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FLASH GENE
Symbol KDM3B contributors: mct/npt - updated : 15-05-2019
HGNC name lysine (K)-specific demethylase 3B
HGNC id 1337
Corresponding disease
IDSFD intellectual disability, short stature, and facial dysmorphism
Location 5q31.2      Physical location : 137.688.284 - 137.772.716
Synonym name
  • rat zinc finger proteinTS1GA homolog
  • chromosome 5 open reading frame 7
  • jumonji domain containing 1B
  • nuclear protein 5qNCA
  • Synonym symbol(s) KIAA1082, 5qNCA, C5orf7, JMJD1B, JHDM2B, NET22
    EC.number 1.14.11.-
    DNA
    TYPE functioning gene
    STRUCTURE 84.43 kb     24 Exon(s)
    MAPPING cloned Y linked N status provisional
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    24 - 6830 - 1761 - 2001 11687974
    EXPRESSION
    Type
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    blood / hematopoieticspleen    
     thymus    
    Cardiovascularheart    
    Digestiveliver   highly
    Reproductivemale systemtestis    Mus musculus
    Urinarykidney   highly
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Blood / Hematopoieticbone marrow   
    Connectivebone   
    Lymphoid    
    Muscularstriatumcardiac  
    Muscularstriatumskeletal  
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Blood/Hematopoieticleukocyte
    cell lineage
    cell lines AML cell lines highly
    fluid/secretion
    at STAGE
    physiological period fetal, pregnancy
    Text liver, placenta highly
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • a N terminal putative zinc finger domain, overlapping a bipartite nuclear localization signals (NLS)
  • a LXLL motif
  • a conserved C terminal zinc finger with the unique spacing
  • Cys-X2-Cys-X7-His-X2-Cys-X2-Cys-X4-Cys-X2-Cys
  • a Jumonji-C domain
  • HOMOLOGY
    interspecies homolog to rattus zinc finger proteinTS1GA
    intraspecies paralog to JMJD1C
    Homologene
    FAMILY
  • JHDM2 histone demethylase family
  • CATEGORY transcription factor , tumor suppressor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus,nucleoplasm
    intracellular,nucleus,chromatin/chromosome
    basic FUNCTION
  • playing a role in meiotic and postmeiotic germ cell development
  • histone H3K9 demethylase implicated in the nuclear hormone receptor-based transcriptional regulation (Katoh 2007)
  • has a role in angiogenesis
  • is likely required for normal spermatogenesis and sexual behaviors in male
  • KDM3A, KDM3B meditated H3K9 demethylation has critical roles for early embryogenesis and embryonic stem cells (ESCs) maintenance
  • is a crucial epigenetic factor in cell cycle regulation that manipulates chromatin dynamics and transcription in hepatocellular carcinoma (HCC)
  • histone demethylase involved in H3K9 demethylation, a crucial part of chromatin modification required for transcriptional regulation
  • CELLULAR PROCESS cell cycle,division,meiosis
    nucleotide, chromatin organization, remodeling
    nucleotide, transcription
    PHYSIOLOGICAL PROCESS reproduction/sex
    text spermatogenesis
    PATHWAY
    metabolism
    signaling
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • displayed histone H3K9-me1/2 demethylase activity and induced leukemogenic oncogene LMO2 expression via a synergistic interaction with CREBBP
  • SCAI, a known transcriptional repressor, interacts specifically with KDM3B
  • KDM3B represses transcription of the angiogenesis regulatory gene, ANGPT1
  • KDM3B-mediated H3K9 demethylation plays essential roles in maintenance of the circulating IGF1, postnatal somatic growth, circulating 17beta-estradiol, and female reproductive function
  • KDM1A, KDM1B preferentially target H3K9 demethylation of gene-dense regions of chromosomes, thereby establishing an H3K9 hypomethylation state in euchromatin
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) IDSFD
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral   LOH    
    loss of chromosome 5 frequently finding in myeloid leukemia and myelodysplasias
    tumoral   deletion    
    frequently finding in myeloid leukemia and myelodysplasias
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    SystemTypeDisorderPubmed
    cancerdigestiveliver
    potential gene therapy target for effective treatment of Hepatocellular carcinoma (HCC)
    ANIMAL & CELL MODELS
  • Jmjd1b -/- mice show defects in hematopoiesis
  • kdm3b-knockout mice present with a somatic growth restriction, possibly explained by decreased concentrations of insulin-like growth factor-1 (IGF1)