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

Gene ID: 13435, updated on 12-Aug-2019

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

Genomic context

See Dnmt3a in Genome Data Viewer
Location:
12; 12 A1.1
Exon count:
30
Annotation release Status Assembly Chr Location
108 current 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_000078.6Genomic Context describing neighboring genes Neighboring gene dystrobrevin, beta Neighboring gene 60S ribosomal protein L36a-like 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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA (cytosine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA (cytosine-5-)-methyltransferase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA (cytosine-5-)-methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
DNA-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding ISO
Inferred from Sequence Orthology
more info
 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methyltransferase activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
DNA methylation IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA methylation ISO
Inferred from Sequence Orthology
more info
 
DNA methylation involved in embryo development IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA methylation involved in embryo development IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA methylation involved in gamete generation IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA methylation on cytosine ISO
Inferred from Sequence Orthology
more info
 
cellular response to amino acid stimulus IDA
Inferred from Direct Assay
more info
PubMed 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
hypermethylation of CpG island IDA
Inferred from Direct Assay
more info
PubMed 
maintenance of DNA methylation TAS
Traceable Author Statement
more info
PubMed 
methylation IEA
Inferred from Electronic Annotation
more info
 
methylation-dependent chromatin silencing IDA
Inferred from Direct Assay
more info
PubMed 
methylation-dependent chromatin silencing IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell death ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting IDA
Inferred from Direct Assay
more info
PubMed 
regulation of gene expression by genetic imprinting IMP
Inferred from Mutant Phenotype
more info
PubMed 
spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
XY body IDA
Inferred from Direct Assay
more info
PubMed 
chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
euchromatin ISO
Inferred from Sequence Orthology
more info
 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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
NP_001258682.1
NP_031898.1
NP_714965.1
XP_006515016.1
XP_006515019.1
XP_030102398.1
XP_030102399.1
XP_030102400.1
XP_030102401.1
XP_030102402.1

NCBI Reference Sequences (RefSeq)

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
    ENSMUSP00000134009.1, ENSMUST00000174817.7
    Conserved Domains (3) 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 ...
    COG0270
    Location:628791
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    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
    ENSMUSP00000020991.8, ENSMUST00000020991.14
    Conserved Domains (3) 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 ...
    COG0270
    Location:628791
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    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
    ENSMUSP00000133543.1, ENSMUST00000172689.7
    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 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000078.6 Reference GRCm38.p6 C57BL/6J

    Range
    3801559..3914443
    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 (3) 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 ...
    COG0270
    Location:628791
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    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 (3) 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 ...
    COG0270
    Location:628791
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    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

  4. XM_030246541.1XP_030102401.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

  5. XM_030246540.1XP_030102400.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

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

  7. XM_030246542.1XP_030102402.1  DNA (cytosine-5)-methyltransferase 3A isoform X2

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