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

Gene ID: 1788, updated on 1-Jun-2020

Summary

Official Symbol
DNMT3Aprovided by HGNC
Official Full Name
DNA methyltransferase 3 alphaprovided by HGNC
Primary source
HGNC:HGNC:2978
See related
Ensembl:ENSG00000119772 MIM:602769
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; HESJAS; 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. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in placenta (RPKM 5.8), ovary (RPKM 3.9) and 25 other tissues See more
Orthologs

Genomic context

See DNMT3A in Genome Data Viewer
Location:
2p23.3
Exon count:
34
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (25227874..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 POMC distal enhancer region Neighboring gene long intergenic non-protein coding RNA 1381 Neighboring gene microRNA 1301 Neighboring gene dystrobrevin beta Neighboring gene DTNB antisense RNA 1 Neighboring gene uncharacterized LOC105374332

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Acute myeloid leukemia Compare labs
HEYN-SPROUL-JACKSON SYNDROME
MedGen: CN263103 OMIM: 618724 GeneReviews: Not available
Compare labs
Tatton-Brown-rahman syndrome
MedGen: C4014545 OMIM: 615879 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-04-29)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2018-04-29)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study identifies susceptibility loci for ossification of the posterior longitudinal ligament of the spine.
NHGRI GWA Catalog
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
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates DNMT1, DNMT3A, and DNMT3B both at the mRNA and protein levels in primary tumors PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-methyltransferase activity TAS
Traceable Author Statement
more info
 
RNA polymerase II proximal promoter sequence-specific 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
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
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
 
aging IEA
Inferred from Electronic Annotation
more info
 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to ethanol IEA
Inferred from Electronic Annotation
more info
 
cellular response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
hepatocyte apoptotic process IEA
Inferred from Electronic Annotation
more info
 
methylation-dependent chromatin silencing IEA
Inferred from Electronic Annotation
more info
 
mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IC
Inferred by Curator
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell death IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting TAS
Traceable Author Statement
more info
PubMed 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to ionizing radiation IEA
Inferred from Electronic Annotation
more info
 
response to lead ion IEA
Inferred from Electronic Annotation
more info
 
response to vitamin A IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
XY body IEA
Inferred from Electronic Annotation
more info
 
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 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA (cytosine-5)-methyltransferase 3A
Names
DNA (cytosine-5-)-methyltransferase 3 alpha
DNA MTase HsaIIIA
DNA cytosine methyltransferase 3A2
NP_001307821.1
NP_001307822.1
NP_001362748.1
NP_072046.2
NP_715640.2
NP_783328.1
NP_783329.1
XP_005264232.1
XP_011530964.1
XP_011530965.1
XP_011530966.1
XP_011530968.1
XP_011530969.1
XP_016859015.1
XP_016859016.1

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.

Genomic

  1. NG_029465.2 RefSeqGene

    Range
    5001..114630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_459

mRNA and Protein(s)

  1. NM_001320892.2NP_001307821.1  DNA (cytosine-5)-methyltransferase 3A isoform c

    Status: REVIEWED

    Source sequence(s)
    AC012074, AL543971, BC032392, BC043617
    Consensus CDS
    CCDS46232.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Conserved Domains (1) summary
    PTZ00449
    Location:482
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
  2. NM_001320893.1NP_001307822.1  DNA (cytosine-5)-methyltransferase 3A isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses a downstream promoter compared to variants 1, 3, 4 and 7.
    Source sequence(s)
    AB208833, AC012074, AF480163, AI376254
    UniProtKB/Swiss-Prot
    Q9Y6K1
    UniProtKB/TrEMBL
    Q59HC6
    Conserved Domains (4) summary
    cd05835
    Location:138224
    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:480643
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:335462
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl26386
    Location:30130
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  3. NM_001375819.1NP_001362748.1  DNA (cytosine-5)-methyltransferase 3A isoform e

    Status: REVIEWED

    Source sequence(s)
    AC012074
    Related
    ENSP00000384237.1, ENST00000402667.1
  4. NM_022552.5NP_072046.2  DNA (cytosine-5)-methyltransferase 3A isoform a

    See identical proteins and their annotated locations for NP_072046.2

    Status: REVIEWED

    Source sequence(s)
    AC012074
    Consensus CDS
    CCDS33157.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000324375.5, ENST00000321117.9
    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 ...
    COG0270
    Location:632795
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:487614
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl25756
    Location:11156
    BASP1; Brain acid soluble protein 1 (BASP1 protein)
  5. NM_153759.3NP_715640.2  DNA (cytosine-5)-methyltransferase 3A isoform b

    See identical proteins and their annotated locations for NP_715640.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a downstream promoter compared to variants 1, 3, 4, and 7.
    Source sequence(s)
    AF331856, AF480163, AI376254, BM470515
    Consensus CDS
    CCDS1718.2
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000370122.4, ENST00000380746.8
    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 ...
    COG0270
    Location:443606
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:298425
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
  6. NM_175629.2NP_783328.1  DNA (cytosine-5)-methyltransferase 3A isoform a

    See identical proteins and their annotated locations for NP_783328.1

    Status: REVIEWED

    Source sequence(s)
    AF331856, AI376254, BC032392
    Consensus CDS
    CCDS33157.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000264709.3, ENST00000264709.7
    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 ...
    COG0270
    Location:632795
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:487614
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl25756
    Location:11156
    BASP1; Brain acid soluble protein 1 (BASP1 protein)
  7. NM_175630.1NP_783329.1  DNA (cytosine-5)-methyltransferase 3A isoform c

    See identical proteins and their annotated locations for NP_783329.1

    Status: REVIEWED

    Source sequence(s)
    BC032392
    Consensus CDS
    CCDS46232.1
    UniProtKB/Swiss-Prot
    Q9Y6K1
    Related
    ENSP00000384852.3, ENST00000406659.3

RNA

  1. NR_135490.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB208833, AC012074, AI376254

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    25227874..25342590 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532663.2XP_011530965.1  DNA (cytosine-5)-methyltransferase 3A isoform X3

    Conserved Domains (3) summary
    cd05835
    Location:235321
    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:577740
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:432559
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
  2. XM_017003526.1XP_016859015.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    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 ...
    COG0270
    Location:632795
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:487614
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl25756
    Location:11156
    BASP1; Brain acid soluble protein 1 (BASP1 protein)
  3. XM_005264175.5XP_005264232.1  DNA (cytosine-5)-methyltransferase 3A isoform X1

    See identical proteins and their annotated locations for 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 ...
    COG0270
    Location:632795
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:487614
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
    cl25756
    Location:11156
    BASP1; Brain acid soluble protein 1 (BASP1 protein)
  4. XM_011532662.2XP_011530964.1  DNA (cytosine-5)-methyltransferase 3A isoform X2

    Conserved Domains (3) summary
    cd05835
    Location:241327
    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:583746
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:438565
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
  5. XM_011532667.3XP_011530969.1  DNA (cytosine-5)-methyltransferase 3A isoform X6

    See identical proteins and their annotated locations for XP_011530969.1

    UniProtKB/Swiss-Prot
    Q9Y6K1
    UniProtKB/TrEMBL
    A0A0C4DG02
    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)
  6. XM_017003527.1XP_016859016.1  DNA (cytosine-5)-methyltransferase 3A isoform X6

    UniProtKB/Swiss-Prot
    Q9Y6K1
    UniProtKB/TrEMBL
    A0A0C4DG02
    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)
  7. XM_011532666.2XP_011530968.1  DNA (cytosine-5)-methyltransferase 3A isoform X5

    See identical proteins and their annotated locations for XP_011530968.1

    Conserved Domains (3) summary
    cd05835
    Location:114200
    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:456619
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:311438
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)
  8. XM_011532664.2XP_011530966.1  DNA (cytosine-5)-methyltransferase 3A isoform X4

    See identical proteins and their annotated locations for XP_011530966.1

    UniProtKB/TrEMBL
    F8WE91
    Related
    ENSP00000370132.3, ENST00000380756.7
    Conserved Domains (3) 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 ...
    COG0270
    Location:632781
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11729
    Location:487614
    ADDz_Dnmt3a; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a)

RNA

  1. XR_001738657.1 RNA Sequence

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