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

KDM3B (lysine demethylase 3B)

Identity

Alias_namesC5orf7
JMJD1B
chromosome 5 open reading frame 7
jumonji domain containing 1B
lysine (K)-specific demethylase 3B
Alias_symbol (synonym)KIAA1082
NET22
Other alias5qNCA
HGNC (Hugo) KDM3B
LocusID (NCBI) 51780
Atlas_Id 50853
Location 5q31.2  [Link to chromosome band 5q31]
Location_base_pair Starts at 138352596 and ends at 138437027 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
KDM3B (5q31.2) / BRK1 (3p25.3)KDM3B (5q31.2) / KDM3B (5q31.2)MATR3 (5q31.2) / KDM3B (5q31.2)
NRXN3 (14q31.1) / KDM3B (5q31.2)PRLR (5p13.2) / KDM3B (5q31.2)SCFD2 (4q12) / KDM3B (5q31.2)
TAGLN3 (3q13.2) / KDM3B (5q31.2)MATR3 5q31.2 / KDM3B 5q31.2PRLR 5p13.2 / KDM3B 5q31.2

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

 


External links

Nomenclature
HGNC (Hugo)KDM3B   1337
Cards
Entrez_Gene (NCBI)KDM3B  51780  lysine demethylase 3B
Aliases5qNCA; C5orf7; JMJD1B; NET22
GeneCards (Weizmann)KDM3B
Ensembl hg19 (Hinxton)ENSG00000120733 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000120733 [Gene_View]  chr5:138352596-138437027 [Contig_View]  KDM3B [Vega]
ICGC DataPortalENSG00000120733
TCGA cBioPortalKDM3B
AceView (NCBI)KDM3B
Genatlas (Paris)KDM3B
WikiGenes51780
SOURCE (Princeton)KDM3B
Genetics Home Reference (NIH)KDM3B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM3B  -     chr5:138352596-138437027 +  5q31.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM3B  -     5q31.2   [Description]    (hg19-Feb_2009)
EnsemblKDM3B - 5q31.2 [CytoView hg19]  KDM3B - 5q31.2 [CytoView hg38]
Mapping of homologs : NCBIKDM3B [Mapview hg19]  KDM3B [Mapview hg38]
OMIM609373   
Gene and transcription
Genbank (Entrez)AB029005 AF251039 AF338242 AK025755 AK304371
RefSeq transcript (Entrez)NM_016604
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM3B
Cluster EST : UnigeneHs.483486 [ NCBI ]
CGAP (NCI)Hs.483486
Alternative Splicing GalleryENSG00000120733
Gene ExpressionKDM3B [ NCBI-GEO ]   KDM3B [ EBI - ARRAY_EXPRESS ]   KDM3B [ SEEK ]   KDM3B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM3B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)51780
GTEX Portal (Tissue expression)KDM3B
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ7LBC6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ7LBC6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ7LBC6
Splice isoforms : SwissVarQ7LBC6
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusQ7LBC6
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)KDM3B
DMDM Disease mutations51780
Blocks (Seattle)KDM3B
PDB (SRS)4C8D   
PDB (PDBSum)4C8D   
PDB (IMB)4C8D   
PDB (RSDB)4C8D   
Structural Biology KnowledgeBase4C8D   
SCOP (Structural Classification of Proteins)4C8D   
CATH (Classification of proteins structures)4C8D   
SuperfamilyQ7LBC6
Human Protein AtlasENSG00000120733
Peptide AtlasQ7LBC6
HPRD11055
IPIIPI00298935   IPI00749486   IPI00748132   IPI01013940   IPI00964799   IPI00964128   
Protein Interaction databases
DIP (DOE-UCLA)Q7LBC6
IntAct (EBI)Q7LBC6
FunCoupENSG00000120733
BioGRIDKDM3B
STRING (EMBL)KDM3B
ZODIACKDM3B
Ontologies - Pathways
QuickGOQ7LBC6
Ontology : AmiGOchromatin  transcription regulatory region sequence-specific DNA binding  nucleus  nucleoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  antioxidant activity  chromatin DNA binding  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  metal ion binding  dioxygenase activity  oxidation-reduction process  response to cisplatin  cellular oxidant detoxification  
Ontology : EGO-EBIchromatin  transcription regulatory region sequence-specific DNA binding  nucleus  nucleoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  antioxidant activity  chromatin DNA binding  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  metal ion binding  dioxygenase activity  oxidation-reduction process  response to cisplatin  cellular oxidant detoxification  
NDEx NetworkKDM3B
Atlas of Cancer Signalling NetworkKDM3B
Wikipedia pathwaysKDM3B
Orthology - Evolution
OrthoDB51780
GeneTree (enSembl)ENSG00000120733
Phylogenetic Trees/Animal Genes : TreeFamKDM3B
HOVERGENQ7LBC6
HOGENOMQ7LBC6
Homologs : HomoloGeneKDM3B
Homology/Alignments : Family Browser (UCSC)KDM3B
Gene fusions - Rearrangements
Fusion : MitelmanMATR3/KDM3B [5q31.2/5q31.2]  [t(5;5)(q31;q31)]  
Fusion : MitelmanPRLR/KDM3B [5p13.2/5q31.2]  [t(5;5)(p13;q31)]  
Fusion: TCGAMATR3 5q31.2 KDM3B 5q31.2 PRAD
Fusion: TCGAPRLR 5p13.2 KDM3B 5q31.2 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM3B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM3B
dbVarKDM3B
ClinVarKDM3B
1000_GenomesKDM3B 
Exome Variant ServerKDM3B
ExAC (Exome Aggregation Consortium)KDM3B (select the gene name)
Genetic variants : HAPMAP51780
Genomic Variants (DGV)KDM3B [DGVbeta]
DECIPHERKDM3B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM3B 
Mutations
ICGC Data PortalKDM3B 
TCGA Data PortalKDM3B 
Broad Tumor PortalKDM3B
OASIS PortalKDM3B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM3B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM3B
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch KDM3B
DgiDB (Drug Gene Interaction Database)KDM3B
DoCM (Curated mutations)KDM3B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM3B (select a term)
intoGenKDM3B
Cancer3DKDM3B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609373   
Orphanet
MedgenKDM3B
Genetic Testing Registry KDM3B
NextProtQ7LBC6 [Medical]
TSGene51780
GENETestsKDM3B
Target ValidationKDM3B
Huge Navigator KDM3B [HugePedia]
snp3D : Map Gene to Disease51780
BioCentury BCIQKDM3B
ClinGenKDM3B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD51780
Chemical/Pharm GKB GenePA25918
Clinical trialKDM3B
Miscellaneous
canSAR (ICR)KDM3B (select the gene name)
Probes
Litterature
PubMed34 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM3B
EVEXKDM3B
GoPubMedKDM3B
iHOPKDM3B
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 : Tue Aug 1 17:04:36 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.