Atlas of Genetics and Cytogenetics in Oncology and Haematology

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KDM4B (lysine demethylase 4B)

Identity

Alias_namesJMJD2B
jumonji domain containing 2B
lysine (K)-specific demethylase 4B
Alias_symbol (synonym)KIAA0876
TDRD14B
Other alias
HGNC (Hugo) KDM4B
LocusID (NCBI) 23030
Atlas_Id 47437
Location 1p34.2  [Link to chromosome band 1p34]
Location_base_pair Starts at 4969113 and ends at 5153597 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)
CHAF1A (19p13.3) / KDM4B (19p13.3)DYRK1A (21q22.13) / KDM4B (19p13.3)KDM4B (19p13.3) / AC011498.1 ()
KDM4B (19p13.3) / AKAP8L (19p13.12)KDM4B (19p13.3) / C19orf44 (19p13.11)KDM4B (19p13.3) / CHAF1A (19p13.3)
KDM4B (19p13.3) / FST (5q11.2)KDM4B (19p13.3) / GTF2F1 (19p13.3)KDM4B (19p13.3) / HP1BP3 (1p36.12)
KDM4B (19p13.3) / KDM4B (19p13.3)KDM4B (19p13.3) / MPND (19p13.3)KDM4B (19p13.3) / SLC25A42 (19p13.11)
KDM4B (19p13.3) / UHRF1 (19p13.3)S100A6 (1q21.3) / KDM4B (19p13.3)STK11 (19p13.3) / KDM4B (19p13.3)
STK24 (13q32.2) / KDM4B (19p13.3)UBR4 (1p36.13) / KDM4B (19p13.3)DYRK1A 21q22.13 / KDM4B 19p13.3
KDM4B 19p13.3 AC011498.1KDM4B 19p13.3 / AKAP8L 19p13.12KDM4B 19p13.3 / C19orf44 19p13.11
KDM4B 19p13.3 / CHAF1A 19p13.3KDM4B 19p13.3 / MPND 19p13.3KDM4B 19p13.3 / SLC25A42 19p13.11
KDM4B 19p13.3 / UHRF1 19p13.3STK11 19p13.3 / KDM4B 19p13.3

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(10;19)(p11;p13) KDM4B/CUL2

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 9 ]
  t(1;19)(p36;p13) UBR4/KDM4B
KDM4B/AKAP8L (19p13)
KDM4B/C19orf44 (19p13)
KDM4B/CHAF1A (19p13)
KDM4B/MPND (19p13)
KDM4B/SLC25A42 (19p13)
KDM4B/UHRF1 (19p13)
STK11/KDM4B (19p13)
t(19;21)(p13;q22) DYRK1A/KDM4B

External links

Nomenclature
HGNC (Hugo)KDM4B   29136
Cards
Entrez_Gene (NCBI)KDM4B  23030  lysine demethylase 4B
AliasesJMJD2B; TDRD14B
GeneCards (Weizmann)KDM4B
Ensembl hg19 (Hinxton)ENSG00000127663 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000127663 [Gene_View]  ENSG00000127663 [Sequence]  chr19:4969113-5153597 [Contig_View]  KDM4B [Vega]
ICGC DataPortalENSG00000127663
TCGA cBioPortalKDM4B
AceView (NCBI)KDM4B
Genatlas (Paris)KDM4B
WikiGenes23030
SOURCE (Princeton)KDM4B
Genetics Home Reference (NIH)KDM4B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM4B  -     chr19:4969113-5153597 +  1p34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM4B  -     1p34.2   [Description]    (hg19-Feb_2009)
EnsemblKDM4B - 1p34.2 [CytoView hg19]  KDM4B - 1p34.2 [CytoView hg38]
Mapping of homologs : NCBIKDM4B [Mapview hg19]  KDM4B [Mapview hg38]
OMIM609765   
Gene and transcription
Genbank (Entrez)AB020683 AF052144 AK026040 AK126854 AL133622
RefSeq transcript (Entrez)NM_015015
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM4B
Cluster EST : UnigeneHs.654816 [ NCBI ]
CGAP (NCI)Hs.654816
Alternative Splicing GalleryENSG00000127663
Gene ExpressionKDM4B [ NCBI-GEO ]   KDM4B [ EBI - ARRAY_EXPRESS ]   KDM4B [ SEEK ]   KDM4B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM4B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23030
GTEX Portal (Tissue expression)KDM4B
Human Protein AtlasENSG00000127663-KDM4B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO94953   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO94953  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO94953
Splice isoforms : SwissVarO94953
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusO94953
Domaine pattern : Prosite (Expaxy)EPHD (PS51805)    JMJC (PS51184)    JMJN (PS51183)   
Domains : Interpro (EBI)EPHD    JmjC_dom    JmjN    Tudor    Znf_FYVE_PHD    Znf_PHD    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)JmjC (PF02373)    JmjN (PF02375)   
Domain families : Pfam (NCBI)pfam02373    pfam02375   
Domain families : Smart (EMBL)JmjC (SM00558)  JmjN (SM00545)  PHD (SM00249)  TUDOR (SM00333)  
Conserved Domain (NCBI)KDM4B
DMDM Disease mutations23030
Blocks (Seattle)KDM4B
PDB (SRS)4LXL    4UC4   
PDB (PDBSum)4LXL    4UC4   
PDB (IMB)4LXL    4UC4   
PDB (RSDB)4LXL    4UC4   
Structural Biology KnowledgeBase4LXL    4UC4   
SCOP (Structural Classification of Proteins)4LXL    4UC4   
CATH (Classification of proteins structures)4LXL    4UC4   
SuperfamilyO94953
Human Protein Atlas [tissue]ENSG00000127663-KDM4B [tissue]
Peptide AtlasO94953
HPRD11056
IPIIPI00013205   IPI00440491   IPI00922876   
Protein Interaction databases
DIP (DOE-UCLA)O94953
IntAct (EBI)O94953
FunCoupENSG00000127663
BioGRIDKDM4B
STRING (EMBL)KDM4B
ZODIACKDM4B
Ontologies - Pathways
QuickGOO94953
Ontology : AmiGOtranscriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding  chromatin binding  nucleus  nucleoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  histone demethylase activity  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  methylated histone binding  histone methyltransferase complex  metal ion binding  histone demethylase activity (H3-K36 specific)  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  
Ontology : EGO-EBItranscriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding  chromatin binding  nucleus  nucleoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  histone demethylase activity  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  methylated histone binding  histone methyltransferase complex  metal ion binding  histone demethylase activity (H3-K36 specific)  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  
NDEx NetworkKDM4B
Atlas of Cancer Signalling NetworkKDM4B
Wikipedia pathwaysKDM4B
Orthology - Evolution
OrthoDB23030
GeneTree (enSembl)ENSG00000127663
Phylogenetic Trees/Animal Genes : TreeFamKDM4B
HOVERGENO94953
HOGENOMO94953
Homologs : HomoloGeneKDM4B
Homology/Alignments : Family Browser (UCSC)KDM4B
Gene fusions - Rearrangements
Fusion : MitelmanDYRK1A/KDM4B [21q22.13/19p13.3]  [t(19;21)(p13;q22)]  
Fusion : MitelmanKDM4B/AKAP8L [19p13.3/19p13.12]  [t(19;19)(p13;p13)]  
Fusion : MitelmanKDM4B/C19orf44 [19p13.3/19p13.11]  [t(19;19)(p13;p13)]  
Fusion : MitelmanKDM4B/CHAF1A [19p13.3/19p13.3]  [t(19;19)(p13;p13)]  
Fusion : MitelmanKDM4B/MPND [19p13.3/19p13.3]  [t(19;19)(p13;p13)]  
Fusion : MitelmanKDM4B/SLC25A42 [19p13.3/19p13.11]  [t(19;19)(p13;p13)]  
Fusion : MitelmanKDM4B/UHRF1 [19p13.3/19p13.3]  [t(19;19)(p13;p13)]  
Fusion : MitelmanSTK11/KDM4B [19p13.3/19p13.3]  [t(19;19)(p13;p13)]  
Fusion : MitelmanUBR4/KDM4B [1p36.13/19p13.3]  [t(1;19)(p36;p13)]  
Fusion PortalDYRK1A 21q22.13 KDM4B 19p13.3 BRCA
Fusion PortalKDM4B 19p13.3 AC011498.1 PRAD
Fusion PortalKDM4B 19p13.3 AKAP8L 19p13.12 LUAD
Fusion PortalKDM4B 19p13.3 C19orf44 19p13.11 BRCA
Fusion PortalKDM4B 19p13.3 CHAF1A 19p13.3 LGG
Fusion PortalKDM4B 19p13.3 MPND 19p13.3 OV
Fusion PortalKDM4B 19p13.3 SLC25A42 19p13.11 SKCM
Fusion PortalKDM4B 19p13.3 UHRF1 19p13.3 BRCA
Fusion PortalSTK11 19p13.3 KDM4B 19p13.3 BRCA
Fusion Cancer (Beijing)S100A6 [1q21.3]  -  KDM4B [19p13.3]  [FUSC003176]
Fusion : QuiverKDM4B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM4B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM4B
dbVarKDM4B
ClinVarKDM4B
1000_GenomesKDM4B 
Exome Variant ServerKDM4B
ExAC (Exome Aggregation Consortium)ENSG00000127663
GNOMAD BrowserENSG00000127663
Varsome BrowserKDM4B
Genetic variants : HAPMAP23030
Genomic Variants (DGV)KDM4B [DGVbeta]
DECIPHERKDM4B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM4B 
Mutations
ICGC Data PortalKDM4B 
TCGA Data PortalKDM4B 
Broad Tumor PortalKDM4B
OASIS PortalKDM4B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM4B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM4B
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 KDM4B
DgiDB (Drug Gene Interaction Database)KDM4B
DoCM (Curated mutations)KDM4B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM4B (select a term)
intoGenKDM4B
Cancer3DKDM4B(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609765   
Orphanet
DisGeNETKDM4B
MedgenKDM4B
Genetic Testing Registry KDM4B
NextProtO94953 [Medical]
TSGene23030
GENETestsKDM4B
Target ValidationKDM4B
Huge Navigator KDM4B [HugePedia]
snp3D : Map Gene to Disease23030
BioCentury BCIQKDM4B
ClinGenKDM4B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23030
Chemical/Pharm GKB GenePA164721452
Clinical trialKDM4B
Miscellaneous
canSAR (ICR)KDM4B (select the gene name)
Probes
Litterature
PubMed59 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM4B
EVEXKDM4B
GoPubMedKDM4B
iHOPKDM4B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Aug 16 11:09:36 CEST 2018
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