Selected-GenAtlas references SOURCE GeneCards NCBI Gene Swiss-Prot Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
FLASH GENE
Symbol KDM5D contributors: SGE/npt - updated : 15-04-2010
HGNC name lysine (K)-specific demethylase 5D
HGNC id 11115
Location Yq11.222      Physical location : 21.867.302 - 21.906.825
Synonym name
  • Jumonji, AT rich interactive domain 1D
  • Smcy homolog, Y chromosome (mouse)
  • histocompatibility Y antigen
  • selected mouse cDNA on Y, human homolog of
  • protein SmcY
  • Jumonji/ARID domain-containing protein 1D
  • Synonym symbol(s) HY, HYA, KIAA0234, SMCY, JARID1D
    EC.number 1.14.11.-
    DNA
    TYPE functioning gene
    STRUCTURE 39.52 kb     28 Exon(s)
    MAPPING cloned Y linked N status confirmed
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    - - 5331 - 1482 - Agulnik (1994)
  • isoform 3
  • 27 - 5502 - 1539 - Agulnik (1994)
  • isoform 2
  • - - 5595 - 1570 - Agulnik (1994)
  • isoform 1
  • EXPRESSION
    Type ubiquitous
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivemouth   moderately
    Endocrineadrenal gland   moderately
    Lymphoid/Immunelymph node   highly
     spleen   moderately
     thymus   predominantly
    Nervousnerve   moderately
    Reproductivemale systemseminal vesicles   
     male systemprostate  moderately
     male systemmale genital tractepididymis  
     male systemtestis   
    Respiratoryrespiratory tracttrachea  highly
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Connectiveadipose  highly
    cell lineage germ cells
    cell lines
    fluid/secretion
    at STAGE
    physiological period fetal
    Text highly in umbilical cord
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • one JMJN domain
  • one ARID domain
  • one JMJC domain
  • two PHD-type zinc fingers
  • one AT-rich interaction domain
  • isoforms Precursor a short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient
    HOMOLOGY
    interspecies homolog to chimpanzee JARID1D (99 pc)
    homolog to murine Kdm5d (81.3 pc)
    intraspecies paralog to HRBBP2
    Homologene
    FAMILY
  • JARID1 histone demethylase family
  • CATEGORY enzyme , antigen
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus
    basic FUNCTION
  • specifically demethylating trimethylated and dimethylated 'Lys-4' of histone H3 thereby playing a central role in histone code
  • may be involved in regulation of transcription, DNA-dependent
  • may play a role in spermatogenesis by recruiting a meiosis-specific protein to condensed DNA (Akimoto 2008)
  • CELLULAR PROCESS cell life, differentiation
    nucleotide, chromatin organization, methylation
    nucleotide, transcription, regulation
    PHYSIOLOGICAL PROCESS reproduction/sex
    PATHWAY
    metabolism
    signaling
    a component
    INTERACTION
    DNA binding
    RNA
    small molecule metal binding, cofactor, other,
  • ascorbate
  • Fe2+
  • Zn2+
  • protein
  • interacting with PCGF6
  • complexing with MSH5 (Akimoto 2008)
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s)
    Susceptibility
    Variant & Polymorphism
    Candidate gene
  • HY-restricting antigen is associated with pregnancy outcome in patients with recurrent miscarriage subsequent to a firsborn boy (Nielsen 2009)
  • antibody responses to HY antigens correlate with chronic graft-versus-host disease and disease remission (Miklos 2005)
  • Marker
    Therapy target
    ANIMAL & CELL MODELS