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COL5A3 (collagen type V alpha 3 chain)

Identity

Alias_namescollagen type V alpha 3
Other alias-
HGNC (Hugo) COL5A3
LocusID (NCBI) 50509
Atlas_Id 53918
Location 19p13.2  [Link to chromosome band 19p13]
Location_base_pair Starts at 9959561 and ends at 10010471 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ASPSCR1 (17q25.3) / COL5A3 (19p13.2)OLFM2 (19p13.2) / COL5A3 (19p13.2)ASPSCR1 17q25.3 / COL5A3 19p13.2
OLFM2 19p13.2 / COL5A3 19p13.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)COL5A3   14864
Cards
Entrez_Gene (NCBI)COL5A3  50509  collagen type V alpha 3 chain
Aliases
GeneCards (Weizmann)COL5A3
Ensembl hg19 (Hinxton)ENSG00000080573 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000080573 [Gene_View]  chr19:9959561-10010471 [Contig_View]  COL5A3 [Vega]
ICGC DataPortalENSG00000080573
TCGA cBioPortalCOL5A3
AceView (NCBI)COL5A3
Genatlas (Paris)COL5A3
WikiGenes50509
SOURCE (Princeton)COL5A3
Genetics Home Reference (NIH)COL5A3
Genomic and cartography
GoldenPath hg38 (UCSC)COL5A3  -     chr19:9959561-10010471 -  19p13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL5A3  -     19p13.2   [Description]    (hg19-Feb_2009)
EnsemblCOL5A3 - 19p13.2 [CytoView hg19]  COL5A3 - 19p13.2 [CytoView hg38]
Mapping of homologs : NCBICOL5A3 [Mapview hg19]  COL5A3 [Mapview hg38]
OMIM120216   
Gene and transcription
Genbank (Entrez)AB209175 AF177941 BQ006883
RefSeq transcript (Entrez)NM_015719
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL5A3
Cluster EST : UnigeneHs.235368 [ NCBI ]
CGAP (NCI)Hs.235368
Alternative Splicing GalleryENSG00000080573
Gene ExpressionCOL5A3 [ NCBI-GEO ]   COL5A3 [ EBI - ARRAY_EXPRESS ]   COL5A3 [ SEEK ]   COL5A3 [ MEM ]
Gene Expression Viewer (FireBrowse)COL5A3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)50509
GTEX Portal (Tissue expression)COL5A3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP25940   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP25940  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP25940
Splice isoforms : SwissVarP25940
PhosPhoSitePlusP25940
Domaine pattern : Prosite (Expaxy)NC1_FIB (PS51461)   
Domains : Interpro (EBI)Collagen    ConA-like_dom    Fib_collagen_C    Laminin_G   
Domain families : Pfam (Sanger)COLFI (PF01410)    Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01410    pfam01391   
Domain families : Smart (EMBL)COLFI (SM00038)  TSPN (SM00210)  
Domain structure : Prodom (Prabi Lyon)Fib_collagen_C (PD002078)   
Conserved Domain (NCBI)COL5A3
DMDM Disease mutations50509
Blocks (Seattle)COL5A3
SuperfamilyP25940
Human Protein AtlasENSG00000080573
Peptide AtlasP25940
HPRD00369
IPIIPI00018279   
Protein Interaction databases
DIP (DOE-UCLA)P25940
IntAct (EBI)P25940
FunCoupENSG00000080573
BioGRIDCOL5A3
STRING (EMBL)COL5A3
ZODIACCOL5A3
Ontologies - Pathways
QuickGOP25940
Ontology : AmiGOextracellular matrix structural constituent  collagen binding  extracellular region  collagen type V trimer  endoplasmic reticulum lumen  cell-matrix adhesion  heparin binding  extracellular matrix organization  collagen fibril organization  collagen catabolic process  proteoglycan binding  skin development  extracellular exosome  
Ontology : EGO-EBIextracellular matrix structural constituent  collagen binding  extracellular region  collagen type V trimer  endoplasmic reticulum lumen  cell-matrix adhesion  heparin binding  extracellular matrix organization  collagen fibril organization  collagen catabolic process  proteoglycan binding  skin development  extracellular exosome  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption    Amoebiasis   
NDEx NetworkCOL5A3
Atlas of Cancer Signalling NetworkCOL5A3
Wikipedia pathwaysCOL5A3
Orthology - Evolution
OrthoDB50509
GeneTree (enSembl)ENSG00000080573
Phylogenetic Trees/Animal Genes : TreeFamCOL5A3
HOVERGENP25940
HOGENOMP25940
Homologs : HomoloGeneCOL5A3
Homology/Alignments : Family Browser (UCSC)COL5A3
Gene fusions - Rearrangements
Fusion : MitelmanASPSCR1/COL5A3 [17q25.3/19p13.2]  [t(17;19)(q25;p13)]  
Fusion : MitelmanOLFM2/COL5A3 [19p13.2/19p13.2]  [t(19;19)(p13;p13)]  
Fusion: TCGAASPSCR1 17q25.3 COL5A3 19p13.2 BRCA
Fusion: TCGAOLFM2 19p13.2 COL5A3 19p13.2 HNSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL5A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL5A3
dbVarCOL5A3
ClinVarCOL5A3
1000_GenomesCOL5A3 
Exome Variant ServerCOL5A3
ExAC (Exome Aggregation Consortium)COL5A3 (select the gene name)
Genetic variants : HAPMAP50509
Genomic Variants (DGV)COL5A3 [DGVbeta]
DECIPHERCOL5A3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL5A3 
Mutations
ICGC Data PortalCOL5A3 
TCGA Data PortalCOL5A3 
Broad Tumor PortalCOL5A3
OASIS PortalCOL5A3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL5A3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL5A3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch COL5A3
DgiDB (Drug Gene Interaction Database)COL5A3
DoCM (Curated mutations)COL5A3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL5A3 (select a term)
intoGenCOL5A3
Cancer3DCOL5A3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120216   
Orphanet
MedgenCOL5A3
Genetic Testing Registry COL5A3
NextProtP25940 [Medical]
TSGene50509
GENETestsCOL5A3
Huge Navigator COL5A3 [HugePedia]
snp3D : Map Gene to Disease50509
BioCentury BCIQCOL5A3
ClinGenCOL5A3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD50509
Chemical/Pharm GKB GenePA26726
Clinical trialCOL5A3
Miscellaneous
canSAR (ICR)COL5A3 (select the gene name)
Probes
Litterature
PubMed14 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL5A3
EVEXCOL5A3
GoPubMedCOL5A3
iHOPCOL5A3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri May 19 12:11:21 CEST 2017

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