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COL4A1 (collagen type IV alpha 1)

Identity

Other namesBSVD
RATOR
HGNC (Hugo) COL4A1
LocusID (NCBI) 1282
Atlas_Id 43831
Location 13q34
Location_base_pair Starts at 110843088 and ends at 110959504 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
COL4A1 (13q34) / COL4A1 (13q34)COL4A1 (13q34) / ELK3 (12q23.1)COL4A1 (13q34) / ZNF827 (4q31.21)
MIRLET7BHG (22q13.31) / COL4A1 (13q34)SLC9A1 (1p36.11) / COL4A1 (13q34)UGGT2 (13q32.1) / COL4A1 (13q34)
COL4A1 13q34 / ELK3 12q23.1COL4A1 13q34 / ZNF827 4q31.21MIRLET7BHG 22q13.31 / COL4A1 13q34
UGGT2 13q32.1 / COL4A1 13q34

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)COL4A1   2202
Cards
Entrez_Gene (NCBI)COL4A1  1282  collagen type IV alpha 1
GeneCards (Weizmann)COL4A1
Ensembl hg19 (Hinxton)ENSG00000187498 [Gene_View]  chr13:110843088-110959504 [Contig_View]  COL4A1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000187498 [Gene_View]  chr13:110843088-110959504 [Contig_View]  COL4A1 [Vega]
ICGC DataPortalENSG00000187498
TCGA cBioPortalCOL4A1
AceView (NCBI)COL4A1
Genatlas (Paris)COL4A1
WikiGenes1282
SOURCE (Princeton)COL4A1
Genomic and cartography
GoldenPath hg19 (UCSC)COL4A1  -     chr13:110843088-110959504 -  13q34   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL4A1  -     13q34   [Description]    (hg38-Dec_2013)
EnsemblCOL4A1 - 13q34 [CytoView hg19]  COL4A1 - 13q34 [CytoView hg38]
Mapping of homologs : NCBICOL4A1 [Mapview hg19]  COL4A1 [Mapview hg38]
OMIM120130   175780   180000   607595   611773   614519   
Gene and transcription
Genbank (Entrez)AA678474 AB209646 AF258349 AF363672 AF400431
RefSeq transcript (Entrez)NM_001303110 NM_001845
RefSeq genomic (Entrez)NC_000013 NC_018924 NG_011544 NT_009952 NW_004929389
Consensus coding sequences : CCDS (NCBI)COL4A1
Cluster EST : UnigeneHs.17441 [ NCBI ]
CGAP (NCI)Hs.17441
Alternative Splicing : Fast-db (Paris)GSHG0008636
Alternative Splicing GalleryENSG00000187498
Gene ExpressionCOL4A1 [ NCBI-GEO ]   COL4A1 [ EBI - ARRAY_EXPRESS ]   COL4A1 [ SEEK ]   COL4A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL4A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)1282
Protein : pattern, domain, 3D structure
UniProt/SwissProtP02462 (Uniprot)
NextProtP02462  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP02462
Splice isoforms : SwissVarP02462 (Swissvar)
PhosPhoSitePlusP02462
Domaine pattern : Prosite (Expaxy)NC1_IV (PS51403)   
Domains : Interpro (EBI)C-type_lectin_fold    Collagen    Collagen_VI_NC   
Domain families : Pfam (Sanger)C4 (PF01413)    Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01413    pfam01391   
Domain families : Smart (EMBL)C4 (SM00111)  
DMDM Disease mutations1282
Blocks (Seattle)COL4A1
PDB (SRS)1LI1   
PDB (PDBSum)1LI1   
PDB (IMB)1LI1   
PDB (RSDB)1LI1   
Structural Biology KnowledgeBase1LI1   
SCOP (Structural Classification of Proteins)1LI1   
CATH (Classification of proteins structures)1LI1   
SuperfamilyP02462
Human Protein AtlasENSG00000187498
Peptide AtlasP02462
HPRD00359
IPIIPI00743696   IPI00873684   IPI01010175   IPI00816684   
Protein Interaction databases
DIP (DOE-UCLA)P02462
IntAct (EBI)P02462
FunCoupENSG00000187498
BioGRIDCOL4A1
STRING (EMBL)COL4A1
ZODIACCOL4A1
Ontologies - Pathways
QuickGOP02462
Ontology : AmiGOpatterning of blood vessels  extracellular matrix structural constituent  protein binding  extracellular region  extracellular region  collagen type IV trimer  basement membrane  endoplasmic reticulum lumen  brain development  neuromuscular junction development  extracellular matrix constituent conferring elasticity  extracellular matrix organization  collagen catabolic process  epithelial cell differentiation  extracellular matrix  extracellular matrix  platelet-derived growth factor binding  blood vessel morphogenesis  retinal blood vessel morphogenesis  renal tubule morphogenesis  cellular response to amino acid stimulus  basement membrane organization  
Ontology : EGO-EBIpatterning of blood vessels  extracellular matrix structural constituent  protein binding  extracellular region  extracellular region  collagen type IV trimer  basement membrane  endoplasmic reticulum lumen  brain development  neuromuscular junction development  extracellular matrix constituent conferring elasticity  extracellular matrix organization  collagen catabolic process  epithelial cell differentiation  extracellular matrix  extracellular matrix  platelet-derived growth factor binding  blood vessel morphogenesis  retinal blood vessel morphogenesis  renal tubule morphogenesis  cellular response to amino acid stimulus  basement membrane organization  
Pathways : BIOCARTARegulators of Bone Mineralization [Genes]    Vitamin C in the Brain [Genes]    Angiotensin-converting enzyme 2 regulates heart function [Genes]    Platelet Amyloid Precursor Protein Pathway [Genes]    Intrinsic Prothrombin Activation Pathway [Genes]    Acute Myocardial Infarction [Genes]   
Pathways : KEGGPI3K-Akt signaling pathway    Focal adhesion    ECM-receptor interaction    Protein digestion and absorption    Amoebiasis    Pathways in cancer    Small cell lung cancer   
NDEx Network
Atlas of Cancer Signalling NetworkCOL4A1
Wikipedia pathwaysCOL4A1
Orthology - Evolution
OrthoDB1282
GeneTree (enSembl)ENSG00000187498
Phylogenetic Trees/Animal Genes : TreeFamCOL4A1
Homologs : HomoloGeneCOL4A1
Homology/Alignments : Family Browser (UCSC)COL4A1
Gene fusions - Rearrangements
Fusion: TCGACOL4A1 13q34 ELK3 12q23.1 HNSC
Fusion: TCGACOL4A1 13q34 ZNF827 4q31.21 KIRC
Fusion: TCGAMIRLET7BHG 22q13.31 COL4A1 13q34 BRCA
Fusion: TCGAUGGT2 13q32.1 COL4A1 13q34 LUAD
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL4A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL4A1
dbVarCOL4A1
ClinVarCOL4A1
1000_GenomesCOL4A1 
Exome Variant ServerCOL4A1
ExAC (Exome Aggregation Consortium)COL4A1 (select the gene name)
SNP (GeneSNP Utah)COL4A1
SNP : HGBaseCOL4A1
Genetic variants : HAPMAPCOL4A1
Genomic Variants (DGV)COL4A1 [DGVbeta]
Mutations
ICGC Data PortalCOL4A1 
TCGA Data PortalCOL4A1 
Broad Tumor PortalCOL4A1
OASIS PortalCOL4A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL4A1 
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)Connective tissue disorders (VUMC Amsterdam)
BioMutasearch COL4A1
DgiDB (Drug Gene Interaction Database)COL4A1
DoCM (Curated mutations)COL4A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL4A1 (select a term)
intoGenCOL4A1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)13:110843088-110959504
CONAN: Copy Number AnalysisCOL4A1 
Mutations and Diseases : HGMDCOL4A1
OMIM120130    175780    180000    607595    611773    614519   
MedgenCOL4A1
Genetic Testing Registry COL4A1
NextProtP02462 [Medical]
TSGene1282
GENETestsCOL4A1
Huge Navigator COL4A1 [HugePedia]  COL4A1 [HugeCancerGEM]
snp3D : Map Gene to Disease1282
BioCentury BCIQCOL4A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1282
Chemical/Pharm GKB GenePA26717
Clinical trialCOL4A1
Miscellaneous
canSAR (ICR)COL4A1 (select the gene name)
Probes
Litterature
PubMed172 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL4A1
GoPubMedCOL4A1
iHOPCOL4A1
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 : Sat Apr 16 17:40:46 CEST 2016

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