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    KDM4A lysine (K)-specific demethylase 4A [ Homo sapiens (human) ]

    Gene ID: 9682, updated on 7-Feb-2016
    Official Symbol
    KDM4Aprovided by HGNC
    Official Full Name
    lysine (K)-specific demethylase 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:22978
    See related
    Ensembl:ENSG00000066135; HPRD:17168; MIM:609764; Vega:OTTHUMG00000007560
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    JMJD2; JHDM3A; JMJD2A; TDRD14A
    Summary
    This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]
    Orthologs
    See KDM4A in Epigenomics, MapViewer
    Location:
    1p34.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 1 NC_000001.11 (43650126..43705518)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44115797..44171189)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene seizure threshold 2 homolog (mouse) Neighboring gene hydroxypyruvate isomerase (putative) Neighboring gene protein tyrosine phosphatase, receptor type F Neighboring gene uncharacterized LOC101929592 Neighboring gene KDM4A antisense RNA 1 Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3 Neighboring gene microRNA 6079

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
    NHGRI GWA Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    NHGRI GWA Catalog
    Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study.
    NHGRI GWA Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    NHGRI GWA Catalog
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • DNA Double Strand Break Response, organism-specific biosystem (from REACTOME)
      DNA Double Strand Break Response, organism-specific biosystemDNA double strand break (DSB) response involves sensing of DNA DSBs by the MRN complex which triggers ATM activation. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signali...
    • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
      DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
    • DNA Repair, organism-specific biosystem (from REACTOME)
      DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
    • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
      HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
    • Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystem (from REACTOME)
      Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystemActivated ATM phosphorylates a number of proteins involved in the DNA damage checkpoint and DNA repair (Thompson and Schild 2002, Ciccia and Elledge 2010), thereby triggering and coordinating accumul...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Clone Names

    • KIAA0677

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    histone demethylase activity (H3-K36 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    DNA repair TAS
    Traceable Author Statement
    more info
     
    cardiac muscle hypertrophy in response to stress IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin organization TAS
    Traceable Author Statement
    more info
     
    double-strand break repair TAS
    Traceable Author Statement
    more info
     
    histone H3-K36 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of histone H3-K9 trimethylation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pericentric heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    lysine-specific demethylase 4A
    Names
    jmjC domain-containing histone demethylation protein 3A
    jumonji C domain-containing histone demethylase 3A
    jumonji domain containing 2
    jumonji domain containing 2A
    jumonji domain-containing protein 2A
    tudor domain containing 14A
    NP_055478.2

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_014663.2NP_055478.2  lysine-specific demethylase 4A

      See identical proteins and their annotated locations for NP_055478.2

      Status: REVIEWED

      Source sequence(s)
      AB014577, BP198064, CA944984, CN361683
      Consensus CDS
      CCDS491.1
      UniProtKB/Swiss-Prot
      O75164
      Related
      ENSP00000361473, OTTHUMP00000008810, ENST00000372396, OTTHUMT00000019960
      Conserved Domains (6) summary
      cd04508
      Location:9601004
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:897953
      TUDOR; Tudor domain
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      cd15575
      Location:667766
      PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p2 Primary Assembly

      Range
      43650126..43705518
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271355.2XP_005271412.1  

      See identical proteins and their annotated locations for XP_005271412.1

      UniProtKB/Swiss-Prot
      O75164
      Conserved Domains (6) summary
      cd04508
      Location:9601004
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:897953
      TUDOR; Tudor domain
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      cd15575
      Location:667766
      PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    2. XM_005271356.2XP_005271413.1  

      Conserved Domains (5) summary
      cd04508
      Location:869913
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00333
      Location:806862
      TUDOR; Tudor domain
      pfam02373
      Location:84200
      JmjC; JmjC domain, hydroxylase
      cd15575
      Location:576675
      PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)
      cd15713
      Location:684793
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    3. XM_005271354.2XP_005271411.1  

      See identical proteins and their annotated locations for XP_005271411.1

      UniProtKB/Swiss-Prot
      O75164
      Conserved Domains (6) summary
      cd04508
      Location:9601004
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:897953
      TUDOR; Tudor domain
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      cd15575
      Location:667766
      PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    4. XM_011542467.1XP_011540769.1  

      UniProtKB/Swiss-Prot
      O75164
      Conserved Domains (4) summary
      cd04508
      Location:377421
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00333
      Location:314370
      TUDOR; Tudor domain
      cd15575
      Location:84183
      PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)
      cl22851
      Location:192301
      PHD_SF; PHD finger superfamily

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

      Range
      44232091..44287481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)