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    Dnmt3a DNA methyltransferase 3A [ Mus musculus (house mouse) ]

    Gene ID: 13435, updated on 13-Jan-2025

    Summary

    Official Symbol
    Dnmt3aprovided by MGI
    Official Full Name
    DNA methyltransferase 3Aprovided by MGI
    Primary source
    MGI:MGI:1261827
    See related
    Ensembl:ENSMUSG00000020661 AllianceGenome:MGI:1261827
    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
    MmuIIIA
    Summary
    This is one of two related genes encoding de novo DNA methyltransferases, which are responsible for the establishment of DNA methylation patterns in embryos. Loss of function of this gene causes developmental defects in multiple different organ systems. There is a pseudogene for this gene located on chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Nov 2012]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 12.7), CNS E11.5 (RPKM 11.1) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Dnmt3a in Genome Data Viewer
    Location:
    12 A1.1; 12 1.99 cM
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (3851559..3964442)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (3801559..3914443)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene dystrobrevin, beta Neighboring gene predicted gene, 53748 Neighboring gene STARR-seq mESC enhancer starr_31423 Neighboring gene STARR-seq mESC enhancer starr_31424 Neighboring gene STARR-positive B cell enhancer ABC_E3047 Neighboring gene predicted gene, 18028 Neighboring gene STARR-seq mESC enhancer starr_31427 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:3855747-3855931 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:3870938-3871047 Neighboring gene DNA methyltransferase 3A, opposite strand Neighboring gene STARR-seq mESC enhancer starr_31429 Neighboring gene predicted gene, 31623 Neighboring gene Pomc distal enhancer region Neighboring gene Pomc promoter region Neighboring gene STARR-positive B cell enhancer mm9_chr12:3959806-3960107 Neighboring gene peptidyl prolyl isomerase H pseudogene Neighboring gene pro-opiomelanocortin-alpha

    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)

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA (cytosine-5-)-methyltransferase activity  
    enables DNA (cytosine-5-)-methyltransferase activity PubMed 
    enables DNA (cytosine-5-)-methyltransferase activity PubMed 
    enables DNA (cytosine-5-)-methyltransferase activity  
    enables DNA (cytosine-5-)-methyltransferase activity  
    enables DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates  
    enables DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates  
    enables DNA binding PubMed 
    enables DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables chromatin binding  
    enables chromatin binding  
    enables identical protein binding  
    enables identical protein binding  
    enables lncRNA binding PubMed 
    enables lncRNA binding  
    enables metal ion binding  
    enables protein binding PubMed 
    enables protein-cysteine methyltransferase activity PubMed 
    enables unmethylated CpG binding  
    Items 1 - 25 of 36
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation PubMed 
    involved_in DNA methylation-dependent constitutive heterochromatin formation  
    involved_in autosome genomic imprinting PubMed 
    acts_upstream_of_or_within autosome genomic imprinting PubMed 
    acts_upstream_of_or_within cellular response to amino acid stimulus PubMed 
    acts_upstream_of_or_within cellular response to bisphenol A PubMed 
    involved_in cellular response to ethanol  
    involved_in cellular response to hypoxia  
    acts_upstream_of_or_within epigenetic programming of gene expression PubMed 
    acts_upstream_of_or_within epigenetic programming of gene expression PubMed 
    acts_upstream_of_or_within genomic imprinting PubMed 
    involved_in genomic imprinting PubMed 
    involved_in hepatocyte apoptotic process  
    acts_upstream_of_or_within heterochromatin formation PubMed 
    involved_in methylation  
    involved_in negative regulation of DNA-templated transcription  
    acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation PubMed 
    involved_in negative regulation of gene expression via chromosomal CpG island methylation PubMed 
    involved_in negative regulation of gene expression via chromosomal CpG island methylation  
    involved_in negative regulation of gene expression via chromosomal CpG island methylation  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in neuron differentiation  
    involved_in positive regulation of cellular response to hypoxia  
    involved_in positive regulation of cellular response to hypoxia  
    acts_upstream_of_or_within post-embryonic development PubMed 
    involved_in regulatory ncRNA-mediated heterochromatin formation  
    involved_in response to cocaine  
    involved_in response to estradiol  
    involved_in response to ionizing radiation  
    involved_in response to lead ion  
    involved_in response to toxic substance  
    involved_in response to vitamin A  
    involved_in response to xenobiotic stimulus  
    acts_upstream_of_or_within spermatogenesis PubMed 
    involved_in transposable element silencing by piRNA-mediated DNA methylation PubMed 
    Items 1 - 25 of 36
    Component Evidence Code Pubs
    located_in XY body PubMed 
    part_of catalytic complex  
    part_of catalytic complex  
    located_in chromosome, centromeric region PubMed 
    is_active_in cytoplasm  
    located_in cytoplasm PubMed 
    located_in cytoplasm  
    located_in cytoplasm  
    located_in euchromatin  
    located_in euchromatin  
    located_in heterochromatin PubMed 
    located_in nuclear matrix  
    located_in nuclear matrix  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    DNA (cytosine-5)-methyltransferase 3A
    Names
    DNA MTase MmuIIIA
    DNA methyltransferase MmuIIIA
    cysteine methyltransferase DNMT3A
    NP_001258682.1
    NP_001408786.1
    NP_031898.1
    NP_714965.1
    XP_006515019.1
    XP_030102398.1
    XP_030102399.1
    XP_030102400.1

    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_001271753.2NP_001258682.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

      See identical proteins and their annotated locations for NP_001258682.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same isoform (1, also known as Dnmt3a1).
      Source sequence(s)
      AC159324, CR974568
      Consensus CDS
      CCDS36397.1
      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Related
      ENSMUSP00000134009.2, ENSMUST00000174817.8
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    2. NM_001421857.1NP_001408786.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC159324, CR974568
      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
    3. NM_007872.5NP_031898.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

      See identical proteins and their annotated locations for NP_031898.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1, also known as Dnmt3a1). Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AC159324, CR974568
      Consensus CDS
      CCDS36397.1
      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Related
      ENSMUSP00000020991.9, ENSMUST00000020991.15
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    4. NM_153743.5NP_714965.1  DNA (cytosine-5)-methyltransferase 3A isoform 2

      See identical proteins and their annotated locations for NP_714965.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter, compared to variant 1. It differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon. The encoded isoform (2, also known as Dnmt3a2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC159324
      Consensus CDS
      CCDS25784.1
      UniProtKB/Swiss-Prot
      O88508
      Related
      ENSMUSP00000133543.2, ENSMUST00000172689.8
      Conserved Domains (3) summary
      cd05835
      Location:67153
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      COG0270
      Location:409572
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd11729
      Location:264391
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)

    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_000078.7 Reference GRCm39 C57BL/6J

      Range
      3851559..3964442
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006514956.4XP_006515019.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      See identical proteins and their annotated locations for XP_006515019.1

      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    2. XM_030246538.1XP_030102398.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    3. XM_030246540.2XP_030102400.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    4. XM_030246539.2XP_030102399.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      UniProtKB/Swiss-Prot
      O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1
      Conserved Domains (5) summary
      cd05835
      Location:286372
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      PTZ00449
      Location:1121
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      COG0270
      Location:628791
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      TIGR00927
      Location:17282
      2A1904; K+-dependent Na+/Ca+ exchanger
      cd11729
      Location:483610
      ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
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