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COL9A2 (collagen type IX alpha 2 chain)

Identity

Alias_namesEDM2
collagen
Alias_symbol (synonym)MED
Other aliasDJ39G22.4
STL5
HGNC (Hugo) COL9A2
LocusID (NCBI) 1298
Atlas_Id 40129
Location 1p34.2  [Link to chromosome band 1p34]
Location_base_pair Starts at 40300491 and ends at 40317267 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
FBRSL1 (12q24.33) / COL9A2 (1p34.2)HEYL (1p34.3) / COL9A2 (1p34.2)RLF (1p34.2) / COL9A2 (1p34.2)
HEYL 1p34.3 / COL9A2 1p34.2

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

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Small Cell Carcinoma


External links

Nomenclature
HGNC (Hugo)COL9A2   2218
Cards
Entrez_Gene (NCBI)COL9A2  1298  collagen type IX alpha 2 chain
AliasesDJ39G22.4; EDM2; MED; STL5
GeneCards (Weizmann)COL9A2
Ensembl hg19 (Hinxton)ENSG00000049089 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000049089 [Gene_View]  chr1:40300491-40317267 [Contig_View]  COL9A2 [Vega]
ICGC DataPortalENSG00000049089
TCGA cBioPortalCOL9A2
AceView (NCBI)COL9A2
Genatlas (Paris)COL9A2
WikiGenes1298
SOURCE (Princeton)COL9A2
Genetics Home Reference (NIH)COL9A2
Genomic and cartography
GoldenPath hg38 (UCSC)COL9A2  -     chr1:40300491-40317267 -  1p34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL9A2  -     1p34.2   [Description]    (hg19-Feb_2009)
EnsemblCOL9A2 - 1p34.2 [CytoView hg19]  COL9A2 - 1p34.2 [CytoView hg38]
Mapping of homologs : NCBICOL9A2 [Mapview hg19]  COL9A2 [Mapview hg38]
OMIM120260   600204   603932   614284   
Gene and transcription
Genbank (Entrez)BC041479 BC065715 BC136326 BC136327 M95610
RefSeq transcript (Entrez)NM_001852
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL9A2
Cluster EST : UnigeneHs.418012 [ NCBI ]
CGAP (NCI)Hs.418012
Alternative Splicing GalleryENSG00000049089
Gene ExpressionCOL9A2 [ NCBI-GEO ]   COL9A2 [ EBI - ARRAY_EXPRESS ]   COL9A2 [ SEEK ]   COL9A2 [ MEM ]
Gene Expression Viewer (FireBrowse)COL9A2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1298
GTEX Portal (Tissue expression)COL9A2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14055   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14055  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14055
Splice isoforms : SwissVarQ14055
PhosPhoSitePlusQ14055
Domains : Interpro (EBI)Collagen   
Domain families : Pfam (Sanger)Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01391   
Conserved Domain (NCBI)COL9A2
DMDM Disease mutations1298
Blocks (Seattle)COL9A2
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   
SuperfamilyQ14055
Human Protein AtlasENSG00000049089
Peptide AtlasQ14055
HPRD00373
IPIIPI00019088   IPI00647776   IPI00513850   IPI00844058   
Protein Interaction databases
DIP (DOE-UCLA)Q14055
IntAct (EBI)Q14055
FunCoupENSG00000049089
BioGRIDCOL9A2
STRING (EMBL)COL9A2
ZODIACCOL9A2
Ontologies - Pathways
QuickGOQ14055
Ontology : AmiGOskeletal system development  extracellular region  proteinaceous extracellular matrix  collagen type IX trimer  endoplasmic reticulum lumen  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  
Ontology : EGO-EBIskeletal system development  extracellular region  proteinaceous extracellular matrix  collagen type IX trimer  endoplasmic reticulum lumen  extracellular matrix structural constituent conferring tensile strength  extracellular matrix organization  
Pathways : KEGGProtein digestion and absorption   
NDEx NetworkCOL9A2
Atlas of Cancer Signalling NetworkCOL9A2
Wikipedia pathwaysCOL9A2
Orthology - Evolution
OrthoDB1298
GeneTree (enSembl)ENSG00000049089
Phylogenetic Trees/Animal Genes : TreeFamCOL9A2
HOVERGENQ14055
HOGENOMQ14055
Homologs : HomoloGeneCOL9A2
Homology/Alignments : Family Browser (UCSC)COL9A2
Gene fusions - Rearrangements
Fusion : MitelmanHEYL/COL9A2 [1p34.3/1p34.2]  [t(1;1)(p34;p34)]  
Fusion : MitelmanRLF/COL9A2 [1p34.2/1p34.2]  [t(1;1)(p34;p34)]  
Fusion: TCGAHEYL 1p34.3 COL9A2 1p34.2 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL9A2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL9A2
dbVarCOL9A2
ClinVarCOL9A2
1000_GenomesCOL9A2 
Exome Variant ServerCOL9A2
ExAC (Exome Aggregation Consortium)COL9A2 (select the gene name)
Genetic variants : HAPMAP1298
Genomic Variants (DGV)COL9A2 [DGVbeta]
DECIPHERCOL9A2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL9A2 
Mutations
ICGC Data PortalCOL9A2 
TCGA Data PortalCOL9A2 
Broad Tumor PortalCOL9A2
OASIS PortalCOL9A2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL9A2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL9A2
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 COL9A2
DgiDB (Drug Gene Interaction Database)COL9A2
DoCM (Curated mutations)COL9A2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL9A2 (select a term)
intoGenCOL9A2
Cancer3DCOL9A2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120260    600204    603932    614284   
Orphanet17597    19597   
MedgenCOL9A2
Genetic Testing Registry COL9A2
NextProtQ14055 [Medical]
TSGene1298
GENETestsCOL9A2
Target ValidationCOL9A2
Huge Navigator COL9A2 [HugePedia]
snp3D : Map Gene to Disease1298
BioCentury BCIQCOL9A2
ClinGenCOL9A2 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1298
Chemical/Pharm GKB GenePA26734
Clinical trialCOL9A2
Miscellaneous
canSAR (ICR)COL9A2 (select the gene name)
Probes
Litterature
PubMed51 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL9A2
EVEXCOL9A2
GoPubMedCOL9A2
iHOPCOL9A2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Aug 1 16:58:22 CEST 2017

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