LocusLink sequence format
From BioPerl
Description
LocusLink is no longer maintained at NCBI, it has been replaced by the Entrez Gene database. It is included here for historical interest and legacy use.
This file format can be parsed by the Bio::SeqIO system using the Bio::SeqIO::locuslink module.
Example
>>26 LOCUSID: 26 LOCUS_CONFIRMED: yes LOCUS_TYPE: gene with protein product, function known or inferred ORGANISM: Homo sapiens STATUS: REVIEWED NM: NM_001091|4501850|na NP: NP_001082|4501851 CDD: Copper amine oxidase|pfam01179|1775|na|6.883370e+02 PRODUCT: amiloride binding protein 1 precursor ASSEMBLY: X78212 CONTIG: NT_007914.10|22047859|na|11083771|11092582|+|7|reference EVID: supported by alignment with mRNA XM: XM_032220|14745402|na XP: XP_032220|14745403|na ACCNUM: X78212|463242|na|na|na TYPE: g PROT: CAA55046|463243 ACCNUM: BC014093|15559450|na|na|na TYPE: m PROT: AAH14093|15559451 ACCNUM: M55602|387655|na|na|na TYPE: m PROT: AAA58358|177960 ACCNUM: U11862|533535|na|na|na TYPE: m PROT: AAC50270|533536 ACCNUM: U11863|533537|na|na|na TYPE: m PROT: AAB60381|533538 OFFICIAL_SYMBOL: ABP1 OFFICIAL_GENE_NAME: amiloride binding protein 1 (amine oxidase (copper-containing)) ALIAS_SYMBOL: DAO ALIAS_SYMBOL: AOC1 PREFERRED_PRODUCT: amiloride binding protein 1 precursor SUMMARY: Summary: This gene encodes a membrane glycoprotein that binds amiloride, a diuretic that acts by closing epithelial sodium ion channels. Experimental evidence indicates, however, that the formation of an amiloride sensitive, sodium channel requires complex formation with additional proteins. Although an association was proposed between this gene and cystic fibrosis, a disorder involving sodium and water imbalance in the lungs, genetic evidence showed that it was not involved in producing that disorder. CHR: 7 STS: RH71199|7|8014|na|seq_map|epcr STS: ABP1|7|32801|ABP1|seq_map|epcr COMP: 10090|Abp1|6|6 cM|76507|7|ABP1|ncbi_mgd COMP: 10090|1600012D06Rik|6|6 cM|76507|7|ABP1|ucsc_mgd ALIAS_PROT: diamine oxidase ALIAS_PROT: Amiloride-binding protein-1 UNIGENE: Hs.75741 BUTTON: unigene.gif LINK: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=75741 OMIM: 104610 ECNUM: 1.4.3.6 MAP: 7q34-q36|RefSeq|C| MAPLINK: default_human_gene|ABP1 BUTTON: snp.gif LINK: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=26 BUTTON: homol.gif LINK: http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=26[loc]&TAXID=9606 BUTTON: gdb.gif LINK: http://gdbwww.gdb.org/gdb-bin/genera/accno?GDB:127105 BUTTON: ensembl.gif LINK: http://www.ensembl.org/Homo_sapiens/contigview?geneid=NM_001091 BUTTON: ucsc.gif LINK: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg12&position=NM_001091 DB_DESCR: GeneCards DB_LINK: http://bioinformatics.weizmann.ac.il/cards-bin/carddisp?ABP1 DB_DESCR: KEGG pathway: Tyrosine metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00350 DB_DESCR: KEGG pathway: Histidine metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00340 DB_DESCR: KEGG pathway: Tryptophan metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00380 DB_DESCR: KEGG pathway: beta-Alanine metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00410 DB_DESCR: KEGG pathway: Alkaloid biosynthesis II DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00960 DB_DESCR: KEGG pathway: Phenylalanine metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00360 DB_DESCR: KEGG pathway: Arginine and proline metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00330 DB_DESCR: KEGG pathway: Glycine, serine and threonine metabolism DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00260 PMID: 11603849,8595053,8182053,8144586,2217167,1356107 GRIF: 11603849|could be detected at the feto-maternal interface of human SUMFUNC: Diamine oxidase (D-amino-acid oxidase histaminase, amiloride-binding protein); deaminates putrescine and histamine|Proteome GO: biological process|metabolism|NR|GO:0008152|Proteome|na GO: cellular component|peroxisome|NR|GO:0005777|Proteome|na GO: molecular function|amine oxidase|E|GO:0008131|Proteome|8144586 GO: molecular function|drug binding|NR|GO:0008144|Proteome|na EXTANNOT: cellular role|Other metabolism|E|Proteome|1356107 EXTANNOT: biochemical function|Oxidoreductase|E|Proteome|1356107 EXTANNOT: biochemical function|Small molecule-binding protein|E|Proteome|8182053
