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KDM6B (lysine demethylase 6B)

Identity

Alias_namesJMJD3
jumonji domain containing 3
jumonji domain containing 3, histone lysine demethylase
lysine (K)-specific demethylase 6B
Alias_symbol (synonym)KIAA0346
Other alias
HGNC (Hugo) KDM6B
LocusID (NCBI) 23135
Atlas_Id 50868
Location 17p13.1  [Link to chromosome band 17p13]
Location_base_pair Starts at 7839917 and ends at 7854790 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ACTN1 (14q24.1) / KDM6B (17p13.1)KDM6B (17p13.1) / DNAH2 (17p13.1)KDM6B (17p13.1) / KDM6B (17p13.1)
KDM6B 17p13.1 / DNAH2 17p13.1

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)KDM6B   29012
Cards
Entrez_Gene (NCBI)KDM6B  23135  lysine demethylase 6B
AliasesJMJD3
GeneCards (Weizmann)KDM6B
Ensembl hg19 (Hinxton)ENSG00000132510 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000132510 [Gene_View]  chr17:7839917-7854790 [Contig_View]  KDM6B [Vega]
ICGC DataPortalENSG00000132510
TCGA cBioPortalKDM6B
AceView (NCBI)KDM6B
Genatlas (Paris)KDM6B
WikiGenes23135
SOURCE (Princeton)KDM6B
Genetics Home Reference (NIH)KDM6B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM6B  -     chr17:7839917-7854790 +  17p13.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM6B  -     17p13.1   [Description]    (hg19-Feb_2009)
EnsemblKDM6B - 17p13.1 [CytoView hg19]  KDM6B - 17p13.1 [CytoView hg38]
Mapping of homologs : NCBIKDM6B [Mapview hg19]  KDM6B [Mapview hg38]
OMIM611577   
Gene and transcription
Genbank (Entrez)AB002344 BC009994 BC035897
RefSeq transcript (Entrez)NM_001080424 NM_001348716
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM6B
Cluster EST : UnigeneHs.223678 [ NCBI ]
CGAP (NCI)Hs.223678
Alternative Splicing GalleryENSG00000132510
Gene ExpressionKDM6B [ NCBI-GEO ]   KDM6B [ EBI - ARRAY_EXPRESS ]   KDM6B [ SEEK ]   KDM6B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM6B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23135
GTEX Portal (Tissue expression)KDM6B
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15054   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15054  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15054
Splice isoforms : SwissVarO15054
PhosPhoSitePlusO15054
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)   
Domains : Interpro (EBI)JmjC_dom    KDM6B    TPR-like_helical_dom   
Domain families : Pfam (Sanger)JmjC (PF02373)   
Domain families : Pfam (NCBI)pfam02373   
Domain families : Smart (EMBL)JmjC (SM00558)  
Conserved Domain (NCBI)KDM6B
DMDM Disease mutations23135
Blocks (Seattle)KDM6B
PDB (SRS)2XUE    2XXZ    4ASK    5FP3   
PDB (PDBSum)2XUE    2XXZ    4ASK    5FP3   
PDB (IMB)2XUE    2XXZ    4ASK    5FP3   
PDB (RSDB)2XUE    2XXZ    4ASK    5FP3   
Structural Biology KnowledgeBase2XUE    2XXZ    4ASK    5FP3   
SCOP (Structural Classification of Proteins)2XUE    2XXZ    4ASK    5FP3   
CATH (Classification of proteins structures)2XUE    2XXZ    4ASK    5FP3   
SuperfamilyO15054
Human Protein AtlasENSG00000132510
Peptide AtlasO15054
IPIIPI00848052   IPI00550090   
Protein Interaction databases
DIP (DOE-UCLA)O15054
IntAct (EBI)O15054
FunCoupENSG00000132510
BioGRIDKDM6B
STRING (EMBL)KDM6B
ZODIACKDM6B
Ontologies - Pathways
QuickGOO15054
Ontology : AmiGOinflammatory response to antigenic stimulus  chromatin binding  protein binding  nucleus  nucleoplasm  beta-catenin binding  response to activity  hippocampus development  histone demethylase activity  sequence-specific DNA binding  cell fate commitment  endothelial cell differentiation  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  mesodermal cell differentiation  dioxygenase activity  cardiac muscle cell differentiation  oxidation-reduction process  response to fungicide  cellular response to hydrogen peroxide  histone H3-K27 demethylation  histone demethylase activity (H3-K27 specific)  
Ontology : EGO-EBIinflammatory response to antigenic stimulus  chromatin binding  protein binding  nucleus  nucleoplasm  beta-catenin binding  response to activity  hippocampus development  histone demethylase activity  sequence-specific DNA binding  cell fate commitment  endothelial cell differentiation  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  mesodermal cell differentiation  dioxygenase activity  cardiac muscle cell differentiation  oxidation-reduction process  response to fungicide  cellular response to hydrogen peroxide  histone H3-K27 demethylation  histone demethylase activity (H3-K27 specific)  
NDEx NetworkKDM6B
Atlas of Cancer Signalling NetworkKDM6B
Wikipedia pathwaysKDM6B
Orthology - Evolution
OrthoDB23135
GeneTree (enSembl)ENSG00000132510
Phylogenetic Trees/Animal Genes : TreeFamKDM6B
HOVERGENO15054
HOGENOMO15054
Homologs : HomoloGeneKDM6B
Homology/Alignments : Family Browser (UCSC)KDM6B
Gene fusions - Rearrangements
Fusion : MitelmanKDM6B/DNAH2 [17p13.1/17p13.1]  
Fusion: TCGAKDM6B 17p13.1 DNAH2 17p13.1 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM6B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM6B
dbVarKDM6B
ClinVarKDM6B
1000_GenomesKDM6B 
Exome Variant ServerKDM6B
ExAC (Exome Aggregation Consortium)KDM6B (select the gene name)
Genetic variants : HAPMAP23135
Genomic Variants (DGV)KDM6B [DGVbeta]
DECIPHERKDM6B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM6B 
Mutations
ICGC Data PortalKDM6B 
TCGA Data PortalKDM6B 
Broad Tumor PortalKDM6B
OASIS PortalKDM6B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM6B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM6B
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
BioMutasearch KDM6B
DgiDB (Drug Gene Interaction Database)KDM6B
DoCM (Curated mutations)KDM6B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM6B (select a term)
intoGenKDM6B
Cancer3DKDM6B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611577   
Orphanet
MedgenKDM6B
Genetic Testing Registry KDM6B
NextProtO15054 [Medical]
TSGene23135
GENETestsKDM6B
Huge Navigator KDM6B [HugePedia]
snp3D : Map Gene to Disease23135
BioCentury BCIQKDM6B
ClinGenKDM6B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23135
Chemical/Pharm GKB GenePA165431973
Clinical trialKDM6B
Miscellaneous
canSAR (ICR)KDM6B (select the gene name)
Probes
Litterature
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM6B
EVEXKDM6B
GoPubMedKDM6B
iHOPKDM6B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri May 19 12:21:25 CEST 2017

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