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    KDM4D lysine demethylase 4D [ Homo sapiens (human) ]

    Gene ID: 55693, updated on 27-Nov-2024

    Summary

    Official Symbol
    KDM4Dprovided by HGNC
    Official Full Name
    lysine demethylase 4Dprovided by HGNC
    Primary source
    HGNC:HGNC:25498
    See related
    Ensembl:ENSG00000186280 MIM:609766; AllianceGenome:HGNC:25498
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    JMJD2D
    Summary
    Enables histone H3K9me2/H3K9me3 demethylase activity. Involved in inflammatory response. Acts upstream of or within several processes, including cellular response to ionizing radiation; double-strand break repair via homologous recombination; and positive regulation of double-strand break repair via nonhomologous end joining. Located in site of double-strand break. Biomarker of nephroblastoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 26.3) and brain (RPKM 0.6) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See KDM4D in Genome Data Viewer
    Location:
    11q21
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (94973709..94999519)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (94980727..95006531)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (94706873..94732683)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ST13, Hsp70 interacting protein pseudogene 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:94705997-94706772 Neighboring gene CWC15 spliceosome associated protein homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5407 Neighboring gene general transcription factor IIE subunit 2 pseudogene Neighboring gene lysine demethylase 4D pseudogene Neighboring gene lysine demethylase 4E

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of lysine (K)-specific demethylase 4D (KDM4D) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10251, MGC141909

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables damaged DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K9me2/H3K9me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in blood microparticle HDA PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IC
    Inferred by Curator
    more info
    PubMed 
    located_in pericentric heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    lysine-specific demethylase 4D
    Names
    [histone H3]-trimethyl-L-lysine(9) demethylase 4D
    jmjC domain-containing histone demethylation protein 3D
    jumonji domain containing 2D
    jumonji domain-containing protein 2D
    lysine (K)-specific demethylase 4D
    NP_060509.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_018039.3NP_060509.2  lysine-specific demethylase 4D

      See identical proteins and their annotated locations for NP_060509.2

      Status: VALIDATED

      Source sequence(s)
      AK056162, AP002383, AW593120, BC031862, CA311555
      Consensus CDS
      CCDS8302.1
      UniProtKB/Swiss-Prot
      B3KPC4, Q0VF39, Q6B0I6, Q9NT41, Q9NW76
      Related
      ENSP00000334181.5, ENST00000335080.6
      Conserved Domains (2) summary
      pfam02373
      Location:179295
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:1953
      JmjN; jmjN domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      94973709..94999519
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      94980727..95006531
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)