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

    Gene ID: 230674, updated on 5-Sep-2021

    Summary

    Official Symbol
    Kdm4aprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 4Aprovided by MGI
    Primary source
    MGI:MGI:2446210
    See related
    Ensembl:ENSMUSG00000033326
    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
    JHDM3; Jmjd2; JHDM3A; Jmjd2a; D4Ertd222; mKIAA0677; D4Ertd222e
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 27.6), CNS E14 (RPKM 25.9) and 28 other tissues See more
    Orthologs
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    Genomic context

    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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (117809609..117852648, 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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 H3-methyl-lysine-36 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables histone H3-methyl-lysine-36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3-tri/dimethyl-lysine-36 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3-tri/dimethyl-lysine-9 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
     
    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

    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)

    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_001161823.1NP_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
      Related
      ENSMUSP00000102014.3, ENSMUST00000106406.9
      Conserved Domains (5) summary
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:960994
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:667766
      PHD_SF; PHD finger superfamily
    2. NM_172382.2NP_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:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:899946
      TUDOR; Tudor domain
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
      cl22851
      Location:667766
      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_006503010.2XP_006503073.1  lysine-specific demethylase 4A isoform X1

      See identical proteins and their annotated locations for XP_006503073.1

      UniProtKB/Swiss-Prot
      Q8BW72
      Related
      ENSMUSP00000095524.3, ENSMUST00000097911.9
      Conserved Domains (5) summary
      smart00545
      Location:1355
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15713
      Location:775884
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
      pfam02373
      Location:175291
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:960994
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:667766
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_003954917.2 RNA Sequence

    2. XR_003954916.2 RNA Sequence

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