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DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha [ Homo sapiens (human) ]

Gene ID: 1788, updated on 11-Sep-2014
Official Symbol
DNMT3Aprovided by HGNC
Official Full Name
DNA (cytosine-5-)-methyltransferase 3 alphaprovided by HGNC
Primary source
HGNC:HGNC:2978
See related
Ensembl:ENSG00000119772; HPRD:04141; MIM:602769; Vega:OTTHUMG00000094777
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TBRS; DNMT3A2; M.HsaIIIA
Summary
CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase that is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes to the cytoplasm and nucleus and its expression is developmentally regulated. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
See DNMT3A in Epigenomics, MapViewer
Location:
2p23
Exon count:
29
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (25228552..25342590, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (25451421..25565459, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EFR3 homolog B (S. cerevisiae) Neighboring gene succinate-CoA ligase, ADP-forming, beta subunit pseudogene 3 Neighboring gene proopiomelanocortin Neighboring gene microRNA 1301 Neighboring gene uncharacterized LOC101929272 Neighboring gene dystrobrevin, beta Neighboring gene additional sex combs like transcriptional regulator 2 Neighboring gene tropomyosin 3 pseudogene 7

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
TATTON-BROWN-RAHMAN SYNDROME
MedGen: CN189716 OMIM: 615879 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Cysteine and methionine metabolism, organism-specific biosystem (from KEGG)
    Cysteine and methionine metabolism, organism-specific biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • Cysteine and methionine metabolism, conserved biosystem (from KEGG)
    Cysteine and methionine metabolism, conserved biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Methionine degradation, organism-specific biosystem (from KEGG)
    Methionine degradation, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • Methionine degradation, conserved biosystem (from KEGG)
    Methionine degradation, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • One Carbon Metabolism, organism-specific biosystem (from WikiPathways)
    One Carbon Metabolism, organism-specific biosystemThis one-carbon metabolism pathway is centered around folate. Folate has two key carbon-carbon double bonds. Saturating one of them yields dihydrofolate (DHF) and adding an additional molecule of hyd...
  • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
    PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism
  • Validated targets of C-MYC transcriptional repression, organism-specific biosystem (from Pathway Interaction Database)
    Validated targets of C-MYC transcriptional repression, organism-specific biosystem
    Validated targets of C-MYC transcriptional repression
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA (cytosine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates IEA
Inferred from Electronic Annotation
more info
 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
unmethylated CpG binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
C-5 methylation of cytosine IDA
Inferred from Direct Assay
more info
PubMed 
C-5 methylation of cytosine IEA
Inferred from Electronic Annotation
more info
 
DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
DNA methylation involved in embryo development IEA
Inferred from Electronic Annotation
more info
 
DNA methylation involved in gamete generation IEA
Inferred from Electronic Annotation
more info
 
DNA methylation on cytosine within a CG sequence IEA
Inferred from Electronic Annotation
more info
 
S-adenosylhomocysteine metabolic process IEA
Inferred from Electronic Annotation
more info
 
S-adenosylmethioninamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
hypermethylation of CpG island IEA
Inferred from Electronic Annotation
more info
 
methylation-dependent chromatin silencing IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting TAS
Traceable Author Statement
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear heterochromatin IEA
Inferred from Electronic Annotation
more info
 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
DNA (cytosine-5)-methyltransferase 3A
Names
DNA (cytosine-5)-methyltransferase 3A
DNA MTase HsaIIIA
DNA cytosine methyltransferase 3A2
NP_072046.2
NP_715640.2
NP_783328.1
NP_783329.1

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.

Genomic

  1. NG_029465.1 

    Range
    5001..114630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_022552.4NP_072046.2  DNA (cytosine-5)-methyltransferase 3A isoform a

    See proteins identical to NP_072046.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both transcript variants 1 and 3 encode isoform a.
    Source sequence(s)
    AC012074, AF331856, AI376254, BC043617
    Consensus CDS
    CCDS33157.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000324375, OTTHUMP00000201147, ENST00000321117, OTTHUMT00000325147
    Conserved Domains (4) summary
    cd05835
    Location:290376
    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:478614
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:632795
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    pfam15327
    Location:12107
    Tankyrase_bdg_C; Tankyrase binding protein C terminal domain
  2. NM_153759.3NP_715640.2  DNA (cytosine-5)-methyltransferase 3A isoform b

    See proteins identical to NP_715640.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region but maintains the reading frame, compared to variant 1. Variant 2 encodes isoform b, which has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AF331856, AF480163, AI376254, BM470515
    Consensus CDS
    CCDS1718.2
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000370122, OTTHUMP00000120006, ENST00000380746, OTTHUMT00000211588
    Conserved Domains (3) summary
    cd05835
    Location:101187
    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:289425
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:443606
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
  3. NM_175629.2NP_783328.1  DNA (cytosine-5)-methyltransferase 3A isoform a

    See proteins identical to NP_783328.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF331856, AI376254, BC032392
    Consensus CDS
    CCDS33157.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000370132, OTTHUMP00000201150, ENST00000380756, OTTHUMT00000324946
    Conserved Domains (4) summary
    cd05835
    Location:290376
    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:478614
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:632795
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    pfam15327
    Location:12107
    Tankyrase_bdg_C; Tankyrase binding protein C terminal domain
  4. NM_175630.1NP_783329.1  DNA (cytosine-5)-methyltransferase 3A isoform c

    See proteins identical to NP_783329.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region, compared to variant 1. Variant 4 encodes isoform c, which is shorter and has a unique C-terminus compared to isoform a.
    Source sequence(s)
    BC032392
    Consensus CDS
    CCDS46232.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000384852, OTTHUMP00000201148, ENST00000406659, OTTHUMT00000325148
    Conserved Domains (1) summary
    PTZ00449
    Location:482
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    25228552..25342590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005264176.1XP_005264233.1  

    See proteins identical to XP_005264233.1

    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000264709, OTTHUMP00000120005, ENST00000264709, OTTHUMT00000211587
    Conserved Domains (4) summary
    cd05835
    Location:290376
    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:478614
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:632795
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    pfam15327
    Location:12107
    Tankyrase_bdg_C; Tankyrase binding protein C terminal domain
  2. XM_005264175.2XP_005264232.1  

    See proteins identical to XP_005264232.1

    UniProtKB/Swiss-Prot
    Q9Y6K1
    Conserved Domains (4) summary
    cd05835
    Location:290376
    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:478614
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:632795
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    pfam15327
    Location:12107
    Tankyrase_bdg_C; Tankyrase binding protein C terminal domain
  3. XM_006711958.1XP_006712021.1  

    Conserved Domains (3) summary
    cd05835
    Location:142228
    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:330466
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:484647
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
  4. XM_005264177.2XP_005264234.1  

    See proteins identical to XP_005264234.1

    UniProtKB/Swiss-Prot
    Q9Y6K1
    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:255391
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:409572
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
  5. XM_006711957.1XP_006712020.1  

    Conserved Domains (4) summary
    cd05835
    Location:290376
    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:478614
    ADDz_Dnmt3a; ADDz domain of DNA (cytosine-5) methyltransferases (C5-MTases) 3 a (Dnmt3a)
    COG0270
    Location:632795
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    pfam15327
    Location:12107
    Tankyrase_bdg_C; Tankyrase binding protein C terminal domain

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    25193733..25302862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

    Range
    25385740..25495369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)