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

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: human all
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Genomic context

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Adenosine kinase inhibits beta-cell proliferation by upregulating DNA methyltransferase 3A expression.
Title: Adenosine kinase inhibits β-cell proliferation by upregulating DNA methyltransferase 3A expression.
Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.
Title: Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.
Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1.
Title: Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1.
Loss of Dnmt3a increases self-renewal and resistance to pegIFN-alpha in JAK2-V617F-positive myeloproliferative neoplasms.
Title: Loss of Dnmt3a increases self-renewal and resistance to pegIFN-α in JAK2-V617F-positive myeloproliferative neoplasms.
miR-29b-3p regulates cardiomyocytes pyroptosis in CVB3-induced myocarditis through targeting DNMT3A.
Title: miR-29b-3p regulates cardiomyocytes pyroptosis in CVB3-induced myocarditis through targeting DNMT3A.
Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells.
Title: Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells.
Suppression of DNMT2/3 by proinflammatory cytokines inhibits CtBP1/2-dependent genes to promote the occurrence of atrophic nonunion.
Title: Suppression of DNMT2/3 by proinflammatory cytokines inhibits CtBP1/2-dependent genes to promote the occurrence of atrophic nonunion.
Loss of Claudin-1 incurred by DNMT aberration promotes pancreatic cancer progression.
Title: Loss of Claudin-1 incurred by DNMT aberration promotes pancreatic cancer progression.
Transcriptional and functional consequences of Oncostatin M signaling on young Dnmt3a-mutant hematopoietic stem cells.
Title: Transcriptional and functional consequences of Oncostatin M signaling on young Dnmt3a-mutant hematopoietic stem cells.
Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits.
Title: Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits.

Submit: New GeneRIF Correction See all GeneRIFs (237)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (9) 1 citation
Targeted (16) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:236800

MARC_26721-26722:1034781098:3 (e-PCR)
- UniSTS:269059

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:516617

RH125299 (e-PCR)
- UniSTS:162121

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:467531

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:467532

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:472908

NoName (e-PCR)
- UniSTS:548448

NoName (e-PCR)
- UniSTS:548449

NoName (e-PCR)
- UniSTS:548450

RH139204 (e-PCR)
- UniSTS:221290

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:525683

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:525684

AU015806 (e-PCR)
- UniSTS:208770

AU015806 (e-PCR)
- UniSTS:180363

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:256665

Dnmt3a (e-PCR), detects polymorphism
- UniSTS:256666

RH130466 (e-PCR)
- UniSTS:213750

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

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Preferred Names: DNA (cytosine-5)-methyltransferase 3A

Names: DNA MTase MmuIIIA; DNA methyltransferase MmuIIIA; cysteine methyltransferase DNMT3A

NP_001258682.1

EC 2.1.1.37

NP_001408786.1

EC 2.1.1.37

NP_031898.1

EC 2.1.1.37

NP_714965.1

EC 2.1.1.37

XP_006515019.1

EC 2.1.1.37

XP_030102398.1

EC 2.1.1.37

XP_030102399.1

EC 2.1.1.37

XP_030102400.1

EC 2.1.1.37

NCBI Reference Sequences (RefSeq)

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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)

NM_001271753.2 → NP_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:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
NM_001421857.1 → NP_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
NM_007872.5 → NP_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:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
NM_153743.5 → NP_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:67 → 153

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:409 → 572

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd11729
Location:264 → 391

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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

3851559..3964442

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006514956.4 → XP_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:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
XM_030246538.1 → XP_030102398.1 DNA (cytosine-5)-methyltransferase 3A isoform X1

UniProtKB/Swiss-Prot

O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1

Conserved Domains (5) summary

cd05835
Location:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
XM_030246540.2 → XP_030102400.1 DNA (cytosine-5)-methyltransferase 3A isoform X1

UniProtKB/Swiss-Prot

O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1

Conserved Domains (5) summary

cd05835
Location:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
XM_030246539.2 → XP_030102399.1 DNA (cytosine-5)-methyltransferase 3A isoform X1

UniProtKB/Swiss-Prot

O88508, Q3TZK8, Q3UH24, Q8CJ60, Q922J0, Q9CSE1

Conserved Domains (5) summary

cd05835
Location:286 → 372

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:1 → 121

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

COG0270
Location:628 → 791

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

TIGR00927
Location:17 → 282

2A1904; K+-dependent Na+/Ca+ exchanger

cd11729
Location:483 → 610

ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)