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COL5A1 (collagen type V alpha 1 chain)

Identity

Alias_namescollagen type V alpha 1
Other aliasEDSC
HGNC (Hugo) COL5A1
LocusID (NCBI) 1289
Atlas_Id 53661
Location 9q34.3  [Link to chromosome band 9q34]
Location_base_pair Starts at 134641805 and ends at 134844842 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ACTG1 (17q25.3) / COL5A1 (9q34.3)COL5A1 (9q34.3) / COL5A1 (9q34.3)COL5A1 (9q34.3) / PTGES2 (9q34.11)
EDF1 (9q34.3) / COL5A1 (9q34.3)EHMT1 (9q34.3) / COL5A1 (9q34.3)SPCS2 (11q13.4) / COL5A1 (9q34.3)
ZNF83 (19q13.41) / COL5A1 (9q34.3)COL5A1 9q34.3 / PTGES2 9q34.11

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)COL5A1   2209
LRG (Locus Reference Genomic)LRG_737
Cards
Entrez_Gene (NCBI)COL5A1  1289  collagen type V alpha 1 chain
AliasesEDSC
GeneCards (Weizmann)COL5A1
Ensembl hg19 (Hinxton)ENSG00000130635 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000130635 [Gene_View]  chr9:134641805-134844842 [Contig_View]  COL5A1 [Vega]
ICGC DataPortalENSG00000130635
TCGA cBioPortalCOL5A1
AceView (NCBI)COL5A1
Genatlas (Paris)COL5A1
WikiGenes1289
SOURCE (Princeton)COL5A1
Genetics Home Reference (NIH)COL5A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL5A1  -     chr9:134641805-134844842 +  9q34.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL5A1  -     9q34.3   [Description]    (hg19-Feb_2009)
EnsemblCOL5A1 - 9q34.3 [CytoView hg19]  COL5A1 - 9q34.3 [CytoView hg38]
Mapping of homologs : NCBICOL5A1 [Mapview hg19]  COL5A1 [Mapview hg38]
OMIM120215   130000   
Gene and transcription
Genbank (Entrez)AB209864 AB371583 AI190929 AK057231 AK122763
RefSeq transcript (Entrez)NM_000093 NM_001278074
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL5A1
Cluster EST : UnigeneHs.210283 [ NCBI ]
CGAP (NCI)Hs.210283
Alternative Splicing GalleryENSG00000130635
Gene ExpressionCOL5A1 [ NCBI-GEO ]   COL5A1 [ EBI - ARRAY_EXPRESS ]   COL5A1 [ SEEK ]   COL5A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL5A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1289
GTEX Portal (Tissue expression)COL5A1
Human Protein AtlasENSG00000130635-COL5A1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP20908   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP20908  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP20908
Splice isoforms : SwissVarP20908
PhosPhoSitePlusP20908
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)  LamG (SM00282)  TSPN (SM00210)  
Domain structure : Prodom (Prabi Lyon)Fib_collagen_C (PD002078)   
Conserved Domain (NCBI)COL5A1
DMDM Disease mutations1289
Blocks (Seattle)COL5A1
PDB (SRS)1A89    1A9A   
PDB (PDBSum)1A89    1A9A   
PDB (IMB)1A89    1A9A   
PDB (RSDB)1A89    1A9A   
Structural Biology KnowledgeBase1A89    1A9A   
SCOP (Structural Classification of Proteins)1A89    1A9A   
CATH (Classification of proteins structures)1A89    1A9A   
SuperfamilyP20908
Human Protein Atlas [tissue]ENSG00000130635-COL5A1 [tissue]
Peptide AtlasP20908
HPRD00368
IPIIPI00844090   IPI00552815   
Protein Interaction databases
DIP (DOE-UCLA)P20908
IntAct (EBI)P20908
FunCoupENSG00000130635
BioGRIDCOL5A1
STRING (EMBL)COL5A1
ZODIACCOL5A1
Ontologies - Pathways
QuickGOP20908
Ontology : AmiGOblood vessel development  heart morphogenesis  integrin binding  extracellular matrix structural constituent  extracellular region  collagen type V trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  cell adhesion  heparin binding  cell migration  extracellular matrix organization  0030199 TARGET=Amigo>collagen fibril organization  collagen fibril organization  collagen catabolic process  extracellular matrix  extracellular matrix  collagen biosynthetic process  wound healing, spreading of epidermal cells  tendon development  proteoglycan binding  skin development  integrin biosynthetic process  metal ion binding  platelet-derived growth factor binding  eye morphogenesis  regulation of cellular component organization  extracellular exosome  supramolecular fiber organization  negative regulation of endodermal cell differentiation  
Ontology : EGO-EBIblood vessel development  heart morphogenesis  integrin binding  extracellular matrix structural constituent  extracellular region  collagen type V trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  cell adhesion  heparin binding  cell migration  extracellular matrix organization  collagen fibril organization  collagen fibril organization  collagen catabolic process  extracellular matrix  extracellular matrix  collagen biosynthetic process  wound healing, spreading of epidermal cells  tendon development  proteoglycan binding  skin development  integrin biosynthetic process  metal ion binding  platelet-derived growth factor binding  eye morphogenesis  regulation of cellular component organization  extracellular exosome  supramolecular fiber organization  negative regulation of endodermal cell differentiation  
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption    Amoebiasis   
NDEx NetworkCOL5A1
Atlas of Cancer Signalling NetworkCOL5A1
Wikipedia pathwaysCOL5A1
Orthology - Evolution
OrthoDB1289
GeneTree (enSembl)ENSG00000130635
Phylogenetic Trees/Animal Genes : TreeFamCOL5A1
HOVERGENP20908
HOGENOMP20908
Homologs : HomoloGeneCOL5A1
Homology/Alignments : Family Browser (UCSC)COL5A1
Gene fusions - Rearrangements
Fusion : MitelmanCOL5A1/PTGES2 [9q34.3/9q34.11]  
Fusion: TCGACOL5A1 9q34.3 PTGES2 9q34.11 BLCA
Fusion: Tumor Portal COL5A1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL5A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL5A1
dbVarCOL5A1
ClinVarCOL5A1
1000_GenomesCOL5A1 
Exome Variant ServerCOL5A1
ExAC (Exome Aggregation Consortium)ENSG00000130635
GNOMAD BrowserENSG00000130635
Genetic variants : HAPMAP1289
Genomic Variants (DGV)COL5A1 [DGVbeta]
DECIPHERCOL5A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL5A1 
Mutations
ICGC Data PortalCOL5A1 
TCGA Data PortalCOL5A1 
Broad Tumor PortalCOL5A1
OASIS PortalCOL5A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL5A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL5A1
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
LOVD (Leiden Open Variation Database)Ehlers Danlos Syndrome Variant Database
BioMutasearch COL5A1
DgiDB (Drug Gene Interaction Database)COL5A1
DoCM (Curated mutations)COL5A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL5A1 (select a term)
intoGenCOL5A1
Cancer3DCOL5A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120215    130000   
Orphanet4042    12007    12006   
MedgenCOL5A1
Genetic Testing Registry COL5A1
NextProtP20908 [Medical]
TSGene1289
GENETestsCOL5A1
Target ValidationCOL5A1
Huge Navigator COL5A1 [HugePedia]
snp3D : Map Gene to Disease1289
BioCentury BCIQCOL5A1
ClinGenCOL5A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1289
Chemical/Pharm GKB GenePA26724
Clinical trialCOL5A1
Miscellaneous
canSAR (ICR)COL5A1 (select the gene name)
Probes
Litterature
PubMed126 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL5A1
EVEXCOL5A1
GoPubMedCOL5A1
iHOPCOL5A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Nov 9 12:45:30 CET 2017

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