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COL9A3 (collagen type IX alpha 3 chain)

Identity

Alias (NCBI)DJ885L7.4.1
EDM3
IDD
MED
HGNC (Hugo) COL9A3
HGNC Alias symbIDD
MED
EDM3
FLJ90759
DJ885L7.4.1
HGNC Alias namecollagen type IX proteoglycan
HGNC Previous namecollagen, type IX, alpha 3
LocusID (NCBI) 1299
Atlas_Id 62004
Location 20q13.33  [Link to chromosome band 20q13]
Location_base_pair Starts at 62817050 and ends at 62841159 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)
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    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]  ENSG00000092758 [Sequence]  chr20:62817050-62841159 [Contig_View]  COL9A3 [Vega]
ICGC DataPortalENSG00000092758
TCGA cBioPortalCOL9A3
AceView (NCBI)COL9A3
Genatlas (Paris)COL9A3
SOURCE (Princeton)COL9A3
Genetics Home Reference (NIH)COL9A3
Genomic and cartography
GoldenPath hg38 (UCSC)COL9A3  -     chr20:62817050-62841159 +  20q13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL9A3  -     20q13.33   [Description]    (hg19-Feb_2009)
GoldenPathCOL9A3 - 20q13.33 [CytoView hg19]  COL9A3 - 20q13.33 [CytoView hg38]
ImmunoBaseENSG00000092758
Genome Data Viewer NCBICOL9A3 [Mapview hg19]  
OMIM120270   600969   603932   
Gene and transcription
Genbank (Entrez)AK075240 BC004412 BC007574 BC011705 DQ598196
RefSeq transcript (Entrez)NM_001853
Consensus coding sequences : CCDS (NCBI)COL9A3
Gene ExpressionCOL9A3 [ NCBI-GEO ]   COL9A3 [ EBI - ARRAY_EXPRESS ]   COL9A3 [ SEEK ]   COL9A3 [ MEM ]
Gene Expression Viewer (FireBrowse)COL9A3 [ Firebrowse - Broad ]
GenevisibleExpression of COL9A3 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1299
GTEX Portal (Tissue expression)COL9A3
Human Protein AtlasENSG00000092758-COL9A3 [pathology]   [cell]   [tissue]
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
PhosPhoSitePlusQ14050
Domains : Interpro (EBI)Collagen   
Domain families : Pfam (Sanger)Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01391   
Conserved Domain (NCBI)COL9A3
PDB (RSDB)5CTD    5CTI    5CVA    5CVB   
PDB Europe5CTD    5CTI    5CVA    5CVB   
PDB (PDBSum)5CTD    5CTI    5CVA    5CVB   
PDB (IMB)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
AlphaFold pdb e-kbQ14050   
Human Protein Atlas [tissue]ENSG00000092758-COL9A3 [tissue]
HPRD00374
Protein Interaction databases
DIP (DOE-UCLA)Q14050
IntAct (EBI)Q14050
BioGRIDCOL9A3
STRING (EMBL)COL9A3
ZODIACCOL9A3
Ontologies - Pathways
QuickGOQ14050
Ontology : AmiGOextracellular matrix structural constituent  extracellular region  collagen type IX trimer  collagen type IX trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  male gonad development  female gonad development  extracellular matrix structural constituent conferring tensile strength  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  extracellular matrix organization  collagen fibril organization  extracellular matrix  collagen-containing extracellular matrix  
Ontology : EGO-EBIextracellular matrix structural constituent  extracellular region  collagen type IX trimer  collagen type IX trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  male gonad development  female gonad development  extracellular matrix structural constituent conferring tensile strength  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  extracellular matrix organization  collagen fibril organization  extracellular matrix  collagen-containing extracellular matrix  
NDEx NetworkCOL9A3
Atlas of Cancer Signalling NetworkCOL9A3
Wikipedia pathwaysCOL9A3
Orthology - Evolution
OrthoDB1299
GeneTree (enSembl)ENSG00000092758
Phylogenetic Trees/Animal Genes : TreeFamCOL9A3
Homologs : HomoloGeneCOL9A3
Homology/Alignments : Family Browser (UCSC)COL9A3
Gene fusions - Rearrangements
Fusion : QuiverCOL9A3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL9A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL9A3
dbVarCOL9A3
ClinVarCOL9A3
MonarchCOL9A3
1000_GenomesCOL9A3 
Exome Variant ServerCOL9A3
GNOMAD BrowserENSG00000092758
Varsome BrowserCOL9A3
ACMGCOL9A3 variants
VarityQ14050
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]  
Somatic Mutations in Cancer : COSMIC3DCOL9A3
Mutations and Diseases : HGMDCOL9A3
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaCOL9A3
DgiDB (Drug Gene Interaction Database)COL9A3
DoCM (Curated mutations)COL9A3
CIViC (Clinical Interpretations of Variants in Cancer)COL9A3
Cancer3DCOL9A3
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120270    600969    603932   
Orphanet17597    19597   
DisGeNETCOL9A3
MedgenCOL9A3
Genetic Testing Registry COL9A3
NextProtQ14050 [Medical]
GENETestsCOL9A3
Target ValidationCOL9A3
Huge Navigator COL9A3 [HugePedia]
ClinGenCOL9A3
Clinical trials, drugs, therapy
MyCancerGenomeCOL9A3
Protein Interactions : CTDCOL9A3
Pharm GKB GenePA26735
PharosQ14050
Clinical trialCOL9A3
Miscellaneous
canSAR (ICR)COL9A3
HarmonizomeCOL9A3
DataMed IndexCOL9A3
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXCOL9A3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:46:34 CEST 2021

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