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Dnmt3a DNA methyltransferase 3 alpha [ Rattus norvegicus (Norway rat) ]

Gene ID: 444984, updated on 4-Jan-2025

Summary

Official Symbol
Dnmt3aprovided by RGD
Official Full Name
DNA methyltransferase 3 alphaprovided by RGD
Primary source
RGD:1303336
See related
EnsemblRapid:ENSRNOG00000026649 AllianceGenome:RGD:1303336
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables chromatin binding activity. Involved in several processes, including cellular response to ethanol; hepatocyte apoptotic process; and positive regulation of cellular response to hypoxia. Located in nucleus. Used to study lung carcinoma and middle cerebral artery infarction. Biomarker of congenital heart disease; hepatocellular carcinoma; and prostatitis. Human ortholog(s) of this gene implicated in Tatton-Brown-Rahman syndrome; hematologic cancer (multiple); and stomach cancer. Orthologous to human DNMT3A (DNA methyltransferase 3 alpha). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Thymus (RPKM 116.0), Brain (RPKM 112.0) and 9 other tissues See more
Orthologs
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Genomic context

See Dnmt3a in Genome Data Viewer
Location:
6q14
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (32507316..32621678)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (26791517..26902161)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (28205375..28346052)

Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene ASXL transcriptional regulator 2 Neighboring gene RNA pseudouridine synthase D4, pseudogene 1 Neighboring gene dystrobrevin, beta Neighboring gene basic transcription factor 3, pseudogene 5 Neighboring gene uncharacterized LOC120103494 Neighboring gene Yip1 domain family, member 4 like 1 Neighboring gene EFR3 homolog B Neighboring gene proopiomelanocortin

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC109195

Gene Ontology Provided by RGD

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 ISO
Inferred from Sequence Orthology
more info
 
enables DNA (cytosine-5-)-methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates IEA
Inferred from Electronic Annotation
more info
 
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables lncRNA binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein-cysteine methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables protein-cysteine methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
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 constitutive heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
involved_in DNA methylation-dependent constitutive heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within autosome genomic imprinting ISO
Inferred from Sequence Orthology
more info
 
involved_in autosome genomic imprinting ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cellular response to amino acid stimulus ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cellular response to bisphenol A ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to ethanol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to hypoxia IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within epigenetic programming of gene expression ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within genomic imprinting ISO
Inferred from Sequence Orthology
more info
 
involved_in genomic imprinting ISO
Inferred from Sequence Orthology
more info
 
involved_in hepatocyte apoptotic process IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
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
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in neuron differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in positive regulation of cellular response to hypoxia IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within post-embryonic development ISO
Inferred from Sequence Orthology
more info
 
involved_in regulatory ncRNA-mediated heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
involved_in response to cocaine IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to estradiol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ethanol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ionizing radiation IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to lead ion IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to nutrient levels IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to toxic substance IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to vitamin A IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within spermatogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in transposable element silencing by piRNA-mediated DNA methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in transposable element silencing by piRNA-mediated DNA methylation ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in XY body ISO
Inferred from Sequence Orthology
more info
 
part_of catalytic complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in euchromatin ISO
Inferred from Sequence Orthology
more info
 
located_in euchromatin ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in heterochromatin ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear matrix ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear matrix ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
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
PubMed 

General protein information

Preferred Names
DNA (cytosine-5)-methyltransferase 3A
Names
DNA (cytosine-5-)-methyltransferase 3 alpha
DNA methyltransferase 3A
cysteine methyltransferase DNMT3A
NP_001003957.1
NP_001003958.1
XP_017449756.1
XP_017449757.1
XP_038968589.1
XP_038968590.1
XP_038968591.1
XP_038968592.1
XP_038968594.1
XP_038968595.1
XP_038968596.1
XP_063118331.1

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_001003957.1NP_001003957.1  DNA (cytosine-5)-methyltransferase 3A isoform 2

    See identical proteins and their annotated locations for NP_001003957.1

    Status: PROVISIONAL

    Source sequence(s)
    BN000396
    UniProtKB/Swiss-Prot
    Q1LZ53
    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 ...
    cd11729
    Location:264391
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:409572
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  2. NM_001003958.1NP_001003958.1  DNA (cytosine-5)-methyltransferase 3A isoform 1

    See identical proteins and their annotated locations for NP_001003958.1

    Status: PROVISIONAL

    Source sequence(s)
    BN000395
    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086024.1 Reference GRCr8

    Range
    32507316..32621678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017594268.3XP_017449757.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  2. XM_017594267.3XP_017449756.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  3. XM_039112664.1XP_038968592.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Related
    ENSRNOP00000046524.2, ENSRNOT00000047210.5
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  4. XM_039112661.2XP_038968589.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  5. XM_039112666.2XP_038968594.1  DNA (cytosine-5)-methyltransferase 3A isoform X2

    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  6. XM_039112663.2XP_038968591.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  7. XM_039112662.2XP_038968590.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    UniProtKB/Swiss-Prot
    Q1LZ52, Q1LZ53
    Conserved Domains (4) 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
    cd11729
    Location:483610
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:628791
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  8. XM_063262261.1XP_063118331.1  DNA (cytosine-5)-methyltransferase 3A isoform X4

  9. XM_039112667.2XP_038968595.1  DNA (cytosine-5)-methyltransferase 3A isoform X3

    UniProtKB/TrEMBL
    A6HAG2
    Conserved Domains (3) summary
    cd05835
    Location:106192
    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 ...
    cd11729
    Location:303430
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:448611
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...
  10. XM_039112668.2XP_038968596.1  DNA (cytosine-5)-methyltransferase 3A isoform X5

    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 ...
    cd11729
    Location:264391
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl30459
    Location:409572
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...