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

Gene ID: 9682, updated on 22-Aug-2021

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
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
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Genomic context

See KDM4A in Genome Data Viewer
Location:
1p34.2-p34.1
Exon count:
23
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (43650149..43705518)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44115820..44171189)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4928 Neighboring gene protein tyrosine phosphatase receptor type F Neighboring gene ST3GAL3 antisense RNA 1 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
GeneReviews: Not available
Biological insights from 108 schizophrenia-associated genetic loci.
GeneReviews: Not available
Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study.
GeneReviews: Not available
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
GeneReviews: Not available

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
enables histone H3-methyl-lysine-36 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3-methyl-lysine-36 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3-methyl-lysine-9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3-methyl-lysine-9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
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
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
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in 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
XP_005271411.1
XP_005271412.1

NCBI Reference Sequences (RefSeq)

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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
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    43650149..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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