LocusLink sequence format

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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LocusLink is no longer maintained at NCBI, it has been replaced by the Entrez Gene database.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
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