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

    Gene ID: 9682, updated on 17-Jun-2024

    Summary

    Official Symbol
    KDM4Aprovided by HGNC
    Official Full Name
    lysine demethylase 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:22978
    See related
    Ensembl:ENSG00000066135 MIM:609764; AllianceGenome:HGNC:22978
    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]
    Expression
    Ubiquitous expression in duodenum (RPKM 11.5), thyroid (RPKM 10.1) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See KDM4A in Genome Data Viewer
    Location:
    1p34.2-p34.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (43650149..43705518)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (43520658..43576010)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44115820..44171189)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SZT2 subunit of KICSTOR complex Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 785 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:43937485-43938684 Neighboring gene Sharpr-MPRA regulatory region 4928 Neighboring gene HYI antisense RNA 1 Neighboring gene hydroxypyruvate isomerase (putative) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43986941-43987441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43997400-43997972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43998601-43999102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43999103-43999602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44000549-44001411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44014162-44014968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44014969-44015773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44022869-44023446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44023447-44024024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44026337-44026914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44030770-44031565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44038483-44038984 Neighboring gene protein tyrosine phosphatase receptor type F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44041269-44042129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44040406-44041268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44046933-44047754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44061284-44061784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44061785-44062285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44063935-44064436 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44086190-44086364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 788 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:44125453-44126129 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44126130-44126805 Neighboring gene uncharacterized LOC124904165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 921 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:44131983-44133182 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44142744-44142920 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44172642-44173159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 790 Neighboring gene ST3GAL3 antisense RNA 1 Neighboring gene uncharacterized LOC124904721 Neighboring gene KDM4A antisense RNA 1 Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 924 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:44232560-44233095 Neighboring gene uncharacterized LOC124904166

    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
    Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0677

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K36 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K36 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K36me2/H3K36me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9me2/H3K9me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of pericentric heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 4A
    Names
    [histone H3]-trimethyl-L-lysine(36) demethylase 4A
    [histone H3]-trimethyl-L-lysine(9) demethylase 4A
    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
    lysine (K)-specific demethylase 4A
    tudor domain containing 14A
    NP_055478.2

    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_014663.3NP_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, Q5VVB1
      Related
      ENSP00000361473.3, ENST00000372396.4
      Conserved Domains (5) summary
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:9551010
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      43650149..43705518
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      43520658..43576010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)