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

    Gene ID: 13435, updated on 14-Sep-2021

    Summary

    Official Symbol
    Dnmt3aprovided by MGI
    Official Full Name
    DNA methyltransferase 3Aprovided by MGI
    Primary source
    MGI:MGI:1261827
    See related
    Ensembl:ENSMUSG00000020661
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    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; 12 A1.1
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (3851559..3964443)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (3801559..3914443)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 12 NC_000078.5 (3806980..3914443)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene dystrobrevin, beta Neighboring gene predicted gene, 53748 Neighboring gene predicted gene, 18028 Neighboring gene DNA methyltransferase 3A, opposite strand Neighboring gene predicted gene, 31623 Neighboring gene Pomc distal enhancer region Neighboring gene peptidyl prolyl isomerase H pseudogene

    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

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    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, acting on CpN substrates TAS
    Traceable Author Statement
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-methyltransferase activity 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 chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methyltransferase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    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 transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in DNA methylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within DNA methylation involved in embryo development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation involved in embryo development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA methylation involved in embryo development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA methylation involved in gamete generation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA methylation on cytosine ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within DNA methylation-dependent heterochromatin assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation-dependent heterochromatin assembly IGI
    Inferred from Genetic Interaction
    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 chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hypermethylation of CpG island IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in maintenance of DNA methylation TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell death ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of gene expression by genetic imprinting IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression by genetic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in XY body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in chromosome, centromeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in euchromatin ISO
    Inferred from Sequence Orthology
    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 nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    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_031898.1
    NP_714965.1
    XP_006515016.1
    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_001271753.1NP_001258682.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

      See identical proteins and their annotated locations for NP_001258682.1

      Status: REVIEWED

      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, AK147263, CN526792
      Consensus CDS
      CCDS36397.1
      UniProtKB/Swiss-Prot
      O88508
      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_007872.4NP_031898.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

      See identical proteins and their annotated locations for NP_031898.1

      Status: REVIEWED

      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, AK147676, CJ104461
      Consensus CDS
      CCDS36397.1
      UniProtKB/Swiss-Prot
      O88508
      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)
    3. NM_153743.4NP_714965.1  DNA (cytosine-5)-methyltransferase 3A isoform 2

      See identical proteins and their annotated locations for NP_714965.1

      Status: REVIEWED

      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, AK147676, AK157792, CN526792
      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: 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_000078.7 Reference GRCm39 C57BL/6J

      Range
      3851559..3964443
      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
      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_006514953.4XP_006515016.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      See identical proteins and their annotated locations for XP_006515016.1

      UniProtKB/Swiss-Prot
      O88508
      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_030246538.1XP_030102398.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      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_030246540.2XP_030102400.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      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)
    5. XM_030246539.2XP_030102399.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

      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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