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collagen, type I

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GeneName col1a1
Aliases ENSDARG:ENSDARG00000012405; cb21, sb: cb21, sb:cb384, alpha1(I), wu:fa99c12, wu:fb02c06, col1a1
Description collagen, type I
GenomicLocation chromosome 3 23512288-23530699 forward strand
ExternalIDs Entrez:337158; EMBL:AY380817; UniGene:20097; ZFIN:ZDB-GENE-030131-9102;
TranscriptID ENSDART:ENSDART00000009393 ENSDART:ENSDART00000047010 ENSDART:ENSDART00000140586
mRNA NCBI:NM_199214
GeneDescription Zebrafish col1a1 has an human ortholog COL1A1. col1a1 is one of the three subunits of collagen protein.
GeneFunction Fisher et al., 2003 successfully characterized a zebrafish skeletal mutant as a model for human osteogenesis imperfecta. col1a1 is strongly expressed in the larval fin folds and in numerous bony skeletal elements during development. The group has shown that in chi mutants there is substitution of a glycine to aspertate which interrupts the conserved triplet repeat domain. Analysis of bone in chi mutant fish by electron microscopy has revealed defects in the collagenous matrix and accumulation of collagen fibrils in the endoplasmic reticulum of osteoblasts .
GeneCloning col1a1 was isolated from zebrafish whole embryo (72 hpf) , cloned in vector pCMV-SPORT6.1 in DH10B phagemid in the clone library NCI_CGAP_ZEmb3.( GI:171846459) source : Zebrafish Gene Collection
GeneStructure The gene encodes for three transcritps.Transcript (ENSDART00000009393) consist of51exons and is 5,797bps in length. The product (ENSDARP00000003177) Consist of 1447 residues. Transcript (ENSDART00000047010) consist of 52 exons and is 4,861bps in length. The product (ENSDARP00000047009) Consist of 1366 residues. Transcript (ENSDART00000140586) consist of 5 exons and is 697 bps in length. It does not code for any protein
Protein ENSDARP00000003177 ENSDARP00000047009
ProteinDomainandFamilies has domain InterPro:IPR008160; InterPro:IPR001007; InterPro:IPR000885;
Motifs has motif Prosite:PS01208; PFAM:PF00093; PFAM:PF01391; PFAM:PF01410; PRINTS:PR01845; PRINTS:PR01878;
Expression ArrayExpress:ENSDARG00000012405;
GeneOntology GO:0005737; GO:0005581; GO:0006817; GO:0030574; GO:0030278; GO:0005201;
Orthologs Gene:1277
VariationAndRepeats RSID:rs41171904; RSID:rs41171904; RSID:rs40969062; RSID:rs40969062; RSID:rs41075098; RSID:rs41075098; RSID:rs41025812; RSID:rs41025812; RSID:rs40981609; RSID:rs40981609; RSID:rs40866764; RSID:rs40866764; RSID:rs40771828; RSID:rs40771828; RSID:rs40870559; RSID:rs40870559; RSID:rs40908477; RSID:rs40908477; RSID:rs41163511; RSID:rs41163511; RSID:rs41175659; RSID:rs41175659; RSID:rs40804268; RSID:rs40804268; RSID:rs41086275; RSID:rs41086275; RSID:rs40887439; RSID:rs40887439; RSID:rs40730519; RSID:rs40730519; RSID:rs40921499; RSID:rs40921499; RSID:rs40772942; RSID:rs40772942; RSID:rs40767464; RSID:rs40767464; RSID:rs41192436; RSID:rs41192436; RSID:rs40911085; RSID:rs40911085; RSID:rs40895027; RSID:rs40895027; RSID:rs41017474; RSID:rs41017474; RSID:rs40696612; RSID:rs40696612; RSID:rs41110014; RSID:rs41110014; RSID:rs40956112; RSID:rs40956112; RSID:rs40714551; RSID:rs40714551; RSID:rs41202982; RSID:rs41202982; RSID:rs40634477; RSID:rs40634477; RSID:rs40921592; RSID:rs40921592; RSID:rs40920741; RSID:rs40920741; RSID:rs40680477; RSID:rs40680477; RSID:rs40908239; RSID:rs40908239; RSID:rs40797570; RSID:rs40797570; RSID:rs41077336; RSID:rs41077336; RSID:rs41049705; RSID:rs41049705; RSID:rs41104898; RSID:rs41104898; RSID:rs40825772; RSID:rs40825772; RSID:rs40959990; RSID:rs40959990; RSID:rs41126944; RSID:rs41126944; RSID:rs40691110; RSID:rs40691110; RSID:rs41197411; RSID:rs41197411; RSID:rs41195228; RSID:rs41195228; RSID:rs40694807; RSID:rs40694807; RSID:rs41212894; RSID:rs41212894; RSID:rs40807070; RSID:rs40807070; RSID:rs40874228; RSID:rs40874228; RSID:rs41227939; RSID:rs41227939; RSID:rs41180279; RSID:rs41180279; RSID:rs40798889; RSID:rs40798889; RSID:rs41160439; RSID:rs41160439; RSID:rs41063016; RSID:rs41063016; RSID:rs40710280; RSID:rs40710280; RSID:rs40824481; RSID:rs40824481; RSID:rs41205802; RSID:rs41205802; RSID:rs40857382; RSID:rs40857382; RSID:rs41056121; RSID:rs41056121; RSID:rs40954887; RSID:rs40954887; RSID:rs40780941; RSID:rs40780941; RSID:rs40875922; RSID:rs40875922; RSID:rs41229019; RSID:rs41229019; RSID:rs40963812; RSID:rs40963812; RSID:rs41185393; RSID:rs41185393; RSID:rs40750099; RSID:rs40750099; RSID:rs41161706; RSID:rs41161706; RSID:rs41150768; RSID:rs41150768; RSID:rs41150768; RSID:rs41051026; RSID:rs41051026; RSID:rs41051026; RSID:rs40958150; RSID:rs40958150; RSID:rs40958150; RSID:rs41128394; RSID:rs41128394; RSID:rs41128394; RSID:rs40612213; RSID:rs40612213; RSID:rs40612213; RSID:rs41245617; RSID:rs41245617; RSID:rs41245617; RSID:rs40750589; RSID:rs40750589; RSID:rs40750589; RSID:rs40813669; RSID:rs40813669; RSID:rs40813669; RSID:rs40829612; RSID:rs40829612; RSID:rs40829612; RSID:rs40986002; RSID:rs40986002; RSID:rs40986002; RSID:rs40746514; RSID:rs40746514; RSID:rs40746514; RSID:rs40860431; RSID:rs40860431; RSID:rs40860431; RSID:rs41064850; RSID:rs41064850; RSID:rs41064850; RSID:rs41074275; RSID:rs41074275; RSID:rs41074275; RSID:rs41238658; RSID:rs41238658; RSID:rs41238658; RSID:rs40979917; RSID:rs40979917; RSID:rs40979917; RSID:rs41042587; RSID:rs41042587; RSID:rs41042587; RSID:rs41086236; RSID:rs41086236; RSID:rs41086236; RSID:rs40858508; RSID:rs40858508; RSID:rs40858508; RSID:rs41003305; RSID:rs41003305; RSID:rs41003305; RSID:rs40693490; RSID:rs40693490; RSID:rs40693490; RSID:rs41055999; RSID:rs41055999; RSID:rs41055999; RSID:rs41125863; RSID:rs41125863; RSID:rs41125863; RSID:rs41124362; RSID:rs41124362; RSID:rs41124362; RSID:rs40820268; RSID:rs40820268; RSID:rs40820268; RSID:rs41070283; RSID:rs41070283; RSID:rs41070283

RelatedPubMedArticles Fisher S, Jagadeeswaran P, Halpern ME. Radiographic analysis of zebrafish skeletal defects. Dev Biol. 2003 Dec 1;264(1):64-76.NCBI Resource Coordinators.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41(Database issue):D8-D20. 2013. PMID:23193264
Kersey, P. J.; Allen, J. E.; Christensen, M.; et al.: Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2013. PMID:24163254
Sigrist, C. J. A.; de, Castro, E; Cerutti, L; Cuche, B. A.; Hulo, N.; Bridge, A.; Bougueleret, L. Xenarios, I.: New and continuing developments at PROSITE. Nucleic Acids Res. doi: 10.1093/nar/gks1067. 2012. PMID:23161676
Punta, M.; Coggill, P. C.; Eberhardt, et al.: The Pfam protein families database. Nucleic Acids Res. 40(Database Issue):D290-D301. 2012. PMID:22127870
Hunter, S.; Jones P.; Mitchell A.; et al.: Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. doi: 10.1093/nar/gkr948. 2011. PMID:22096229
Carbon, S.; Ireland, A.; Mungall, C. J.; Shu, S.; Marshall, B.; Lewis, S.; AMIGO Hub; Web Presence Working Group.: AMIGO: online access to ontology and annotation data. Bioinformatics. 25(2):288-9. 2009. PMID:19033274
Ashburner, M.; Ball, C. A.; Blake, J. A.; et al. The Gene Ontology Consortium.: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1):25-9. 2000. PMID:10802651
Sherry, S. T.; Ward, M. H.; Kholodov, M.; Baker, J.; Phan, L.; Smigielski, E. M.; Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 1;29(1):308-11. 2001. PMID:11125122
Bradford, Y.; Conlin, T.; Dunn, N.; et al.: ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(suppl 1):D822-D829. 2011. PMID:21036866
Kapushesky, M.; Adamusiak, T.; Burdett, T.; et al.: Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 40(Database isue):D1077-81. 2012. PMID:22064864

Web resources:
NCBI: http://www.ncbi.nlm.nih.gov/
PFAM: http://pfam.sanger.ac.uk/
PROSITE: http://prosite.expasy.org/
Interpro: http://www.ebi.ac.uk/interpro/
ZFIN: http://zfin.org/
Expression Atlas (EMBL): http://www.ebi.ac.uk/gxa/
Ensembl: http://asia.ensembl.org/Danio_rerio/
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine.: http://www.ncbi.nlm.nih.gov/SNP/
PRINTS from Genomenet: http://www.genome.jp/
European Nucleotide Archive: http://www.ebi.ac.uk/ena/home
UNIGENE: http://www.ncbi.nlm.nih.gov/unigene/
AMIGO Gene Ontology: http://amigo.geneontology.org
Topic revision: r2 - 2013-07-26 - ParasSehgal
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