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Kdm4a lysine (K)-specific demethylase 4A [ Mus musculus (house mouse) ]

Gene ID: 230674, updated on 12-Mar-2023

Summary

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Official Symbol
Kdm4aprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Aprovided by MGI
Primary source
MGI:MGI:2446210
See related
Ensembl:ENSMUSG00000033326 AllianceGenome:MGI:2446210
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Jmjd2; JHDM3A; Jmjd2a; mKIAA0677; D4Ertd222e
Summary
Enables histone demethylase activity. Acts upstream of or within cardiac muscle hypertrophy in response to stress and negative regulation of histone H3-K9 trimethylation. Located in pericentric heterochromatin. Is expressed in several structures, including branchial arch; central nervous system; dorsal root ganglion; early conceptus; and genitourinary system. Orthologous to human KDM4A (lysine demethylase 4A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 27.6), CNS E14 (RPKM 25.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Kdm4a in Genome Data Viewer
Location:
4 D2.1; 4 54.31 cM
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (117994154..118037242, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (118136957..118180090, complement)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3 Neighboring gene RIKEN cDNA 9530034E10 gene Neighboring gene predicted gene, 54253 Neighboring gene predicted gene, 23382 Neighboring gene predicted gene, 54252 Neighboring gene microRNA 7226 Neighboring gene protein tyrosine phosphatase, receptor type, F Neighboring gene predicted gene, 40235

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. KDM4A, involved in the inflammatory and oxidative stress caused by traumatic brain injury-hemorrhagic shock, partly through the regulation of the microglia M1 polarization. Cai J, et al. BMC Neurosci, 2023 Mar 3. PMID 36869312, Free PMC Article
  2. Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling. Qi Q, et al. Cell Mol Life Sci, 2020 Jun. PMID 31515577
  3. Maternal expression of the histone demethylase Kdm4a is crucial for pre-implantation development. Sankar A, et al. Development, 2017 Sep 15. PMID 28827393
  4. Inhibition of KDM4A activity as a strategy to suppress interleukin-6 production and attenuate colitis induction. Ishiguro K, et al. Clin Immunol, 2017 Jul. PMID 28511912
  5. Histone Lysine Demethylases of JMJD2 or KDM4 Family are Important Epigenetic Regulators in Reward Circuitry in the Etiopathology of Depression. Pathak SS, et al. Neuropsychopharmacology, 2017 Mar. PMID 27711046, Free PMC Article

See all (60) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KDM4A, involved in the inflammatory and oxidative stress caused by traumatic brain injury-hemorrhagic shock, partly through the regulation of the microglia M1 polarization.
    Title: KDM4A, involved in the inflammatory and oxidative stress caused by traumatic brain injury-hemorrhagic shock, partly through the regulation of the microglia M1 polarization.
  2. IRX2 activated by jumonji domain-containing protein 2A is crucial for cardiac hypertrophy and dysfunction in response to the hypertrophic stimuli.
    Title: IRX2 activated by jumonji domain-containing protein 2A is crucial for cardiac hypertrophy and dysfunction in response to the hypertrophic stimuli.
  3. KDM4A regulates myogenesis by demethylating H3K9me3 of myogenic regulatory factors.
    Title: KDM4A regulates myogenesis by demethylating H3K9me3 of myogenic regulatory factors.
  4. Targeting KDM4A epigenetically activates tumor-cell-intrinsic immunity by inducing DNA replication stress.
    Title: Targeting KDM4A epigenetically activates tumor-cell-intrinsic immunity by inducing DNA replication stress.
  5. KDM4 knockdown resulted in the down-regulation of miR-29 expression.
    Title: The histone demethylase Kdm4 suppresses activation of hepatic stellate cell by inducing MiR-29 transcription.
  6. KDM4A inhibition as a potential therapeutic target for treating metabolic disorders.
    Title: Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling.
  7. KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes.
    Title: KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes.
  8. The knockout of the KDM4 demethylases leads to accumulation of H3K9me3 on transcription start sites and the corresponding downregulation of expression of several genes in hematopoietic stem cell.
    Title: The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance.
  9. Jmjd2 class demethylases are critical epigenetic regulators involved in etiopathology of depression and related disorders.
    Title: Histone Lysine Demethylases of JMJD2 or KDM4 Family are Important Epigenetic Regulators in Reward Circuitry in the Etiopathology of Depression.
  10. High Jmjd2a expression is associated with neuropathic pain.
    Title: The histone demethylase JMJD2A regulates the expression of BDNF and mediates neuropathic pain in mice.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (3) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC28562

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K36 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
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
 PubMed 
enables histone H3K9 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cardiac muscle hypertrophy in response to stress IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of astrocyte differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of autophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of cell death ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of neuron differentiation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in pericentric heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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 domain containing 2A
jumonji domain-containing protein 2A
NP_001155295.1
NP_759014.2
XP_006503073.1

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_001161823.1 → NP_001155295.1  lysine-specific demethylase 4A isoform 1

    See identical proteins and their annotated locations for NP_001155295.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK054095, AL626764, BY308642
    Consensus CDS
    CCDS51282.1
    UniProtKB/Swiss-Prot
    Q8BW72, Q8K137
    Related
    ENSMUSP00000102014.3, ENSMUST00000106406.9
    Conserved Domains (5) summary
    smart00545
    Location:13 → 55
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15713
    Location:775 → 884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    pfam02373
    Location:175 → 291
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:960 → 994
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:667 → 766
    PHD_SF; PHD finger superfamily

  2. NM_172382.2 → NP_759014.2  lysine-specific demethylase 4A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 3' terminal exon, compared to variant 1, that results in a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK054095, AL626764, BY308642
    Consensus CDS
    CCDS18545.1
    UniProtKB/Swiss-Prot
    Q8BW72
    UniProtKB/TrEMBL
    A2A8L9
    Related
    ENSMUSP00000062910.9, ENSMUST00000050288.9
    Conserved Domains (5) summary
    smart00545
    Location:13 → 55
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:899 → 946
    TUDOR; Tudor domain
    pfam02373
    Location:175 → 291
    JmjC; JmjC domain, hydroxylase
    cd15713
    Location:775 → 884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    cl22851
    Location:667 → 766
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Mus musculus 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 GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    117994154..118037242 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006503010.2 → XP_006503073.1  lysine-specific demethylase 4A isoform X1

    See identical proteins and their annotated locations for XP_006503073.1

    UniProtKB/Swiss-Prot
    Q8BW72, Q8K137
    Related
    ENSMUSP00000095524.3, ENSMUST00000097911.9
    Conserved Domains (5) summary
    smart00545
    Location:13 → 55
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15713
    Location:775 → 884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    pfam02373
    Location:175 → 291
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:960 → 994
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:667 → 766
    PHD_SF; PHD finger superfamily

RNA

  1. XR_003954917.2 RNA Sequence

  2. XR_003954916.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BW72.3 GenPept UniProtKB/Swiss-Prot:Q8BW72

Gene LinkOut

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