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KDM3A (lysine demethylase 3A)

Identity

Alias_namesJMJD1
JMJD1A
jumonji domain containing 1
jumonji domain containing 1A
lysine (K)-specific demethylase 3A
Alias_symbol (synonym)TSGA
KIAA0742
JHMD2A
Other aliasJHDM2A
HGNC (Hugo) KDM3A
LocusID (NCBI) 55818
Atlas_Id 51339
Location 2p11.2  [Link to chromosome band 2p11]
Location_base_pair Starts at 86441148 and ends at 86492716 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)
ACTR3 (2q14.1) / KDM3A (2p11.2)ADCY1 (7p12.3) / KDM3A (2p11.2)KDM3A (2p11.2) / ADCY1 (7p12.3)
KDM3A (2p11.2) / PUS10 (2p16.1)KDM3A (2p11.2) / RFX8 (2q11.2)PARD3 (10p11.22) / KDM3A (2p11.2)
KDM3A 2p11.2 / PUS10 2p16.1KDM3A 2p11.2 / RFX8 2q11.2

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) [ 2 ]
  t(2;2)(p11;p16) KDM3A/PUS10
t(2;2)(p11;q11) KDM3A/RFX8

External links

Nomenclature
HGNC (Hugo)KDM3A   20815
Cards
Entrez_Gene (NCBI)KDM3A  55818  lysine demethylase 3A
AliasesJHDM2A; JHMD2A; JMJD1; JMJD1A; 
TSGA
GeneCards (Weizmann)KDM3A
Ensembl hg19 (Hinxton)ENSG00000115548 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000115548 [Gene_View]  ENSG00000115548 [Sequence]  chr2:86441148-86492716 [Contig_View]  KDM3A [Vega]
ICGC DataPortalENSG00000115548
TCGA cBioPortalKDM3A
AceView (NCBI)KDM3A
Genatlas (Paris)KDM3A
WikiGenes55818
SOURCE (Princeton)KDM3A
Genetics Home Reference (NIH)KDM3A
Genomic and cartography
GoldenPath hg38 (UCSC)KDM3A  -     chr2:86441148-86492716 +  2p11.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM3A  -     2p11.2   [Description]    (hg19-Feb_2009)
GoldenPathKDM3A - 2p11.2 [CytoView hg19]  KDM3A - 2p11.2 [CytoView hg38]
ImmunoBaseENSG00000115548
Mapping of homologs : NCBIKDM3A [Mapview hg19]  KDM3A [Mapview hg38]
OMIM611512   
Gene and transcription
Genbank (Entrez)AB018285 AI911797 AK074314 AK125045 AK304276
RefSeq transcript (Entrez)NM_001146688 NM_018433
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM3A
Cluster EST : UnigeneHs.557425 [ NCBI ]
CGAP (NCI)Hs.557425
Alternative Splicing GalleryENSG00000115548
Gene ExpressionKDM3A [ NCBI-GEO ]   KDM3A [ EBI - ARRAY_EXPRESS ]   KDM3A [ SEEK ]   KDM3A [ MEM ]
Gene Expression Viewer (FireBrowse)KDM3A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55818
GTEX Portal (Tissue expression)KDM3A
Human Protein AtlasENSG00000115548-KDM3A [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y4C1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y4C1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y4C1
Splice isoforms : SwissVarQ9Y4C1
PhosPhoSitePlusQ9Y4C1
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)   
Domains : Interpro (EBI)JmjC_dom   
Domain families : Pfam (Sanger)JmjC (PF02373)   
Domain families : Pfam (NCBI)pfam02373   
Domain families : Smart (EMBL)JmjC (SM00558)  
Conserved Domain (NCBI)KDM3A
DMDM Disease mutations55818
Blocks (Seattle)KDM3A
SuperfamilyQ9Y4C1
Human Protein Atlas [tissue]ENSG00000115548-KDM3A [tissue]
Peptide AtlasQ9Y4C1
HPRD11054
IPIIPI00479545   IPI01014138   IPI01013795   IPI00747470   IPI00915748   IPI00925151   IPI00915904   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y4C1
IntAct (EBI)Q9Y4C1
FunCoupENSG00000115548
BioGRIDKDM3A
STRING (EMBL)KDM3A
ZODIACKDM3A
Ontologies - Pathways
QuickGOQ9Y4C1
Ontology : AmiGOchromatin  transcription regulatory region sequence-specific DNA binding  RNA polymerase II core promoter sequence-specific DNA binding  DNA-binding transcription factor activity  iron ion binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  spermatid nucleus elongation  hormone-mediated signaling pathway  membrane  androgen receptor signaling pathway  chromatin DNA binding  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  histone H3-K9 demethylation  histone H3-K9 dimethylation  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  formaldehyde biosynthetic process  androgen receptor binding  dioxygenase activity  negative regulation of histone H3-K9 methylation  oxidation-reduction process  positive regulation of cold-induced thermogenesis  cellular response to leukemia inhibitory factor  regulation of stem cell population maintenance  regulation of stem cell differentiation  
Ontology : EGO-EBIchromatin  transcription regulatory region sequence-specific DNA binding  RNA polymerase II core promoter sequence-specific DNA binding  DNA-binding transcription factor activity  iron ion binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  spermatid nucleus elongation  hormone-mediated signaling pathway  membrane  androgen receptor signaling pathway  chromatin DNA binding  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  histone H3-K9 demethylation  histone H3-K9 dimethylation  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  formaldehyde biosynthetic process  androgen receptor binding  dioxygenase activity  negative regulation of histone H3-K9 methylation  oxidation-reduction process  positive regulation of cold-induced thermogenesis  cellular response to leukemia inhibitory factor  regulation of stem cell population maintenance  regulation of stem cell differentiation  
NDEx NetworkKDM3A
Atlas of Cancer Signalling NetworkKDM3A
Wikipedia pathwaysKDM3A
Orthology - Evolution
OrthoDB55818
GeneTree (enSembl)ENSG00000115548
Phylogenetic Trees/Animal Genes : TreeFamKDM3A
HOGENOMQ9Y4C1
Homologs : HomoloGeneKDM3A
Homology/Alignments : Family Browser (UCSC)KDM3A
Gene fusions - Rearrangements
Fusion : MitelmanKDM3A/PUS10 [2p11.2/2p16.1]  
Fusion : MitelmanKDM3A/RFX8 [2p11.2/2q11.2]  [t(2;2)(p11;q11)]  
Fusion PortalKDM3A 2p11.2 PUS10 2p16.1 LUSC
Fusion PortalKDM3A 2p11.2 RFX8 2q11.2 BRCA
Fusion : QuiverKDM3A
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM3A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM3A
dbVarKDM3A
ClinVarKDM3A
1000_GenomesKDM3A 
Exome Variant ServerKDM3A
ExAC (Exome Aggregation Consortium)ENSG00000115548
GNOMAD BrowserENSG00000115548
Varsome BrowserKDM3A
Genetic variants : HAPMAP55818
Genomic Variants (DGV)KDM3A [DGVbeta]
DECIPHERKDM3A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM3A 
Mutations
ICGC Data PortalKDM3A 
TCGA Data PortalKDM3A 
Broad Tumor PortalKDM3A
OASIS PortalKDM3A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM3A  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DKDM3A
Mutations and Diseases : HGMDKDM3A
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch KDM3A
DgiDB (Drug Gene Interaction Database)KDM3A
DoCM (Curated mutations)KDM3A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM3A (select a term)
intoGenKDM3A
Cancer3DKDM3A(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611512   
Orphanet
DisGeNETKDM3A
MedgenKDM3A
Genetic Testing Registry KDM3A
NextProtQ9Y4C1 [Medical]
TSGene55818
GENETestsKDM3A
Target ValidationKDM3A
Huge Navigator KDM3A [HugePedia]
snp3D : Map Gene to Disease55818
BioCentury BCIQKDM3A
ClinGenKDM3A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55818
Chemical/Pharm GKB GenePA164721293
Clinical trialKDM3A
Miscellaneous
canSAR (ICR)KDM3A (select the gene name)
DataMed IndexKDM3A
Probes
Litterature
PubMed79 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM3A
EVEXKDM3A
GoPubMedKDM3A
iHOPKDM3A
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 : Wed Nov 13 17:49:27 CET 2019
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