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

Gene ID: 9682, updated on 9-Sep-2018

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; 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]
Expression
Ubiquitous expression in duodenum (RPKM 11.5), thyroid (RPKM 10.1) and 25 other tissues See more
Orthologs

Genomic context

See KDM4A in Genome Data Viewer
Location:
1p34.2-p34.1
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 SZT2, KICSTOR complex subunit 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

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

Pathways from BioSystems

  • 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...
  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0677

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
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 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
cytosol IDA
Inferred from Direct Assay
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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
lysine (K)-specific demethylase 4A
tudor domain containing 14A
NP_055478.2
XP_005271411.1
XP_005271412.1

NCBI Reference Sequences (RefSeq)

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
    ENSP00000361473.3, OTTHUMP00000008810, ENST00000372396.3, OTTHUMT00000019960
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005271355.3XP_005271412.1  lysine-specific demethylase 4A isoform X1

    See identical proteins and their annotated locations for XP_005271412.1

    UniProtKB/Swiss-Prot
    O75164
    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)
  2. XM_005271354.3XP_005271411.1  lysine-specific demethylase 4A isoform X1

    See identical proteins and their annotated locations for XP_005271411.1

    UniProtKB/Swiss-Prot
    O75164
    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)
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