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COL9A3 (collagen type IX alpha 3 chain)

Identity

Alias_namescollagen, type IX, alpha 3
Alias_symbol (synonym)IDD
MED
EDM3
FLJ90759
DJ885L7.4.1
Other alias
HGNC (Hugo) COL9A3
LocusID (NCBI) 1299
Atlas_Id 62004
Location 20q13.33  [Link to chromosome band 20q13]
Location_base_pair Starts at 62817062 and ends at 62841159 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
COL9A3 (20q13.33) / ELK3 (12q23.1)GDE1 (16p12.3) / COL9A3 (20q13.33)

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)COL9A3   2219
Cards
Entrez_Gene (NCBI)COL9A3  1299  collagen type IX alpha 3 chain
AliasesDJ885L7.4.1; EDM3; IDD; MED
GeneCards (Weizmann)COL9A3
Ensembl hg19 (Hinxton)ENSG00000092758 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000092758 [Gene_View]  chr20:62817062-62841159 [Contig_View]  COL9A3 [Vega]
ICGC DataPortalENSG00000092758
TCGA cBioPortalCOL9A3
AceView (NCBI)COL9A3
Genatlas (Paris)COL9A3
WikiGenes1299
SOURCE (Princeton)COL9A3
Genetics Home Reference (NIH)COL9A3
Genomic and cartography
GoldenPath hg38 (UCSC)COL9A3  -     chr20:62817062-62841159 +  20q13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL9A3  -     20q13.33   [Description]    (hg19-Feb_2009)
EnsemblCOL9A3 - 20q13.33 [CytoView hg19]  COL9A3 - 20q13.33 [CytoView hg38]
Mapping of homologs : NCBICOL9A3 [Mapview hg19]  COL9A3 [Mapview hg38]
OMIM120270   600969   603932   
Gene and transcription
Genbank (Entrez)AK075240 BC004412 BC007574 BC011705 DQ598196
RefSeq transcript (Entrez)NM_001853
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL9A3
Cluster EST : UnigeneHs.716639 [ NCBI ]
CGAP (NCI)Hs.716639
Alternative Splicing GalleryENSG00000092758
Gene ExpressionCOL9A3 [ NCBI-GEO ]   COL9A3 [ EBI - ARRAY_EXPRESS ]   COL9A3 [ SEEK ]   COL9A3 [ MEM ]
Gene Expression Viewer (FireBrowse)COL9A3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1299
GTEX Portal (Tissue expression)COL9A3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14050   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14050  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14050
Splice isoforms : SwissVarQ14050
PhosPhoSitePlusQ14050
Domains : Interpro (EBI)Collagen   
Domain families : Pfam (Sanger)Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01391   
Conserved Domain (NCBI)COL9A3
DMDM Disease mutations1299
Blocks (Seattle)COL9A3
PDB (SRS)5CTD    5CTI    5CVA    5CVB   
PDB (PDBSum)5CTD    5CTI    5CVA    5CVB   
PDB (IMB)5CTD    5CTI    5CVA    5CVB   
PDB (RSDB)5CTD    5CTI    5CVA    5CVB   
Structural Biology KnowledgeBase5CTD    5CTI    5CVA    5CVB   
SCOP (Structural Classification of Proteins)5CTD    5CTI    5CVA    5CVB   
CATH (Classification of proteins structures)5CTD    5CTI    5CVA    5CVB   
SuperfamilyQ14050
Human Protein AtlasENSG00000092758
Peptide AtlasQ14050
HPRD00374
IPIIPI00289999   IPI00386694   IPI00607653   
Protein Interaction databases
DIP (DOE-UCLA)Q14050
IntAct (EBI)Q14050
FunCoupENSG00000092758
BioGRIDCOL9A3
STRING (EMBL)COL9A3
ZODIACCOL9A3
Ontologies - Pathways
QuickGOQ14050
Ontology : AmiGOextracellular region  proteinaceous extracellular matrix  collagen type IX trimer  endoplasmic reticulum lumen  male gonad development  female gonad development  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  
Ontology : EGO-EBIextracellular region  proteinaceous extracellular matrix  collagen type IX trimer  endoplasmic reticulum lumen  male gonad development  female gonad development  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  
Pathways : KEGGProtein digestion and absorption   
NDEx NetworkCOL9A3
Atlas of Cancer Signalling NetworkCOL9A3
Wikipedia pathwaysCOL9A3
Orthology - Evolution
OrthoDB1299
GeneTree (enSembl)ENSG00000092758
Phylogenetic Trees/Animal Genes : TreeFamCOL9A3
HOVERGENQ14050
HOGENOMQ14050
Homologs : HomoloGeneCOL9A3
Homology/Alignments : Family Browser (UCSC)COL9A3
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL9A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL9A3
dbVarCOL9A3
ClinVarCOL9A3
1000_GenomesCOL9A3 
Exome Variant ServerCOL9A3
ExAC (Exome Aggregation Consortium)COL9A3 (select the gene name)
Genetic variants : HAPMAP1299
Genomic Variants (DGV)COL9A3 [DGVbeta]
DECIPHERCOL9A3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL9A3 
Mutations
ICGC Data PortalCOL9A3 
TCGA Data PortalCOL9A3 
Broad Tumor PortalCOL9A3
OASIS PortalCOL9A3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL9A3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL9A3
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)Mendelian genes
BioMutasearch COL9A3
DgiDB (Drug Gene Interaction Database)COL9A3
DoCM (Curated mutations)COL9A3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL9A3 (select a term)
intoGenCOL9A3
Cancer3DCOL9A3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120270    600969    603932   
Orphanet17597    19597   
MedgenCOL9A3
Genetic Testing Registry COL9A3
NextProtQ14050 [Medical]
TSGene1299
GENETestsCOL9A3
Target ValidationCOL9A3
Huge Navigator COL9A3 [HugePedia]
snp3D : Map Gene to Disease1299
BioCentury BCIQCOL9A3
ClinGenCOL9A3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1299
Chemical/Pharm GKB GenePA26735
Clinical trialCOL9A3
Miscellaneous
canSAR (ICR)COL9A3 (select the gene name)
Probes
Litterature
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL9A3
EVEXCOL9A3
GoPubMedCOL9A3
iHOPCOL9A3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 15:44:14 CEST 2017

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