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KDM5B (lysine demethylase 5B)

Identity

Alias_namesJARID1B
Jumonji, AT rich interactive domain 1B (RBP2-like)
jumonji, AT rich interactive domain 1B
lysine (K)-specific demethylase 5B
Alias_symbol (synonym)RBBP2H1A
PLU-1
CT31
PPP1R98
Other aliasPLU1
PUT1
RBP2-H1
HGNC (Hugo) KDM5B
LocusID (NCBI) 10765
Atlas_Id 50846
Location 1q32.1  [Link to chromosome band 1q32]
Location_base_pair Starts at 202725185 and ends at 202809470 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CANX (5q35.3) / KDM5B (1q32.1)HSPB8 (12q24.23) / KDM5B (1q32.1)KDM5B (1q32.1) / KDM5B (1q32.1)
KDM5B (1q32.1) / OXR1 (8q23.1)KDM5B (1q32.1) / RABGAP1L (1q25.1)KDM5B (1q32.1) / UAP1 (1q23.3)
LIN9 (1q42.12) / KDM5B (1q32.1)KDM5B 1q32.1 / RABGAP1L 1q25.1KDM5B 1q32.1 / UAP1 1q23.3
LIN9 1q42.12 / KDM5B 1q32.1

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)KDM5B   18039
Cards
Entrez_Gene (NCBI)KDM5B  10765  lysine demethylase 5B
AliasesCT31; JARID1B; PLU-1; PLU1; 
PPP1R98; PUT1; RBBP2H1A; RBP2-H1
GeneCards (Weizmann)KDM5B
Ensembl hg19 (Hinxton)ENSG00000117139 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000117139 [Gene_View]  chr1:202725185-202809470 [Contig_View]  KDM5B [Vega]
ICGC DataPortalENSG00000117139
TCGA cBioPortalKDM5B
AceView (NCBI)KDM5B
Genatlas (Paris)KDM5B
WikiGenes10765
SOURCE (Princeton)KDM5B
Genetics Home Reference (NIH)KDM5B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM5B  -     chr1:202725185-202809470 -  1q32.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM5B  -     1q32.1   [Description]    (hg19-Feb_2009)
EnsemblKDM5B - 1q32.1 [CytoView hg19]  KDM5B - 1q32.1 [CytoView hg38]
Mapping of homologs : NCBIKDM5B [Mapview hg19]  KDM5B [Mapview hg38]
OMIM605393   
Gene and transcription
Genbank (Entrez)AB015348 AF087481 AI262935 AJ132440 AJ243706
RefSeq transcript (Entrez)NM_001314042 NM_001347591 NM_006618
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM5B
Cluster EST : UnigeneHs.443650 [ NCBI ]
CGAP (NCI)Hs.443650
Alternative Splicing GalleryENSG00000117139
Gene ExpressionKDM5B [ NCBI-GEO ]   KDM5B [ EBI - ARRAY_EXPRESS ]   KDM5B [ SEEK ]   KDM5B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10765
GTEX Portal (Tissue expression)KDM5B
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UGL1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UGL1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UGL1
Splice isoforms : SwissVarQ9UGL1
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusQ9UGL1
Domaine pattern : Prosite (Expaxy)ARID (PS51011)    JMJC (PS51184)    JMJN (PS51183)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)ARID_dom    JmjC_dom    JmjN    Lys_sp_deMease-like_dom    Zinc_finger_PHD-type_CS    Znf_C5HC2    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)ARID (PF01388)    JmjC (PF02373)    JmjN (PF02375)    PHD (PF00628)    PLU-1 (PF08429)    zf-C5HC2 (PF02928)   
Domain families : Pfam (NCBI)pfam01388    pfam02373    pfam02375    pfam00628    pfam08429    pfam02928   
Domain families : Smart (EMBL)BRIGHT (SM00501)  JmjC (SM00558)  JmjN (SM00545)  PHD (SM00249)  
Conserved Domain (NCBI)KDM5B
DMDM Disease mutations10765
Blocks (Seattle)KDM5B
PDB (SRS)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
PDB (PDBSum)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
PDB (IMB)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
PDB (RSDB)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
Structural Biology KnowledgeBase2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
SCOP (Structural Classification of Proteins)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
CATH (Classification of proteins structures)2MA5    2MNY    2MNZ    5A1F    5A3N    5A3P    5A3T    5A3W    5FPL    5FPU    5FUN    5FUP    5FV3    5FYT    5FYU    5FYY    5FYZ    5FZ0    5FZ1    5FZ3    5FZ4    5FZ6    5FZ7    5FZ9    5FZA    5FZB    5FZC    5FZH    5FZK    5FZL    5LW9    5LWB   
SuperfamilyQ9UGL1
Human Protein AtlasENSG00000117139
Peptide AtlasQ9UGL1
HPRD09251
IPIIPI00873956   IPI00847436   IPI01009119   IPI00877939   
Protein Interaction databases
DIP (DOE-UCLA)Q9UGL1
IntAct (EBI)Q9UGL1
FunCoupENSG00000117139
BioGRIDKDM5B
STRING (EMBL)KDM5B
ZODIACKDM5B
Ontologies - Pathways
QuickGOQ9UGL1
Ontology : AmiGODNA binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  protein binding  nucleus  nucleoplasm  cytosol  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  single fertilization  zinc ion binding  post-embryonic development  positive regulation of gene expression  oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors  histone demethylase activity  histone demethylase activity (H3-K4 specific)  positive regulation of mammary gland epithelial cell proliferation  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  cellular response to fibroblast growth factor stimulus  negative regulation of transcription, DNA-templated  rhythmic process  oxidation-reduction process  branching involved in mammary gland duct morphogenesis  mammary duct terminal end bud growth  response to fungicide  uterus morphogenesis  lens fiber cell differentiation  sequence-specific double-stranded DNA binding  regulation of estradiol secretion  
Ontology : EGO-EBIDNA binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  protein binding  nucleus  nucleoplasm  cytosol  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  single fertilization  zinc ion binding  post-embryonic development  positive regulation of gene expression  oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors  histone demethylase activity  histone demethylase activity (H3-K4 specific)  positive regulation of mammary gland epithelial cell proliferation  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  cellular response to fibroblast growth factor stimulus  negative regulation of transcription, DNA-templated  rhythmic process  oxidation-reduction process  branching involved in mammary gland duct morphogenesis  mammary duct terminal end bud growth  response to fungicide  uterus morphogenesis  lens fiber cell differentiation  sequence-specific double-stranded DNA binding  regulation of estradiol secretion  
NDEx NetworkKDM5B
Atlas of Cancer Signalling NetworkKDM5B
Wikipedia pathwaysKDM5B
Orthology - Evolution
OrthoDB10765
GeneTree (enSembl)ENSG00000117139
Phylogenetic Trees/Animal Genes : TreeFamKDM5B
HOVERGENQ9UGL1
HOGENOMQ9UGL1
Homologs : HomoloGeneKDM5B
Homology/Alignments : Family Browser (UCSC)KDM5B
Gene fusions - Rearrangements
Fusion : MitelmanKDM5B/RABGAP1L [1q32.1/1q25.1]  
Fusion : MitelmanKDM5B/UAP1 [1q32.1/1q23.3]  [t(1;1)(q23;q32)]  
Fusion : MitelmanLIN9/KDM5B [1q42.12/1q32.1]  [t(1;1)(q32;q42)]  
Fusion: TCGAKDM5B 1q32.1 RABGAP1L 1q25.1 BRCA
Fusion: TCGAKDM5B 1q32.1 UAP1 1q23.3 LGG
Fusion: TCGALIN9 1q42.12 KDM5B 1q32.1 LGG
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5B
dbVarKDM5B
ClinVarKDM5B
1000_GenomesKDM5B 
Exome Variant ServerKDM5B
ExAC (Exome Aggregation Consortium)KDM5B (select the gene name)
Genetic variants : HAPMAP10765
Genomic Variants (DGV)KDM5B [DGVbeta]
DECIPHERKDM5B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM5B 
Mutations
ICGC Data PortalKDM5B 
TCGA Data PortalKDM5B 
Broad Tumor PortalKDM5B
OASIS PortalKDM5B [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDKDM5B
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 KDM5B
DgiDB (Drug Gene Interaction Database)KDM5B
DoCM (Curated mutations)KDM5B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM5B (select a term)
intoGenKDM5B
Cancer3DKDM5B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605393   
Orphanet
MedgenKDM5B
Genetic Testing Registry KDM5B
NextProtQ9UGL1 [Medical]
TSGene10765
GENETestsKDM5B
Target ValidationKDM5B
Huge Navigator KDM5B [HugePedia]
snp3D : Map Gene to Disease10765
BioCentury BCIQKDM5B
ClinGenKDM5B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10765
Chemical/Pharm GKB GenePA164721626
Clinical trialKDM5B
Miscellaneous
canSAR (ICR)KDM5B (select the gene name)
Probes
Litterature
PubMed77 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM5B
EVEXKDM5B
GoPubMedKDM5B
iHOPKDM5B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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