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COL9A1 (collagen type IX alpha 1 chain)

Identity

Alias_namescollagen, type IX, alpha 1
Other aliasDJ149L1.1.2
EDM6
MED
STL4
HGNC (Hugo) COL9A1
LocusID (NCBI) 1297
Atlas_Id 62003
Location 6q13  [Link to chromosome band 6q13]
Location_base_pair Starts at 70216040 and ends at 70303083 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)
ZNF638 (2p13.2) / COL9A1 (6q13)

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)COL9A1   2217
Cards
Entrez_Gene (NCBI)COL9A1  1297  collagen type IX alpha 1 chain
AliasesDJ149L1.1.2; EDM6; MED; STL4
GeneCards (Weizmann)COL9A1
Ensembl hg19 (Hinxton)ENSG00000112280 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000112280 [Gene_View]  ENSG00000112280 [Sequence]  chr6:70216040-70303083 [Contig_View]  COL9A1 [Vega]
ICGC DataPortalENSG00000112280
TCGA cBioPortalCOL9A1
AceView (NCBI)COL9A1
Genatlas (Paris)COL9A1
WikiGenes1297
SOURCE (Princeton)COL9A1
Genetics Home Reference (NIH)COL9A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL9A1  -     chr6:70216040-70303083 -  6q13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL9A1  -     6q13   [Description]    (hg19-Feb_2009)
EnsemblCOL9A1 - 6q13 [CytoView hg19]  COL9A1 - 6q13 [CytoView hg38]
Mapping of homologs : NCBICOL9A1 [Mapview hg19]  COL9A1 [Mapview hg38]
OMIM120210   614134   614135   
Gene and transcription
Genbank (Entrez)AK097582 AK125738 AU118474 AW021120 AW022764
RefSeq transcript (Entrez)NM_001851 NM_078485
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL9A1
Cluster EST : UnigeneHs.590892 [ NCBI ]
CGAP (NCI)Hs.590892
Alternative Splicing GalleryENSG00000112280
Gene ExpressionCOL9A1 [ NCBI-GEO ]   COL9A1 [ EBI - ARRAY_EXPRESS ]   COL9A1 [ SEEK ]   COL9A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL9A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1297
GTEX Portal (Tissue expression)COL9A1
Human Protein AtlasENSG00000112280-COL9A1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP20849   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP20849  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP20849
Splice isoforms : SwissVarP20849
PhosPhoSitePlusP20849
Domains : Interpro (EBI)Collagen    ConA-like_dom    Laminin_G   
Domain families : Pfam (Sanger)Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01391   
Domain families : Smart (EMBL)TSPN (SM00210)  
Conserved Domain (NCBI)COL9A1
DMDM Disease mutations1297
Blocks (Seattle)COL9A1
PDB (SRS)2UUR    5CTD    5CTI    5CVA    5CVB   
PDB (PDBSum)2UUR    5CTD    5CTI    5CVA    5CVB   
PDB (IMB)2UUR    5CTD    5CTI    5CVA    5CVB   
PDB (RSDB)2UUR    5CTD    5CTI    5CVA    5CVB   
Structural Biology KnowledgeBase2UUR    5CTD    5CTI    5CVA    5CVB   
SCOP (Structural Classification of Proteins)2UUR    5CTD    5CTI    5CVA    5CVB   
CATH (Classification of proteins structures)2UUR    5CTD    5CTI    5CVA    5CVB   
SuperfamilyP20849
Human Protein Atlas [tissue]ENSG00000112280-COL9A1 [tissue]
Peptide AtlasP20849
HPRD00367
IPIIPI00874229   IPI00295999   IPI00645204   IPI00745219   IPI00903058   IPI00852933   
Protein Interaction databases
DIP (DOE-UCLA)P20849
IntAct (EBI)P20849
FunCoupENSG00000112280
BioGRIDCOL9A1
STRING (EMBL)COL9A1
ZODIACCOL9A1
Ontologies - Pathways
QuickGOP20849
Ontology : AmiGO###############################################################################################################################################################################################################################################################                  
Ontology : EGO-EBI###############################################################################################################################################################################################################################################################                  
NDEx NetworkCOL9A1
Atlas of Cancer Signalling NetworkCOL9A1
Wikipedia pathwaysCOL9A1
Orthology - Evolution
OrthoDB1297
GeneTree (enSembl)ENSG00000112280
Phylogenetic Trees/Animal Genes : TreeFamCOL9A1
HOVERGENP20849
HOGENOMP20849
Homologs : HomoloGeneCOL9A1
Homology/Alignments : Family Browser (UCSC)COL9A1
Gene fusions - Rearrangements
Fusion : QuiverCOL9A1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL9A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL9A1
dbVarCOL9A1
ClinVarCOL9A1
1000_GenomesCOL9A1 
Exome Variant ServerCOL9A1
ExAC (Exome Aggregation Consortium)ENSG00000112280
GNOMAD BrowserENSG00000112280
Varsome BrowserCOL9A1
Genetic variants : HAPMAP1297
Genomic Variants (DGV)COL9A1 [DGVbeta]
DECIPHERCOL9A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL9A1 
Mutations
ICGC Data PortalCOL9A1 
TCGA Data PortalCOL9A1 
Broad Tumor PortalCOL9A1
OASIS PortalCOL9A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL9A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL9A1
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
LOVD (Leiden Open Variation Database)Eye diseases - LOVD
BioMutasearch COL9A1
DgiDB (Drug Gene Interaction Database)COL9A1
DoCM (Curated mutations)COL9A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL9A1 (select a term)
intoGenCOL9A1
Cancer3DCOL9A1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM120210    614134    614135   
Orphanet17597    19597   
DisGeNETCOL9A1
MedgenCOL9A1
Genetic Testing Registry COL9A1
NextProtP20849 [Medical]
TSGene1297
GENETestsCOL9A1
Target ValidationCOL9A1
Huge Navigator COL9A1 [HugePedia]
snp3D : Map Gene to Disease1297
BioCentury BCIQCOL9A1
ClinGenCOL9A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1297
Chemical/Pharm GKB GenePA26733
Clinical trialCOL9A1
Miscellaneous
canSAR (ICR)COL9A1 (select the gene name)
Probes
Litterature
PubMed1 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL9A1
EVEXCOL9A1
GoPubMedCOL9A1
iHOPCOL9A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Jul 30 13:41:10 CEST 2018

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