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KDM1B (lysine demethylase 1B)

Identity

Alias_namesC6orf193
AOF1
amine oxidase, flavin containing 1
chromosome 6 open reading frame 193
amine oxidase (flavin containing) domain 1
lysine (K)-specific demethylase 1B
Alias_symbol (synonym)FLJ34109
FLJ33898
dJ298J15.2
bA204B7.3
FLJ43328
LSD2
Other alias
HGNC (Hugo) KDM1B
LocusID (NCBI) 221656
Atlas_Id 54403
Location 6p22.3  [Link to chromosome band 6p22]
Location_base_pair Starts at 18155388 and ends at 18223853 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)
IL6ST (5q11.2) / KDM1B (6p22.3)KDM1B (6p22.3) / DENR (12q24.31)KDM1B (6p22.3) / RUNDC1 (17q21.31)
SMG9 (19q13.31) / KDM1B (6p22.3)TMEM242 (6q25.3) / KDM1B (6p22.3)

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 Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Adenocarcinoma


External links

Nomenclature
HGNC (Hugo)KDM1B   21577
Cards
Entrez_Gene (NCBI)KDM1B  221656  lysine demethylase 1B
AliasesAOF1; C6orf193; LSD2
GeneCards (Weizmann)KDM1B
Ensembl hg19 (Hinxton)ENSG00000165097 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000165097 [Gene_View]  ENSG00000165097 [Sequence]  chr6:18155388-18223853 [Contig_View]  KDM1B [Vega]
ICGC DataPortalENSG00000165097
TCGA cBioPortalKDM1B
AceView (NCBI)KDM1B
Genatlas (Paris)KDM1B
WikiGenes221656
SOURCE (Princeton)KDM1B
Genetics Home Reference (NIH)KDM1B
Genomic and cartography
GoldenPath hg38 (UCSC)KDM1B  -     chr6:18155388-18223853 +  6p22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM1B  -     6p22.3   [Description]    (hg19-Feb_2009)
EnsemblKDM1B - 6p22.3 [CytoView hg19]  KDM1B - 6p22.3 [CytoView hg38]
Mapping of homologs : NCBIKDM1B [Mapview hg19]  KDM1B [Mapview hg38]
OMIM613081   
Gene and transcription
Genbank (Entrez)AA332652 AJ420481 AK091217 AK125318 BC113093
RefSeq transcript (Entrez)NM_001364614 NM_153042
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM1B
Cluster EST : UnigeneHs.709336 [ NCBI ]
CGAP (NCI)Hs.709336
Alternative Splicing GalleryENSG00000165097
Gene ExpressionKDM1B [ NCBI-GEO ]   KDM1B [ EBI - ARRAY_EXPRESS ]   KDM1B [ SEEK ]   KDM1B [ MEM ]
Gene Expression Viewer (FireBrowse)KDM1B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)221656
GTEX Portal (Tissue expression)KDM1B
Human Protein AtlasENSG00000165097-KDM1B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8NB78   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8NB78  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8NB78
Splice isoforms : SwissVarQ8NB78
Catalytic activity : Enzyme1.-.-.- [ Enzyme-Expasy ]   1.-.-.-1.-.-.- [ IntEnz-EBI ]   1.-.-.- [ BRENDA ]   1.-.-.- [ KEGG ]   
PhosPhoSitePlusQ8NB78
Domaine pattern : Prosite (Expaxy)SWIRM (PS50934)    ZF_CW (PS51050)   
Domains : Interpro (EBI)Amino_oxidase    FAD/NAD-bd_sf    Homeobox-like_sf    SWIRM    WH-like_DNA-bd_sf    Znf_CW   
Domain families : Pfam (Sanger)Amino_oxidase (PF01593)    SWIRM (PF04433)    zf-CW (PF07496)   
Domain families : Pfam (NCBI)pfam01593    pfam04433    pfam07496   
Conserved Domain (NCBI)KDM1B
DMDM Disease mutations221656
Blocks (Seattle)KDM1B
PDB (SRS)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
PDB (PDBSum)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
PDB (IMB)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
PDB (RSDB)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
Structural Biology KnowledgeBase4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
SCOP (Structural Classification of Proteins)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
CATH (Classification of proteins structures)4FWE    4FWF    4FWJ    4GU0    4GU1    4GUR    4GUS    4GUT    4GUU    4HSU   
SuperfamilyQ8NB78
Human Protein Atlas [tissue]ENSG00000165097-KDM1B [tissue]
Peptide AtlasQ8NB78
HPRD18524
IPIIPI00646410   IPI00783535   IPI00973534   IPI00784464   
Protein Interaction databases
DIP (DOE-UCLA)Q8NB78
IntAct (EBI)Q8NB78
FunCoupENSG00000165097
BioGRIDKDM1B
STRING (EMBL)KDM1B
ZODIACKDM1B
Ontologies - Pathways
QuickGOQ8NB78
Ontology : AmiGOnucleosome  DNA binding  protein binding  nucleus  nucleoplasm  regulation of gene expression by genetic imprinting  multicellular organism development  zinc ion binding  oxidoreductase activity  protein deubiquitination  histone demethylase activity  histone demethylase activity (H3-dimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone demethylase activity (H3-monomethyl-K4 specific)  histone demethylase activity (H3-monomethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation  histone binding  DNA methylation involved in gamete generation  regulation of DNA methylation  oxidation-reduction process  FAD binding  
Ontology : EGO-EBInucleosome  DNA binding  protein binding  nucleus  nucleoplasm  regulation of gene expression by genetic imprinting  multicellular organism development  zinc ion binding  oxidoreductase activity  protein deubiquitination  histone demethylase activity  histone demethylase activity (H3-dimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone demethylase activity (H3-monomethyl-K4 specific)  histone demethylase activity (H3-monomethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation  histone binding  DNA methylation involved in gamete generation  regulation of DNA methylation  oxidation-reduction process  FAD binding  
NDEx NetworkKDM1B
Atlas of Cancer Signalling NetworkKDM1B
Wikipedia pathwaysKDM1B
Orthology - Evolution
OrthoDB221656
GeneTree (enSembl)ENSG00000165097
Phylogenetic Trees/Animal Genes : TreeFamKDM1B
HOVERGENQ8NB78
HOGENOMQ8NB78
Homologs : HomoloGeneKDM1B
Homology/Alignments : Family Browser (UCSC)KDM1B
Gene fusions - Rearrangements
Fusion : MitelmanIL6ST/KDM1B [5q11.2/6p22.3]  [t(5;6)(q11;p22)]  
Fusion : QuiverKDM1B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM1B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM1B
dbVarKDM1B
ClinVarKDM1B
1000_GenomesKDM1B 
Exome Variant ServerKDM1B
ExAC (Exome Aggregation Consortium)ENSG00000165097
GNOMAD BrowserENSG00000165097
Varsome BrowserKDM1B
Genetic variants : HAPMAP221656
Genomic Variants (DGV)KDM1B [DGVbeta]
DECIPHERKDM1B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM1B 
Mutations
ICGC Data PortalKDM1B 
TCGA Data PortalKDM1B 
Broad Tumor PortalKDM1B
OASIS PortalKDM1B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM1B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM1B
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 KDM1B
DgiDB (Drug Gene Interaction Database)KDM1B
DoCM (Curated mutations)KDM1B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM1B (select a term)
intoGenKDM1B
Cancer3DKDM1B(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM613081   
Orphanet
DisGeNETKDM1B
MedgenKDM1B
Genetic Testing Registry KDM1B
NextProtQ8NB78 [Medical]
TSGene221656
GENETestsKDM1B
Target ValidationKDM1B
Huge Navigator KDM1B [HugePedia]
snp3D : Map Gene to Disease221656
BioCentury BCIQKDM1B
ClinGenKDM1B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD221656
Chemical/Pharm GKB GenePA165617946
Clinical trialKDM1B
Miscellaneous
canSAR (ICR)KDM1B (select the gene name)
Probes
Litterature
PubMed28 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM1B
EVEXKDM1B
GoPubMedKDM1B
iHOPKDM1B
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 Nov 6 11:14:46 CET 2018

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