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

Gene ID: 13435, updated on 27-May-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
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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

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, 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 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 ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
 
enables chromatin binding ISO
Inferred from Sequence Orthology
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity 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 transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables unmethylated CpG binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation IDA
Inferred from Direct Assay
more info
 
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in DNA methylation-dependent heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
involved_in S-adenosylmethionine metabolic process 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 
acts_upstream_of_or_within chromatin organization 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 
involved_in 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 
acts_upstream_of_or_within heterochromatin formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within 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
 
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
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cellular response to hypoxia ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
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 
part_of catalytic complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome IEA
Inferred from Electronic Annotation
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
 
part_of euchromatin ISO
Inferred from Sequence Orthology
more info
 
part_of 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
 
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
 

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)