Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

KDM2B (lysine demethylase 2B)

Identity

Alias_namesFBXL10
F-box and leucine-rich repeat protein 10
lysine (K)-specific demethylase 2B
Alias_symbol (synonym)PCCX2
CXXC2
Fbl10
JHDM1B
Other alias
HGNC (Hugo) KDM2B
LocusID (NCBI) 84678
Atlas_Id 53197
Location 12q24.31  [Link to chromosome band 12q24]
Location_base_pair Starts at 121429096 and ends at 121580459 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ANAPC5 (12q24.31) / KDM2B (12q24.31)KDM2B (12q24.31) / AFF4 (5q31.1)KDM2B (12q24.31) / CCDC60 (12q24.23)
KDM2B (12q24.31) / KDM2B (12q24.31)KDM2B (12q24.31) / KSR2 (12q24.22)KDM2B (12q24.31) / UTY (Yq11.221)
SCN2A (2q24.3) / KDM2B (12q24.31)SETD1B (12q24.31) / KDM2B (12q24.31)TNFAIP2 (14q32.32) / KDM2B (12q24.31)
ANAPC5 12q24.31 / KDM2B 12q24.31KDM2B 12q24.31 / KSR2 12q24.22SETD1B 12q24.31 / KDM2B 12q24.31

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)KDM2B   13610
Cards
Entrez_Gene (NCBI)KDM2B  84678  lysine demethylase 2B
AliasesCXXC2; FBXL10; Fbl10; JHDM1B; 
PCCX2
GeneCards (Weizmann)KDM2B
Ensembl hg19 (Hinxton)ENSG00000089094 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000089094 [Gene_View]  chr12:121429096-121580459 [Contig_View]  KDM2B [Vega]
ICGC DataPortalENSG00000089094
TCGA cBioPortalKDM2B
AceView (NCBI)KDM2B
Genatlas (Paris)KDM2B
WikiGenes84678
SOURCE (Princeton)KDM2B
Genetics Home Reference (NIH)KDM2B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM2B  -     chr12:121429096-121580459 -  12q24.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM2B  -     12q24.31   [Description]    (hg19-Feb_2009)
EnsemblKDM2B - 12q24.31 [CytoView hg19]  KDM2B - 12q24.31 [CytoView hg38]
Mapping of homologs : NCBIKDM2B [Mapview hg19]  KDM2B [Mapview hg38]
OMIM609078   
Gene and transcription
Genbank (Entrez)AA504464 AB031230 AJ459424 AK027440 AK027692
RefSeq transcript (Entrez)NM_001005366 NM_032590
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM2B
Cluster EST : UnigeneHs.524800 [ NCBI ]
CGAP (NCI)Hs.524800
Alternative Splicing GalleryENSG00000089094
Gene ExpressionKDM2B [ NCBI-GEO ]   KDM2B [ EBI - ARRAY_EXPRESS ]   KDM2B [ SEEK ]   KDM2B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM2B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84678
GTEX Portal (Tissue expression)KDM2B
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8NHM5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8NHM5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8NHM5
Splice isoforms : SwissVarQ8NHM5
Catalytic activity : Enzyme1.14.11.27 [ Enzyme-Expasy ]   1.14.11.271.14.11.27 [ IntEnz-EBI ]   1.14.11.27 [ BRENDA ]   1.14.11.27 [ KEGG ]   
PhosPhoSitePlusQ8NHM5
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)    ZF_CXXC (PS51058)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)F-box_dom    JmjC_dom    L_dom-like    Leu-rich_rpt_Cys-con_subtyp    Znf_CXXC    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)F-box (PF00646)    PHD_4 (PF16866)    zf-CXXC (PF02008)   
Domain families : Pfam (NCBI)pfam00646    pfam16866    pfam02008   
Domain families : Smart (EMBL)JmjC (SM00558)  LRR_CC (SM00367)  PHD (SM00249)  
Conserved Domain (NCBI)KDM2B
DMDM Disease mutations84678
Blocks (Seattle)KDM2B
PDB (SRS)4O64    5JH5   
PDB (PDBSum)4O64    5JH5   
PDB (IMB)4O64    5JH5   
PDB (RSDB)4O64    5JH5   
Structural Biology KnowledgeBase4O64    5JH5   
SCOP (Structural Classification of Proteins)4O64    5JH5   
CATH (Classification of proteins structures)4O64    5JH5   
SuperfamilyQ8NHM5
Human Protein AtlasENSG00000089094
Peptide AtlasQ8NHM5
HPRD12362
IPIIPI00185326   IPI00747262   IPI00737594   IPI00455183   IPI00982326   IPI00984774   IPI01008849   IPI01011349   IPI01010215   IPI01015941   IPI01015145   IPI00940436   IPI01014615   IPI01015056   IPI01013943   IPI01014339   IPI01013034   IPI01013475   
Protein Interaction databases
DIP (DOE-UCLA)Q8NHM5
IntAct (EBI)Q8NHM5
FunCoupENSG00000089094
BioGRIDKDM2B
STRING (EMBL)KDM2B
ZODIACKDM2B
Ontologies - Pathways
QuickGOQ8NHM5
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core promoter sequence-specific DNA binding  DNA binding  protein binding  nucleus  nucleoplasm  nucleolus  transcription, DNA-templated  spermatogenesis  zinc ion binding  rRNA binding  midbrain-hindbrain boundary morphogenesis  fourth ventricle development  lateral ventricle development  third ventricle development  initiation of neural tube closure  positive regulation of cell growth  forebrain development  midbrain development  hindbrain development  PcG protein complex  histone demethylase activity  histone H2A monoubiquitination  negative regulation of neuron apoptotic process  embryonic camera-type eye morphogenesis  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  positive regulation of stem cell population maintenance  negative regulation of neural precursor cell proliferation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core promoter sequence-specific DNA binding  DNA binding  protein binding  nucleus  nucleoplasm  nucleolus  transcription, DNA-templated  spermatogenesis  zinc ion binding  rRNA binding  midbrain-hindbrain boundary morphogenesis  fourth ventricle development  lateral ventricle development  third ventricle development  initiation of neural tube closure  positive regulation of cell growth  forebrain development  midbrain development  hindbrain development  PcG protein complex  histone demethylase activity  histone H2A monoubiquitination  negative regulation of neuron apoptotic process  embryonic camera-type eye morphogenesis  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  positive regulation of stem cell population maintenance  negative regulation of neural precursor cell proliferation  
NDEx NetworkKDM2B
Atlas of Cancer Signalling NetworkKDM2B
Wikipedia pathwaysKDM2B
Orthology - Evolution
OrthoDB84678
GeneTree (enSembl)ENSG00000089094
Phylogenetic Trees/Animal Genes : TreeFamKDM2B
HOVERGENQ8NHM5
HOGENOMQ8NHM5
Homologs : HomoloGeneKDM2B
Homology/Alignments : Family Browser (UCSC)KDM2B
Gene fusions - Rearrangements
Fusion : MitelmanANAPC5/KDM2B [12q24.31/12q24.31]  [t(12;12)(q24;q24)]  
Fusion : MitelmanKDM2B/CCDC60 [12q24.31/12q24.23]  [t(12;12)(q24;q24)]  
Fusion : MitelmanKDM2B/KSR2 [12q24.31/12q24.22]  [t(12;12)(q24;q24)]  
Fusion : MitelmanSETD1B/KDM2B [12q24.31/12q24.31]  [t(12;12)(q24;q24)]  
Fusion: TCGAANAPC5 12q24.31 KDM2B 12q24.31 BRCA
Fusion: TCGAKDM2B 12q24.31 KSR2 12q24.22 GBM
Fusion: TCGASETD1B 12q24.31 KDM2B 12q24.31 GBM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM2B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM2B
dbVarKDM2B
ClinVarKDM2B
1000_GenomesKDM2B 
Exome Variant ServerKDM2B
ExAC (Exome Aggregation Consortium)KDM2B (select the gene name)
Genetic variants : HAPMAP84678
Genomic Variants (DGV)KDM2B [DGVbeta]
DECIPHERKDM2B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM2B 
Mutations
ICGC Data PortalKDM2B 
TCGA Data PortalKDM2B 
Broad Tumor PortalKDM2B
OASIS PortalKDM2B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM2B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM2B
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch KDM2B
DgiDB (Drug Gene Interaction Database)KDM2B
DoCM (Curated mutations)KDM2B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM2B (select a term)
intoGenKDM2B
Cancer3DKDM2B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609078   
Orphanet
MedgenKDM2B
Genetic Testing Registry KDM2B
NextProtQ8NHM5 [Medical]
TSGene84678
GENETestsKDM2B
Huge Navigator KDM2B [HugePedia]
snp3D : Map Gene to Disease84678
BioCentury BCIQKDM2B
ClinGenKDM2B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84678
Chemical/Pharm GKB GenePA164721242
Clinical trialKDM2B
Miscellaneous
canSAR (ICR)KDM2B (select the gene name)
Probes
Litterature
PubMed41 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM2B
EVEXKDM2B
GoPubMedKDM2B
iHOPKDM2B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri May 19 12:21:23 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.