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

Gene ID: 9682, updated on 26-Aug-2014
Official Symbol
KDM4Aprovided by HGNC
Official Full Name
lysine (K)-specific demethylase 4Aprovided by HGNC
Primary source
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]
See KDM4A in Epigenomics, MapViewer
Location:
1p34.1
Exon count:
24
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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
Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study.
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...
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

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
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cardiac muscle hypertrophy in response to stress IEA
Inferred from Electronic Annotation
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 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
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
lysine-specific demethylase 4A
Names
lysine-specific demethylase 4A
jumonji domain containing 2
tudor domain containing 14A
jumonji domain containing 2A
jumonji domain-containing protein 2A
jumonji C domain-containing histone demethylase 3A
jmjC domain-containing histone demethylation protein 3A
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 proteins identical to 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
    Blast Score: 95
    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
    Blast Score: 179
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:897953
    Blast Score: 137
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    Blast Score: 434
    JmjC; JmjC domain, hydroxylase
    pfam13831
    Location:733766
    Blast Score: 145
    PHD_2; PHD-finger
    pfam13832
    Location:774884
    Blast Score: 455
    zf-HC5HC2H_2; PHD-zinc-finger like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

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

mRNA and Protein(s)

  1. XM_005271355.1XP_005271412.1  

    See proteins identical to XP_005271412.1

    UniProtKB/Swiss-Prot
    O75164
    Conserved Domains (6) summary
    cd04508
    Location:9601004
    Blast Score: 95
    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
    Blast Score: 179
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:897953
    Blast Score: 137
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    Blast Score: 434
    JmjC; JmjC domain, hydroxylase
    pfam13831
    Location:733766
    Blast Score: 145
    PHD_2; PHD-finger
    pfam13832
    Location:774884
    Blast Score: 455
    zf-HC5HC2H_2; PHD-zinc-finger like domain
  2. XM_005271356.1XP_005271413.1  

    Conserved Domains (5) summary
    cd04508
    Location:869913
    Blast Score: 95
    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
    Blast Score: 136
    TUDOR; Tudor domain
    pfam02373
    Location:84200
    Blast Score: 434
    JmjC; JmjC domain, hydroxylase
    pfam13831
    Location:642675
    Blast Score: 143
    PHD_2; PHD-finger
    pfam13832
    Location:683793
    Blast Score: 449
    zf-HC5HC2H_2; PHD-zinc-finger like domain
  3. XM_005271354.1XP_005271411.1  

    See proteins identical to XP_005271411.1

    UniProtKB/Swiss-Prot
    O75164
    Conserved Domains (6) summary
    cd04508
    Location:9601004
    Blast Score: 95
    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
    Blast Score: 179
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:897953
    Blast Score: 137
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    Blast Score: 434
    JmjC; JmjC domain, hydroxylase
    pfam13831
    Location:733766
    Blast Score: 145
    PHD_2; PHD-finger
    pfam13832
    Location:774884
    Blast Score: 455
    zf-HC5HC2H_2; PHD-zinc-finger like domain

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    42236372..42291619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

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