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

    Gene ID: 230674, updated on 27-Nov-2024

    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 H3K9 demethylase activity. Acts upstream of or within cardiac muscle hypertrophy in response to stress. 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, Nov 2024]
    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
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (117994154..118037216, 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 STARR-seq mESC enhancer starr_11191 Neighboring gene STARR-seq mESC enhancer starr_11192 Neighboring gene STARR-positive B cell enhancer ABC_E6201 Neighboring gene STARR-positive B cell enhancer ABC_E1037 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:117852549-117852732 Neighboring gene predicted gene, 23382 Neighboring gene predicted gene, 54252 Neighboring gene STARR-seq mESC enhancer starr_11193 Neighboring gene STARR-seq mESC enhancer starr_11196 Neighboring gene microRNA 7226 Neighboring gene protein tyrosine phosphatase receptor type F Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:117930044-117930297 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. 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, Free PMC Article
    2. 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
    3. 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
    4. Maternal expression of the histone demethylase Kdm4a is crucial for pre-implantation development. Sankar A, et al. Development, 2017 Sep 15. PMID 28827393
    5. JMJD2A attenuation affects cell cycle and tumourigenic inflammatory gene regulation in lipopolysaccharide stimulated neuroectodermal stem cells. Das A, et al. Exp Cell Res, 2014 Nov 1. PMID 25193078

    See all (65) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. JMJD2A mediates transcriptional activation of SFRP4 and regulates oxidative stress and mitochondrial dysfunction in heart failure.
      Title: JMJD2A mediates transcriptional activation of SFRP4 and regulates oxidative stress and mitochondrial dysfunction in heart failure.
    2. Astrocyte KDM4A mediates chemokines and drives neutrophil infiltration to aggravate cerebral ischemia and reperfusion injury.
      Title: Astrocyte KDM4A mediates chemokines and drives neutrophil infiltration to aggravate cerebral ischemia and reperfusion injury.
    3. 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.
    4. 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.
    5. KDM4A regulates myogenesis by demethylating H3K9me3 of myogenic regulatory factors.
      Title: KDM4A regulates myogenesis by demethylating H3K9me3 of myogenic regulatory factors.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Variation

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    Alleles

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

    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 histone H3K36 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9me2/H3K9me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ubiquitin protein ligase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in apoptotic chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in apoptotic chromosome condensation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cardiac muscle hypertrophy in response to stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of astrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of astrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to nutrient levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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
    		  
    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_001413184.1
    NP_001413185.1
    NP_001413186.1
    NP_001413187.1
    NP_001413188.1
    NP_759014.2

    NCBI Reference Sequences (RefSeq)

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    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_001161823.2 → NP_001155295.1  lysine-specific demethylase 4A isoform 1

      See identical proteins and their annotated locations for NP_001155295.1

      Status: VALIDATED

      Source sequence(s)
      AL626764
      Consensus CDS
      CCDS51282.1
      UniProtKB/Swiss-Prot
      A2A8L8, Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, 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_001426255.1 → NP_001413184.1  lysine-specific demethylase 4A isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL626764
      UniProtKB/Swiss-Prot
      A2A8L8, Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, Q8BW72, Q8K137

    3. NM_001426256.1 → NP_001413185.1  lysine-specific demethylase 4A isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL626764
      UniProtKB/Swiss-Prot
      A2A8L8, Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, Q8BW72, Q8K137
      Related
      ENSMUSP00000095524.3, ENSMUST00000097911.9

    4. NM_001426257.1 → NP_001413186.1  lysine-specific demethylase 4A isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL626764
      UniProtKB/Swiss-Prot
      A2A8L8, Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, Q8BW72, Q8K137
      Related
      ENSMUSP00000102011.2, ENSMUST00000106403.8

    5. NM_001426258.1 → NP_001413187.1  lysine-specific demethylase 4A isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL626764
      UniProtKB/TrEMBL
      A2A8L9

    6. NM_001426259.1 → NP_001413188.1  lysine-specific demethylase 4A isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL626764

    7. NM_172382.3 → NP_759014.2  lysine-specific demethylase 4A isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL626764
      Consensus CDS
      CCDS18545.1
      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

    RNA

    1. NR_189679.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL626764

    2. NR_189680.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL626764

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    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..118037216 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BW72.3 GenPept UniProtKB/Swiss-Prot:Q8BW72

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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