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

    Gene ID: 13435, updated on 9-Dec-2024

    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
    Try the new Gene table
    Try the new Transcript table

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA (cytosine-5-)-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA (cytosine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA (cytosine-5-)-methyltransferase activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables DNA (cytosine-5-)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA (cytosine-5-)-methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates TAS
    Traceable Author Statement
    more info
     
    enables DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables lncRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lncRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-cysteine methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables unmethylated CpG binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in DNA methylation-dependent constitutive heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in autosome genomic imprinting IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within autosome genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to amino acid stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to bisphenol A IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to ethanol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within epigenetic programming of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within epigenetic programming of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hepatocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of gene expression via chromosomal CpG island methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of gene expression via chromosomal CpG island methylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of gene expression via chromosomal CpG island methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cellular response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cellular response to hypoxia ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within post-embryonic development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulatory ncRNA-mediated heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to cocaine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to estradiol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to ionizing radiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to lead ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to toxic substance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to vitamin A IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in transposable element silencing by piRNA-mediated DNA methylation IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in XY body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of catalytic complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromosome, centromeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in euchromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in euchromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    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)