053" } } , source { { src { db "UniGene" , tag str "Mm.262053" } , anchor "Mm.262053" , url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=26 2053" } } } , { type comment , version 0 , source { { src { db "HomoloGene" , tag str "11306" } , anchor "HomoloGene" , url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT= 11306[loc]&TAXID=10090" } } } , { type comment , version 0 , source { { src { db "MGI" , tag id 109533 } , anchor "MGI" , url "http://www.informatics.jax.org/searches/accession_report.cg i?id=MGI:109533" } } } , { type comment , version 0 , source { { src { db "Ensembl" , tag str "" } , url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC035 534" } } } , { type comment , version 0 , source { { src { db "UCSC" , tag str "" } , url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position= BC035534" } } } , { type comment , text "Gene Expression Database (GXD) at MGI" , version 0 , source { { src { db "Gene Expression Database (GXD) at MGI" , tag str "MGI:109533" } , anchor "MGI:109533" , url "http://www.informatics.jax.org/searches/expression_report.c gi?id=MGI:109533" } } } , { type comment , text "Human ABC-Transporter Proteins" , version 0 , source { { src { db "Human ABC-Transporter Proteins" , tag str "Human ABC-Transporter Proteins" } , anchor "Human ABC-Transporter Proteins" , url "http://nutrigene.4t.com/humanabc.htm" } } } } } , { type generif , text "ABC7 positively regulates the expression of extramitochondrial thioredoxin & that of an intramitochondrial iron-sulfur-containing protein, ferrochelatase. ABC7 contributes to the production of heme during the differentiation of erythroid cells." , version 0 , refs { pmid 12480705 } , create-date str "May 23 2003 12:00AM" , update-date str "Jun 22 2003 7:07AM" } } , unique-keys { { db "LocusID" , tag id 11306 } , { db "MGI" , tag id 109533 } } , xtra-index-terms { "LOC11306" } } Entrezgene ::= { track-info { geneid 171590 , status live , create-date std { year 2005 , month 4 , day 7 , hour 13 , minute 32 , second 25 } , update-date std { year 2005 , month 1 , day 18 , hour 23 , minute 7 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Caenorhabditis elegans" , db { { db "taxon" , tag id 6239 } } , orgname { name binomial { genus "Caenorhabditis" , species "elegans" } , lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" , gcode 1 , mgcode 5 , div "INV" } } , subtype { { subtype chromosome , name "I" } } } , gene { locus "1A478" , maploc "I;-17.75 cM (interpolated genetic position)" , db { { db "AceView/WormGenes" , tag str "1A478" } , { db "LocusID" , tag id 171590 } , { db "WormBase" , tag str "Y74C9A.3" } } , syn { "Y74C9A.3" , "CELK05052" } , locus-tag "1A478" } , prot { name { "AD-003 protein (26.6 kD) (1A478)" } } , rna { type mRNA } , location { { display-str "I;-17.75 cM (interpolated genetic position)" , method map-type cM } } , gene-source { src "Entrez Genomes" , src-int 25167480 , src-str1 "NC_003279" , src-str2 "CE:1A478" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , label "1A478" , accession "NC_003279" , version 2 , seqs { int { from 4220 , to 10147 , strand minus , id gi 25167480 } } , products { { type mRNA , accession "NM_058260" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 10094 , to 10147 , strand minus , id gi 25167480 } , int { from 9726 , to 9845 , strand minus , id gi 25167480 } , int { from 6036 , to 6326 , strand minus , id gi 25167480 } , int { from 5194 , to 5295 , strand minus , id gi 25167480 } , int { from 4220 , to 4357 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510630 } , products { { type peptide , label "AD-003 protein (26.6 kD) (1A478)" , accession "NP_490660" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 10094 , to 10147 , strand minus , id gi 25167480 } , int { from 9726 , to 9845 , strand minus , id gi 25167480 } , int { from 6036 , to 6326 , strand minus , id gi 25167480 } , int { from 5194 , to 5295 , strand minus , id gi 25167480 } , int { from 4220 , to 4357 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510631 } } } , comment { { type comment , text "" , version 0 } } } } , comment { { type comment , text "Title: Caenorhabditis elegans gene 1A478, AD-003 protein." , version 0 } } } } , comments { { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_058260" , version 1 , source { { src { db "Nucleotide" , tag id 17510630 } , anchor "NM_058260" } } , seqs { whole gi 17510630 } , products { { type peptide , heading "Product" , accession "NP_490660" , version 1 , source { { src { db "Protein" , tag id 17510631 } , anchor "NP_490660" } } , seqs { whole gi 17510631 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 17510631 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 24115 } , anchor "pfam05891: DUF858; Eukaryotic protein of unknown function (DUF858)" } } , comment { { type other , text "Location: 11 - 225 Blast Score: 824" , version 0 } } } } } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC024206" , version 1 , source { { src { db "Nucleotide" , tag id 7105656 } , anchor "AC024206" } } , seqs { whole gi 7105656 } , products { { type peptide , accession "AAF36050" , version 2 , source { { src { db "Protein" , tag id 14550391 } , anchor "AAF36050" } } , seqs { whole gi 14550391 } } } } } } , { type comment , heading "RefSeq Status" , label "Reviewed" , version 0 } } , unique-keys { { db "LocusID" , tag id 171590 } } , xtra-iq { { tag "NUCLEOTIDE" , value "7105656" } , { tag "PROTEIN" , value "14550391" } } , non-unique-keys { { db "ID" , tag id 25167480 } } } Entrezgene ::= { track-info { geneid 171591 , status live , create-date std { year 2005 , month 4 , day 6 , hour 18 , minute 33 , second 30 } , update-date std { year 2005 , month 1 , day 18 , hour 23 , minute 7 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Caenorhabditis elegans" , db { { db "taxon" , tag id 6239 } } , orgname { name binomial { genus "Caenorhabditis" , species "elegans" } , lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" , gcode 1 , mgcode 5 , div "INV" } } , subtype { { subtype chromosome , name "I" } } } , gene { locus "1A489" , maploc "I;-17.80 cM (interpolated genetic position)" , db { { db "AceView/WormGenes" , tag str "1A489" } , { db "LocusID" , tag id 171591 } , { db "WormBase" , tag str "Y74C9A.2" } } , syn { "Y74C9A.2" , "CELK01753" } , locus-tag "1A489" } , prot { name { "putative protein, with a coiled coil-4 domain (13.7 kD) (1A489)" } } , rna { type mRNA } , location { { display-str "I;-17.80 cM (interpolated genetic position)" , method map-type cM } } , gene-source { src "Entrez Genomes" , src-int 25167480 , src-str1 "NC_003279" , src-str2 "CE:1A489" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , label "1A489" , accession "NC_003279" , version 2 , seqs { int { from 11640 , to 16584 , strand plus , id gi 25167480 } } , products { { type mRNA , accession "NM_058259" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 11640 , to 11688 , strand plus , id gi 25167480 } , int { from 14950 , to 15159 , strand plus , id gi 25167480 } , int { from 16472 , to 16584 , strand plus , id gi 25167480 } } } , seqs { whole gi 17510628 } , products { { type peptide , label "putative protein, with a coiled coil-4 domain (13.7 kD) (1A489)" , accession "NP_490661" , version 1 , refs { pmid 9851916 , pmid 11231151 } , genomic-coords { mix { int { from 11640 , to 11688 , strand plus , id gi 25167480 } , int { from 14950 , to 15159 , strand plus , id gi 25167480 } , int { from 16472 , to 16584 , strand plus , id gi 25167480 } } } , seqs { whole gi 17510629 } } } , comment { { type comment , text "" , version 0 } } } } , comment { { type comment , text "Title: Caenorhabditis elegans essential expressed gene 1A489." , version 0 } } } } , comments { { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_058259" , version 1 , source { { src { db "Nucleotide" , tag id 17510628 } , anchor "NM_058259" } } , seqs { whole gi 17510628 } , products { { type peptide , heading "Product" , accession "NP_490661" , version 1 , source { { src { db "Protein" , tag id 17510629 } , anchor "NP_490661" } } , seqs { whole gi 17510629 } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC024206" , version 1 , source { { src { db "Nucleotide" , tag id 7105656 } , anchor "AC024206" } } , seqs { whole gi 7105656 } , products { { type peptide , accession "AAF36049" , version 1 , source { { src { db "Protein" , tag id 7105658 } , anchor "AAF36049" } } , seqs { whole gi 7105658 } } } } } } , { type comment , heading "RefSeq Status" , label "Reviewed" , version 0 } } , unique-keys { { db "LocusID" , tag id 171591 } } , xtra-iq { { tag "NUCLEOTIDE" , value "7105656" } , { tag "PROTEIN" , value "7105658" } } , non-unique-keys { { db "ID" , tag id 25167480 } } } Entrezgene ::= { track-info { geneid 171592 , status live , create-date std { year 2005 , month 4 , day 6 , hour 18 , minute 31 , second 55 } , update-date std { year 2005 , month 1 , day 18 , hour 23 , minute 7 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Caenorhabditis elegans" , db { { db "taxon" , tag id 6239 } } , orgname { name binomial { genus "Caenorhabditis" , species "elegans" } , lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" , gcode 1 , mgcode 5 , div "INV" } } , subtype { { subtype chromosome , name "I" } } } , gene { locus "1A492" , maploc "I;-17.86 cM (interpolated genetic position)" , db { { db "AceView/WormGenes" , tag str "1A492" } , { db "LocusID" , tag id 171592 } , { db "WormBase" , tag str "Y74C9A.4a" } } , syn { "Y74C9A.4a" , "Y74C9A.4b" , "CELK08126" } , locus-tag "1A492" } , prot { name { "suppressor of PResenilin defect SPR-1 related; similar to co-repressor of REST RE1-silencing transcription factor (65.9 kD) (1A492)" , "suppressor of PResenilin defect SPR-1 related; similar to co-repressor of REST RE1-silencing transcription factor (65.6 kD) (1A492)" } } , location { { display-str "I;-17.86 cM (interpolated genetic position)" , method map-type cM } } , gene-source { src "Entrez Genomes" , src-int 25167480 , src-str1 "NC_003279" , src-str2 "CE:1A492" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , label "1A492" , accession "NC_003279" , version 2 , seqs { int { from 17910 , to 26777 , strand minus , id gi 25167480 } } , products { { type mRNA , accession "NM_058261" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 26732 , to 26777 , strand minus , id gi 25167480 } , int { from 26589 , to 26689 , strand minus , id gi 25167480 } , int { from 26370 , to 26523 , strand minus , id gi 25167480 } , int { from 25272 , to 25471 , strand minus , id gi 25167480 } , int { from 24928 , to 25089 , strand minus , id gi 25167480 } , int { from 24650 , to 24844 , strand minus , id gi 25167480 } , int { from 21012 , to 21138 , strand minus , id gi 25167480 } , int { from 20847 , to 20963 , strand minus , id gi 25167480 } , int { from 20270 , to 20477 , strand minus , id gi 25167480 } , int { from 19014 , to 19240 , strand minus , id gi 25167480 } , int { from 18005 , to 18114 , strand minus , id gi 25167480 } , int { from 17910 , to 17957 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510632 } , products { { type peptide , label "suppressor of PResenilin defect SPR-1 related; similar to co-repressor of REST RE1-silencing transcription factor (65.9 kD) (1A492)" , accession "NP_490662" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 26732 , to 26777 , strand minus , id gi 25167480 } , int { from 26589 , to 26689 , strand minus , id gi 25167480 } , int { from 26370 , to 26523 , strand minus , id gi 25167480 } , int { from 25272 , to 25471 , strand minus , id gi 25167480 } , int { from 24928 , to 25089 , strand minus , id gi 25167480 } , int { from 24650 , to 24844 , strand minus , id gi 25167480 } , int { from 21012 , to 21138 , strand minus , id gi 25167480 } , int { from 20847 , to 20963 , strand minus , id gi 25167480 } , int { from 20270 , to 20477 , strand minus , id gi 25167480 } , int { from 19014 , to 19240 , strand minus , id gi 25167480 } , int { from 18005 , to 18114 , strand minus , id gi 25167480 } , int { from 17910 , to 17957 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510633 } } } , comment { { type comment , text "" , version 0 } } } , { type mRNA , accession "NM_058262" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 26732 , to 26777 , strand minus , id gi 25167480 } , int { from 26589 , to 26680 , strand minus , id gi 25167480 } , int { from 26370 , to 26523 , strand minus , id gi 25167480 } , int { from 25272 , to 25471 , strand minus , id gi 25167480 } , int { from 24928 , to 25089 , strand minus , id gi 25167480 } , int { from 24650 , to 24844 , strand minus , id gi 25167480 } , int { from 21012 , to 21138 , strand minus , id gi 25167480 } , int { from 20847 , to 20963 , strand minus , id gi 25167480 } , int { from 20270 , to 20477 , strand minus , id gi 25167480 } , int { from 19014 , to 19240 , strand minus , id gi 25167480 } , int { from 18005 , to 18114 , strand minus , id gi 25167480 } , int { from 17910 , to 17957 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510634 } , products { { type peptide , label "suppressor of PResenilin defect SPR-1 related; similar to co-repressor of REST RE1-silencing transcription factor (65.6 kD) (1A492)" , accession "NP_490663" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 26732 , to 26777 , strand minus , id gi 25167480 } , int { from 26589 , to 26680 , strand minus , id gi 25167480 } , int { from 26370 , to 26523 , strand minus , id gi 25167480 } , int { from 25272 , to 25471 , strand minus , id gi 25167480 } , int { from 24928 , to 25089 , strand minus , id gi 25167480 } , int { from 24650 , to 24844 , strand minus , id gi 25167480 } , int { from 21012 , to 21138 , strand minus , id gi 25167480 } , int { from 20847 , to 20963 , strand minus , id gi 25167480 } , int { from 20270 , to 20477 , strand minus , id gi 25167480 } , int { from 19014 , to 19240 , strand minus , id gi 25167480 } , int { from 18005 , to 18114 , strand minus , id gi 25167480 } , int { from 17910 , to 17957 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510635 } } } , comment { { type comment , text "" , version 0 } } } } , comment { { type comment , text "Title: Caenorhabditis elegans gene 1A492, suppressor of PResenilin defect SPR-1 related; similar to co-repressor of REST RE1-silencing transcription factor." , version 0 } } } } , comments { { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_058261" , version 1 , source { { src { db "Nucleotide" , tag id 17510632 } , anchor "NM_058261" } } , seqs { whole gi 17510632 } , products { { type peptide , heading "Product" , accession "NP_490662" , version 1 , source { { src { db "Protein" , tag id 17510633 } , anchor "NP_490662" } } , seqs { whole gi 17510633 } } } } , { type mRNA , heading "mRNA Sequence" , accession "NM_058262" , version 1 , source { { src { db "Nucleotide" , tag id 17510634 } , anchor "NM_058262" } } , seqs { whole gi 17510634 } , products { { type peptide , heading "Product" , accession "NP_490663" , version 1 , source { { src { db "Protein" , tag id 17510635 } , anchor "NP_490663" } } , seqs { whole gi 17510635 } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC024206" , version 1 , source { { src { db "Nucleotide" , tag id 7105656 } , anchor "AC024206" } } , seqs { whole gi 7105656 } , products { { type peptide , accession "AAK67240" , version 1 , source { { src { db "Protein" , tag id 14550392 } , anchor "AAK67240" } } , seqs { whole gi 14550392 } } } } , { type genomic , heading "Genomic" , accession "AC024206" , version 1 , source { { src { db "Nucleotide" , tag id 7105656 } , anchor "AC024206" } } , seqs { whole gi 7105656 } , products { { type peptide , accession "AAF36052" , version 1 , source { { src { db "Protein" , tag id 7105661 } , anchor "AAF36052" } } , seqs { whole gi 7105661 } } } } } } , { type comment , heading "RefSeq Status" , label "Reviewed" , version 0 } } , unique-keys { { db "LocusID" , tag id 171592 } } , xtra-iq { { tag "NUCLEOTIDE" , value "7105656" } , { tag "PROTEIN" , value "14550392" } , { tag "PROTEIN" , value "7105661" } } , non-unique-keys { { db "ID" , tag id 25167480 } } } Entrezgene ::= { track-info { geneid 171593 , status live , create-date std { year 2005 , month 4 , day 7 , hour 13 , minute 31 , second 41 } , update-date std { year 2005 , month 1 , day 18 , hour 23 , minute 7 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Caenorhabditis elegans" , db { { db "taxon" , tag id 6239 } } , orgname { name binomial { genus "Caenorhabditis" , species "elegans" } , lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" , gcode 1 , mgcode 5 , div "INV" } } , subtype { { subtype chromosome , name "I" } } } , gene { locus "1A502" , maploc "I;-17.91 cM (interpolated genetic position)" , db { { db "AceView/WormGenes" , tag str "1A502" } , { db "LocusID" , tag id 171593 } , { db "WormBase" , tag str "Y74C9A.5" } } , syn { "Y74C9A.5" , "CELK09643" } , locus-tag "1A502" } , prot { name { "sestrin (1A502)" } } , rna { type mRNA } , location { { display-str "I;-17.91 cM (interpolated genetic position)" , method map-type cM } } , gene-source { src "Entrez Genomes" , src-int 25167480 , src-str1 "NC_003279" , src-str2 "CE:1A502" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , label "1A502" , accession "NC_003279" , version 2 , seqs { int { from 28279 , to 34904 , strand minus , id gi 25167480 } } , products { { type mRNA , accession "NM_058263" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 34694 , to 34904 , strand minus , id gi 25167480 } , int { from 32598 , to 32764 , strand minus , id gi 25167480 } , int { from 32411 , to 32541 , strand minus , id gi 25167480 } , int { from 31768 , to 32071 , strand minus , id gi 25167480 } , int { from 29768 , to 30423 , strand minus , id gi 25167480 } , int { from 29099 , to 29366 , strand minus , id gi 25167480 } , int { from 28915 , to 29025 , strand minus , id gi 25167480 } , int { from 28279 , to 28404 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510636 } , products { { type peptide , label "sestrin (1A502)" , accession "NP_490664" , version 1 , refs { pmid 9851916 } , genomic-coords { mix { int { from 34694 , to 34904 , strand minus , id gi 25167480 } , int { from 32598 , to 32764 , strand minus , id gi 25167480 } , int { from 32411 , to 32541 , strand minus , id gi 25167480 } , int { from 31768 , to 32071 , strand minus , id gi 25167480 } , int { from 29768 , to 30423 , strand minus , id gi 25167480 } , int { from 29099 , to 29366 , strand minus , id gi 25167480 } , int { from 28915 , to 29025 , strand minus , id gi 25167480 } , int { from 28279 , to 28404 , strand minus , id gi 25167480 } } } , seqs { whole gi 17510637 } } } , comment { { type comment , text "" , version 0 } } } } , comment { { type comment , text "Title: Caenorhabditis elegans gene 1A502, sestrin." , version 0 } } } } , comments { { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_058263" , version 1 , source { { src { db "Nucleotide" , tag id 17510636 } , anchor "NM_058263" } } , seqs { whole gi 17510636 } , products { { type peptide , heading "Product" , accession "NP_490664" , version 1 , source { { src { db "Protein" , tag id 17510637 } , anchor "NP_490664" } } , seqs { whole gi 17510637 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 17510637 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 15933 } , anchor "pfam04636: PA26; PA26 p53-induced protein (sestrin)" } } , comment { { type other , text "Location: 88 - 644 Blast Score: 1457" , version 0 } } } } } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC024206" , version 1 , source { { src { db "Nucleotide" , tag id 7105656 } , anchor "AC024206" } } , seqs { whole gi 7105656 } , products { { type peptide , accession "AAF36051" , version 1 , source { { src { db "Protein" , tag id 7105660 } , anchor "AAF36051" } } , seqs { whole gi 7105660 } } } } } } , { type comment , heading "RefSeq Status" , label "Reviewed" , version 0 } } , unique-keys { { db "LocusID" , tag id 171593 } } , xtra-iq { { tag "NUCLEOTIDE" , value "7105656" } , { tag "PROTEIN" , value "7105660" } } , non-unique-keys { { db "ID" , tag id 25167480 } } } Entrezgene ::= { track-info { geneid 171594 , status live , create-date std { year 2005 , month 4 , day 7 , hour 13 , minute 31 , second 47 } , update-date std { year 2005 , month 1 , day 18 , hour 23 , minute 7 , second 0 } } , type protein-coding , source { genome genomic , origin natural , org { taxname "Caenorhabditis elegans" , db { { db "taxon" , tag id 6239 } } , orgname { name binomial { genus "Caenorhabditis" , species "elegans" } , lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" , gcode 1 , mgcode 5 , div "INV" } } , subtype { { subtype chromosome , name "I" } } } , gene { locus "1A527" , maploc "I;-18.07 cM (interpolated genetic position)" , db { { db "AceView/WormGenes" , tag str "1A527" } , { db "LocusID" , tag id 171594 } , { db "WormBase" , tag str "Y48G1C.4" } } , syn { "Y48G1C.4" , "CELK05819" } , locus-tag "1A527" } , prot { name { "putative phosphatidylglycerophosphate synthase, similar to silencer-associated factor (51.7 kD) (1A527)" } } , rna { type mRNA } , location { { display-str "I;-18.07 cM (interpolated genetic position)" , method map-type cM } } , gene-source { src "Entrez Genomes" , src-int 25167480 , src-str1 "NC_003279" , src-str2 "CE:1A527" , gene-display FALSE , locus-display FALSE , extra-terms FALSE } , locus { { type genomic , label "1A527" , accession "NC_003279" , version 2 , seqs { int { from 49920 , to 54359 , strand plus , id gi 25167480 } } , products { { type mRNA , accession "NM_058265" , version 2 , refs { pmid 9851916 } , genomic-coords { mix { int { from 49920 , to 50015 , strand plus , id gi 25167480 } , int { from 50814 , to 51029 , strand plus , id gi 25167480 } , int { from 52282 , to 52409 , strand plus , id gi 25167480 } , int { from 52465 , to 52571 , strand plus , id gi 25167480 } , int { from 53265 , to 53336 , strand plus , id gi 25167480 } , int { from 53390 , to 53694 , strand plus , id gi 25167480 } , int { from 53943 , to 54359 , strand plus , id gi 25167480 } } } , seqs { whole gi 25143330 } , products { { type peptide , label "putative phosphatidylglycerophosphate synthase, similar to silencer-associated factor (51.7 kD) (1A527)" , accession "NP_490666" , version 2 , refs { pmid 9851916 , pmid 11231151 } , genomic-coords { mix { int { from 49920 , to 50015 , strand plus , id gi 25167480 } , int { from 50814 , to 51029 , strand plus , id gi 25167480 } , int { from 52282 , to 52409 , strand plus , id gi 25167480 } , int { from 52465 , to 52571 , strand plus , id gi 25167480 } , int { from 53265 , to 53336 , strand plus , id gi 25167480 } , int { from 53390 , to 53694 , strand plus , id gi 25167480 } , int { from 53943 , to 54359 , strand plus , id gi 25167480 } } } , seqs { whole gi 25143331 } } } , comment { { type comment , text "" , version 0 } } } } , comment { { type comment , text "Title: Caenorhabditis elegans essential gene 1A527, putative phosphatidylglycerophosphate synthase, similar to silencer-associated factor." , version 0 } } } } , comments { { type comment , heading "NCBI Reference Sequences (RefSeq)" , version 0 , products { { type mRNA , heading "mRNA Sequence" , accession "NM_058265" , version 2 , source { { src { db "Nucleotide" , tag id 25143330 } , anchor "NM_058265" } } , seqs { whole gi 25143330 } , products { { type peptide , heading "Product" , accession "NP_490666" , version 2 , source { { src { db "Protein" , tag id 25143331 } , anchor "NP_490666" } } , seqs { whole gi 25143331 } , comment { { type other , heading "Conserved Domains" , version 0 , source { { src { db "PROT_CDD" , tag id 25143331 } , pre-text "(1)" , anchor "summary" } } , comment { { type other , version 0 , source { { src { db "CDD" , tag id 5372 } , anchor "cd00138: PLDc; Phospholipase D" } } , comment { { type other , text "Location: 20 - 172 Blast Score: 135" , version 0 } } } } } } } } } } } , { type comment , heading "Related Sequences" , version 0 , products { { type genomic , heading "Genomic" , accession "AC024796" , version 1 , source { { src { db "Nucleotide" , tag id 7140352 } , anchor "AC024796" } } , seqs { whole gi 7140352 } , products { { type peptide , accession "AAK29892" , version 2 , source { { src { db "Protein" , tag id 16950493 } , anchor "AAK29892" } } , seqs { whole gi 16950493 } } } } } } , { type comment , heading "RefSeq Status" , label "Reviewed" , version 0 } } , unique-keys { { db "LocusID" , tag id 171594 } } , xtra-iq { { tag "NUCLEOTIDE" , value "7140352" } , { tag "PROTEIN" , value "16950493" } } , non-unique-keys { { db "ID" , tag id 25167480 } } } author-pod-syntax.t100644000765000024 45413352317004 21070 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. use strict; use warnings; use Test::More; use Test::Pod 1.41; all_pod_files_ok(); author-pod-coverage.t100644000765000024 53613352317004 21336 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodCoverageTests. use Test::Pod::Coverage 1.08; use Pod::Coverage::TrustPod; all_pod_coverage_ok({ coverage_class => 'Pod::Coverage::TrustPod' }); examples000755000765000024 013352317004 16525 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73indexer_test.pl100755000765000024 300713352317004 21722 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/examples#!/usr/bin/perl # launch it like "perl indexer_test.pl Homo_sapiens" (Homo_sapiens can be downloaded # and decompressed from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN/Mammalia/Homo_sapiens.gz) # or use the included test file "perl indexer_test.pl ../t/input.asn ../t/input1.asn" use strict; use lib 'lib'; use lib '/home/liu/cvs/bioperl-1.5.0'; use lib '/home/liu/important/scripts/ari_geneindex'; use Bio::ASN1::EntrezGene::Indexer; use Dumpvalue; use Benchmark; # creation of index: my $file = 'entrezgene.idx'; my $inx = Bio::ASN1::EntrezGene::Indexer->new( -filename => $file, -write_flag => 'WRITE'); my $t0 = new Benchmark; $inx->make_index(@ARGV); my $t1 = new Benchmark; print "Indexing @ARGV took:",timestr(timediff($t1, $t0)),"\n"; # using the index: my $geneid = 3; # below is not needed in this script but it's the preferred calling way if # one's just using an existing index file # my $inx = Bio::ASN1::EntrezGene::Indexer->new(-filename => 'entrezgene.idx'); print "there are a total of " . $inx->count_records . " records\n"; my $t0 = new Benchmark; # uncomment below to test retrieving Bio::Seq obj # my $seq = $inx->fetch($geneid); # Bio::Seq obj returned by Bio::SeqIO::entrezgene.pm my $seq1 = $inx->fetch_hash($geneid); # a hash produced by Bio::ASN1::EntrezGene # that contains all data in the Entrez Gene record my $t1 = new Benchmark; print "Retrieving Entrez Gene #$geneid took:",timestr(timediff($t1, $t0)),"\n"; # Dumpvalue->new->dumpValue($seq); Dumpvalue->new->dumpValue($seq1); ASN1000755000765000024 013352317004 16670 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/BioSequence.pm100755000765000024 4703713352317004 21174 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1package Bio::ASN1::Sequence; $Bio::ASN1::Sequence::VERSION = '1.73'; use utf8; use strict; use warnings; use Carp qw(carp croak); # ABSTRACT: Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences. # AUTHOR: Dr. Mingyi Liu # OWNER: 2005 Mingyi Liu # OWNER: 2005 GPC Biotech AG # OWNER: 2005 Altana Research Institute # LICENSE: Perl_5 sub new { my $class = shift; $class = ref($class) if(ref($class)); my $self = { maxerrstr => 20, @_ }; bless $self, $class; map { $self->input_file($self->{$_}) if($self->{$_}) } qw(file -file); map { $self->fh($self->{$_}) if($self->{$_}) } qw(fh -fh); return $self; } sub maxerrstr { my ($self, $value) = @_; $self->{maxerrstr} = $value if $value > 0; return $self->{maxerrstr}; } sub parse { my ($self, $input, $compact, $noreset) = @_; $input || croak "must have input!\n"; $self->{input} = $input; $self->{filename} = "input" unless $self->{filename}; $self->{linenumber} = 1 unless $self->{linenumber} && $noreset; $self->{depth} = 0; my $result; eval { $result = $self->_parse(); # no need to reset $self->{depth} or linenumber }; if($@) { if($@ !~ /^Data Error:/) { croak "non-conforming data broke parser on line $self->{linenumber} in $self->{filename}\n". "possible cause includes randomly inserted brackets in input file before line $self->{linenumber}\n". "first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" . substr($self->{input}, pos($self->{input}), $self->{maxerrstr}) . "\nRaw error mesg: $@\n"; } else { die $@ } } trimdata($result, $compact); return $result; } sub input_file { my ($self, $filename) = @_; # in case user's Perl system can't handle large file. Assuming Unix, otherwise raise error local *IN; # older styled code to enable module to work with perl 5.005_03 open(*IN, $filename) || ($! =~ /too large/i && open(*IN, "cat $filename |")) || croak "can't open $filename! -- $!\n"; $self->{fh} = *IN; $self->{filename} = $filename; $self->{linenumber} = 0; # reset line number } sub next_seq { my ($self, $compact) = @_; $self->{fh} || croak "you must pass in a file name or handle through new() or input_file() first before calling next_seq!\n"; local $/ = "Seq-entry ::= set {"; # set record separator while($_ = readline($self->{fh})) { chomp; next unless /\S/; my $tmp = (/^\s*Seq-entry ::= set (\{.*)/si)? $1 : "{" . $_; # get rid of the 'Seq-entry ::= set ' at the beginning of Sequence record return $self->parse($tmp, $compact, 1); # 1 species no resetting line number } } sub _parse { my ($self, $flag) = @_; my $data; while(1) { # changing orders of regex if/elsif statements made little difference. current order is close to optimal if($self->{input} =~ /\G[ \t]*,?[ \t]*\n/cg) # cleanup leftover { $self->{linenumber}++; next; } if($self->{input} =~ /\G[ \t]*}/cg) { if(!($self->{depth}--) && $self->{input} =~ /\S/) { croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n"; } return $data } elsif($self->{input} =~ /\G[ \t]*{/cg) { $self->{depth}++; push(@$data, $self->_parse()) } elsif($self->{input} =~ /\G[ \t]*([\w-]+)(\s*)/cg) { my ($id, $lines) = ($1, $2); # we're prepared for NCBI to make the format even worse: # note: to count line numbers right for text files on different OS, I'm sacrificing much speed (maybe I shouldn't worry so much) $self->{linenumber} += $lines =~ s/\n//g || $lines =~ s/\r//g; # count by *NIX/Win or Mac my ($tmp, $tmp1); # we put \s* in lookahead for linenumber counting purpose (which slows things down) if(($self->{input} =~ /\G"((?:[^"]+|"")*)"(?=\s*[,}])/cg && ++$tmp) || ($self->{input} =~ /\G'([^']+)'\s*H/icg && ++$tmp1) || # this is the only difference b/w sequence and entrez gene formats so far $self->{input} =~ /\G([\w-]+)(?=\s*[,}])/cg) { my $value = $1; if($tmp) # slight speed optimization, not really necessary since regex is fast enough { $value =~ s/""/"/g; $self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac $value =~ s/[\r\n]+//g; # in case it's Win format } elsif($tmp1) # slight speed optimization, not really necessary since regex is fast enough { $value =~ tr/fF8421/NNTGCA/; # good for NCBI4na. But if NCBI8na was used, then more needs to be transliterated $self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac $value =~ s/[\r\n0]+//g; # in case it's Win format (get rid of '0' at end of seq too) } if(ref($data->{$id})) { push(@{$data->{$id}}, $value) } # hash value is not a terminal (or have multiple values), create array to avoid multiple same-keyed hash overwrite each other elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # hash value has a second terminal value now! else { $data->{$id} = $value } # the first terminal value } elsif($self->{input} =~ /\G\{/cg) { $self->{depth}++; push(@{$data->{$id}}, $self->_parse()); } elsif($self->{input} =~ /\G(?=[,}])/cg) { push(@$data, $id) } else # must be "id value value" format { $self->{depth}++; push(@{$data->{$id}}, $self->_parse(1)) } if($flag) { if(!($self->{depth}--) && $self->{input} =~ /\S/) { croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n"; } return $data; } } elsif($self->{input} =~ /\G[ \t]*"((?:[^"]+|"")*)"(?=\s*[,}])/cg) { my $value = $1; $value =~ s/""/"/g; $self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac $value =~ s/[\r\n]+//g; # in case it's Win format push(@$data, $value) } else # end of input { my ($pos, $len) = (pos($self->{input}), length($self->{input})); if($pos != $len && $self->{input} =~ /\G\s*\S/cg) # problem with parsing, must be non-conforming data { croak "Data Error: none conforming data found on line $self->{linenumber} in $self->{filename}!\n" . "first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" . substr($self->{input}, $pos, $self->{maxerrstr}) . "\n"; } elsif($self->{depth} > 0) { croak "Data Error: missing '}' found at end of input in $self->{filename}!"; } elsif($self->{depth} < 0) { croak "Data Error: extra (mismatched) '}' found at end of input in $self->{filename}!"; } return $data; } } } # following copied directly from my Pipeline::Util::util just to make this module # more self-sufficient. Changes should be made over in that module though. # trims arrayrefs that points to one-element array to slims the # data structure down (calls Pipeline::Util::util::trimdata) # something like # 'comments' => ARRAY(0x898be94) # 0 ARRAY(0x883fc54) # 0 ARRAY(0x886aef4) # 0 HASH(0x884d554) # 'heading' => 'LocusTagLink' # 'source' => ARRAY(0x8810714) # 0 ARRAY(0x8a7df18) # 0 ARRAY(0x889f940) # 0 HASH(0x886ada4) # 'src' => ARRAY(0x88454fc) # 0 ARRAY(0x8845598) # 0 HASH(0x898c0ec) # 'db' => 'HGNC' # 'tag' => ARRAY(0x898bfb4) # 0 HASH(0x898c164) # 'id' => 5 # becomes this if $flag == 1: # 'comments' => ARRAY(0x8840014) # 0 HASH(0x884d8a4) # 'heading' => 'LocusTagLink' # 'source' => HASH(0x8a9869c) # 'src' => HASH(0x884534c) # 'db' => 'HGNC' # 'tag' => HASH(0x88453c4) # 'id' => 5 # so now $hash->{comments}->[0]->[0]->[0]->{source}->[0]->[0]->[0]->{src}->[0]->[0]->{tag}->[0]->{id} # becomes $hash->{comments}->[0]->{source}->{src}->{tag}->{id} # this may create problem as array might suddenly change to hash depending on whether it # has multiple elements or not. So set $flag to 2 or 0/undef would disallow trimming that # would lead to data type change, thus resulting in data structure like: # 'comments' => ARRAY(0x88617e8) # 0 HASH(0x889d578) # 'heading' => 'LocusTagLink' # 'source' => ARRAY(0x8912244) # 0 HASH(0x8a5d648) # 'src' => ARRAY(0x8a2203c) # 0 HASH(0x8a1af10) # 'db' => 'HGNC' # 'tag' => ARRAY(0x8a1add8) # 0 HASH(0x8a1af88) # 'id' => 5 # still not the safest, but saves some hassle writing code sub trimdata { my ($ref, $flag) = @_; $flag = 2 unless $flag; return if $flag == 3 || !ref($ref); if(ref($ref) ne 'ARRAY') # allows for object refs { my @keys; eval { @keys = keys %$ref }; # let's be careful and check if it can work as a hash return if $@; foreach my $key (@keys) { my $tmp = $ref->{$key}; while(ref($tmp) eq 'ARRAY' && @$tmp == 1) { last if($flag == 2 && ref($tmp->[0]) ne 'ARRAY'); $tmp = $tmp->[0] } $ref->{$key} = $tmp; trimdata($ref->{$key}, $flag) if(ref($ref->{$key})) } } else { # since the only situations where we would get an array of array is # when ASN file has a bracket of brackets (otherwise we'd get at least # a hash), it makes sense to reduce the arrayrefs to one level foreach my $item (@$ref) { my $tmp = $item; while(ref($tmp) eq 'ARRAY' && @$tmp == 1) { $tmp = $tmp->[0]; } $item = $tmp; trimdata($item, $flag) if(ref($item)) } } } sub fh { my ($self, $filehandle) = @_; if($filehandle) { $self->{fh} = $filehandle; $self->{linenumber} = 0; # reset line number } return $self->{fh}; } sub rawdata { my $self = shift; return "Seq-entry ::= set $self->{input}"; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::ASN1::Sequence - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences. =head1 VERSION version 1.73 =head1 SYNOPSIS use Bio::ASN1::Sequence; my $parser = Bio::ASN1::Sequence->new('file' => "downloaded.asn1"); while(my $result = $parser->next_seq) { # extract data from $result, or Dumpvalue->new->dumpValue($result); } # a new way to get the $result data hash for a particular sequence id: use Bio::ASN1::Sequence::Indexer; my $inx = Bio::ASN1::Sequence::Indexer->new(-filename => 'seq.idx'); my $seq = $inx->fetch_hash('AF093062'); # for creation of .idx index files please refer to # Bio::ASN1::Sequence::Indexer perldoc =head1 DESCRIPTION Bio::ASN1::Sequence is a regular expression-based Perl Parser for ASN.1-formatted NCBI sequences. It parses an ASN.1-formatted sequence record and returns a data structure that contains all data items from the sequence record. The parser will report error & line number if input data does not conform to the NCBI Sequence annotation file format. The sequence parser is basically a modified version of the high-performance Bio::ASN1::EntrezGene parser. However, I created a standalone module for sequence since it is more efficient to keep Sequence-specific code out of EntrezGene.pm. In fact it is possible to provide reading of all NCBI's ASN.1-formatted files through simple variations of the Entrez Gene parser (I need more investigation to be sure, but at least the sequence parser works well). Since demand for parsing NCBI ASN.1-formatted sequences is much lower than EntrezGene, this module is more like a beta version that works on the examples I checked, but I did not check all available records or data definitions. The error-reporting function of this module has to be useful sometimes. :) =head1 ATTRIBUTES =head2 maxerrstr Parameters: $maxerrstr (optional) - maximum number of characters after offending element, used by error reporting, default is 20 Example: $parser->maxerrstr(20); Function: get/set maxerrstr. Returns: maxerrstr. Notes: =head2 input_file Parameters: $filename for file that contains Sequence record(s) Example: $parser->input_file($filename); Function: Takes in name of a file containing Sequence records. opens the file and stores file handle Returns: none. Notes: Attempts to open file larger than 2 GB even on Perl that does not support 2 GB file (accomplished by calling "cat" and piping output. On OS that does not have "cat" error message will be displayed) =head1 METHODS =head2 new Parameters: maxerrstr => 20 (optional) - maximum number of characters after offending element, used by error reporting, default is 20 file or -file => $filename (optional) - name of the file to be parsed. call next_seq to parse! fh or -fh => $filehandle (optional) - handle of the file to be parsed. Example: my $parser = Bio::ASN1::Sequence->new(); Function: Instantiate a parser object Returns: Object reference Notes: Setting file or fh will reset line numbers etc. that are used for error reporting purposes, and seeking on file handle would mess up linenumbers! =head2 parse Parameters: $string that contains Sequence record, $trimopt (optional) that specifies how the data structure returned should be trimmed. 2 is recommended and default $noreset (optional) that species that line number should not be reset DEPRECATED as external function!!! Do not call this function directly! Call next_seq() instead Example: my $value = $parser->parse($text); # DEPRECATED as # external function!!! Do not call this function # directly! Call next_seq() instead Function: Takes in a string representing Sequence record, parses the record and returns a data structure. Returns: A data structure containing all data items from the sequence record. Notes: DEPRECATED as external function!!! Do not call this function directly! Call next_seq() instead $string should not contain 'Seq-entry ::= set' at beginning! =head2 next_seq Parameters: $trimopt (optional) that specifies how the data structure returned should be trimmed. option 2 is recommended and default Example: my $value = $parser->next_seq(); Function: Use the file handle generated by input_file, parses the next the record and returns a data structure. Returns: A data structure containing all data items from the sequence record. Notes: Must pass in a filename through new() or input_file() first! For details on how to use the $trimopt data trimming option please see comment for the trimdata method. An option of 2 is recommended and default The acceptable values for $trimopt include: 1 - trim as much as possible 2 (or 0, undef) - trim to an easy-to-use structure 3 - no trimming (in version 1.06, prior to version 1.06, 0 or undef means no trimming) =head2 trimdata Parameters: $hashref or $arrayref $trimflag (optional, see Notes) Example: trimdata($datahash); # using the default flag Function: recursively process all attributes of a hash/array hybrid and get rid of any arrayref that points to one-element arrays (trims data structure) depending on the optional flag. Returns: none - trimming happenes in-place Notes: This function is useful to compact a data structure produced by Bio::ASN1::Sequence::parse. The acceptable values for $trimopt include: 1 - trim as much as possible 2 (or 0, undef) - trim to an easy-to-use structure 3 - no trimming (in version 1.06, prior to version 1.06, 0 or undef means no trimming) This function is duplicate to EntrezGene.pm's and code should be compressed in the future (using util module & subclass). =head2 fh Parameters: $filehandle (optional) Example: trimdata($datahash); # using the default flag Function: getter/setter for file handle Returns: file handle for current file being parsed. Notes: Use with care! Line number report would not be corresponding to file's line number if seek operation is performed on the file handle! =head2 rawdata Parameters: none Example: my $data = $parser->rawdata(); Function: Get the sequence data file that was just parsed Returns: a string containing the ASN1-formatted sequence record Notes: Must first parse a record then call this function! Could be useful in interpreting line number value in error report (if user did a seek on file handle right before parsing call) =head1 INTERNAL METHODS =head2 _parse NCBI's Apr 05, 2005 format change forced much usage of lookahead, which would for sure slows parser down. But can't code efficiently without it. =head1 PREREQUISITE None. =head1 INSTALLATION Bio::ASN1::Sequence is part of the Bio::ASN1::EntrezGene package. Bio::ASN1::EntrezGene package can be installed & tested as follows: perl Makefile.PL make make test make install =head1 SEE ALSO The parse_sequence_example.pl script included in this package (please see the Bio-ASN1-EntrezGene-x.xx/examples directory) shows the usage. Please check out perldoc for Bio::ASN1::EntrezGene for more info. =head1 CITATION Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190. =head1 OPERATION SYSTEMS SUPPORTED Any OS that Perl runs on. =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-asn1-entrezgene/issues =head1 AUTHOR Dr. Mingyi Liu =head1 COPYRIGHT This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute. This software is available under the same terms as the perl 5 programming language system itself. =cut EntrezGene.pm100755000765000024 4722513352317004 21471 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1package Bio::ASN1::EntrezGene; $Bio::ASN1::EntrezGene::VERSION = '1.73'; use utf8; use strict; use warnings; use Carp qw(carp croak); # ABSTRACT: Regular expression-based Perl Parser for NCBI Entrez Gene. # AUTHOR: Dr. Mingyi Liu # OWNER: 2005 Mingyi Liu # OWNER: 2005 GPC Biotech AG # OWNER: 2005 Altana Research Institute # LICENSE: Perl_5 sub new { my $class = shift; $class = ref($class) if(ref($class)); my $self = { maxerrstr => 20, @_ }; bless $self, $class; map { $self->input_file($self->{$_}) if($self->{$_}) } qw(file -file); map { $self->fh($self->{$_}) if($self->{$_}) } qw(fh -fh); return $self; } sub maxerrstr { my ($self, $value) = @_; $self->{maxerrstr} = $value if $value > 0; return $self->{maxerrstr}; } sub parse { my ($self, $input, $compact, $noreset) = @_; $input || croak "must have input!\n"; $self->{input} = $input; $self->{filename} = "input" unless $self->{filename}; $self->{linenumber} = 1 unless $self->{linenumber} && $noreset; $self->{depth} = 0; my $result; eval { $result = $self->_parse(); # no need to reset $self->{depth} or linenumber }; if($@) { if($@ !~ /^Data Error:/) { croak "non-conforming data broke parser on line $self->{linenumber} in $self->{filename}\n". "possible cause includes randomly inserted brackets in input file before line $self->{linenumber}\n". "first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" . substr($self->{input}, pos($self->{input}), $self->{maxerrstr}) . "\nRaw error mesg: $@\n"; } else { die $@ } } trimdata($result, $compact); return $result; } sub input_file { my ($self, $filename) = @_; # in case user's Perl system can't handle large file. Assuming Unix, otherwise raise error local *IN; # older styled code to enable module to work with perl 5.005_03 open(*IN, $filename) || ($! =~ /too large/i && open(*IN, "cat $filename |")) || croak "can't open $filename! -- $!\n"; $self->{fh} = *IN; $self->{filename} = $filename; $self->{linenumber} = 0; # reset line number } sub next_seq { my ($self, $compact) = @_; $self->{fh} || croak "you must pass in a file name or handle through new() or input_file() first before calling next_seq!\n"; local $/ = "Entrezgene ::= {"; # set record separator while($_ = readline($self->{fh})) { chomp; next unless /\S/; my $tmp = (/^\s*Entrezgene(-Set)? ::= (\{.*)/si)? $2 : "{" . $_; # get rid of the 'Entrezgene ::= ' at the beginning of Entrez Gene record return $self->parse($tmp, $compact, 1); # 1 species no resetting line number } } sub _parse { my ($self, $flag) = @_; my $data; while(1) { # changing orders of regex if/elsif statements made little difference. current order is close to optimal if($self->{input} =~ /\G[ \t]*,?[ \t]*\n/cg) # cleanup leftover { $self->{linenumber}++; next; } if($self->{input} =~ /\G[ \t]*}/cg) { if(!($self->{depth}--) && $self->{input} =~ /\S/) { croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n"; } return $data } elsif($self->{input} =~ /\G[ \t]*{/cg) { $self->{depth}++; push(@$data, $self->_parse()) } elsif($self->{input} =~ /\G[ \t]*([\w-]+)(\s*)/cg) { my ($id, $lines) = ($1, $2); # we're prepared for NCBI to make the format even worse: # note: to count line numbers right for text files on different OS, I'm sacrificing much speed (maybe I shouldn't worry so much) $self->{linenumber} += $lines =~ s/\n//g || $lines =~ s/\r//g; # count by *NIX/Win or Mac my $tmp; # we put \s* in lookahead for linenumber counting purpose (which slows things down) if(($self->{input} =~ /\G"((?:[^"]+|"")*)"(?=\s*[,}])/cg && ++$tmp) || $self->{input} =~ /\G([\w-]+)(?=\s*[,}])/cg) { my $value = $1; if($tmp) # slight speed optimization, not really necessary since regex is fast enough { $value =~ s/""/"/g; $self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac $value =~ s/[\r\n]+//g; # in case it's Win format } if(ref($data->{$id})) { push(@{$data->{$id}}, $value) } # hash value is not a terminal (or have multiple values), create array to avoid multiple same-keyed hash overwrite each other elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # hash value has a second terminal value now! else { $data->{$id} = $value } # the first terminal value } elsif($self->{input} =~ /\G\{/cg) { $self->{depth}++; push(@{$data->{$id}}, $self->_parse()); } elsif($self->{input} =~ /\G(?=[,}])/cg) { push(@$data, $id) } else # must be "id value value" format { $self->{depth}++; push(@{$data->{$id}}, $self->_parse(1)) } if($flag) { if(!($self->{depth}--) && $self->{input} =~ /\S/) { croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n"; } return $data; } } elsif($self->{input} =~ /\G[ \t]*"((?:[^"]+|"")*)"(?=\s*[,}])/cg) { my $value = $1; $value =~ s/""/"/g; $self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac $value =~ s/[\r\n]+//g; # in case it's Win format push(@$data, $value) } else # end of input { my ($pos, $len) = (pos($self->{input}), length($self->{input})); if($pos != $len && $self->{input} =~ /\G\s*\S/cg) # problem with parsing, must be non-conforming data { croak "Data Error: none conforming data found on line $self->{linenumber} in $self->{filename}!\n" . "first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" . substr($self->{input}, $pos, $self->{maxerrstr}) . "\n"; } elsif($self->{depth} > 0) { croak "Data Error: missing '}' found at end of input in $self->{filename}!"; } elsif($self->{depth} < 0) { croak "Data Error: extra (mismatched) '}' found at end of input in $self->{filename}!"; } return $data; } } } # following copied directly from my Pipeline::Util::util just to make this module # more self-sufficient. Changes should be made over in that module though. # trims arrayrefs that points to one-element array to slims the # data structure down (calls Pipeline::Util::util::trimdata) # something like # 'comments' => ARRAY(0x898be94) # 0 ARRAY(0x883fc54) # 0 ARRAY(0x886aef4) # 0 HASH(0x884d554) # 'heading' => 'LocusTagLink' # 'source' => ARRAY(0x8810714) # 0 ARRAY(0x8a7df18) # 0 ARRAY(0x889f940) # 0 HASH(0x886ada4) # 'src' => ARRAY(0x88454fc) # 0 ARRAY(0x8845598) # 0 HASH(0x898c0ec) # 'db' => 'HGNC' # 'tag' => ARRAY(0x898bfb4) # 0 HASH(0x898c164) # 'id' => 5 # becomes this if $flag == 1: # 'comments' => ARRAY(0x8840014) # 0 HASH(0x884d8a4) # 'heading' => 'LocusTagLink' # 'source' => HASH(0x8a9869c) # 'src' => HASH(0x884534c) # 'db' => 'HGNC' # 'tag' => HASH(0x88453c4) # 'id' => 5 # so now $hash->{comments}->[0]->[0]->[0]->{source}->[0]->[0]->[0]->{src}->[0]->[0]->{tag}->[0]->{id} # becomes $hash->{comments}->[0]->{source}->{src}->{tag}->{id} # this may create problem as array might suddenly change to hash depending on whether it # has multiple elements or not. So set $flag to 2 or 0/undef would disallow trimming that # would lead to data type change, thus resulting in data structure like: # 'comments' => ARRAY(0x88617e8) # 0 HASH(0x889d578) # 'heading' => 'LocusTagLink' # 'source' => ARRAY(0x8912244) # 0 HASH(0x8a5d648) # 'src' => ARRAY(0x8a2203c) # 0 HASH(0x8a1af10) # 'db' => 'HGNC' # 'tag' => ARRAY(0x8a1add8) # 0 HASH(0x8a1af88) # 'id' => 5 # still not the safest, but saves some hassle writing code sub trimdata { my ($ref, $flag) = @_; $flag = 2 unless $flag; return if $flag == 3 || !ref($ref); if(ref($ref) ne 'ARRAY') # allows for object refs { my @keys; eval { @keys = keys %$ref }; # let's be careful and check if it can work as a hash return if $@; foreach my $key (@keys) { my $tmp = $ref->{$key}; while(ref($tmp) eq 'ARRAY' && @$tmp == 1) { last if($flag == 2 && ref($tmp->[0]) ne 'ARRAY'); $tmp = $tmp->[0] } $ref->{$key} = $tmp; trimdata($ref->{$key}, $flag) if(ref($ref->{$key})) } } else { # since the only situations where we would get an array of array is # when ASN file has a bracket of brackets (otherwise we'd get at least # a hash), it makes sense to reduce the arrayrefs to one level foreach my $item (@$ref) { my $tmp = $item; while(ref($tmp) eq 'ARRAY' && @$tmp == 1) { $tmp = $tmp->[0]; } $item = $tmp; trimdata($item, $flag) if(ref($item)) } } } sub fh { my ($self, $filehandle) = @_; if($filehandle) { $self->{fh} = $filehandle; $self->{linenumber} = 0; # reset line number } return $self->{fh}; } sub rawdata { my $self = shift; return "Entrezgene ::= $self->{input}"; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::ASN1::EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene. =head1 VERSION version 1.73 =head1 SYNOPSIS use Bio::ASN1::EntrezGene; my $parser = Bio::ASN1::EntrezGene->new('file' => "Homo_sapiens"); while(my $result = $parser->next_seq) { # extract data from $result, or Dumpvalue->new->dumpValue($result); } # a new way to get the $result data hash for a particular gene id: use Bio::ASN1::EntrezGene::Indexer; my $inx = Bio::ASN1::EntrezGene::Indexer->new(-filename => 'entrezgene.idx'); my $seq = $inx->fetch_hash(10); # returns $result for Entrez Gene record # with geneid 10 # note that the index file 'entrezgene.idx' can be created as follows my $inx = Bio::ASN1::EntrezGene::Indexer->new( -filename => 'entrezgene.idx', -write_flag => 'WRITE'); $inx->make_index('Homo_sapiens', 'Mus_musculus'); # files come from NCBI download # for more detail please refer to Bio::ASN1::EntrezGene::Indexer perldoc =head1 DESCRIPTION Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez Gene genome databases (L). It parses an ASN.1-formatted Entrez Gene record and returns a data structure that contains all data items from the gene record. The parser will report error & line number if input data does not conform to the NCBI Entrez Gene genome annotation file format. Note that it is possible to provide reading of all NCBI's ASN.1-formatted files through simple variations of the Entrez Gene parser (I need more investigation to be sure, but at least the sequence parser is a very simple variation on Entrez Gene parser and works well). It took the parser version 1.0 11 minutes to parse the human genome Entrez Gene file on one 2.4 GHz Intel Xeon processor. The addition of validation and error reporting in 1.03 and handling of new Entrez Gene format slowed the parser down about 40%. Since V1.07, this package also included an indexer that runs pretty fast (it takes 21 seconds for the indexer to index the human genome on the same processor). Therefore the combination of the modules would allow user to retrieve and parse arbitrary records. =head1 ATTRIBUTES =head2 maxerrstr Parameters: $maxerrstr (optional) - maximum number of characters after offending element, used by error reporting, default is 20 Example: $parser->maxerrstr(20); Function: get/set maxerrstr. Returns: maxerrstr. Notes: =head2 input_file Parameters: $filename for file that contains Entrez Gene record(s) Example: $parser->input_file($filename); Function: Takes in name of a file containing Entrez Gene records. opens the file and stores file handle Returns: none. Notes: Attempts to open file larger than 2 GB even on Perl that does not support 2 GB file (accomplished by calling "cat" and piping output. On OS that does not have "cat" error message will be displayed) =head1 METHODS =head2 new Parameters: maxerrstr => 20 (optional) - maximum number of characters after offending element, used by error reporting, default is 20 file or -file => $filename (optional) - name of the file to be parsed. call next_seq to parse! fh or -fh => $filehandle (optional) - handle of the file to be parsed. Example: my $parser = Bio::ASN1::EntrezGene->new(); Function: Instantiate a parser object Returns: Object reference Notes: Setting file or fh will reset line numbers etc. that are used for error reporting purposes, and seeking on file handle would mess up linenumbers! =head2 parse Parameters: $string that contains Entrez Gene record, $trimopt (optional) that specifies how the data structure returned should be trimmed. 2 is recommended and default $noreset (optional) that species that line number should not be reset DEPRECATED as external function!!! Do not call this function directly! Call next_seq() instead Example: my $value = $parser->parse($text); # DEPRECATED as # external function!!! Do not call this function # directly! Call next_seq() instead Function: Takes in a string representing Entrez Gene record, parses the record and returns a data structure. Returns: A data structure containing all data items from the Entrez Gene record. Notes: DEPRECATED as external function!!! Do not call this function directly! Call next_seq() instead $string should not contain 'EntrezGene ::=' at beginning! =head2 next_seq Parameters: $trimopt (optional) that specifies how the data structure returned should be trimmed. option 2 is recommended and default Example: my $value = $parser->next_seq(); Function: Use the file handle generated by input_file, parses the next the record and returns a data structure. Returns: A data structure containing all data items from the Entrez Gene record. Notes: Must pass in a filename through new() or input_file() first! For details on how to use the $trimopt data trimming option please see comment for the trimdata method. An option of 2 is recommended and default The acceptable values for $trimopt include: 1 - trim as much as possible 2 (or 0, undef) - trim to an easy-to-use structure 3 - no trimming (in version 1.06, prior to version 1.06, 0 or undef means no trimming) =head2 trimdata Parameters: $hashref or $arrayref $trimflag (optional, see Notes) Example: trimdata($datahash); # using the default flag Function: recursively process all attributes of a hash/array hybrid and get rid of any arrayref that points to one-element arrays (trims data structure) depending on the optional flag. Returns: none - trimming happenes in-place Notes: This function is useful to compact a data structure produced by Bio::ASN1::EntrezGene::parse. The acceptable values for $trimopt include: 1 - trim as much as possible 2 (or 0, undef) - trim to an easy-to-use structure 3 - no trimming (in version 1.06, prior to version 1.06, 0 or undef means no trimming) =head2 fh Parameters: $filehandle (optional) Example: trimdata($datahash); # using the default flag Function: getter/setter for file handle Returns: file handle for current file being parsed. Notes: Use with care! Line number report would not be corresponding to file's line number if seek operation is performed on the file handle! =head2 rawdata Parameters: none Example: my $data = $parser->rawdata(); Function: Get the entrez gene data file that was just parsed Returns: a string containing the ASN1-formatted Entrez Gene record Notes: Must first parse a record then call this function! Could be useful in interpreting line number value in error report (if user did a seek on file handle right before parsing call) =head1 INTERNAL METHODS =head2 _parse NCBI's Apr 05, 2005 format change forced much usage of lookahead, which would for sure slows parser down. But can't code efficiently without it. =head1 PREREQUISITE None. =head1 INSTALLATION Bio::ASN1::EntrezGene package can be installed & tested as follows: perl Makefile.PL make make test make install =head1 SEE ALSO The parse_entrez_gene_example.pl script included in this package (please see the Bio-ASN1-EntrezGene-x.xx/examples directory) is a very important and near-complete demo on using this module to extract all data items from Entrez Gene records. Do check it out because in fact, this script took me about 3-4 times more time to make for my project than the parser V1.0 itself. Note that the example script was edited to leave out stuff specific to my internal project. For details on various parsers I generated for Entrez Gene, example scripts that uses/benchmarks the modules, please see L. Those other parsers etc. are included in V1.05 download. =head1 CITATION Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190. =head1 OPERATION SYSTEMS SUPPORTED Any OS that Perl runs on. =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-asn1-entrezgene/issues =head1 AUTHOR Dr. Mingyi Liu =head1 COPYRIGHT This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute. This software is available under the same terms as the perl 5 programming language system itself. =cut SeqIO000755000765000024 013352317004 17146 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bioentrezgene.pm100644000765000024 12301113352317004 22050 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/SeqIOpackage Bio::SeqIO::entrezgene; $Bio::SeqIO::entrezgene::VERSION = '1.73'; use utf8; use strict; use warnings; # ABSTRACT: Entrez Gene ASN1 parser # AUTHOR: Stefan Kirov # OWNER: Stefan Kirov # CONTRIBUTOR: Hilmar Lapp # LICENSE: Perl_5 use Bio::ASN1::EntrezGene; use Bio::Seq; use Bio::Species; use Bio::Annotation::SimpleValue; use Bio::Annotation::DBLink; use Bio::Annotation::Comment; use Bio::SeqFeature::Generic; use Bio::Annotation::Reference; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use Bio::Cluster::SequenceFamily; #use Bio::Ontology::Ontology; Relationships.... later use Bio::Ontology::Term; use Bio::Annotation::OntologyTerm; use Data::Dumper; use base qw(Bio::SeqIO); %main::eg_to_ll = ( 'Official Full Name' => 'OFFICIAL_GENE_NAME', 'chromosome' => 'CHR', 'cyto' => 'MAP', 'Official Symbol' => 'OFFICIAL_SYMBOL' ); @main::egonly = keys %main::eg_to_ll; # We define $xval and some other variables so we don't have # to pass them as arguments my ( $seq, $ann, $xval, %seqcollection, $buf ); sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys $self->{_debug} = $param{-debug} || 'off'; $self->{_locuslink} = $param{-locuslink} || 'no'; $self->{_service_record} = $param{-service_record} || 'no'; $self->{_parser} = Bio::ASN1::EntrezGene->new( file => $param{-file} ); #Instantiate the low level parser here (it is -file in Bioperl #-should tell M.) #$self->{_parser}->next_seq; #First empty record- bug in Bio::ASN::Parser } sub next_seq { my $self = shift; my $value = $self->{_parser}->next_seq(1); # $value contains data structure for the # record being parsed. 2 indicates the recommended # trimming mode of the data structure #I use 1 as I prefer not to descend into size 0 arrays return unless ($value); my $debug = $self->{_debug}; $self->{_ann} = Bio::Annotation::Collection->new(); $self->{_currentann} = Bio::Annotation::Collection->new(); my @alluncaptured; # parse the entry #my @keys=keys %{$value}; obsolete $xval = $value->[0]; return Bio::Seq->new( -id => 'Generif service record', -seq => '' ) if ( ( $self->{_service_record} ne 'yes' ) && ( $xval->{gene}->{desc} =~ /record to support submission of generifs for a gene not in entrez/i ) ); #Basic data #$xval->{summary}=~s/\n//g; $seq = Bio::Seq->new( -display_id => $xval->{gene}{locus}, -accession_number => $xval->{'track-info'}{geneid}, -desc => $xval->{summary} ); #Source data here $self->_add_to_ann( $xval->{'track-info'}->{status}, 'Entrez Gene Status' ); my $lineage = $xval->{source}{org}{orgname}{lineage}; $lineage =~ s/[\s\n]//g; my ( $comp, @lineage ); while ($lineage) { ( $comp, $lineage ) = split( /;/, $lineage, 2 ); unshift @lineage, $comp; } unless ( exists( $xval->{source}{org}{orgname}{name}{binomial} ) ) { shift @lineage; my ( $gen, $sp ) = split( /\s/, $xval->{source}{org}{taxname} ); if ( ($sp) && ( $sp ne '' ) ) { if ( $gen =~ /plasmid/i ) { $sp = $gen . $sp; } unshift @lineage, $sp; } else { unshift @lineage, 'unknown'; } } else { my $sp = $xval->{source}{org}{orgname}{name}{binomial}{species}; if ( ($sp) && ( $sp ne '' ) ) { my ( $spc, $strain ) = split( 'sp.', $sp ); #Do we need strain? $spc =~ s/\s//g; if ( ($spc) && ( $spc ne '' ) ) { unshift @lineage, $spc; } else { unshift @lineage, 'unknown'; } } else { unshift @lineage, 'unknown'; } } #print Dumper($xval->{source}{org}); my $ncbiid; if ( ref( $xval->{source}{org}{db} ) eq 'ARRAY' ) { foreach my $taxonomy ( @{ $xval->{source}{org}{db} } ) { if ( lc( $taxonomy->{db} ) eq 'taxon' ) { $ncbiid = $taxonomy->{tag}{id}; } else { push @alluncaptured, $taxonomy; } delete $xval->{source}{org}{db}; } } $ncbiid = $ncbiid || $xval->{source}{org}{db}{tag}{id}; my $s1 = shift @lineage; my $s2 = shift @lineage; my $specie = Bio::Species->new( -classification => [ $s1, $s2 ], -ncbi_taxid => $ncbiid ); $specie->common_name( $xval->{source}{org}{common} ); if ( exists( $xval->{source}->{subtype} ) && ( $xval->{source}->{subtype} ) ) { if ( ref( $xval->{source}->{subtype} ) eq 'ARRAY' ) { foreach my $subtype ( @{ $xval->{source}->{subtype} } ) { $self->_add_to_ann( $subtype->{name}, $subtype->{subtype} ); } } else { $self->_add_to_ann( $xval->{source}->{subtype}->{name}, $xval->{source}->{subtype}->{subtype} ); } } #Synonyms if ( ref( $xval->{gene}->{syn} ) eq 'ARRAY' ) { foreach my $symsyn ( @{ $xval->{gene}->{syn} } ) { $self->_add_to_ann( $symsyn, 'ALIAS_SYMBOL' ); } } else { $self->_add_to_ann( $xval->{gene}->{syn}, 'ALIAS_SYMBOL' ) if ( $xval->{gene}->{syn} ); } #COMMENTS (STS not dealt with yet) if ( exists( $xval->{comments} ) ) { if ( ref( $xval->{comments} ) eq 'ARRAY' ) { for my $i ( 0 .. $#{ $xval->{comments} } ) { $self->{_current} = $xval->{comments}->[$i]; push @alluncaptured, $self->_process_all_comments(); } } else { $self->{_current} = $xval->{comments}; push @alluncaptured, $self->_process_all_comments(); } } #Gene if ( exists( $xval->{gene}->{db} ) ) { if ( ref( $xval->{gene}->{db} ) eq 'ARRAY' ) { foreach my $genedb ( @{ $xval->{gene}->{db} } ) { my $id = exists( $genedb->{tag}->{id} ) ? $genedb->{tag}->{id} : $genedb->{tag}->{str}; $self->_add_to_ann( $id, $genedb->{db} ); } } else { my $id = ( $xval->{gene}->{db}->{tag}->{id} ) ? $xval->{gene}->{db}->{tag}->{id} : $xval->{gene}->{db}->{tag}->{str}; $self->_add_to_ann( $id, $xval->{gene}->{db}->{db} ); } $self->_add_to_ann( $xval->{gene}->{'locus-tag'}, 'LOCUS_SYNONYM' ); delete $xval->{gene}->{db} unless ( $debug eq 'off' ); } #LOCATION To do: uncaptured stuff if ( exists( $xval->{location} ) ) { if ( ref( $xval->{location} ) eq 'ARRAY' ) { foreach my $loc ( @{ $xval->{location} } ) { $self->_add_to_ann( $loc->{'display-str'}, $loc->{method}->{'map-type'} ); } } else { $self->_add_to_ann( $xval->{location}->{'display-str'}, $xval->{location}->{method}->{'map-type'} ); } delete $xval->{location} unless ( $debug eq 'off' ); } #LOCUS if ( ref( $xval->{locus} ) eq 'ARRAY' ) { foreach my $locus ( @{ $xval->{locus} } ) { $self->{_current} = $locus; push @alluncaptured, $self->_process_locus(); } } else { push @alluncaptured, $self->_process_locus( $xval->{locus} ); } #Homology my @homologies; # Sometimes there are multiple entries if (ref $xval->{homology} eq 'ARRAY') { @homologies = @{ $xval->{homology} }; } else { push @homologies, $xval->{homology}; } foreach my $homology (@homologies) { my ( $uncapt, $hom, $anchor ) = _process_src( $homology->{source} ); foreach my $homann (@$hom) { $self->{_ann}->add_Annotation( 'dblink', $homann ); } push @alluncaptured, $uncapt; } #Index terms if ( ( exists( $xval->{'xtra-index-terms'} ) ) && ( $xval->{'xtra-index-terms'} ) ) { if ( ref( $xval->{'xtra-index-terms'} ) eq 'ARRAY' ) { foreach my $term ( @{ $xval->{'xtra-index-terms'} } ) { $self->_add_to_ann( $term, 'Index terms' ); } } else { $self->_add_to_ann( $xval->{'xtra-index-terms'}, 'Index terms' ); } } #PROPERTIES my @prop; if ( exists( $xval->{properties} ) ) { if ( ref( $xval->{properties} ) eq 'ARRAY' ) { foreach my $property ( @{ $xval->{properties} } ) { push @alluncaptured, $self->_process_prop($property); } } else { push @alluncaptured, $self->_process_prop( $xval->{properties} ); } } $seq->annotation( $self->{_ann} ); $seq->species($specie); my @seqs; foreach my $key ( keys %seqcollection ) { #Optimize this, no need to go through hash? push @seqs, @{ $seqcollection{$key} }; } my $cluster = Bio::Cluster::SequenceFamily->new( -family_id => $seq->accession_number, -description => "Entrez Gene " . $seq->accession_number, -members => \@seqs ); #Our EntrezGene object #clean unless ( $debug eq 'off' ) { delete $xval->{homology}->{source}; delete( $xval->{summary} ); delete( $xval->{'track-info'} ); delete( $xval->{gene}{locus} ); delete( $xval->{source}{org}{orgname}{lineage} ); delete $xval->{source}{org}{orgname}{name}{binomial}{species}; delete $xval->{gene}{syn}; delete $xval->{source}->{subtype}; delete $xval->{comments}; delete $xval->{properties}; delete $xval->{'xtra-index-terms'}; delete $xval->{status}; } push @alluncaptured, $xval; undef %seqcollection; $seq->annotation( _backcomp_ll( $self->{_ann} ) ) if ( $self->{_locuslink} eq 'convert' ); #Fix this! return wantarray ? ( $seq, $cluster, \@alluncaptured ) : $seq; #Hilmar's suggestion } sub _process_refseq { my $self = shift; my $products = shift; my $ns = shift; my $iter = shift; $iter++; my $pid; my ( @uncaptured, @products ); if ( ref($products) eq 'ARRAY' ) { @products = @{$products}; } else { push @products, $products; } foreach my $product (@products) { if ( ( ref($product) eq 'ARRAY' ) && ( $#{$product} > -1 ) ) { $self->_process_refseq( $product, $ns, $iter ); next; } if ( ( exists( $product->{products} ) && ( !exists( $product->{accession} ) ) ) ) { $self->_process_refseq( $product->{products}, $ns ); next; } if ( ( exists( $product->{seqs}->{whole}->{gi} ) ) && ( ref( $product->{seqs}->{whole}->{gi} ) eq 'ARRAY' ) ) { $product->{seqs}->{whole}->{gi} = $product->{seqs}->{whole}->{gi}->[0]; } #Lose some data if ( ( exists( $product->{seqs}->{whole}->{gi} ) ) || ( exists( $product->{accession} ) ) ) { #Minimal data required my $cann = Bio::Annotation::Collection->new(); $pid = $product->{accession}; my $authority = exists( $product->{type} ) ? $product->{type} : $product->{heading}; my $nseq = Bio::Seq->new( -accession_number => $product->{seqs}->{whole}->{gi}, -display_id => $product->{accession}, -authority => $authority, -namespace => $ns ); if ( exists( $product->{source} ) && ( $product->{source} ) ) { if ( ( !defined( $nseq->authority ) ) && ( exists( $product->{source}->{src} ) ) && ( exists( $product->{source}->{src}->{db} ) ) ) { $nseq->authority( $product->{source}->{src}->{db} ); } my ( $uncapt, $allann ) = _process_src( $product->{source} ); push @uncaptured, $uncapt; delete $product->{source}; foreach my $annotation ( @{$allann} ) { $cann->add_Annotation( 'dblink', $annotation ); } } delete $product->{seqs}->{whole}->{gi}; delete $product->{accession}; delete $product->{source}; delete $product->{heading}; my ( $uncapt, $ann, $cfeat ) = $self->_process_comments( $product->{comment} ) if ( exists( $product->{comment} ) ); push @uncaptured, $uncapt; foreach my $feat ( @{$cfeat} ) { $nseq->add_SeqFeature($feat); } if ( exists( $product->{products} ) && ( $product->{products} ) ) { my ( $uncapt, $prodid ) = $self->_process_refseq( $product->{products} ); push @uncaptured, $uncapt; my $simann = Bio::Annotation::SimpleValue->new( -value => $prodid, -tagname => 'product' ); $cann->add_Annotation($simann); } foreach my $key ( keys %$ann ) { foreach my $val ( @{ $ann->{$key} } ) { $cann->add_Annotation( $key, $val ); } } $nseq->annotation($cann); push @{ $seqcollection{seq} }, $nseq; } } undef @products; undef $products; return \@uncaptured, $pid, $seqcollection{seq}, $iter; } sub _process_links { my $self = shift; my $links = shift; my ( @annot, @uncapt ); if ( ref($links) eq 'ARRAY' ) { foreach my $link (@$links) { my ( $uncapt, $annot ) = _process_src( $link->{source} ) if ( exists( $link->{source} ) ); push @uncapt, $uncapt; foreach my $annotation (@$annot) { $self->{_ann}->add_Annotation( 'dblink', $annotation ); } } } else { my ( $uncapt, $annot ) = _process_src( $links->{source} ) if ( exists( $links->{source} ) ); push @uncapt, $uncapt; foreach my $annotation (@$annot) { $self->{_ann}->add_Annotation( 'dblink', $annotation ); } } return @uncapt; } sub _add_to_ann { #Highest level only my ( $self, $val, $tag ) = @_; # $val=~s/\n//g;#Low level EG parser leaves this so we take care of them here unless ($tag) { $self->warn( "No tagname for value $val, tag $tag " . $seq->id . "\n" ); return; } my $simann = Bio::Annotation::SimpleValue->new( -value => $val, -tagname => $tag ); $self->{_ann}->add_Annotation($simann); } sub _process_comments { my $self = shift; my $prod = shift; my ( %cann, @feat, @uncaptured, @comments, @sfann ); if ( ( ref($prod) eq 'HASH' ) && ( exists( $prod->{comment} ) ) ) { $prod = $prod->{comment}; } if ( ref($prod) eq 'ARRAY' ) { @comments = @{$prod}; } else { push @comments, $prod; } my $i = 0; for my $comm (@comments) { # Each comments is a hash reference $self->throw("Comment not a hash reference") unless ref($comm) eq 'HASH'; my ( $desc, $nfeat, $add, @ann, @comm ); my $heading = $comm->{heading} || 'description'; if ( !exists( $comm->{comment} ) ) { if ( ( exists( $comm->{type} ) ) && ( $comm->{type} ) && ( $self->{_current_heading} ) ) { $comm->{type} = $self->{_current_heading}; } if ( ( exists( $comm->{source} ) ) && ( exists( $comm->{type} ) ) && ( exists( $comm->{text} ) ) && ( $comm->{type} ne 'comment' ) ) { my ( $uncapt, $annot, $anchor ) = _process_src( $comm->{source} ); my $cann = shift(@$annot); if ( defined $cann ) { $cann->optional_id( $comm->{text} ); $cann->authority( $comm->{type} ); $cann->version( $comm->{version} ); push @sfann, $cann; } } } while (ref($comm) eq 'HASH' && ( exists( $comm->{comment} ) ) && ( $comm->{comment} ) ) { if ( ( exists( $comm->{source} ) ) && ( $comm->{source} ) ) { my ( $uncapt, $allann, $anchor ) = _process_src( $comm->{source} ); if ($allann) { delete $comm->{source}; push @uncaptured, $uncapt; foreach my $annotation ( @{$allann} ) { if ( $annotation->{_anchor} ) { $desc .= $annotation->{_anchor} . ' '; } $annotation->optional_id($heading); push @sfann, $annotation; push @{ $cann{'dblink'} }, $annotation; } } } $comm = $comm->{comment}; if ( ref($comm) eq 'ARRAY' ) { @comm = @{$comm}; } else { push @comm, $comm if ($comm); } foreach my $ccomm (@comm) { next unless ($ccomm); if ( exists( $ccomm->{source} ) ) { my ( $uncapt, $allann, $anchor ) = _process_src( $ccomm->{source} ); if ($allann) { @sfann = @{$allann}; delete $ccomm->{source}; push @uncaptured, $uncapt; } } $ccomm = $ccomm->{comment} if ( exists( $ccomm->{comment} ) ); #Alice in Wonderland??? my @loc; if ($ccomm) { if ( ref($ccomm) eq 'ARRAY' ) { @loc = @{$ccomm}; } else { push @loc, $ccomm; } } foreach my $loc (@loc) { if ( ( exists( $loc->{text} ) ) && ( $loc->{text} =~ /Location/i ) ) { my ( $l1, $rest ) = split( /-/, $loc->{text} ); $l1 =~ s/\D//g; $rest =~ s/^\s//; my ( $l2, $scorestr ) = split( /\s/, $rest, 2 ); my ( $scoresrc, $score ); if (defined $scorestr) { my ( $scoresrc, $score ) = split( /:/, $scorestr ); $score =~ s/\D//g; } my ( %tags, $tag ); unless ($l1) { next; } $nfeat = Bio::SeqFeature::Generic->new( -start => $l1, -end => $l2, -strand => $tags{strand}, -source => $loc->{type}, -seq_id => $desc, -primary => $heading, -score => $score, -tag => { score_src => $scoresrc } ); my $sfeatann = Bio::Annotation::Collection->new(); foreach my $sfann (@sfann) { $sfeatann->add_Annotation( 'dblink', $sfann ); } undef @sfann; $nfeat->annotation($sfeatann) ; #Thus the annotation will be available both in the seq and seqfeat? push @feat, $nfeat; delete $loc->{text}; delete $loc->{type}; } elsif ( exists( $loc->{label} ) ) { my $simann = Bio::Annotation::SimpleValue->new( -value => $loc->{text}, -tagname => $loc->{label} ); delete $loc->{text}; delete $loc->{label}; push @{ $cann{'simple'} }, $simann; push @uncaptured, $loc; } elsif ( exists( $loc->{text} ) ) { my $simann = Bio::Annotation::SimpleValue->new( -value => $loc->{text}, -tagname => $heading ); delete $loc->{text}; push @{ $cann{'simple'} }, $simann; push @uncaptured, $loc; } } } #Bit clumsy but that's what we get from the low level parser } $i++; } if (@sfann) { push @{ $cann{'dblink'} }, @sfann; } #Annotation that is not location specific, for example phenotype #undef $self->{_current_heading}; return \@uncaptured, \%cann, \@feat; } sub _process_src { my $src = shift; #Trick we do because sometimes we have an array ref my ( @ann, $anch, @uncapt ); if ( ref($src) eq 'ARRAY' ) { foreach my $msrc (@$src) { my ( $uncapt, $ann, $anchor ) = _process_src($msrc); push @ann, @$ann; push @uncapt, $uncapt; $anch = $anchor; } return \@uncapt, \@ann, $anch; } return unless ( exists( $src->{src}->{tag} ) ); #my $t0=new Benchmark my $db = $src->{src}->{db}; delete $src->{src}->{db}; my $anchor = $src->{anchor} || ''; delete $src->{anchor}; my $url; if ( exists( $src->{url} ) && ( $src->{url} ) ) { $url = $src->{url}; $url =~ s/\n//g; delete $src->{url}; } if ( ( exists( $src->{src}->{tag}->{str} ) ) && ( $src->{src}->{tag}->{str} ) ) { my @sq = split( /[,;]/, $src->{src}->{tag}->{str} ); delete $src->{src}->{tag}; foreach my $id (@sq) { $id =~ s/\n//g; undef $anchor if ( $anchor eq 'id' ); my $simann = Bio::Annotation::DBLink->new( -database => $db, -primary_id => $id, -authority => $src->{heading} ); $simann->url($url) if ($url); #DBLink should have URL! push @ann, $simann; } } else { my $id = $src->{src}->{tag}->{id} || ''; delete $src->{src}->{tag}; undef $anchor if ( $anchor eq 'id' ); $id =~ s/\n//g; my $simann = Bio::Annotation::DBLink->new( -database => $db, -primary_id => $id, -authority => $src->{heading} ); if ($anchor) { $simann->{_anchor} = $anchor; $simann->optional_id($anchor); } $simann->url($url) if ($url); #DBLink should have URL! push @ann, $simann; } return $src, \@ann, $anchor; } sub _add_references { my $self = shift; my $refs = shift; if ( ref($refs) eq 'ARRAY' ) { foreach my $ref (@$refs) { my $refan = Bio::Annotation::Reference->new( -database => 'Pubmed', -primary_id => $ref ); $self->{_ann}->add_Annotation( 'Reference', $refan ); } } else { my $refan = Bio::Annotation::Reference->new( -database => 'Pubmed', -primary_id => $refs ); $self->{_ann}->add_Annotation( 'Reference', $refan ); } } #Should we do this at all if no seq coord are present? sub _process_locus { my $self = shift; my @uncapt; return $self unless ( exists( $self->{_current}->{accession} ) && ( $self->{_current}->{accession} ) ); my $gseq = Bio::Seq->new( -display_id => $self->{_current}->{accession}, -version => $self->{_current}->{version}, -accession_number => $self->{_current}->{seqs}->{'int'}->{id}->{gi}, -authority => $self->{_current}->{type}, -namespace => $self->{_current}->{heading} ); delete $self->{_current}->{accession}; delete $self->{_current}->{version}; delete $self->{_current}->{'int'}->{id}->{gi}; my ( $start, $end, $strand ); if ( exists( $self->{_current}->{seqs}->{'int'}->{from} ) ) { $start = $self->{_current}->{seqs}->{'int'}->{from}; delete $self->{_current}->{seqs}->{'int'}->{from}; $end = $self->{_current}->{seqs}->{'int'}->{to}; delete $self->{_current}->{seqs}->{'int'}->{to}; delete $self->{_current}->{seqs}->{'int'}->{strand}; $strand = $self->{_current}->{seqs}->{'int'}->{strand} eq 'minus' ? -1 : 1 if ( exists( $self->{_current}->{seqs}->{'int'}->{strand} ) ) ; #1 being default my $nfeat = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -strand => $strand, primary => 'gene location' ); $gseq->add_SeqFeature($nfeat); } my @products; if ( ref( $self->{_current}->{products} ) eq 'ARRAY' ) { @products = @{ $self->{_current}->{products} }; } else { push @products, $self->{_current}->{products}; } delete $self->{_current}->{products}; my $gstruct = Bio::SeqFeature::Gene::GeneStructure->new(); foreach my $product (@products) { my ( $tr, $uncapt ) = _process_products_coordinates( $product, $start, $end, $strand ); $gstruct->add_transcript($tr) if ($tr); undef $tr->{parent}; #Because of a cycleG push @uncapt, $uncapt; } $gseq->add_SeqFeature($gstruct); push @{ $seqcollection{genestructure} }, $gseq; return @uncapt; } sub _process_products_coordinates { my $coord = shift; my $start = shift || 0; #In case it is not known: should there be an entry at all? my $end = shift || 1; my $strand = shift || 1; return unless ( exists( $coord->{accession} ) ); my ( @coords, @uncapt ); my $transcript = Bio::SeqFeature::Gene::Transcript->new( -primary => $coord->{accession}, #Desc is actually non functional... -start => $start, -end => $end, -strand => $strand, -desc => $coord->{type} ); if ( ( exists( $coord->{'genomic-coords'}->{mix}->{'int'} ) ) || ( exists( $coord->{'genomic-coords'}->{'packed-int'} ) ) ) { @coords = exists( $coord->{'genomic-coords'}->{mix}->{'int'} ) ? @{ $coord->{'genomic-coords'}->{mix}->{'int'} } : @{ $coord->{'genomic-coords'}->{'packed-int'} }; foreach my $exon (@coords) { next unless ( exists( $exon->{from} ) ); my $exonobj = Bio::SeqFeature::Gene::Exon->new( -start => $exon->{from}, -end => $exon->{to}, -strand => $strand ); $transcript->add_exon($exonobj); delete $exon->{from}; delete $exon->{to}; delete $exon->{strand}; push @uncapt, $exon; } } my ( $prot, $uncapt ); if ( exists( $coord->{products} ) ) { my @products; # Sometimes there are multiple entries if (ref $coord->{products} eq 'ARRAY') { @products = @{ $coord->{products} }; } else { push @products, $coord->{products}; } foreach my $product (@products) { my ( $prot, $uncapt ) = _process_products_coordinates( $product, $start, $end, $strand ); $transcript->add_SeqFeature($prot); push @uncapt, $uncapt; } } return $transcript, \@uncapt; } sub _process_prop { my $self = shift; my $prop = shift; my @uncapt; if ( exists( $prop->{properties} ) ) { #Iterate if ( ref( $prop->{properties} ) eq 'ARRAY' ) { foreach my $propn ( @{ $prop->{properties} } ) { push @uncapt, $self->_process_prop($propn); } } else { push @uncapt, $self->_process_prop( $prop->{properties} ); } } unless ( ( exists( $prop->{heading} ) ) && ( $prop->{heading} eq 'GeneOntology' ) ) { $self->_add_to_ann( $prop->{text}, $prop->{label} ) if ( exists( $prop->{text} ) ); delete $prop->{text}; delete $prop->{label}; push @uncapt, $prop; return \@uncapt; } #Will do GO later if ( exists( $prop->{comment} ) ) { push @uncapt, $self->_process_go( $prop->{comment} ); } } sub _process_all_comments { my $self = shift; my $product = $self->{_current}; #Better without copying my @alluncaptured; my $heading = $product->{heading} if ( exists( $product->{heading} ) ); if ($heading) { #my $tx1=new Benchmark; delete $product->{heading}; CLASS: { if ( $heading =~ 'RefSeq Status' ) { #IN case NCBI changes slightly the spacing:-) $self->_add_to_ann( $product->{label}, 'RefSeq status' ); last CLASS; } if ( $heading =~ 'NCBI Reference Sequences' ) { #IN case NCBI changes slightly the spacing:-) if ( ( exists( $product->{comment} ) ) && ( !exists( $product->{products} ) ) ) { $product->{products} = $product->{comment}; } my @uncaptured = $self->_process_refseq( $product->{products}, 'refseq' ); push @alluncaptured, @uncaptured; last CLASS; } if ( ( $heading =~ 'Related Sequences' ) && ( exists( $product->{products} ) ) ) { #IN case NCBI changes slightly the spacing:-) my @uncaptured = $self->_process_refseq( $product->{products} ); push @alluncaptured, @uncaptured; last CLASS; } if ( ( $heading =~ 'Additional Links' ) && ( exists( $product->{comment} ) ) ) { #IN case NCBI changes slightly the spacing:-) push @alluncaptured, $self->_process_links( $product->{comment} ); last CLASS; } if ( $heading =~ 'LocusTagLink' ) { #IN case NCBI changes slightly the spacing:-) $self->_add_to_ann( $product->{source}->{src}->{tag}->{id}, $product->{source}->{src}->{db} ); last CLASS; } if ( ( $heading =~ 'Sequence Tagged Sites' ) && ( exists( $product->{comment} ) ) ) { #IN case NCBI changes slightly the spacing:-) push @alluncaptured, $self->_process_STS( $product->{comment} ); delete $product->{comment}; last CLASS; } if ( $heading =~ 'Pathways' ) { $self->{_current_heading} = 'Pathways'; last CLASS; } } # my $tx2=new Benchmark; # my $td= timediff($tx2, $tx1); #print "\t\t$heading:",timestr($td),"\n"; } if ( exists( $product->{type} ) && ( $product->{type} eq 'generif' ) ) { push @alluncaptured, $self->_process_grif($product); return @alluncaptured; #Maybe still process the comments? } if ( exists( $product->{refs} ) ) { $self->_add_references( $product->{refs}->{pmid} ); delete $product->{refs}->{pmid}; push @alluncaptured, $product; } if ( exists( $product->{comment} ) ) { my ( $uncapt, $allan, $allfeat ) = $self->_process_comments( $product->{comment} ); foreach my $key ( keys %$allan ) { foreach my $val ( @{ $allan->{$key} } ) { $self->{_ann}->add_Annotation( $key, $val ); } } delete $product->{refs}->{comment}; push @alluncaptured, $uncapt; } return @alluncaptured; } sub _process_STS { my $self = shift; my $comment = shift; my @comm; push @comm, ( ref($comment) eq 'ARRAY' ) ? @{$comment} : $comment; foreach my $product (@comm) { my $sts = Bio::Ontology::Term->new( -identifier => $product->{source}->{src}->{tag}->{id}, -name => $product->{source}->{anchor}, -comment => $product->{source}->{'post-text'} ); $sts->namespace( $product->{source}->{src}->{db} ); $sts->authority('STS marker'); my @alt; if ( exists( $product->{comment} ) ) { push @alt, ( ref( $product->{comment} ) eq 'ARRAY' ) ? @{ $product->{comment} } : $product->{comment}; foreach my $alt (@alt) { $sts->add_synonym( $alt->{text} ); } } my $annterm = Bio::Annotation::OntologyTerm->new(); $annterm->term($sts); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } sub _process_go { my $self = shift; my $comm = shift; my @comm; push @comm, ( ref($comm) eq 'ARRAY' ) ? @{$comm} : $comm; foreach my $comp (@comm) { my $category = $comp->{label}; if ( ref( $comp->{comment} ) eq 'ARRAY' ) { foreach my $go ( @{ $comp->{comment} } ) { my $term = _get_go_term( $go, $category ); my $annterm = Bio::Annotation::OntologyTerm->new( -tagname => 'Gene Ontology' ); $annterm->term($term); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } else { my $term = _get_go_term( $comp->{comment}, $category ); my $annterm = Bio::Annotation::OntologyTerm->new( -tagname => 'Gene Ontology' ); $annterm->term($term); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } } sub _process_grif { my $self = shift; my $grif = shift; if ( ( exists( $grif->{comment} ) ) && ( ref( $grif->{comment} ) eq 'ARRAY' ) ) { my @uncapt; foreach my $product ( @{ $grif->{comment} } ) { next unless ( exists( $product->{text} ) ); my $uproduct = $self->_process_grif($product); #$self->{_ann->add_Annotation($type,$grifobj); push @uncapt, $uproduct; } return \@uncapt; } if ( exists( $grif->{comment}->{comment} ) ) { $grif = $grif->{comment}; } my $ref = ( ref( $grif->{refs} ) eq 'ARRAY' ) ? shift @{ $grif->{refs} } : $grif->{refs}; my $refergene = ''; my $refdb = ''; my ( $obj, $type ); if ( $ref->{pmid} ) { if ( exists( $grif->{source} ) ) { #unfortunatrely we cannot put yet everything in $refergene = $grif->{source}->{src}->{tag}->{id}; $refdb = $grif->{source}->{src}->{db}; } my $grifobj = Bio::Annotation::Comment->new( -text => $grif->{text} ); $obj = Bio::Annotation::DBLink->new( -database => 'generif', -primary_id => $ref->{pmid} , #The pubmed id (at least the first one) which is a base for the conclusion -version => $grif->{version}, -optional_id => $refergene, -authority => $refdb ); $obj->comment($grifobj); $type = 'dblink'; } else { $obj = Bio::Annotation::SimpleValue->new( $grif->{text}, 'generif' ); $type = 'generif'; } delete $grif->{text}; delete $grif->{version}; delete $grif->{type}; delete $grif->{refs}; $self->{_ann}->add_Annotation( $type, $obj ); return $grif; } sub _get_go_term { my $go = shift; my $category = shift; my $refan = Bio::Annotation::Reference->new( #We expect one ref per GO -medline => $go->{refs}->{pmid}, -title => 'no title' ); my $term = Bio::Ontology::Term->new( -identifier => $go->{source}->{src}->{tag}->{id}, -name => $go->{source}->{anchor}, -definition => $go->{source}->{anchor}, -comment => $go->{source}->{'post-text'}, -version => $go->{version} ); $term->add_reference($refan); $term->namespace($category); return $term; } sub _backcomp_ll { my $ann = shift; my $newann = Bio::Annotation::Collection->new(); foreach my $tagmap ( keys %{ $ann->{_typemap}->{_type} } ) { next if ( grep( /$tagmap/, @main::egonly ) ); $newann->{_annotation}->{$tagmap} = $ann->{_annotation}->{$tagmap}; } $newann->{_typemap}->{_type} = $ann->{_typemap}->{_type}; foreach my $ftype ( keys %main::eg_to_ll ) { my $newkey = $main::eg_to_ll{$ftype}; $newann->{_annotation}->{$newkey} = $ann->{_annotation}->{$ftype}; $newann->{_typemap}->{_type}->{$newkey} = 'Bio::Annotation::SimpleValue'; delete $newann->{_typemap}->{_type}->{$ftype}; $newann->{_annotation}->{$newkey}->[0]->{tagname} = $newkey; } foreach my $dblink ( @{ $newann->{_annotation}->{dblink} } ) { next unless ( $dblink->{_url} ); my $simann = Bio::Annotation::SimpleValue->new( -value => $dblink->{_url}, -tagname => 'URL' ); $newann->add_Annotation($simann); } return $newann; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser =head1 VERSION version 1.73 =head1 SYNOPSIS use Bio::SeqIO; # don't instantiate directly - instead do my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file); my $gene = $seqio->next_seq; =head1 DESCRIPTION This is EntrezGene ASN bioperl parser. It is built on top of L, a low level ASN parser built by Mingyi Liu (L). The easiest way to use it is shown above. You will get most of the Entrez Gene annotation such as gene symbol, gene name and description, accession numbers associated with the gene, etc. Almost all of these are given as L objects. If you need all the data do: my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file, -debug => 'on' ); my ($gene,$genestructure,$uncaptured) = $seqio->next_seq; The second variable returned, C<$genestructure>, is a L object. It contains all Refseqs and the genomic contigs that are associated with the particular gene. The third variable, C<$uncaptured>, is a reference to a plain array. You can also modify the output to allow back compatibility with the old LocusLink parser: my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file, -locuslink => 'convert'); The C<-debug> and C<-locuslink> options slow down the parser. Example code which looks for ontology terms: my $eio = new Bio::SeqIO(-file => $file, -format => 'entrezgene', -service_record => 'yes'); while (my $seq = $eio->next_seq) { my $gid = $seq->accession_number; foreach my $ot ($ann->get_Annotations('OntologyTerm')) { next if ($ot->term->authority eq 'STS marker'); # No STS markers my $evid = $ot->comment; $evid =~ s/evidence: //i; my @ref = $ot->term->get_references; my $id = $ot->identifier; my $fid = 'GO:' . sprintf("%07u",$id); print join("\t",$gid, $ot->ontology->name, $ot->name, $evid, $fid, @ref?$ref[0]->medline:''), "\n"; } } =head1 _process_products_coordinates To do: =head1 _process_prop To do: process GO =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-asn1-entrezgene/issues =head1 AUTHOR Stefan Kirov =head1 COPYRIGHT This software is copyright (c) by Stefan Kirov . This software is available under the same terms as the perl 5 programming language system itself. =cut entrezgene_bug3453.dat100644000765000024 51220313352317004 22302 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/t/dataEntrezgene ::= { track-info { geneid 3581, status live, create-date std { year 1997, month 11, day 18 }, update-date std { year 2013, month 12, day 8, hour 11, minute 11, second 0 } }, type protein-coding, source { genome genomic, origin natural, org { taxname "Homo sapiens", common "human", db { { db "taxon", tag id 9606 } }, syn { "man" }, orgname { name binomial { genus "Homo", species "sapiens" }, lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo", gcode 1, mgcode 2, div "PRI", pgcode 0 } }, subtype { { subtype chromosome, name "X" }, { subtype chromosome, name "Y" } } }, gene { locus "IL9R", desc "interleukin 9 receptor", maploc "Xq28 and Yq12", db { { db "HGNC", tag id 6030 }, { db "Ensembl", tag str "ENSG00000124334" }, { db "HPRD", tag str "02052" }, { db "MIM", tag id 300007 }, { db "Vega", tag str "OTTHUMG00000022720" } }, syn { "CD129", "IL-9R" } }, prot { name { "interleukin-9 receptor", "IL-9 receptor" }, desc "interleukin-9 receptor" }, summary "The protein encoded by this gene is a cytokine receptor that specifically mediates the biological effects of interleukin 9 (IL9). The functional IL9 receptor complex requires this protein as well as the interleukin 2 receptor, gamma (IL2RG), a common gamma subunit shared by the receptors of many different cytokines. The ligand binding of this receptor leads to the activation of various JAK kinases and STAT proteins, which connect to different biologic responses. This gene is located at the pseudoautosomal regions of X and Y chromosomes. Genetic studies suggested an association of this gene with the development of asthma. Multiple pseudogenes on chromosome 9, 10, 16, and 18 have been described. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]", location { { display-str "Xq28 and Yq12", method map-type cyto } }, gene-source { src "LocusLink", src-int 3581, src-str2 "3581" }, locus { { type genomic, heading "Reference GRCh37.p13 Primary Assembly", label "chromosome Y reference GRCh37.p13 Primary Assembly", accession "NC_000024", version 9, seqs { int { from 59330251, to 59343487, strand plus, id gi 224589823 } }, products { { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_176786", version 1, genomic-coords { mix { int { from 59330251, to 59330457, strand plus, id gi 224589823 }, int { from 59334078, to 59334178, strand plus, id gi 224589823 }, int { from 59335552, to 59335689, strand plus, id gi 224589823 }, int { from 59336119, to 59336230, strand plus, id gi 224589823 }, int { from 59336354, to 59336525, strand plus, id gi 224589823 }, int { from 59337119, to 59337235, strand plus, id gi 224589823 }, int { from 59337948, to 59338149, strand plus, id gi 224589823 }, int { from 59338753, to 59338858, strand plus, id gi 224589823 }, int { from 59342486, to 59343487, strand plus, id gi 224589823 } } }, seqs { whole gi 29171683 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_789743", version 2, source { { src { db "CCDS", tag str "CCDS59180.1" }, anchor "CCDS59180.1" } }, genomic-coords { mix { int { from 59330414, to 59330457, strand plus, id gi 224589823 }, int { from 59334078, to 59334178, strand plus, id gi 224589823 }, int { from 59335552, to 59335689, strand plus, id gi 224589823 }, int { from 59336119, to 59336230, strand plus, id gi 224589823 }, int { from 59336354, to 59336525, strand plus, id gi 224589823 }, int { from 59337119, to 59337235, strand plus, id gi 224589823 }, int { from 59337948, to 59338149, strand plus, id gi 224589823 }, int { from 59338753, to 59338858, strand plus, id gi 224589823 }, int { from 59342486, to 59342522, strand plus, id gi 224589823 } } }, seqs { whole gi 388490122 } } } }, { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_002186", version 2, genomic-coords { mix { int { from 59330251, to 59330457, strand plus, id gi 224589823 }, int { from 59335576, to 59335689, strand plus, id gi 224589823 }, int { from 59336119, to 59336230, strand plus, id gi 224589823 }, int { from 59336347, to 59336525, strand plus, id gi 224589823 }, int { from 59337090, to 59337235, strand plus, id gi 224589823 }, int { from 59337948, to 59338149, strand plus, id gi 224589823 }, int { from 59338753, to 59338858, strand plus, id gi 224589823 }, int { from 59340193, to 59340277, strand plus, id gi 224589823 }, int { from 59342486, to 59343487, strand plus, id gi 224589823 } } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_002177", version 2, source { { src { db "CCDS", tag str "CCDS14771.4" }, anchor "CCDS14771.4" } }, genomic-coords { mix { int { from 59330430, to 59330457, strand plus, id gi 224589823 }, int { from 59335576, to 59335689, strand plus, id gi 224589823 }, int { from 59336119, to 59336230, strand plus, id gi 224589823 }, int { from 59336347, to 59336525, strand plus, id gi 224589823 }, int { from 59337090, to 59337235, strand plus, id gi 224589823 }, int { from 59337948, to 59338149, strand plus, id gi 224589823 }, int { from 59338753, to 59338858, strand plus, id gi 224589823 }, int { from 59340193, to 59340277, strand plus, id gi 224589823 }, int { from 59342486, to 59343079, strand plus, id gi 224589823 } } }, seqs { whole gi 29171682 } } } } } }, { type genomic, heading "Reference GRCh37.p13 Primary Assembly", label "chromosome X reference GRCh37.p13 Primary Assembly", accession "NC_000023", version 10, seqs { int { from 155227245, to 155240481, strand plus, id gi 224589822 } }, products { { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_176786", version 1, genomic-coords { mix { int { from 155227245, to 155227451, strand plus, id gi 224589822 }, int { from 155231072, to 155231172, strand plus, id gi 224589822 }, int { from 155232546, to 155232683, strand plus, id gi 224589822 }, int { from 155233113, to 155233224, strand plus, id gi 224589822 }, int { from 155233348, to 155233519, strand plus, id gi 224589822 }, int { from 155234113, to 155234229, strand plus, id gi 224589822 }, int { from 155234942, to 155235143, strand plus, id gi 224589822 }, int { from 155235747, to 155235852, strand plus, id gi 224589822 }, int { from 155239480, to 155240481, strand plus, id gi 224589822 } } }, seqs { whole gi 29171683 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_789743", version 2, source { { src { db "CCDS", tag str "CCDS59180.1" }, anchor "CCDS59180.1" } }, genomic-coords { mix { int { from 155227408, to 155227451, strand plus, id gi 224589822 }, int { from 155231072, to 155231172, strand plus, id gi 224589822 }, int { from 155232546, to 155232683, strand plus, id gi 224589822 }, int { from 155233113, to 155233224, strand plus, id gi 224589822 }, int { from 155233348, to 155233519, strand plus, id gi 224589822 }, int { from 155234113, to 155234229, strand plus, id gi 224589822 }, int { from 155234942, to 155235143, strand plus, id gi 224589822 }, int { from 155235747, to 155235852, strand plus, id gi 224589822 }, int { from 155239480, to 155239516, strand plus, id gi 224589822 } } }, seqs { whole gi 388490122 } } } }, { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_002186", version 2, genomic-coords { mix { int { from 155227245, to 155227451, strand plus, id gi 224589822 }, int { from 155232570, to 155232683, strand plus, id gi 224589822 }, int { from 155233113, to 155233224, strand plus, id gi 224589822 }, int { from 155233341, to 155233519, strand plus, id gi 224589822 }, int { from 155234084, to 155234229, strand plus, id gi 224589822 }, int { from 155234942, to 155235143, strand plus, id gi 224589822 }, int { from 155235747, to 155235852, strand plus, id gi 224589822 }, int { from 155237187, to 155237271, strand plus, id gi 224589822 }, int { from 155239480, to 155240481, strand plus, id gi 224589822 } } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_002177", version 2, source { { src { db "CCDS", tag str "CCDS14771.4" }, anchor "CCDS14771.4" } }, genomic-coords { mix { int { from 155227424, to 155227451, strand plus, id gi 224589822 }, int { from 155232570, to 155232683, strand plus, id gi 224589822 }, int { from 155233113, to 155233224, strand plus, id gi 224589822 }, int { from 155233341, to 155233519, strand plus, id gi 224589822 }, int { from 155234084, to 155234229, strand plus, id gi 224589822 }, int { from 155234942, to 155235143, strand plus, id gi 224589822 }, int { from 155235747, to 155235852, strand plus, id gi 224589822 }, int { from 155237187, to 155237271, strand plus, id gi 224589822 }, int { from 155239480, to 155240073, strand plus, id gi 224589822 } } }, seqs { whole gi 29171682 } } } } } }, { type genomic, heading "Reference assembly", label "RefSeqGene", accession "NG_013238", version 1, seqs { int { from 5000, to 18236, strand plus, id gi 261823945 } }, products { { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_002186", version 2, genomic-coords { mix { int { from 5000, to 5206, strand plus, id gi 261823945 }, int { from 10325, to 10438, strand plus, id gi 261823945 }, int { from 10868, to 10979, strand plus, id gi 261823945 }, int { from 11096, to 11274, strand plus, id gi 261823945 }, int { from 11839, to 11984, strand plus, id gi 261823945 }, int { from 12697, to 12898, strand plus, id gi 261823945 }, int { from 13502, to 13607, strand plus, id gi 261823945 }, int { from 14942, to 15026, strand plus, id gi 261823945 }, int { from 17235, to 18236, strand plus, id gi 261823945 } } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_002177", version 2, source { { src { db "CCDS", tag str "CCDS14771.4" }, anchor "CCDS14771.4" } }, genomic-coords { mix { int { from 5179, to 5206, strand plus, id gi 261823945 }, int { from 10325, to 10438, strand plus, id gi 261823945 }, int { from 10868, to 10979, strand plus, id gi 261823945 }, int { from 11096, to 11274, strand plus, id gi 261823945 }, int { from 11839, to 11984, strand plus, id gi 261823945 }, int { from 12697, to 12898, strand plus, id gi 261823945 }, int { from 13502, to 13607, strand plus, id gi 261823945 }, int { from 14942, to 15026, strand plus, id gi 261823945 }, int { from 17235, to 17828, strand plus, id gi 261823945 } } }, seqs { whole gi 29171682 } } } } } }, { type genomic, heading "Alternate CHM1_1.1", label "chromosome X alternate CHM1_1.1", accession "NC_018934", version 2, seqs { int { from 155138862, to 155152088, strand plus, id gi 528476524 } }, products { { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_176786", version 1, genomic-coords { mix { int { from 155138862, to 155139068, strand plus, id gi 528476524 }, int { from 155142688, to 155142788, strand plus, id gi 528476524 }, int { from 155144166, to 155144303, strand plus, id gi 528476524 }, int { from 155144733, to 155144844, strand plus, id gi 528476524 }, int { from 155144968, to 155145139, strand plus, id gi 528476524 }, int { from 155145733, to 155145849, strand plus, id gi 528476524 }, int { from 155146562, to 155146763, strand plus, id gi 528476524 }, int { from 155147367, to 155147472, strand plus, id gi 528476524 }, int { from 155151087, to 155152088, strand plus, id gi 528476524 } } }, seqs { whole gi 29171683 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_789743", version 2, genomic-coords { mix { int { from 155139025, to 155139068, strand plus, id gi 528476524 }, int { from 155142688, to 155142788, strand plus, id gi 528476524 }, int { from 155144166, to 155144303, strand plus, id gi 528476524 }, int { from 155144733, to 155144844, strand plus, id gi 528476524 }, int { from 155144968, to 155145139, strand plus, id gi 528476524 }, int { from 155145733, to 155145849, strand plus, id gi 528476524 }, int { from 155146562, to 155146763, strand plus, id gi 528476524 }, int { from 155147367, to 155147472, strand plus, id gi 528476524 }, int { from 155151087, to 155151123, strand plus, id gi 528476524 } } }, seqs { whole gi 388490122 } } } }, { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_002186", version 2, genomic-coords { mix { int { from 155138862, to 155139068, strand plus, id gi 528476524 }, int { from 155144190, to 155144303, strand plus, id gi 528476524 }, int { from 155144733, to 155144844, strand plus, id gi 528476524 }, int { from 155144961, to 155145139, strand plus, id gi 528476524 }, int { from 155145704, to 155145849, strand plus, id gi 528476524 }, int { from 155146562, to 155146763, strand plus, id gi 528476524 }, int { from 155147367, to 155147472, strand plus, id gi 528476524 }, int { from 155148808, to 155148892, strand plus, id gi 528476524 }, int { from 155151087, to 155152088, strand plus, id gi 528476524 } } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_002177", version 2, genomic-coords { mix { int { from 155139041, to 155139068, strand plus, id gi 528476524 }, int { from 155144190, to 155144303, strand plus, id gi 528476524 }, int { from 155144733, to 155144844, strand plus, id gi 528476524 }, int { from 155144961, to 155145139, strand plus, id gi 528476524 }, int { from 155145704, to 155145849, strand plus, id gi 528476524 }, int { from 155146562, to 155146763, strand plus, id gi 528476524 }, int { from 155147367, to 155147472, strand plus, id gi 528476524 }, int { from 155148808, to 155148892, strand plus, id gi 528476524 }, int { from 155151087, to 155151680, strand plus, id gi 528476524 } } }, seqs { whole gi 29171682 } } } } } }, { type genomic, heading "Alternate HuRef", label "chromosome X alternate HuRef", accession "AC_000155", version 1, seqs { int { from 143710175, to 143723406, strand plus, id gi 157734237 } }, products { { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_176786", version 1, genomic-coords { mix { int { from 143710175, to 143710381, strand plus, id gi 157734237 }, int { from 143714002, to 143714102, strand plus, id gi 157734237 }, int { from 143715480, to 143715617, strand plus, id gi 157734237 }, int { from 143716047, to 143716158, strand plus, id gi 157734237 }, int { from 143716282, to 143716453, strand plus, id gi 157734237 }, int { from 143717047, to 143717163, strand plus, id gi 157734237 }, int { from 143717876, to 143718077, strand plus, id gi 157734237 }, int { from 143718681, to 143718786, strand plus, id gi 157734237 }, int { from 143722405, to 143723406, strand plus, id gi 157734237 } } }, seqs { whole gi 29171683 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_789743", version 2, genomic-coords { mix { int { from 143710338, to 143710381, strand plus, id gi 157734237 }, int { from 143714002, to 143714102, strand plus, id gi 157734237 }, int { from 143715480, to 143715617, strand plus, id gi 157734237 }, int { from 143716047, to 143716158, strand plus, id gi 157734237 }, int { from 143716282, to 143716453, strand plus, id gi 157734237 }, int { from 143717047, to 143717163, strand plus, id gi 157734237 }, int { from 143717876, to 143718077, strand plus, id gi 157734237 }, int { from 143718681, to 143718786, strand plus, id gi 157734237 }, int { from 143722405, to 143722441, strand plus, id gi 157734237 } } }, seqs { whole gi 388490122 } } } }, { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_002186", version 2, genomic-coords { mix { int { from 143710175, to 143710381, strand plus, id gi 157734237 }, int { from 143715504, to 143715617, strand plus, id gi 157734237 }, int { from 143716047, to 143716158, strand plus, id gi 157734237 }, int { from 143716275, to 143716453, strand plus, id gi 157734237 }, int { from 143717018, to 143717163, strand plus, id gi 157734237 }, int { from 143717876, to 143718077, strand plus, id gi 157734237 }, int { from 143718681, to 143718786, strand plus, id gi 157734237 }, int { from 143720118, to 143720202, strand plus, id gi 157734237 }, int { from 143722405, to 143723406, strand plus, id gi 157734237 } } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_002177", version 2, genomic-coords { mix { int { from 143710354, to 143710381, strand plus, id gi 157734237 }, int { from 143715504, to 143715617, strand plus, id gi 157734237 }, int { from 143716047, to 143716158, strand plus, id gi 157734237 }, int { from 143716275, to 143716453, strand plus, id gi 157734237 }, int { from 143717018, to 143717163, strand plus, id gi 157734237 }, int { from 143717876, to 143718077, strand plus, id gi 157734237 }, int { from 143718681, to 143718786, strand plus, id gi 157734237 }, int { from 143720118, to 143720202, strand plus, id gi 157734237 }, int { from 143722405, to 143722998, strand plus, id gi 157734237 } } }, seqs { whole gi 29171682 } } } } } } }, properties { { type comment, label "Nomenclature", source { { anchor "HUGO Gene Nomenclature Committee" } }, properties { { type property, label "Official Symbol", text "IL9R" }, { type property, label "Official Full Name", text "interleukin 9 receptor" } } }, { type comment, heading "GeneOntology", source { { pre-text "Provided by", anchor "GOA", url "http://www.ebi.ac.uk/GOA/" } }, comment { { type comment, label "Function", comment { { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 4919 }, anchor "interleukin-9 receptor activity", post-text "evidence: TAS" } } } } }, { type comment, label "Process", comment { { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 8283 }, anchor "cell proliferation", post-text "evidence: TAS" } } }, { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 38113 }, anchor "interleukin-9-mediated signaling pathway", post-text "evidence: TAS" } } }, { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 7165 }, anchor "signal transduction", post-text "evidence: TAS" } } } } }, { type comment, label "Component", comment { { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 5615 }, anchor "extracellular space", post-text "evidence: TAS" } } }, { type comment, refs { pmid 1376929 }, source { { src { db "GO", tag id 5887 }, anchor "integral to plasma membrane", post-text "evidence: TAS" } } } } } } } }, homology { { type comment, heading "Mouse, Rat", source { { src { db "HomoloGene", tag id 37591 }, anchor "Map Viewer", url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=X&M APS=genes-r-org/rat-chr/human%3AX,genes-r-org/mouse-chr/human%3AX,genes-r-org/ human-chrX&query=e%3A3581[egene_id]+AND+gene[obj_type]&QSTR=il9r&cmd=focus&fil l=10", post-text "(chromosome X)" } } }, { type comment, heading "Mouse, Rat", source { { src { db "HomoloGene", tag id 37591 }, anchor "Map Viewer", url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=Y&M APS=genes-r-org/rat-chr/human%3AY,genes-r-org/mouse-chr/human%3AY,genes-r-org/ human-chrY&query=e%3A3581[egene_id]+AND+gene[obj_type]&QSTR=il9r&cmd=focus&fil l=10", post-text "(chromosome Y)" } } } }, comments { { type comment, heading "RefSeq Status", label "REVIEWED" }, { type comment, heading "Annotation Information", properties { { type property, label "Annotation category", text "partial on reference assembly" } } }, { type gene-group, heading "Related pseudogene(s)", source { { pre-text "5 found", anchor "Review record(s) in Gene" } } }, { type comment, refs { pmid 23638223, pmid 22638550, pmid 21371865, pmid 20673868, pmid 20595916, pmid 20503287, pmid 20452482, pmid 20424473, pmid 19723899, pmid 19692168, pmid 19401191, pmid 19258923, pmid 19139102, pmid 18829468, pmid 18633131, pmid 18339896, pmid 17919707, pmid 17703412, pmid 17207965, pmid 17192395, pmid 17083349, pmid 15621723, pmid 15591265, pmid 12477932, pmid 11868823, pmid 11588013, pmid 11418623, pmid 11160343, pmid 11039580, pmid 10657622, pmid 10655549, pmid 10642536, pmid 10486269, pmid 10329852, pmid 9535918, pmid 9002663, pmid 8756628, pmid 8666384, pmid 8193355, pmid 7718508, pmid 1376929 } }, { type comment, heading "NCBI Reference Sequences (RefSeq)", comment { { type comment, heading "RefSeqs maintained independently of Annotated Genomes", products { { type mRNA, heading "mRNA Sequence", accession "NM_002186", version 2, source { { src { db "Nucleotide", tag id 29171681 }, anchor "NM_002186" } }, seqs { whole gi 29171681 }, products { { type peptide, heading "Product", accession "NP_002177", version 2, source { { src { db "Protein", tag id 29171682 }, anchor "NP_002177", post-text "interleukin-9 receptor isoform 1 precursor" } }, seqs { whole gi 29171682 }, comment { { type other, heading "Related", source { { src { db "Ensembl", tag str "ENSP00000244174" } } } }, { type other, heading "UniProtKB", source { }, comment { { type other, source { { src { db "UniProtKB/Swiss-Prot", tag str "Q01113" }, anchor "Q01113" } } } } }, { type other, heading "Consensus CDS (CCDS)", source { { src { db "CCDS", tag str "CCDS14771.4" }, anchor "CCDS14771.4" } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMP00000024332" } } } } } } }, comment { { type comment, label "RefSeq Status", text "REVIEWED" }, { type comment, heading "Transcriptional Variant", comment { { type comment, text "Transcript Variant: This variant (1) represent the longer transcript and encodes the longer isoform (1)." } } }, { type other, heading "Source Sequence", source { { src { db "Nucleotide", tag str "BC025298,M84747" }, anchor "BC025298,M84747" } } }, { type other, heading "Related", source { { src { db "Ensembl", tag str "ENST00000244174" } } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMT00000058981" } } } } } }, { type mRNA, heading "mRNA Sequence", accession "NM_176786", version 1, source { { src { db "Nucleotide", tag id 29171683 }, anchor "NM_176786" } }, seqs { whole gi 29171683 }, products { { type peptide, heading "Product", accession "NP_789743", version 2, source { { src { db "Protein", tag id 388490122 }, anchor "NP_789743", post-text "interleukin-9 receptor isoform 2" } }, seqs { whole gi 388490122 }, comment { { type other, heading "Related", source { { src { db "Ensembl", tag str "ENSP00000358431" } } } }, { type other, heading "UniProtKB", source { }, comment { { type other, source { { src { db "UniProtKB/Swiss-Prot", tag str "Q01113" }, anchor "Q01113" } } } } }, { type other, heading "Consensus CDS (CCDS)", source { { src { db "CCDS", tag str "CCDS59180.1" }, anchor "CCDS59180.1" } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMP00000024331" } } } } } } }, comment { { type comment, label "RefSeq Status", text "REVIEWED" }, { type comment, heading "Transcriptional Variant", comment { { type comment, text "Transcript Variant: This variant (2) differs in the 5' and 3' UTR and has multiple coding region differences, compared to variant 1. Some of these differences result in translational frameshifts. The resulting isoform (2) has distinct N- and C-termini and is shorter than isoform 1." } } }, { type other, heading "Source Sequence", source { { src { db "Nucleotide", tag str "AJ271736,BC025298" }, anchor "AJ271736,BC025298" } } }, { type other, heading "Related", source { { src { db "Ensembl", tag str "ENST00000369423" } } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMT00000058980" } } } } } } }, comment { { type genomic, heading "RefSeqGene", accession "NG_013238", version 1, source { { src { db "Nucleotide", tag id 261823945 }, anchor "NG_013238" } }, seqs { int { from 5000, to 18236, strand plus, id gi 261823945 } } } } }, { type comment, heading "RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 105", products { { type genomic, heading "Reference GRCh37.p13 Primary Assembly", accession "NC_000023", version 10, source { { src { db "Nucleotide", tag id 224589822 } } }, seqs { int { from 155227245, to 155240481, strand plus, id gi 224589822 } } }, { type genomic, heading "Alternate HuRef", accession "AC_000155", version 1, source { { src { db "Nucleotide", tag id 157734237 } } }, seqs { int { from 143710175, to 143723406, strand plus, id gi 157734237 } } }, { type genomic, heading "Alternate CHM1_1.1", accession "NC_018934", version 2, source { { src { db "Nucleotide", tag id 528476524 } } }, seqs { int { from 155138862, to 155152088, strand plus, id gi 528476524 } } } } } } }, { type comment, heading "Related Sequences", products { { type genomic, heading "Genomic", accession "ABBA01028635", version 1, source { { src { db "Nucleotide", tag id 148163528 }, anchor "ABBA01028635" } }, seqs { int { from 28050, to 41281, strand plus, id gi 148163528 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AJ271736", version 1, source { { src { db "Nucleotide", tag id 8979791 }, anchor "AJ271736" } }, seqs { whole gi 8979791 }, products { { type peptide, accession "CAB96817", version 1, source { { src { db "Protein", tag id 8979793 }, anchor "CAB96817" } }, seqs { whole gi 8979793 } } } }, { type genomic, heading "Genomic", accession "AMYH02040904", version 1, source { { src { db "Nucleotide", tag id 511784226 }, anchor "AMYH02040904" } }, seqs { int { from 17496, to 30722, strand plus, id gi 511784226 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AY071830", version 1, source { { src { db "Nucleotide", tag id 18071671 }, anchor "AY071830" } }, seqs { whole gi 18071671 }, products { { type peptide, accession "AAL55435", version 1, source { { src { db "Protein", tag id 18071672 }, anchor "AAL55435" } }, seqs { whole gi 18071672 } } } }, { type genomic, heading "Genomic", accession "CH471247", version 1, source { { src { db "Nucleotide", tag id 71514074 }, anchor "CH471247" } }, seqs { whole gi 71514074 }, products { { type peptide, accession "EAW55884", version 1, source { { src { db "Protein", tag id 119576288 }, anchor "EAW55884" } }, seqs { whole gi 119576288 } }, { type peptide, accession "EAW55885", version 1, source { { src { db "Protein", tag id 119576289 }, anchor "EAW55885" } }, seqs { whole gi 119576289 } }, { type peptide, accession "EAW55886", version 1, source { { src { db "Protein", tag id 119576290 }, anchor "EAW55886" } }, seqs { whole gi 119576290 } } } }, { type genomic, heading "Genomic", accession "L39064", version 1, source { { src { db "Nucleotide", tag id 632992 }, anchor "L39064" } }, seqs { whole gi 632992 }, products { { type peptide, accession "AAC29513", version 1, source { { src { db "Protein", tag id 632993 }, anchor "AAC29513" } }, seqs { whole gi 632993 } } } }, { type genomic, heading "Genomic", accession "S71420", version 1, source { { src { db "Nucleotide", tag id 551360 }, anchor "S71420" } }, seqs { whole gi 551360 }, products { { type peptide, accession "AAD14081", version 1, source { { src { db "Protein", tag id 4261781 }, anchor "AAD14081" } }, seqs { whole gi 4261781 } } } }, { type mRNA, heading "mRNA", accession "AK303178", version 1, source { { src { db "Nucleotide", tag id 194381807 }, anchor "AK303178" } }, seqs { whole gi 194381807 }, products { { type peptide, accession "BAG64273", version 1, source { { src { db "Protein", tag id 194381808 }, anchor "BAG64273" } }, seqs { whole gi 194381808 } } } }, { type mRNA, heading "mRNA", accession "BC025298", version 1, source { { src { db "Nucleotide", tag id 22137637 }, anchor "BC025298" } }, seqs { whole gi 22137637 }, products { { type peptide, text "None" } } }, { type mRNA, heading "mRNA", accession "BC051337", version 1, source { { src { db "Nucleotide", tag id 30410903 }, anchor "BC051337" } }, seqs { whole gi 30410903 }, products { { type peptide, accession "AAH51337", version 1, source { { src { db "Protein", tag id 30410904 }, anchor "AAH51337" } }, seqs { whole gi 30410904 } } } }, { type mRNA, heading "mRNA", accession "M84747", version 1, source { { src { db "Nucleotide", tag id 184508 }, anchor "M84747" } }, seqs { whole gi 184508 }, products { { type peptide, accession "AAA58679", version 1, source { { src { db "Protein", tag id 184509 }, anchor "AAA58679" } }, seqs { whole gi 184509 } } } }, { type mRNA, heading "mRNA", accession "S71404", version 1, source { { src { db "Nucleotide", tag id 551356 }, anchor "S71404" } }, seqs { whole gi 551356 }, products { { type peptide, accession "AAB30844", version 2, source { { src { db "Protein", tag id 13236921 }, anchor "AAB30844" } }, seqs { whole gi 13236921 } } } }, { type other, text "None", products { { type peptide, accession "Q01113", version 3, source { { src { db "Protein", tag id 116242526 } }, { src { db "UniProtKB/Swiss-Prot", tag str "Q01113" } } }, seqs { whole gi 116242526 } } } }, { type other-genetic, heading "Synthetic", accession "HQ447710", version 1, source { { src { db "Nucleotide", tag id 312151365 }, anchor "HQ447710" } }, seqs { whole gi 312151365 }, products { { type peptide, accession "ADQ32195", version 1, source { { src { db "Protein", tag id 312151366 }, anchor "ADQ32195" } }, seqs { whole gi 312151366 } } } } } }, { type comment, heading "Additional Links", comment { { type comment, source { { src { db "Evidence Viewer", tag str "3581" }, anchor "Evidence Viewer", url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_167198.1&gene=IL9R&lid=3581&from=6145183&to=6158419" } } }, { type comment, source { { src { db "Evidence Viewer", tag str "3581" }, anchor "Evidence Viewer", url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_167206.1&gene=IL9R&lid=3581&from=296202&to=309438" } } }, { type comment, text "MIM", source { { src { db "MIM", tag id 300007 }, anchor "300007" } } }, { type comment, source { { src { db "AceView", tag id 3581 }, anchor "AceView", url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=g eneid&org=9606&l=3581" } } }, { type comment, text "IL9R @ LOVD", source { { src { db "IL9R", tag str "IL9R" }, anchor "IL9R", url "http://www.LOVD.nl/IL9R" } } }, { type comment, text "UCSC", source { { src { db "UCSC", tag str "UCSC" }, anchor "UCSC", url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= NM_176786" } } }, { type comment, source { { src { db "MGC", tag str "BC051337" }, anchor "MGC", url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC051337" } } }, { type comment, source { { src { db "HuGE Navigator", tag str "3581" }, anchor "HuGE Navigator", url "http://hugenavigator.net/HuGENavigator/huGEPedia.do?firstQu ery=IL9R&geneID=3581&typeOption=gene&which=2&pubOrderType=pubD&typeSubmit=GO&c heck=y" } } }, { type comment, source { { src { db "KEGG", tag str "hsa:3581" }, url "http://www.genome.jp/dbget-bin/www_bget?hsa:3581" } } }, { type comment, text "UniGene", xtra-properties { { tag "UNIGENE", value "Hs.406228" } }, source { { src { db "UniGene", tag str "Hs.406228" }, anchor "Hs.406228", url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=40 6228" } } } } }, { type generif, text "Our findings suggest that overexpression of IL-9R may contribute to the pathogenesis of diffuse large B-cell lymphoma", refs { pmid 23638223 }, create-date std { year 2013, month 11, day 30, hour 10, minute 1, second 0 }, update-date std { year 2013, month 11, day 30, hour 12, minute 36, second 0 } }, { type generif, text "One of the identified peptide sequences corresponded to a fragment of the human interleukin-9 receptor alpha (IL-9Ralpha).", refs { pmid 22638550 }, create-date std { year 2013, month 5, day 11, hour 10, minute 1, second 0 }, update-date std { year 2013, month 5, day 11, hour 10, minute 42, second 0 } }, { type generif, text "analysis of IL-9 and IL-9 receptor gene polymorphisms and atopic dermatitis in a Korean population", refs { pmid 21371865 }, create-date std { year 2011, month 7, day 23, hour 10, minute 1, second 0 }, update-date std { year 2011, month 7, day 23, hour 10, minute 31, second 0 } }, { type generif, text "There is an association of at least 2 X-chromosomal genes with rheumatoid arthritis: TIMP1 and IL9R.", refs { pmid 19723899 }, create-date std { year 2010, month 2, day 15, hour 11, minute 2, second 0 }, update-date std { year 2010, month 2, day 15, hour 11, minute 13, second 0 } }, { type generif, text "These results reveal a regulatory function for IFN-gamma and IL-10 on modulating the inducible IL-9Ralpha expression levels on peripheral blood neutrophils by T(H)2 cytokines.", refs { pmid 19401191 }, create-date std { year 2009, month 6, day 15, hour 11, minute 2, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "IL-9Ralpha and IL-2Rbeta homodimers efficiently mediate constitutive activation of ALL-associated JAK1 mutants.", refs { pmid 19139102 }, create-date std { year 2009, month 5, day 9, hour 10, minute 1, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)", refs { pmid 20595916, pmid 19258923 }, source { { src { db "HuGENet", tag str "3581.19258923" }, anchor "HuGENet" } }, create-date std { year 2009, month 3, day 25, hour 21, minute 36, second 0 }, update-date std { year 2009, month 3, day 25, hour 21, minute 36, second 0 } }, { type generif, text "Observational study of gene-disease association. (HuGE Navigator)", refs { pmid 20673868, pmid 20503287, pmid 20452482, pmid 20424473, pmid 19723899, pmid 19692168, pmid 17703412 }, source { { src { db "HuGENet", tag str "3581.17703412" }, anchor "HuGENet" } }, create-date std { year 2009, month 3, day 25, hour 21, minute 36, second 0 }, update-date std { year 2009, month 3, day 25, hour 21, minute 36, second 0 } }, { type generif, text "the preformed complexes between gamma c and IL-2Rbeta or IL-9Ralpha promote signaling by the JAK3 A572V mutant without ligand, identified in several human cancers.", refs { pmid 18829468 }, create-date std { year 2009, month 1, day 31, hour 10, minute 1, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)", refs { pmid 18633131 }, source { { src { db "HuGENet", tag str "3581.18633131" }, anchor "HuGENet" } }, create-date std { year 2008, month 9, day 24, hour 21, minute 30, second 0 }, update-date std { year 2008, month 9, day 24, hour 21, minute 30, second 0 } }, { type generif, text "primary ATL cells, via IL-9, support the action of IL-9Ralpha/CD14-expressing monocytes, which subsequently support the ex vivo spontaneous proliferation of malignant T cells", refs { pmid 18339896 }, create-date std { year 2008, month 7, day 12, hour 10, minute 1, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "IL-9R alpha was expressed on human tonsillar B cells, with an ability to transduce signals through activation of signal transducer and activator of transcription 3 and 5.", refs { pmid 17919707 }, create-date std { year 2008, month 2, day 9, hour 10, minute 1, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "Human bronchial epithelium expresses interleukin-9 receptors.", refs { pmid 11868823 }, create-date std { year 2007, month 8, day 25, hour 10, minute 2, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "Variants in the IL4RA gene alone may not exert any major influence on susceptibility to asthma-related diseases in childhood, but in combination with other genes, such as IL9R, IL4RA may be an important gene for disease susceptibility", refs { pmid 17083349 }, create-date std { year 2007, month 8, day 25, hour 10, minute 2, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "IL-9 and its receptor have roles in cell growth and malignant transformation of lymphoid cells associated with constitutive activation of the Jak/STAT pathway [review]", refs { pmid 15621723 }, create-date std { year 2007, month 8, day 25, hour 10, minute 2, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, text "variations in the IL9R gene may influence susceptibility to childhood wheezing and atopy, and data support the notion that different haplotypes may have sex specific influences", refs { pmid 15591265 }, create-date std { year 2007, month 8, day 25, hour 10, minute 2, second 0 }, update-date std { year 2010, month 1, day 21, hour 0, minute 0, second 0 } }, { type generif, heading "Interactions", comment { { type generif, text "Two-hybrid", refs { pmid 21988832 }, source { { src { db "BioGRID", tag id 109795 }, anchor "BioGRID" } }, comment { { type other, source { { src { db "BioGRID", tag id 109795 } } } }, { type other, source { { src { db "GeneID", tag id 8738 }, anchor "CRADD" }, { src { db "BioGRID", tag id 114275 } } } } }, create-date std { year 2013, month 4, day 7, hour 10, minute 36, second 0 }, update-date std { year 2013, month 12, day 8, hour 11, minute 11, second 0 } }, { type generif, text "Affinity Capture-Western; Two-hybrid", refs { pmid 10486269 }, source { { src { db "BioGRID", tag id 109795 }, anchor "BioGRID" } }, comment { { type other, source { { src { db "BioGRID", tag id 109795 } } } }, { type other, source { { src { db "GeneID", tag id 10524 }, anchor "KAT5" }, { src { db "BioGRID", tag id 115779 } } } } }, create-date std { year 2012, month 7, day 8, hour 10, minute 24, second 0 }, update-date std { year 2013, month 12, day 8, hour 11, minute 11, second 0 } }, { type generif, refs { pmid 10486269 }, source { { src { db "HPRD", tag str "02052" }, anchor "HPRD" } }, comment { { type peptide, source { { src { db "Protein", tag id 116242526 }, anchor "Q01113" } } }, { type peptide, source { { src { db "GeneID", tag id 10524 }, anchor "KAT5" }, { src { db "Protein", tag id 30923328 }, anchor "Q92993" } } } }, create-date std { year 2009, month 12, day 17, hour 15, minute 28, second 0 }, update-date std { year 2009, month 12, day 17, hour 15, minute 31, second 0 } }, { type generif, refs { pmid 10642536 }, source { { src { db "HPRD", tag str "02052" }, anchor "HPRD" } }, comment { { type peptide, source { { src { db "Protein", tag id 116242526 }, anchor "Q01113" } } }, { type peptide, source { { src { db "GeneID", tag id 7534 }, anchor "YWHAZ" }, { src { db "Protein", tag id 52000887 }, anchor "P63104" } } } }, create-date std { year 2009, month 12, day 17, hour 15, minute 28, second 0 }, update-date std { year 2009, month 12, day 17, hour 15, minute 31, second 0 } }, { type generif, refs { pmid 11418623 }, source { { src { db "HPRD", tag str "02052" }, anchor "HPRD" } }, comment { { type peptide, source { { src { db "Protein", tag id 116242526 }, anchor "Q01113" } } }, { type peptide, source { { src { db "GeneID", tag id 3561 }, anchor "IL2RG" }, { src { db "Protein", tag id 400048 }, anchor "P31785" } } } }, create-date std { year 2009, month 12, day 17, hour 15, minute 28, second 0 }, update-date std { year 2009, month 12, day 17, hour 15, minute 31, second 0 } }, { type generif, refs { pmid 8756628 }, source { { src { db "HPRD", tag str "02052" }, anchor "HPRD" } }, comment { { type peptide, source { { src { db "Protein", tag id 116242526 }, anchor "Q01113" } } }, { type peptide, source { { src { db "GeneID", tag id 3716 }, anchor "JAK1" }, { src { db "Protein", tag id 215274013 }, anchor "P23458" } } } }, create-date std { year 2009, month 12, day 17, hour 15, minute 28, second 0 }, update-date std { year 2009, month 12, day 17, hour 15, minute 31, second 0 } }, { type generif, refs { pmid 11588013 }, source { { src { db "HPRD", tag str "02052" }, anchor "HPRD" } }, comment { { type peptide, source { { src { db "Protein", tag id 116242526 }, anchor "Q01113" } } }, { type peptide, source { { src { db "GeneID", tag id 3578 }, anchor "IL9" }, { src { db "Protein", tag id 124362 }, anchor "P15248" } } } }, create-date std { year 2009, month 12, day 17, hour 15, minute 28, second 0 }, update-date std { year 2009, month 12, day 17, hour 15, minute 31, second 0 } }, { type generif, text "Affinity Capture-Western; Two-hybrid", refs { pmid 10642536 }, source { { src { db "BioGRID", tag id 109795 }, anchor "BioGRID" } }, comment { { type other, source { { src { db "BioGRID", tag id 109795 } } } }, { type other, source { { src { db "GeneID", tag id 7534 }, anchor "YWHAZ" }, { src { db "BioGRID", tag id 113366 } } } } }, create-date std { year 2008, month 12, day 23, hour 9, minute 6, second 0 }, update-date std { year 2013, month 12, day 8, hour 11, minute 11, second 0 } }, { type generif, text "Affinity Capture-Western", refs { pmid 8756628 }, source { { src { db "BioGRID", tag id 109795 }, anchor "BioGRID" } }, comment { { type other, source { { src { db "BioGRID", tag id 109795 } } } }, { type other, source { { src { db "GeneID", tag id 3716 }, anchor "JAK1" }, { src { db "BioGRID", tag id 109919 } } } } }, create-date std { year 2008, month 12, day 23, hour 9, minute 6, second 0 }, update-date std { year 2013, month 12, day 8, hour 11, minute 11, second 0 } } } }, { type comment, heading "Pathways", comment { { type comment, text "KEGG pathway: Cytokine-cytokine receptor interaction", source { { src { db "KEGG pathway", tag str "04060" }, anchor "04060", url "http://www.genome.jp/dbget-bin/show_pathway?hsa04060+3581" } } }, { type comment, text "KEGG pathway: Hematopoietic cell lineage", source { { src { db "KEGG pathway", tag str "04640" }, anchor "04640", url "http://www.genome.jp/dbget-bin/show_pathway?hsa04640+3581" } } }, { type comment, text "KEGG pathway: Jak-STAT signaling pathway", source { { src { db "KEGG pathway", tag str "04630" }, anchor "04630", url "http://www.genome.jp/dbget-bin/show_pathway?hsa04630+3581" } } } } }, { type comment, heading "Markers (Sequence Tagged Sites/STS)", comment { { type comment, source { { src { db "UniSTS", tag id 85806 }, anchor "RH69191", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 296037 }, anchor "ECD15020", post-text "(e-PCR)" } } } } }, { type comment, heading "Gene Location History", comment { { type comment, heading "Homo sapiens Annotation Release 105", comment { { type assembly, heading "GRCh37.p13", label "Reference", accession "GCF_000001405", version 25, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome X", accession "NC_000023", version 10, seqs { int { from 155227245, to 155240481, strand plus, id gi 224589822 } } }, { type genomic, label "chromosome Chromosome Y", accession "NC_000024", version 9, seqs { int { from 59330251, to 59343487, strand plus, id gi 224589823 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type genomic, label "chromosome Chromosome X", accession "AC_000155", version 1, seqs { int { from 143710175, to 143723406, strand plus, id gi 157734237 } } } } }, { type assembly, heading "CHM1_1.1", label "Alternate", accession "GCF_000306695", version 2, comment { { type genomic, label "chromosome Chromosome X", accession "NC_018934", version 2, seqs { int { from 155138862, to 155152088, strand plus, id gi 528476524 } } } } } } }, { type comment, heading "Homo sapiens Annotation Release 104", comment { { type assembly, heading "GRCh37.p10", label "Reference", accession "GCF_000001405", version 22, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome X", accession "NC_000023", version 10, seqs { int { from 155227245, to 155240481, strand plus, id gi 224589822 } } }, { type genomic, label "chromosome Chromosome Y", accession "NC_000024", version 9, seqs { int { from 59330251, to 59343487, strand plus, id gi 224589823 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type genomic, label "chromosome Chromosome X", accession "AC_000155", version 1, seqs { int { from 143710175, to 143723406, strand plus, id gi 157734237 } } } } }, { type assembly, heading "CHM1_1.0", label "Alternate", accession "GCF_000306695", version 1, comment { { type genomic, label "chromosome Chromosome X", accession "NC_018934", version 1, seqs { int { from 155094217, to 155107460, strand plus, id gi 409253441 } } } } } } }, { type comment, heading "Build 37.3", comment { { type assembly, heading "GRCh37.p5", label "Reference", accession "GCF_000001405", version 17, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome X", accession "NC_000023", version 10, seqs { int { from 155227245, to 155240481, strand plus, id gi 224589822 } } }, { type genomic, label "chromosome Chromosome Y", accession "NC_000024", version 9, seqs { int { from 59330251, to 59343487, strand plus, id gi 224589823 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000000025", version 1, comment { { type genomic, label "chromosome Chromosome X", accession "AC_000155", version 1, seqs { int { from 143710175, to 143723406, strand plus, id gi 157734237 } } } } } } } } } } } }, unique-keys { { db "HGNC", tag id 6030 }, { db "LocusID", tag id 3581 }, { db "MIM", tag id 300007 } }, xtra-index-terms { "LOC3581" } } Entrezgene ::= { track-info { geneid 56111, status live, create-date std { year 2000, month 7, day 13 }, update-date std { year 2013, month 12, day 3, hour 17, minute 40, second 0 } }, type protein-coding, source { genome genomic, origin natural, org { taxname "Homo sapiens", common "human", db { { db "taxon", tag id 9606 } }, syn { "man" }, orgname { name binomial { genus "Homo", species "sapiens" }, lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo", gcode 1, mgcode 2, div "PRI", pgcode 0 } }, subtype { { subtype chromosome, name "5" } } }, gene { locus "PCDHGA4", desc "protocadherin gamma subfamily A, 4", maploc "5q31", db { { db "HGNC", tag id 8702 }, { db "Ensembl", tag str "ENSG00000262576" }, { db "HPRD", tag str "09381" }, { db "MIM", tag id 606291 }, { db "Vega", tag str "OTTHUMG00000177593" } }, syn { "PCDH-GAMMA-A4" } }, prot { name { "protocadherin gamma-A4" }, desc "protocadherin gamma-A4" }, summary "This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]", location { { display-str "5q31", method map-type cyto } }, gene-source { src "LocusLink", src-int 56111, src-str2 "56111" }, locus { { type genomic, heading "Reference GRCh37.p13 Primary Assembly", label "chromosome 5 reference GRCh37.p13 Primary Assembly", accession "NC_000005", version 9, seqs { int { from 140734767, to 140892545, strand plus, id gi 224589817 } }, products { { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_018917", version 2, genomic-coords { mix { int { from 140734767, to 140737187, strand plus, id gi 224589817 }, int { from 140874373, to 140874431, strand plus, id gi 224589817 }, int { from 140884959, to 140885047, strand plus, id gi 224589817 }, int { from 140890513, to 140892545, strand plus, id gi 224589817 } } }, seqs { whole gi 14196466 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_061740", version 1, source { { src { db "CCDS", tag str "CCDS58979.1" }, anchor "CCDS58979.1" } }, genomic-coords { mix { int { from 140734767, to 140737187, strand plus, id gi 224589817 }, int { from 140874373, to 140874431, strand plus, id gi 224589817 }, int { from 140884959, to 140885047, strand plus, id gi 224589817 }, int { from 140890513, to 140890739, strand plus, id gi 224589817 } } }, seqs { whole gi 11056026 } } } }, { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_032053", version 1, genomic-coords { int { from 140734767, to 140737295, strand plus, id gi 224589817 } }, seqs { whole gi 14196467 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_114442", version 1, genomic-coords { int { from 140734767, to 140737229, strand plus, id gi 224589817 } }, seqs { whole gi 14196468 } } } } } }, { type genomic, heading "Reference assembly", label "genomic region", accession "NG_000012", version 2, seqs { int { from 65221, to 223175, strand plus, id gi 50284693 } }, products { { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_018917", version 3, genomic-coords { mix { int { from 65221, to 67817, strand plus, id gi 50284693 }, int { from 205003, to 205061, strand plus, id gi 50284693 }, int { from 215589, to 215677, strand plus, id gi 50284693 }, int { from 221143, to 223175, strand plus, id gi 50284693 } } }, seqs { whole gi 523567547 } }, { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_032053", version 2, genomic-coords { int { from 65221, to 67926, strand plus, id gi 50284693 } }, seqs { whole gi 523567549 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_061740", version 2, source { { src { db "CCDS", tag str "CCDS58979.1" }, anchor "CCDS58979.1" } }, genomic-coords { mix { int { from 65304, to 67817, strand plus, id gi 50284693 }, int { from 205003, to 205061, strand plus, id gi 50284693 }, int { from 215589, to 215677, strand plus, id gi 50284693 }, int { from 221143, to 221369, strand plus, id gi 50284693 } } }, seqs { whole gi 523567548 } }, { type peptide, heading "Reference", label "isoform 2 precursor", accession "NP_114442", version 2, genomic-coords { int { from 65304, to 67859, strand plus, id gi 50284693 } }, seqs { whole gi 523567550 } } } } } }, { type genomic, heading "Alternate CHM1_1.1", label "chromosome 5 alternate CHM1_1.1", accession "NC_018916", version 2, seqs { int { from 140167974, to 140325822, strand plus, id gi 528476642 } }, products { { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_018917", version 2, genomic-coords { mix { int { from 140167974, to 140170394, strand plus, id gi 528476642 }, int { from 140307638, to 140307696, strand plus, id gi 528476642 }, int { from 140318237, to 140318325, strand plus, id gi 528476642 }, int { from 140323790, to 140325822, strand plus, id gi 528476642 } } }, seqs { whole gi 14196466 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_061740", version 1, genomic-coords { mix { int { from 140167974, to 140170394, strand plus, id gi 528476642 }, int { from 140307638, to 140307696, strand plus, id gi 528476642 }, int { from 140318237, to 140318325, strand plus, id gi 528476642 }, int { from 140323790, to 140324016, strand plus, id gi 528476642 } } }, seqs { whole gi 11056026 } } } }, { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_032053", version 1, genomic-coords { int { from 140167974, to 140170502, strand plus, id gi 528476642 } }, seqs { whole gi 14196467 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_114442", version 1, genomic-coords { int { from 140167974, to 140170436, strand plus, id gi 528476642 } }, seqs { whole gi 14196468 } } } } } }, { type genomic, heading "Alternate HuRef", label "chromosome 5 alternate HuRef", accession "AC_000137", version 1, seqs { int { from 135879842, to 136037385, strand plus, id gi 157734151 } }, products { { type mRNA, heading "Reference", label "transcript variant 1", accession "NM_018917", version 2, genomic-coords { mix { int { from 135879842, to 135882262, strand plus, id gi 157734151 }, int { from 136019211, to 136019269, strand plus, id gi 157734151 }, int { from 136029799, to 136029887, strand plus, id gi 157734151 }, int { from 136035353, to 136037385, strand plus, id gi 157734151 } } }, seqs { whole gi 14196466 }, products { { type peptide, heading "Reference", label "isoform 1 precursor", accession "NP_061740", version 1, genomic-coords { mix { int { from 135879842, to 135882262, strand plus, id gi 157734151 }, int { from 136019211, to 136019269, strand plus, id gi 157734151 }, int { from 136029799, to 136029887, strand plus, id gi 157734151 }, int { from 136035353, to 136035579, strand plus, id gi 157734151 } } }, seqs { whole gi 11056026 } } } }, { type mRNA, heading "Reference", label "transcript variant 2", accession "NM_032053", version 1, genomic-coords { int { from 135879842, to 135882370, strand plus, id gi 157734151 } }, seqs { whole gi 14196467 }, products { { type peptide, heading "Reference", label "isoform 2", accession "NP_114442", version 1, genomic-coords { int { from 135879842, to 135882304, strand plus, id gi 157734151 } }, seqs { whole gi 14196468 } } } } } } }, properties { { type comment, label "Nomenclature", source { { anchor "HUGO Gene Nomenclature Committee" } }, properties { { type property, label "Official Symbol", text "PCDHGA4" }, { type property, label "Official Full Name", text "protocadherin gamma subfamily A, 4" } } }, { type comment, heading "GeneOntology", source { { pre-text "Provided by", anchor "GOA", url "http://www.ebi.ac.uk/GOA/" } }, comment { { type comment, label "Function", comment { { type comment, source { { src { db "GO", tag id 5509 }, anchor "calcium ion binding", post-text "evidence: IEA" } } } } }, { type comment, label "Process", comment { { type comment, source { { src { db "GO", tag id 7156 }, anchor "homophilic cell adhesion", post-text "evidence: IEA" } } } } }, { type comment, label "Component", comment { { type comment, source { { src { db "GO", tag id 16021 }, anchor "integral to membrane", post-text "evidence: IEA" } } }, { type comment, source { { src { db "GO", tag id 5886 }, anchor "plasma membrane", post-text "evidence: IEA" } } } } } } } }, homology { { type comment, heading "Mouse, Rat", source { { src { db "HomoloGene", tag id 81866 }, anchor "Map Viewer", url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&M APS=genes-r-org/rat-chr/human%3A5,genes-r-org/mouse-chr/human%3A5,genes-r-org/ human-chr5&query=e%3A56111[egene_id]+AND+gene[obj_type]&QSTR=pcdhga4&cmd=focus &fill=10" } } } }, comments { { type comment, heading "RefSeq Status", label "REVIEWED" }, { type comment, refs { pmid 16344560, pmid 11230163, pmid 10835267, pmid 10817752, pmid 10716726, pmid 10380929 } }, { type comment, heading "NCBI Reference Sequences (RefSeq)", comment { { type comment, heading "RefSeqs maintained independently of Annotated Genomes", products { { type mRNA, heading "mRNA Sequence", accession "NM_018917", version 3, source { { src { db "Nucleotide", tag id 523567547 }, anchor "NM_018917" } }, seqs { whole gi 523567547 }, products { { type peptide, heading "Product", accession "NP_061740", version 2, source { { src { db "Protein", tag id 523567548 }, anchor "NP_061740", post-text "protocadherin gamma-A4 isoform 1 precursor" } }, seqs { whole gi 523567548 }, comment { { type other, heading "Conserved Domains", source { { pre-text "(6)", anchor "summary" } }, comment { { type other, source { { src { db "CDD", tag id 206637 }, anchor "cd11304: Cadherin_repeat; Cadherin tandem repeat domain" } }, comment { { type other, text "Location: 277 - 374 Blast Score: 278" }, { type other, text "Location: 393 - 479 Blast Score: 236" }, { type other, text "Location: 170 - 269 Blast Score: 227" }, { type other, text "Location: 610 - 697 Blast Score: 223" }, { type other, text "Location: 487 - 589 Blast Score: 221" }, { type other, text "Location: 64 - 160 Blast Score: 123" } } } } }, { type other, heading "Related", source { { src { db "Ensembl", tag str "ENSP00000458570" } } } }, { type other, heading "UniProtKB", source { }, comment { { type other, source { { src { db "UniProtKB/Swiss-Prot", tag str "Q9Y5G9" }, anchor "Q9Y5G9" } } } } }, { type other, heading "Consensus CDS (CCDS)", source { { src { db "CCDS", tag str "CCDS58979.1" }, anchor "CCDS58979.1" } }, comment { { type other, heading "CCDS Note", text "The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript and primate conservation data. " } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMP00000257173" } } } } } } }, comment { { type comment, label "RefSeq Status", text "REVIEWED" }, { type comment, heading "Transcriptional Variant", comment { { type comment, text "Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1)." } } }, { type other, heading "Source Sequence", source { { src { db "Nucleotide", tag str "AF152324,DA392480" }, anchor "AF152324,DA392480" } } }, { type other, heading "Related", source { { src { db "Ensembl", tag str "ENST00000571252" } } } }, { type other, heading "Related", source { { src { db "Vega", tag str "OTTHUMT00000437959" } } } } } }, { type mRNA, heading "mRNA Sequence", accession "NM_032053", version 2, source { { src { db "Nucleotide", tag id 523567549 }, anchor "NM_032053" } }, seqs { whole gi 523567549 }, products { { type peptide, heading "Product", accession "NP_114442", version 2, source { { src { db "Protein", tag id 523567550 }, anchor "NP_114442", post-text "protocadherin gamma-A4 isoform 2 precursor" } }, seqs { whole gi 523567550 }, comment { { type other, heading "Conserved Domains", source { { pre-text "(6)", anchor "summary" } }, comment { { type other, source { { src { db "CDD", tag id 206637 }, anchor "cd11304: Cadherin_repeat; Cadherin tandem repeat domain" } }, comment { { type other, text "Location: 277 - 374 Blast Score: 275" }, { type other, text "Location: 393 - 479 Blast Score: 233" }, { type other, text "Location: 170 - 269 Blast Score: 224" }, { type other, text "Location: 610 - 697 Blast Score: 220" }, { type other, text "Location: 487 - 589 Blast Score: 218" }, { type other, text "Location: 64 - 160 Blast Score: 121" } } } } }, { type other, heading "UniProtKB", source { }, comment { { type other, source { { src { db "UniProtKB/Swiss-Prot", tag str "Q9Y5G9" }, anchor "Q9Y5G9" } } } } } } } }, comment { { type comment, label "RefSeq Status", text "REVIEWED" }, { type comment, heading "Transcriptional Variant", comment { { type comment, text "Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes the shorter isoform (2)." } } }, { type other, heading "Source Sequence", source { { src { db "Nucleotide", tag str "AF152511,BX100615,DA392480" }, anchor "AF152511,BX100615,DA392480" } } } } } }, comment { { type genomic, heading "Reference", accession "NG_000012", version 2, source { { src { db "Nucleotide", tag id 50284693 }, anchor "NG_000012" } }, seqs { int { from 65221, to 223175, strand plus, id gi 50284693 } } } } }, { type comment, heading "RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 105", products { { type genomic, heading "Reference GRCh37.p13 Primary Assembly", accession "NC_000005", version 9, source { { src { db "Nucleotide", tag id 224589817 } } }, seqs { int { from 140734767, to 140892545, strand plus, id gi 224589817 } } }, { type genomic, heading "Alternate HuRef", accession "AC_000137", version 1, source { { src { db "Nucleotide", tag id 157734151 } } }, seqs { int { from 135879842, to 136037385, strand plus, id gi 157734151 } } }, { type genomic, heading "Alternate CHM1_1.1", accession "NC_018916", version 2, source { { src { db "Nucleotide", tag id 528476642 } } }, seqs { int { from 140167974, to 140325822, strand plus, id gi 528476642 } } } } } } }, { type comment, heading "Related Sequences", products { { type genomic, heading "Genomic", accession "ABBA01026410", version 1, source { { src { db "Nucleotide", tag id 148165753 }, anchor "ABBA01026410" } }, seqs { int { from 18242, to 75873, strand minus, id gi 148165753 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026411", version 1, source { { src { db "Nucleotide", tag id 148165752 }, anchor "ABBA01026411" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026412", version 1, source { { src { db "Nucleotide", tag id 148165751 }, anchor "ABBA01026412" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026413", version 1, source { { src { db "Nucleotide", tag id 148165750 }, anchor "ABBA01026413" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026414", version 1, source { { src { db "Nucleotide", tag id 148165749 }, anchor "ABBA01026414" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026415", version 1, source { { src { db "Nucleotide", tag id 148165748 }, anchor "ABBA01026415" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026416", version 1, source { { src { db "Nucleotide", tag id 148165747 }, anchor "ABBA01026416" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "ABBA01026417", version 1, source { { src { db "Nucleotide", tag id 148165746 }, anchor "ABBA01026417" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AC005366", version 1, source { { src { db "Nucleotide", tag id 3367508 }, anchor "AC005366" } }, seqs { int { from 17974, to 36136, strand minus, id gi 3367508 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AC005618", version 1, source { { src { db "Nucleotide", tag id 3548785 }, anchor "AC005618" } }, seqs { int { from 66536, to 176713, strand plus, id gi 3548785 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AC008781", version 7, source { { src { db "Nucleotide", tag id 16303400 }, anchor "AC008781" } }, seqs { int { from 138117, to 185893, strand minus, id gi 16303400 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AL832028", version 1, source { { src { db "Nucleotide", tag id 21732568 }, anchor "AL832028" } }, seqs { whole gi 21732568 }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AMYH02012344", version 1, source { { src { db "Nucleotide", tag id 511816418 }, anchor "AMYH02012344" } }, seqs { int { from 151138, to 175836, strand plus, id gi 511816418 } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AMYH02012345", version 1, source { { src { db "Nucleotide", tag id 511816417 }, anchor "AMYH02012345" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "AMYH02012346", version 1, source { { src { db "Nucleotide", tag id 511816416 }, anchor "AMYH02012346" } }, products { { type peptide, text "None" } } }, { type genomic, heading "Genomic", accession "CH471062", version 2, source { { src { db "Nucleotide", tag id 74230048 }, anchor "CH471062" } }, seqs { whole gi 74230048 }, products { { type peptide, accession "EAW61957", version 1, source { { src { db "Protein", tag id 119582361 }, anchor "EAW61957" } }, seqs { whole gi 119582361 } }, { type peptide, accession "EAW61964", version 1, source { { src { db "Protein", tag id 119582368 }, anchor "EAW61964" } }, seqs { whole gi 119582368 } } } }, { type mRNA, heading "mRNA", accession "AF152324", version 1, source { { src { db "Nucleotide", tag id 5456939 }, anchor "AF152324" } }, seqs { whole gi 5456939 }, products { { type peptide, accession "AAD43718", version 1, source { { src { db "Protein", tag id 5456940 }, anchor "AAD43718" } }, seqs { whole gi 5456940 } } } }, { type mRNA, heading "mRNA", accession "AF152511", version 1, source { { src { db "Nucleotide", tag id 5457069 }, anchor "AF152511" } }, seqs { whole gi 5457069 }, products { { type peptide, accession "AAD43771", version 1, source { { src { db "Protein", tag id 5457070 }, anchor "AAD43771" } }, seqs { whole gi 5457070 } } } }, { type mRNA, heading "mRNA", accession "AI805761", version 1, source { { src { db "Nucleotide", tag id 5392327 }, anchor "AI805761" } }, seqs { whole gi 5392327 }, products { { type peptide, text "None" } } }, { type mRNA, heading "mRNA", accession "BX100615", version 1, source { { src { db "Nucleotide", tag id 27830686 }, anchor "BX100615" } }, seqs { whole gi 27830686 }, products { { type peptide, text "None" } } }, { type mRNA, heading "mRNA", accession "DA392480", version 1, source { { src { db "Nucleotide", tag id 80578107 }, anchor "DA392480" } }, seqs { whole gi 80578107 }, products { { type peptide, text "None" } } }, { type other, text "None", products { { type peptide, accession "Q9Y5G9", version 1, source { { src { db "Protein", tag id 37999839 } }, { src { db "UniProtKB/Swiss-Prot", tag str "Q9Y5G9" } } }, seqs { whole gi 37999839 } } } }, { type other-genetic, heading "Synthetic", accession "BC152812", version 1, source { { src { db "Nucleotide", tag id 157170235 }, anchor "BC152812" } }, seqs { whole gi 157170235 }, products { { type peptide, accession "AAI52813", version 1, source { { src { db "Protein", tag id 157170236 }, anchor "AAI52813" } }, seqs { whole gi 157170236 } } } }, { type other-genetic, heading "Synthetic", accession "BC156730", version 1, source { { src { db "Nucleotide", tag id 162318805 }, anchor "BC156730" } }, seqs { whole gi 162318805 }, products { { type peptide, accession "AAI56731", version 1, source { { src { db "Protein", tag id 162318806 }, anchor "AAI56731" } }, seqs { whole gi 162318806 } } } } } }, { type comment, heading "Additional Links", comment { { type comment, source { { src { db "Evidence Viewer", tag str "56111" }, anchor "Evidence Viewer", url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti g=NT_029289.11&gene=PCDHGA4&lid=56111&from=1897694&to=2055472" } } }, { type comment, text "MIM", source { { src { db "MIM", tag id 606291 }, anchor "606291" } } }, { type comment, source { { src { db "AceView", tag id 56111 }, anchor "AceView", url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=g eneid&org=9606&l=56111" } } }, { type comment, text "UCSC", source { { src { db "UCSC", tag str "UCSC" }, anchor "UCSC", url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position= NM_018917" } } }, { type comment, source { { src { db "MGC", tag str "BC152812,BC156730" }, anchor "MGC", url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC152812 ,BC156730" } } }, { type comment, source { { src { db "KEGG", tag str "hsa:56111" }, url "http://www.genome.jp/dbget-bin/www_bget?hsa:56111" } } }, { type comment, text "UniGene", xtra-properties { { tag "UNIGENE", value "Hs.368160" } }, source { { src { db "UniGene", tag str "Hs.368160" }, anchor "Hs.368160", url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=36 8160" } } } } }, { type comment, heading "Markers (Sequence Tagged Sites/STS)", comment { { type comment, source { { src { db "UniSTS", tag id 68872 }, anchor "SHGC-76190", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "HSA.981" }, { type other, label "Alternate name", text "RH101644" }, { type other, label "Alternate name", text "RH50318" }, { type other, label "Alternate name", text "STS-L11373" }, { type other, label "Alternate name", text "WI-18887" } } }, { type comment, source { { src { db "UniSTS", tag id 58378 }, anchor "T03558", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "IB475" } } }, { type comment, source { { src { db "UniSTS", tag id 277566 }, anchor "PCDHGA9_1502", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 277567 }, anchor "PCDHGC3__1203", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 280897 }, anchor "PCDHGA4_2560", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "PCDHGA4_2560.2" } } }, { type comment, source { { src { db "UniSTS", tag id 280898 }, anchor "PCDHGA6_2010", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 280900 }, anchor "PCDHGB4_2544", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 280901 }, anchor "PCDHGC4_2483", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 47440 }, anchor "AF022190", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 87645 }, anchor "RH91455", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "stSG44640" } } }, { type comment, source { { src { db "UniSTS", tag id 256698 }, anchor "5q31-33_24", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 25793 }, anchor "AF053066", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 25794 }, anchor "AF022189", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 466384 }, anchor "PCDHGA10_7046", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 73201 }, anchor "D5S2538", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "GDB:734416" }, { type other, label "Alternate name", text "RH34348" }, { type other, label "Alternate name", text "SHGC-5561" } } }, { type comment, source { { src { db "UniSTS", tag id 256498 }, anchor "5q31-33_16", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 256499 }, anchor "5q31-33_17", post-text "(e-PCR)" } } }, { type comment, source { { src { db "UniSTS", tag id 50676 }, anchor "STS-R97031", post-text "(e-PCR)" } }, comment { { type other, label "Alternate name", text "RH41214" }, { type other, label "Alternate name", text "sts-R97031" } } } } }, { type comment, heading "Gene Location History", comment { { type comment, heading "Homo sapiens Annotation Release 105", comment { { type assembly, heading "GRCh37.p13", label "Reference", accession "GCF_000001405", version 25, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome 5", accession "NC_000005", version 9, seqs { int { from 140734767, to 140892545, strand plus, id gi 224589817 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type genomic, label "chromosome Chromosome 5", accession "AC_000137", version 1, seqs { int { from 135879842, to 136037385, strand plus, id gi 157734151 } } } } }, { type assembly, heading "CHM1_1.1", label "Alternate", accession "GCF_000306695", version 2, comment { { type genomic, label "chromosome Chromosome 5", accession "NC_018916", version 2, seqs { int { from 140167974, to 140325822, strand plus, id gi 528476642 } } } } } } }, { type comment, heading "Homo sapiens Annotation Release 104", comment { { type assembly, heading "GRCh37.p10", label "Reference", accession "GCF_000001405", version 22, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome 5", accession "NC_000005", version 9, seqs { int { from 140734767, to 140892545, strand plus, id gi 224589817 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type genomic, label "chromosome Chromosome 5", accession "AC_000137", version 1, seqs { int { from 135879842, to 136037385, strand plus, id gi 157734151 } } } } }, { type assembly, heading "CHM1_1.0", label "Alternate", accession "GCF_000306695", version 1, comment { { type genomic, label "chromosome Chromosome 5", accession "NC_018916", version 1, seqs { int { from 141011444, to 141169209, strand plus, id gi 409253459 } } } } } } }, { type comment, heading "Build 37.3", comment { { type assembly, heading "GRCh37.p5", label "Reference", accession "GCF_000001405", version 17, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000001305", version 13, comment { { type genomic, label "chromosome Chromosome 5", accession "NC_000005", version 9, seqs { int { from 140734767, to 140892545, strand plus, id gi 224589817 } } } } } } }, { type assembly, heading "HuRef", label "Alternate", accession "GCF_000002125", version 1, comment { { type assembly-unit, heading "Primary Assembly", accession "GCF_000000025", version 1, comment { { type genomic, label "chromosome Chromosome 5", accession "AC_000137", version 1, seqs { int { from 135879842, to 136037385, strand plus, id gi 157734151 } } } } } } } } } } } }, unique-keys { { db "HGNC", tag id 8702 }, { db "LocusID", tag id 56111 }, { db "MIM", tag id 606291 } }, xtra-index-terms { "LOC56111" } } regex_parser_test.pl100755000765000024 150213352317004 22750 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/examples#!/usr/bin/perl # launch it like "perl regex_parser_test.pl Homo_sapiens" (Homo_sapiens can be downloaded # and decompressed from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN/Mammalia/Homo_sapiens.gz) # or use the included test file "perl regex_parser_test.pl ../t/input.asn" use strict; use Dumpvalue; use Bio::ASN1::EntrezGene; use Benchmark; my $parser = Bio::ASN1::EntrezGene->new(file => $ARGV[0]); # instantiate a parser object my ($t0, $end, $i) = (new Benchmark, 10, 0); # process the first 10 records in the input file while(my $value = $parser->next_seq) { # Dumpvalue->new->dumpValue($value); # uncomment to dump the data structure out last if ++$i >= $end; # only process the first 20 records } my $t1 = new Benchmark; print "The first $i records in $ARGV[0] took EntrezGene parser:",timestr(timediff($t1, $t0)),"\n"; Sequence000755000765000024 013352317004 20440 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1Indexer.pm100755000765000024 1434113352317004 22562 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1/Sequencepackage Bio::ASN1::Sequence::Indexer; $Bio::ASN1::Sequence::Indexer::VERSION = '1.73'; use utf8; use strict; use warnings; use Carp qw(carp croak); use Bio::ASN1::Sequence; use Bio::Index::AbstractSeq; use parent qw(Bio::Index::AbstractSeq); # ABSTRACT: Indexes NCBI Sequence files. # AUTHOR: Dr. Mingyi Liu # OWNER: 2005 Mingyi Liu # OWNER: 2005 GPC Biotech AG # OWNER: 2005 Altana Research Institute # LICENSE: Perl_5 # TODO: Should this be deprecated? sub _version { return $Bio::Index::AbstractSeq::VERSION; } sub _type_stamp { return '__Sequence_ASN1__'; } sub _index_file { my($self, $file, $idx) = @_; my $position; open(IN, $file) || $self->throw("Can't open $file - $!"); local $/ = "Seq-entry ::= set {"; while() { chomp; while(/[,{}]\s+accession\s*"([^"]+)"\s+[,{}]/ig) # add both dna and protein { $self->add_record($1, $idx, $position); } $position = tell(IN) - 19; # $/'s length } close(IN); return 1; } sub _file_format { return 'sequence'; } sub fetch_hash { my ($self, $seqid) = @_; if (my $seq = $self->db->{$seqid}) { my ($fileno, $position) = $self->unpack_record($seq); my $parser = Bio::ASN1::Sequence->new('fh' => $self->_file_handle($fileno)); seek($parser->fh, $position, 0); return $parser->next_seq; } } sub _file_handle { my( $self, $i ) = @_; unless ($self->{'_filehandle'}[$i]) { my @rec = $self->unpack_record($self->db->{"__FILE_$i"}) or $self->throw("Can't get filename for index : $i"); my $file = $rec[0]; local *FH; open *FH, $file or $self->throw("Can't read file '$file' : $!"); $self->{'_filehandle'}[$i] = *FH; # Cache filehandle } return $self->{'_filehandle'}[$i]; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files. =head1 VERSION version 1.73 =head1 SYNOPSIS use Bio::ASN1::Sequence::Indexer; # creating & using the index is just a few lines my $inx = Bio::ASN1::Sequence::Indexer->new( -filename => 'seq.idx', -write_flag => 'WRITE'); # needed for make_index call, but if opening # existing index file, don't set write flag! $inx->make_index('seq1.asn', 'seq2.asn'); my $seq = $inx->fetch('AF093062'); # Bio::Seq obj for Sequence (doesn't work yet) # alternatively, if one prefers just a data structure instead of objects $seq = $inx->fetch_hash('AF093062'); # a hash produced by Bio::ASN1::Sequence # that contains all data in the Sequence record =head1 DESCRIPTION Bio::ASN1::Sequence::Indexer is a Perl Indexer for NCBI Sequence genome databases. It processes an ASN.1-formatted Sequence record and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass of Bioperl's index objects). Note that this module does not parse record, because it needs to run fast and grab only the gene ids. For parsing record, use Bio::ASN1::Sequence. As with Bio::ASN1::Sequence, this module is best thought of as beta version - it works, but is not fully tested. =head1 METHODS =head2 fetch Parameters: $geneid - id for the Sequence record to be retrieved Example: my $hash = $indexer->fetch(10); # get Sequence #10 Function: fetch the data for the given Sequence id. Returns: A Bio::Seq object produced by Bio::SeqIO::sequence Notes: Bio::SeqIO::sequence does not exist and probably won't exist for a while! So call fetch_hash instead =head2 fetch_hash Parameters: $seqid - id for the Sequence record to be retrieved Example: my $hash = $indexer->fetch_hash('AF093062'); Function: fetch a hash produced by Bio::ASN1::Sequence for given id Returns: A data structure containing all data items from the Sequence record. Notes: Alternative to fetch() =head1 INTERNAL METHODS =head2 _version =head2 _type_stamp =head2 _index_file =head2 _file_format =head2 _file_handle Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT Notes : This function is copied from Bio::Index::Abstract. Once that module changes file handle code like I do below to fit perl 5.005_03, this sub would be removed from this module =head1 PREREQUISITE Bio::ASN1::Sequence, Bioperl and all dependencies therein. =head1 INSTALLATION Same as Bio::ASN1::EntrezGene =head1 SEE ALSO Please check out perldoc for Bio::ASN1::EntrezGene for more info. =head1 CITATION Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190. =head1 OPERATION SYSTEMS SUPPORTED Any OS that Perl & Bioperl run on. =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-asn1-entrezgene/issues =head1 AUTHOR Dr. Mingyi Liu =head1 COPYRIGHT This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute. This software is available under the same terms as the perl 5 programming language system itself. =cut parse_sequence_example.pl100755000765000024 131013352317004 23735 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/examples#!/usr/bin/perl # launch it like "perl parse_sequence_example.pl seq.asn1" # one can use the included test file "perl parse_sequence_example.pl ../t/seq.asn" use strict; use Dumpvalue; use Bio::ASN1::Sequence; use Benchmark; my $parser = Bio::ASN1::Sequence->new(file => $ARGV[0]); # instantiate a parser object my ($t0, $end, $i) = (new Benchmark, 10, 0); # process the first 10 records in the input file while(my $value = $parser->next_seq) { Dumpvalue->new->dumpValue($value); # uncomment to dump the data structure out last if ++$i >= $end; # only process the first 20 records } my $t1 = new Benchmark; print "The first $i records in $ARGV[0] took Sequence parser:",timestr(timediff($t1, $t0)),"\n"; EntrezGene000755000765000024 013352317004 20736 5ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1Indexer.pm100755000765000024 1527013352317004 23062 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/lib/Bio/ASN1/EntrezGenepackage Bio::ASN1::EntrezGene::Indexer; $Bio::ASN1::EntrezGene::Indexer::VERSION = '1.73'; use utf8; use strict; use warnings; use Carp qw(carp croak); use Bio::ASN1::EntrezGene; use Bio::Index::AbstractSeq; use parent qw(Bio::Index::AbstractSeq); # ABSTRACT: Indexes NCBI Sequence files. # AUTHOR: Dr. Mingyi Liu # OWNER: 2005 Mingyi Liu # OWNER: 2005 GPC Biotech AG # OWNER: 2005 Altana Research Institute # LICENSE: Perl_5 # TODO: Should this be deprecated? sub _version { return $Bio::Index::AbstractSeq::VERSION; } sub _type_stamp { return '__EntrezGene_ASN1__'; } sub _index_file { my($self, $file, $idx) = @_; my $position; open(IN, $file) || $self->throw("Can't open $file - $!"); local $/ = "Entrezgene ::= {"; while() { chomp; $self->add_record($1, $idx, $position) if (/[,{}]\s+geneid\s*(\d+)\s+[,{}]/i); $position = tell(IN) - 16; # $/'s length } close(IN); return 1; } sub _file_format { return 'entrezgene'; } sub fetch_hash { my ($self, $geneid) = @_; if (my $gene = $self->db->{$geneid}) { my ($fileno, $position) = $self->unpack_record($gene); my $parser = Bio::ASN1::EntrezGene->new('fh' => $self->_file_handle($fileno)); seek($parser->fh, $position, 0); return $parser->next_seq; } } sub _file_handle { my( $self, $i ) = @_; unless ($self->{'_filehandle'}[$i]) { my @rec = $self->unpack_record($self->db->{"__FILE_$i"}) or $self->throw("Can't get filename for index : $i"); my $file = $rec[0]; local *FH; open *FH, $file or $self->throw("Can't read file '$file' : $!"); $self->{'_filehandle'}[$i] = *FH; # Cache filehandle } return $self->{'_filehandle'}[$i]; } 1; __END__ =pod =encoding UTF-8 =head1 NAME Bio::ASN1::EntrezGene::Indexer - Indexes NCBI Sequence files. =head1 VERSION version 1.73 =head1 SYNOPSIS use Bio::ASN1::EntrezGene::Indexer; # creating & using the index is just a few lines my $inx = Bio::ASN1::EntrezGene::Indexer->new( -filename => 'entrezgene.idx', -write_flag => 'WRITE'); # needed for make_index call, but if opening # existing index file, don't set write flag! $inx->make_index('Homo_sapiens', 'Mus_musculus', 'Rattus_norvegicus'); my $seq = $inx->fetch(10); # Bio::Seq obj for Entrez Gene #10 # alternatively, if one prefers just a data structure instead of objects $seq = $inx->fetch_hash(10); # a hash produced by Bio::ASN1::EntrezGene # that contains all data in the Entrez Gene record # note that in case you wonder, you can get the files 'Homo_sapiens' # from NCBI Entrez Gene ftp download, DATA/ASN/Mammalia directory =head1 DESCRIPTION Bio::ASN1::EntrezGene::Indexer is a Perl Indexer for NCBI Entrez Gene genome databases. It processes an ASN.1-formatted Entrez Gene record and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass of Bioperl's index objects). Note that this module does not parse record, because it needs to run fast and grab only the gene ids. For parsing record, use Bio::ASN1::EntrezGene, or better yet, use Bio::SeqIO, format 'entrezgene'. It takes this module (version 1.07) 21 seconds to index the human genome Entrez Gene file (Apr. 5/2005 download) on one 2.4 GHz Intel Xeon processor. =head1 METHODS =head2 fetch Parameters: $geneid - id for the Entrez Gene record to be retrieved Example: my $hash = $indexer->fetch(10); # get Entrez Gene #10 Function: fetch the data for the given Entrez Gene id. Returns: A Bio::Seq object produced by Bio::SeqIO::entrezgene Notes: One needs to have Bio::SeqIO::entrezgene installed before calling this function! =head2 fetch_hash Parameters: $geneid - id for the Entrez Gene record to be retrieved Example: my $hash = $indexer->fetch_hash(10); # get Entrez Gene #10 Function: fetch a hash produced by Bio::ASN1::EntrezGene for given Entrez Gene id. Returns: A data structure containing all data items from the Entrez Gene record. Notes: Alternative to fetch() =head1 INTERNAL METHODS =head2 _version =head2 _type_stamp =head2 _index_file =head2 _file_format =head2 _file_handle Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT Notes : This function is copied from Bio::Index::Abstract. Once that module changes file handle code like I do below to fit perl 5.005_03, this sub would be removed from this module =head1 PREREQUISITE Bio::ASN1::EntrezGene, Bioperl version that contains Stefan Kirov's entrezgene.pm and all dependencies therein. =head1 INSTALLATION Same as Bio::ASN1::EntrezGene =head1 SEE ALSO For details on various parsers I generated for Entrez Gene, example scripts that uses/benchmarks the modules, please see L. Those other parsers etc. are included in V1.05 download. =head1 CITATION Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190. =head1 OPERATION SYSTEMS SUPPORTED Any OS that Perl & Bioperl run on. =head1 FEEDBACK =head2 Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bio-asn1-entrezgene/issues =head1 AUTHOR Dr. Mingyi Liu =head1 COPYRIGHT This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute. This software is available under the same terms as the perl 5 programming language system itself. =cut parse_entrez_gene_example.pl100755000765000024 6167613352317004 24477 0ustar00cjfieldsstaff000000000000Bio-ASN1-EntrezGene-1.73/examples#!/usr/bin/perl # launch it like "perl parse_entrez_gene_example.pl Homo_sapiens" (Homo_sapiens can be downloaded # and decompressed from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN/Mammalia/Homo_sapiens.gz) # or use the included test file "perl parse_entrez_gene_example.pl ../t/input.asn" ################################################################################ # parse_entrez_gene_example # Purpose: Demonstrates how to use Mingyi's Entrez Gene parser and retrieve # each data item from Entrez Gene. This data extraction demo is # very important as I spent 3-4 times more time on this script # than on writing, debugging, profiling, optimizing my parser! # It's a tedious task and I hope this script helps you (I'm sure # it will, if you use my parser). # NOTE!!! This example script shows where each data item from Entrez Gene # is in the data structure, but it does not store much data at all! # Therefore you will find little data in the dumpValue($gene) gene call # That's because data storage is project specific. Please store # the extracted data items in your script according to your own plan. # # Although the author tries to show how to get all data out of Entrez Gene, # there is no guarantee that all data from all versions of Entrez Gene will # be extracted using this script. # Copyright: (c) 2005, Mingyi Liu, GPC Biotech, Altana Research Institute. # License: this code is licensed under Perl itself or GPL. # Citation: Liu, M and Grigoriev, A (2005) "Fast Parsers for Entrez Gene" # Bioinformatics. In press ################################################################################ use strict; use Dumpvalue; use Benchmark; use Bio::ASN1::EntrezGene; my $parser = Bio::ASN1::EntrezGene->new('file' => $ARGV[0]); my $i = 0; while(my $result = $parser->next_seq) { unless(defined $result) # this never happens, but doesn't hurt { print STDERR "bad text for round #".++$i."!\n"; next; } $result = $result->[0] if(ref($result) eq 'ARRAY'); # this should always be true Dumpvalue->new->dumpValue($result); # $result contains all Entrez Gene data my $gene = makegene($result); Dumpvalue->new->dumpValue($gene); # although data are extracted, very few are stored (and thus dumped) after I edited out project-specific stuff, user should decide about the storage themselves last; } ################################################################################# # NOTE!!! this is just example that shows where each data item from Entrez Gene # is in the data structure, therefore I did not store all data items! But # for your own script, you'd probably want to store them. # sorry I don't have time to add more comments! I hope they're easy to understand. sub makegene { my $seq = shift; # Dumpvalue->new->dumpValue($seq);exit; my $geneid = safeval($seq, '{track-info}->[0]->{geneid}'); die "no geneid found!\n" unless $geneid; # this never happens, but doesn't hurt my (%protaccs, %protgis); my $llgene = {}; ################################################################################### # it is difficult to process Entrez Gene in event-triggered functions, so # we'll just process items one by one to pick & choose the ones we want safeassign($llgene, 'description', $seq, '{gene}->[0]->{desc}'); safeassign($llgene, 'type', $seq, '{type}'); safeassign($llgene, 'symbol', $seq, '{gene}->[0]->{locus}'); # may be overwritten map { push(@{$llgene->{genenames}}, $_) } @{$seq->{gene}->[0]->{syn}} if(safeval($seq, '{gene}->[0]->{syn}')); $llgene->{summary} = $seq->{summary} if($seq->{summary}); $llgene->{chromosome} = $seq->{source}->[0]->{subtype}->[0]->{name} if(safeval($seq, '{source}->[0]->{subtype}->[0]->{subtype}') eq 'chromosome'); safeassign($llgene, 'chrmap', $seq, '{gene}->[0]->{maploc}'); addxrefs($llgene, 'HGNC', $1) if(safeval($seq, '{gene}->[0]->{locus-tag}') =~ /HGNC:(\S+)/i); ########################################## # HomoloGene if($seq->{homology}) { # Entrez Gene documentation seems to have errors on this one (no label, text, anchor, # otherwise we could provide some description) # NOTE!!! species could be multiple species separated by ',' my $id = safeval($seq, '{homology}->[0]->{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); my $species = safeval($seq, '{homology}->[0]->{heading}'); } ########################################## # OK, let's process the comments my $allseqs = {}; # refseq seqs foreach my $comment (@{$seq->{comments}}) { # pubmed ids addxrefs($llgene, 'PUBMED', $comment->{refs}->[0]->{pmid}) if(ref($comment->{refs}) eq 'ARRAY'); my $status = $comment->{label} if($comment->{heading} eq 'RefSeq Status'); ##################### # STS stuff if($comment->{heading} =~ /Markers.*STS\)$/) { foreach my $c (@{$comment->{comment}}) { addxref($llgene, 'UNISTS', id => safeval($c, '{source}->[0]->{anchor}'), acc => safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}')); } } ############################################################## # refseq stuff, DNA=>protein, domain info, we store it first # and assemble info for future processing # of variants, transcripts and proteins, (dealing with these objects # is by far the most time-consuming task in extracting Entrez Gene data) if($comment->{heading} =~ /\(RefSeq\)$/ && $comment->{products}) { foreach my $product (@{$comment->{products}}) { my ($acc, $gi, $trans, %ids); # we are probably too careful below since refseq should have accession AND gi $acc = $product->{accession}; $gi = safeval($product, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); if($acc) { $ids{acc} = $acc; $trans->{acc} = $ids{acc}; $trans->{gi} = $gi if $gi; $allseqs->{$acc} = $trans; $trans->{type} = $product->{heading} if($product->{type} ne 'mRNA'); } $ids{gi} = $gi if($gi); if($product->{comment}) { foreach my $c (@{$product->{comment}}) { # check assembly info if($c->{heading} eq 'Source Sequence') { $trans->{assembly} = safeval($c, '{source}->[0]->{anchor}'); } # check variant info if($c->{heading} eq 'Transcriptional Variant') { $trans->{variantcomment} = safeval($c, '{comment}->[0]->{text}'); } } } ############################# # now deal with protein if(ref($product->{products}) eq 'ARRAY') # protein { my ($prot); for(my $j = 0; $j < @{$product->{products}}; $j++) { my $p = $product->{products}->[$j]; $acc = $p->{accession}; $gi = safeval($p, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); if($gi) { $ids{'protgi' . ($j+1)} = $gi; $protgis{$gi} = 'protgi' . ($j+1); } if($acc) { $ids{'protacc' . ($j+1)} = $acc; $protgis{$acc} = 'protacc' . ($j+1); $prot->{acc} = $acc; $prot->{gi} = $gi if $gi; $trans->{protein}->{$acc} = $prot; $prot->{type} = $product->{heading} if($p->{type} ne 'peptide'); } safeassign($prot, 'name', $p, '{source}->[0]->{post-text}'); ############################# # check domain info if($p->{comment}) { foreach my $c1 (@{$p->{comment}}) { if($c1->{heading} =~ /Domains$/) { my @domains; foreach my $c2 (@{$c1->{comment}}) { my $dom; my $tmp = safeval($c2, '{comment}->[0]->{text}'); $dom->{score} = $tmp =~ /Blast Score: ([0-9.-]+)/; ($dom->{start}, $dom->{end}) = $tmp =~ /Location: (\d+) - (\d+)/; $dom->{desc} = safeval($c2, '{source}->[0]->{anchor}'); $dom->{xref} = { db => safeval($c2, '{source}->[0]->{src}->[0]->{db}'), ids => [{type=>'id',id=>safeval($c2, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}')}] }; push(@domains, $dom); } $prot->{dom} = \@domains; } elsif($c1->{heading} =~ /\(CCDS\)/) # CCDS database xref { $prot->{ccds} = safeval($c1, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}'); } } } ################ # end domain } } ###################### # end protein addxref($llgene, 'REFSEQ', %ids) if (keys %ids > 0); } } ######################################################### # related seqeunces, goes into xref only if($comment->{heading} eq 'Related Sequences' && $comment->{products}) { foreach my $product (@{$comment->{products}}) { my ($acc, $gi, %ids); $acc = $product->{accession}; $gi = safeval($product, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); $ids{gi} = $gi if $gi; $ids{acc} = $acc if $acc; if(ref($product->{products}) eq 'ARRAY') { # just in case two genbank protein's assigned to one mRNA for(my $j = 0; $j < @{$product->{products}}; $j++) { $acc = $product->{products}->[$j]->{accession}; $gi = safeval($product->{products}->[$j], '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); $ids{'protgi' . ($j+1)} = $gi if $gi; $ids{'protacc' . ($j+1)} = $acc if $acc; } } addxref($llgene, 'GENBANK', %ids) if (keys %ids > 0); } } ###################### # various dblinks if($comment->{heading} eq 'Additional Links' && $comment->{comment}) { foreach my $c (@{$comment->{comment}}) { my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}'); if($id) # add xref to llgene { my $db = uc(safeval($c, '{source}->[0]->{src}->[0]->{db}')); next if $db =~ /\s+/ || $db =~ /HomoloGene/i; # homologene id here is not real id, and some of dblinks' DB name are not real DBs, we temporarily use space to identify those my @ids = trim(split /,/, $id); # MGC sometimes has multiple ids concatenated by ',' map { s/^$db://i; addxref($llgene, $db, 'id' => $_) } @ids; # $db: truncation useful for GDB ids } my $url = safeval($c, '{source}->[0]->{url}'); if($url) { $url =~ s/\s//g; # some urls have linebreaks in them my $desc = safeval($c, '{source}->[0]->{anchor}'); } } } ###################### # Pathways if($comment->{heading} eq 'Pathways' && $comment->{comment}) { foreach my $c (@{$comment->{comment}}) { my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}'); my $url = safeval($c, '{source}->[0]->{url}'); if($url) { $url =~ s/\s//g; # some urls have linebreaks in them my $desc = ($c->{text})? $c->{text} : 'KEGG Pathway'; } if($id) # add xref to llgene { my @ids = trim(split /,/, $id); # MGC sometimes has multiple ids concatenated by ',' map { addxref($llgene, 'KEGG', 'id' => $_) } @ids; # $db: truncation useful for GDB ids } } } ###################### # generif if($comment->{type} eq 'generif') { my @cs = ($comment->{heading} && ref($comment->{comment}) eq 'ARRAY')? @{$comment->{comment}} : $comment; foreach my $c (@cs) { my $generif = $c->{text}; my $pmid => safeval($c, "{refs}->[0]->{pmid}"); if($comment->{heading}) { my $type = $comment->{heading}; my ($db, $id) = makexref($c); my $anchor = safeval($c, '{source}->[0]->{anchor}'); foreach my $c1 (@{$c->{comment}}) { my ($db, $id) = makexref($c1); my ($label, $acc) = ((($c1->{label})? "$c1->{label}:" : ''), $c1->{accession}); } } addxref($llgene, 'PUBMED', 'id' => safeval($c, "{refs}->[0]->{pmid}")); } } ###################### # phenotype if($comment->{heading} eq 'Phenotypes') { my $detail = safeval($comment, '{comment}->[0]->{text}'); if(safeval($comment, '{comment}->[0]->{source}')) { my $db = safeval($comment, '{comment}->[0]->{source}->[0]->{src}->[0]->{db}'); my $id = safeval($comment, '{comment}->[0]->{source}->[0]->{src}->[0]->{tag}->[0]->{id}'); } } ###################### # relationships if($comment->{heading} eq 'Relationships') { foreach my $c (@{$comment->{comment}}) { my $type = ($c->{text} =~ /related (.*)/)? $1 : $c->{text}; my $anchor = safeval($c, '{source}->[0]->{anchor}'); my ($db, $id) = makexref($c); } } ###################### # tRNA if($comment->{heading} eq 'tRNA-ext') { my $trnatext = $comment->{text}; } ######################################################################### # ECNUM (documentation for Entrez Gene says it's here, so I put this in, # but it is actually in locus (see further below) if($comment->{type} =~ /property/i && $comment->{label} eq 'EC') { addxref($llgene, 'EC', 'id' => $comment->{text}); } } my %map = ('FUNCTION' => 'molecular function', 'PROCESS' => 'biological process', 'COMPONENT' => 'cellular component'); ################################## # OK, let's process the GO info if($seq->{properties}) { foreach my $p (@{$seq->{properties}}) { if($p->{heading} eq 'GeneOntology') { foreach my $c (@{$p->{comment}}) { foreach my $c1 (@{$c->{comment}}) { my ($db, $id) = (safeval($c1, '{source}->[0]->{src}->[0]->{db}'), safeval($c1, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}')); addxref($llgene, $db, id => $id); my $category = $map{uc($c->{label})}; my $content = safeval($c1, '{source}->[0]->{anchor}'); } } } elsif($p->{label} eq 'Nomenclature') { foreach my $p1 (@{$p->{properties}}) { if($p1->{label} eq 'Official Symbol') { my $hugosymbol = $p1->{text}; } elsif($p1->{label} eq 'Official Full Name') { my $hugoname = $p1->{text}; } } } } } ################################## # protein aliases if($seq->{prot}) { foreach my $p (@{$seq->{prot}}) { map { my $protalias = $_ } @{$p->{name}} if(ref($p->{name}) eq 'ARRAY'); } } ##################################################################### # now locus, again assemble info into $allseqs for future processing # of variants, transcripts and proteins, (dealing with these objects # is by far the most time-consuming task in extracting Entrez Gene data) if($seq->{locus}) { # judgement call: # we should take NC_ whenever possible and disregard NT_ # but in absence of NC_, we use NT_ to figure out exons foreach my $l (@{$seq->{locus}}) { if($l->{products}) { foreach my $p (@{$l->{products}}) { ######################################## # let's first get the accession numbers my %ids; $ids{acc} = $p->{accession}; my $gi = safeval($p, '{seqs}->[0]->{whole}->[0]->{gi}'); $ids{gi} = $gi if $gi; my $t = $allseqs->{$p->{accession}}; $allseqs->{$p->{accession}}->{acc} = $ids{acc} unless $allseqs->{$p->{accession}}->{acc}; # sometimes NCBI forgot to put refseq IDs into comments about Refseq sequences, e.g. Gene 616. $allseqs->{$p->{accession}}->{gi} = $ids{gi} unless $allseqs->{$p->{accession}}->{gi}; # sometimes NCBI forgot to put refseq IDs into comments about Refseq sequences, e.g. Gene 616. if($p->{products}) { for(my $j = 0; $j < @{$p->{products}}; $j++) { my $p1 = $p->{products}->[$j]; $gi = safeval($p1, '{seqs}->[0]->{whole}->[0]->{gi}'); my ($gino, $accno) = ((($protgis{$gi})? $protgis{$gi} : 'protgi' . ($j+1)), (($protaccs{$p1->{accession}})? $protaccs{$p1->{accession}} : 'protacc' . ($j+1))); if($gi) { $ids{$gino} = $gi; $protgis{$gi} = $gino; } $ids{$accno} = $p1->{accession}; $protaccs{$p1->{accession}} = $accno; $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{acc} = $ids{$accno} unless $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{acc}; # sometimes NCBI forgot to put refseq IDs into comments about Refseq sequences, e.g. Gene 616. $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{gi} = $ids{$gino} unless $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{gi}; # sometimes NCBI forgot to put refseq IDs into comments about Refseq sequences, e.g. Gene 616. if($p1->{comment} && safeval($p1, '{comment}->[0]->{type}') eq 'property' && safeval($p1, '{comment}->[0]->{label}') eq 'EC') { my $ec = safeval($p1, '{comment}->[0]->{text}'); # change dealing with EC number to add to xref addxref($llgene, 'EC', 'id' => $ec); } } } addxref($llgene, 'REFSEQ', %ids); # trans and prots xrefs ############################################################# # now get exon coordinates - only do the work when necessary unless($t && $t->{genomic} && ($t->{genomic} =~ /^NC_/ || $l->{accession} =~ /^NT_/)) { $allseqs->{$p->{accession}}->{genomic} = $l->{accession}; $allseqs->{$p->{accession}}->{type} = $p->{type}; my $tmp = safeval($p, '{genomic-coords}->[0]->{mix}->[0]->{int}') || safeval($p, '{genomic-coords}->[0]->{int}'); $allseqs->{$p->{accession}}->{exons} = $tmp if($tmp); if($p->{products}) { foreach my $p1 (@{$p->{products}}) { ############################################################# # now get protein location - only do the work when necessary $t = $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}; unless($t && $t->{from}) { my $tmp = safeval($p1, '{genomic-coords}->[0]->{packed-int}') || safeval($p1, '{genomic-coords}->[0]->{int}'); if($tmp) { $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{from} = $tmp->[0]->{from}; $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{to} = $tmp->[$#$tmp]->{to}; } } } } } } addxref($llgene, 'REFSEQ', 'acc' => $l->{accession}, 'gi' => safeval($l, '{seqs}->[0]->{int}->[0]->{id}->[0]->{gi}')); # trans and prots xrefs } } } ########################################################################## # now that we got all info for transcripts and proteins # we should assemble info into variants, transcripts and proteins, # (dealing with these objects is by far the most time-consuming task # in extracting Entrez Gene data) # note again I edited out project-specific stuff, so the only purpose is # to show you where data items are, not to store everything my (@variants, @trans, $genestart, $geneend, $genomeacc); foreach my $dnaacc (keys %$allseqs) { my ($variant, $trans, $xref); my $t = $allseqs->{$dnaacc}; if($t->{variantcomment}) { $variant->{comment} = $t->{variantcomment}; } ############################################ # work on transcript $trans->{assembly} = $t->{assembly} if $t->{assembly}; $trans->{type} = $t->{type} if $t->{type}; $trans->{comment} = "Data from $t->{genomic}" if($t->{genomic}); $genomeacc = $t->{genomic} unless $genomeacc; my $dealwithtransxref if($t->{acc} || $t->{gi}); # db should be refseq # now exon if($t->{exons}) { if($t->{genomic} eq $genomeacc) # only process when the trans is on same contig as first one { $genestart = $t->{exons}->[0]->{from} if(!$genestart || $t->{exons}->[0]->{from} < $genestart); $geneend = $t->{exons}->[$#{$t->{exons}}]->{to} if($t->{exons}->[$#{$t->{exons}}]->{to} > $geneend); } foreach my $exon (@{$t->{exons}}) { $trans->{strand} = $exon->{strand} unless $trans->{strand}; my $start = $exon->{from}; # follow Entrez Gene style, start is always smaller than end my $end = $exon->{to}; my $coordSys = "$t->{genomic}"; } # finally protein if($t->{protein}) { foreach my $pacc (keys %{$t->{protein}}) { my $p = $t->{protein}->{$pacc}; my $deal_with_prot_xref if($p->{acc}); # db should be refseq my $add_ccds_xref if($p->{ccds}); # db should be CCDS my $protname = $p->{name} if($p->{name}); if($p->{from} || $p->{to}) # sometimes Entrez Gene forgets to annotate CDS start/end like for gene 574, NP_001178 { my $protcoordSys = "$t->{genomic}"; my $protstart = $p->{from} if $p->{from}; my $protend = $p->{to} if $p->{to}; } # domains if($p->{dom}) { foreach my $dom (@{$p->{dom}}) { my $desc = $dom->{desc}; my $score = $dom->{score} if(defined $dom->{score}); my $loc = { start => $dom->{start}, end=> $dom->{end}, coordSys => "$p->{acc}" }; my $xref = $dom->{xref}; } } } } } # put transcript into variant if annotated, otherwise into transcript if($variant) { # user can decide how to store } else { # user can decide how to store } } if($genestart && $geneend) { # user can decide how to store } # tracking info about how this gene has changed if(safeval($seq, '{track-info}->[0]->{current-id}')) { my (@ids, $newegid, $newllid); foreach my $id (@{$seq->{'track-info'}->[0]->{'current-id'}}) { my $tmpid = safeval($id, '{tag}->[0]->{id}'); push(@ids, "$id->{db}:$tmpid"); $newegid = $tmpid if($id->{db} =~ /^GeneID$/i); $newllid = $tmpid if($id->{db} =~ /^LocusID$/i); } my $comment = "Gene moved: current IDs are: " . join(' ; ', @ids); } return $llgene; } # safely assign a value to $data->{$key} ($data must be hash) sub safeassign { my ($data, $key, $ds, $str) = @_; my $tmp = safeval($ds, $str); $data->{$key} = $tmp if $tmp; return (defined $tmp)? 1 : 0; } # safely extracts a value, another choice is to simply use # eval in-line, if it fails, it fails. Probably faster, but can't # give feedback in-line (always has to add a couple lines dealing with # $@ for error reporting), might still be worth it though because # of the speed. User can make his/her own choice here. sub safeval { my ($ds, $str) = @_; # data structure and string (we need $ds passed in because we use strict) my @items = split('->', $str); foreach (@items) { my $tmp; if(($tmp) = /\[(\d+)\]/) { return undef unless(ref($ds) eq 'ARRAY' && @$ds > $tmp); $ds = $ds->[$tmp]; } elsif(($tmp) = /^{(.*?)}$/) { return undef unless(ref($ds) eq 'HASH' && $ds->{$tmp}); # this is not ideal (since one might want to return '' instead of undef when this hash value is defined as ''), but correct for our situations $ds = $ds->{$tmp}; } else { die "wrong syntax for string:$str\n"; } } return $ds; } sub addxrefs { # left for user implementation since it's project-specific } sub addxref { # left for user implementation since it's project-specific } # used for making xrefs listed under comments sub makexref { my $c = shift; my $db = safeval($c, '{source}->[0]->{src}->[0]->{db}'); my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}') || safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}'); # change the following as suited for your project $id =~ $1 if($id =~ /^"(.*)"$/); if($db =~ /GeneID/) { $db = 'ENTREZGENE'; } elsif($db =~ /Nucleotide/) { $db = 'GENBANK'; } return ($db, $id); } sub trim { my @data = @_; map { s/^\s+//; s/\s+$//; } (@data); return wantarray ? @data : $data[0]; }