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Aliases for DNMT3A Gene

Aliases for DNMT3A Gene

  • DNA (Cytosine-5-)-Methyltransferase 3 Alpha 2 3
  • DNA MTase HsaIIIA 3 4
  • EC 2.1.1.37 4 64
  • M.HsaIIIA 3 4
  • DNA (Cytosine-5)-Methyltransferase 3A 3
  • DNA Cytosine Methyltransferase 3A2 3
  • DNA Methyltransferase HsaIIIA 4
  • DNMT3A2 3
  • Dnmt3a 4
  • TBRS 3

External Ids for DNMT3A Gene

Summaries for DNMT3A Gene

Entrez Gene Summary for DNMT3A Gene

  • 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]

GeneCards Summary for DNMT3A Gene

DNMT3A (DNA (Cytosine-5-)-Methyltransferase 3 Alpha) is a Protein Coding gene. Diseases associated with DNMT3A include tall stature-intellectual disability-facial dysmorphism syndrome and tatton-brown-rahman syndrome. Among its related pathways are MicroRNAs in cancer and Metabolism. GO annotations related to this gene include chromatin binding and unmethylated CpG binding. An important paralog of this gene is DNMT3L.

UniProtKB/Swiss-Prot for DNMT3A Gene

  • Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Recruited to trimethylated Lys-36 of histone H3 (H3K36me3) sites. Can actively repress transcription through the recruitment of HDAC activity.

Tocris Summary for DNMT3A Gene

  • DNA methyltransferase (DNMT) add methyl groups to DNA to effect gene expression. There are three types of DNMTs. DNMT1 is predominately responsible for hemimethylated CpG island methylation, DNMT2 in fact transfers methyl groups to RNA not DNA, hence has been renamed to tRNA aspartic acid methyltransferase 1 (TRDMT1) and DNMT3 is responsible for unmethylated CpG island methylation.

Gene Wiki entry for DNMT3A Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DNMT3A Gene

Genomics for DNMT3A Gene

Genomic Location for DNMT3A Gene

Start:
25,227,855 bp from pter
End:
25,342,590 bp from pter
Size:
114,736 bases
Orientation:
Minus strand

Genomic View for DNMT3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DNMT3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DNMT3A Gene

Regulatory Elements for DNMT3A Gene

Transcription factor binding sites by QIAGEN in the DNMT3A gene promoter:

Proteins for DNMT3A Gene

  • Protein details for DNMT3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6K1-DNM3A_HUMAN
    Recommended name:
    DNA (cytosine-5)-methyltransferase 3A
    Protein Accession:
    Q9Y6K1
    Secondary Accessions:
    • E9PEB8
    • Q86TE8
    • Q86XF5
    • Q8IZV0
    • Q8WXU9

    Protein attributes for DNMT3A Gene

    Size:
    912 amino acids
    Molecular mass:
    101858 Da
    Quaternary structure:
    • Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with UBC9, PIAS1 and PIAS2 (By similarity). Binds the ZBTB18 transcriptional repressor. Interacts with SETDB1. Associates with HDAC1 through its ADD domain. Interacts with UHRF1 (By similarity). Interacts with DNMT1 and DNMT3B. Interacts with the PRC2/EED-EZH2 complex. Interacts with MPHOSPH8. Interacts with histone H3 that is not methylated at Lys-4 (H3K4).
    SequenceCaution:
    • Sequence=AAL57039.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAN40037.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for DNMT3A Gene

    Alternative splice isoforms for DNMT3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DNMT3A Gene

Proteomics data for DNMT3A Gene at MOPED

Post-translational modifications for DNMT3A Gene

  • Sumoylated; sumoylation disrupts the ability to interact with histone deacetylases (HDAC1 and HDAC2) and repress transcription.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys200 and Lys367

Other Protein References for DNMT3A Gene

Domains for DNMT3A Gene

Protein Domains for DNMT3A Gene

UniProtKB/Swiss-Prot:

DNM3A_HUMAN
Domain:
  • The PWWP domain is essential for targeting to pericentric heterochromatin. It specifically recognizes and binds trimethylated Lys-36 of histone H3 (H3K36me3) (By similarity).:
    • Q9Y6K1
  • Contains 1 ADD domain.:
    • Q9Y6K1
  • Contains 1 PWWP domain.:
    • Q9Y6K1
  • Contains 1 SAM-dependent MTase C5-type domain.:
    • Q9Y6K1
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.:
    • Q9Y6K1
Similarity:
  • Contains 1 GATA-type zinc finger.:
    • Q9Y6K1
  • Contains 1 PHD-type zinc finger.:
    • Q9Y6K1
genes like me logo Genes that share domains with DNMT3A: view

No data available for Gene Families for DNMT3A Gene

Function for DNMT3A Gene

Molecular function for DNMT3A Gene

GENATLAS Biochemistry: DNA (cytosine -5)-methyltransferase 3 alpha ,abundantly expressed in ES cells but at very low levels in differentiated embryoid bodies or adult tissues,essential for de novo DNA methylation and development (at least in mouse)
UniProtKB/Swiss-Prot CatalyticActivity: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
UniProtKB/Swiss-Prot EnzymeRegulation: Activated by binding to the regulatory factor DNMT3L.
UniProtKB/Swiss-Prot Function: Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Recruited to trimethylated Lys-36 of histone H3 (H3K36me3) sites. Can actively repress transcription through the recruitment of HDAC activity.

Enzyme Numbers (IUBMB) for DNMT3A Gene

Gene Ontology (GO) - Molecular Function for DNMT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IDA 12138111
GO:0003682 chromatin binding IEA --
GO:0003886 DNA (cytosine-5-)-methyltransferase activity IDA 12138111
GO:0005515 protein binding IPI 16357870
GO:0008168 methyltransferase activity --
genes like me logo Genes that share ontologies with DNMT3A: view
genes like me logo Genes that share phenotypes with DNMT3A: view

Animal Models for DNMT3A Gene

MGI Knock Outs for DNMT3A:

No data available for Transcription Factor Targeting and HOMER Transcription for DNMT3A Gene

Localization for DNMT3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for DNMT3A Gene

Nucleus. Cytoplasm. Note=Accumulates in the major satellite repeats at pericentric heterochromatin. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DNMT3A Gene COMPARTMENTS Subcellular localization image for DNMT3A gene
Compartment Confidence
nucleus 5
cytosol 1
golgi apparatus 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for DNMT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000791 euchromatin IDA 12138111
GO:0000792 heterochromatin --
GO:0001741 XY body IEA --
GO:0005634 nucleus IDA 12138111
genes like me logo Genes that share ontologies with DNMT3A: view

Pathways for DNMT3A Gene

genes like me logo Genes that share pathways with DNMT3A: view

Pathways by source for DNMT3A Gene

1 GeneGo (Thomson Reuters Life Sciences Research) pathway for DNMT3A Gene
1 Qiagen pathway for DNMT3A Gene
1 Cell Signaling Technology pathway for DNMT3A Gene

Gene Ontology (GO) - Biological Process for DNMT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006306 DNA methylation IDA 12138111
GO:0006325 chromatin organization TAS --
GO:0006346 methylation-dependent chromatin silencing IEA --
GO:0006349 regulation of gene expression by genetic imprinting TAS 12138111
genes like me logo Genes that share ontologies with DNMT3A: view

Compounds for DNMT3A Gene

(9) ApexBio Compounds for DNMT3A Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor. Incorporates into DNA forming covalent adducts with cellular DNMT1, depleting enzyme activity. [320-67-2]
Decitabine (NSC127716, 5AZA-CdR) Decitabine is a kind of deoxycytidine analog and an inducer of cellular differentiation. [2353-33-5]
Lomeguatrib Inhibitor of O6-methylguanine-DNA methyltransferase (MGMT); (IC50 = 0.009 uM in cell-free extracts from HeLa S3 cells); [192441-08-0]
Nanaomycin A Selective DNMT3B inhibitor, regulates DNA methylation. [52934-83-5]
Nanaomycin C amide of nanaomycin A [58286-55-8]
RG 108 RG108 is a DNA methyltransferase (DMNT) inhibitor that enhanced reprogramming of OK-transduced MEFs in the presence of BIX. [48208-26-0]
SGI-110 SGI-110 is a second generation DNA-hypomethyating agent. [929901-49-5]
Thioguanine Thioguanine is a purine antimetabolite widely used in the treatment of acute lymphoblastic leukemia, autoimmune disorders (e.g., Crohns disease, rheumatoid arthritis) and organ transplant recipients. [154-42-7]
Zebularine Zebularine, a chemically stable cytidine analog containing a 2-(1H)-pyridimidinone ring, is an effective DNA methylation inhibitor which can act with DNA methyltransferases to form a covalent complex. It has been shown to cause demethylation and reactivat [3690-10-6]

(5) Tocris Compounds for DNMT3A Gene

Compound Action Cas Number
3-Deazaneplanocin A hydrochloride Histone methyltransferase inhibitor [120964-45-6]
BIX 01294 G9a-like protein and G9a histone lysine methyltransferase inhibitor [935693-62-2]
SGC 0946 Highly potent and selective DOT1L inhibitor; cell permeable
UNC 0638 Selective G9a and GLP histone lysine methyltransferase inhibitor [1255517-77-1]
UNC 0646 Potent and selective G9a/GLP inhibitor [1320288-17-2]

(3) HMDB Compounds for DNMT3A Gene

Compound Synonyms Cas Number PubMed IDs
5-Methylcytosine
  • 4-Amino-5-methyl-2-pyrimidinol
554-01-8
S-Adenosylhomocysteine
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
979-92-0
S-Adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
29908-03-0

(8) Novoseek inferred chemical compound relationships for DNMT3A Gene

Compound -log(P) Hits PubMed IDs
5-aza-2deoxycytidine 79.8 8
5-methylcytosine 72.4 1
cytosine 66.3 10
s-adenosylmethionine 53.2 6
azathioprine 16 1
genes like me logo Genes that share compounds with DNMT3A: view

Transcripts for DNMT3A Gene

Unigene Clusters for DNMT3A Gene

DNA (cytosine-5-)-methyltransferase 3 alpha:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3A Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^
SP1: - - - -
SP2:
SP3:
SP4: - - - - - -
SP5: -
SP6: - - - - - - - -
SP7: - -
SP8: -
SP9:
SP10: - - - -
SP11:

ExUns: 17 ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26
SP1: - -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for DNMT3A Gene

GeneLoc Exon Structure for
DNMT3A
ECgene alternative splicing isoforms for
DNMT3A

Expression for DNMT3A Gene

mRNA expression in normal human tissues for DNMT3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DNMT3A Gene

SOURCE GeneReport for Unigene cluster for DNMT3A Gene Hs.515840

mRNA Expression by UniProt/SwissProt for DNMT3A Gene

Q9Y6K1-DNM3A_HUMAN
Tissue specificity: Highly expressed in fetal tissues, skeletal muscle, heart, peripheral blood mononuclear cells, kidney, and at lower levels in placenta, brain, liver, colon, spleen, small intestine and lung.
genes like me logo Genes that share expressions with DNMT3A: view

Orthologs for DNMT3A Gene

This gene was present in the common ancestor of chordates.

Orthologs for DNMT3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DNMT3A 36
  • 99.81 (n)
  • 100 (a)
DNMT3A 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DNMT3A 36
  • 93.14 (n)
  • 97.03 (a)
DNMT3A 37
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DNMT3A 37
  • 96 (a)
OneToOne
LOC482996 36
  • 93.86 (n)
  • 98.76 (a)
mouse
(Mus musculus)
Mammalia Dnmt3a 36
  • 90.68 (n)
  • 96.37 (a)
Dnmt3a 16
Dnmt3a 37
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 37
  • 92 (a)
OneToMany
-- 37
  • 94 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 88 (a)
OneToMany
-- 37
  • 99 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Dnmt3a 36
  • 90.6 (n)
  • 96.15 (a)
chicken
(Gallus gallus)
Aves DNMT3A 36
  • 82.04 (n)
  • 89.15 (a)
DNMT3A 37
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DNMT3A 37
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100496503 36
  • 75.29 (n)
  • 81.47 (a)
zebrafish
(Danio rerio)
Actinopterygii dnmt3aa 37
  • 60 (a)
OneToMany
dnmt3ab 36
  • 75.28 (n)
  • 84.65 (a)
dnmt3ab 37
  • 67 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7801 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 41 (a)
OneToMany
Species with no ortholog for DNMT3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DNMT3A Gene

ENSEMBL:
Gene Tree for DNMT3A (if available)
TreeFam:
Gene Tree for DNMT3A (if available)

Paralogs for DNMT3A Gene

Paralogs for DNMT3A Gene

Selected SIMAP similar genes for DNMT3A Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for DNMT3A Gene

genes like me logo Genes that share paralogs with DNMT3A: view

Variants for DNMT3A Gene

Sequence variations from dbSNP and Humsavar for DNMT3A Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs10538 -- 25,233,303(+) CCACC(A/G)TGAGA utr-variant-3-prime
rs734693 -- 25,241,002(+) GTGGA(C/T)GGCTG intron-variant
rs747792 -- 25,250,678(+) ACACC(A/T)CGCCG intron-variant
rs749130 -- 25,307,159(-) GCTGC(A/G)TGGAA intron-variant
rs749131 -- 25,306,755(-) TTTTT(G/T)AGTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DNMT3A Gene

Variant ID Type Subtype PubMed ID
dgv57n68 CNV Loss 17160897
esv33372 CNV Loss 17666407
nsv455908 CNV Loss 19166990
nsv828653 CNV Loss 20364138
esv27729 CNV Loss 19812545
esv2573580 CNV Loss 19546169
esv988737 CNV Loss 20482838

Relevant External Links for DNMT3A Gene

HapMap Linkage Disequilibrium report
DNMT3A
Human Gene Mutation Database (HGMD)
DNMT3A

Disorders for DNMT3A Gene

UniProtKB/Swiss-Prot

DNM3A_HUMAN
  • Tatton-Brown-Rahman syndrome (TBRS) [MIM:615879]: An overgrowth syndrome characterized by a distinctive facial appearance, tall stature and intellectual disability. Facial gestalt is characterized by a round face, heavy horizontal eyebrows and narrow palpebral fissures. Less common features include atrial septal defects, seizures, umbilical hernia, and scoliosis. {ECO:0000269 PubMed:24614070}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for DNMT3A Gene

(16) Novoseek inferred disease relationships for DNMT3A Gene

Disease -log(P) Hits PubMed IDs
cancer 42.6 8
tumors 37.1 12
hepatocellular carcinoma 28.3 4
colon cancer 20 2
ovarian cancer 19.7 2

Relevant External Links for DNMT3A

Genetic Association Database (GAD)
DNMT3A
Human Genome Epidemiology (HuGE) Navigator
DNMT3A
genes like me logo Genes that share disorders with DNMT3A: view

Publications for DNMT3A Gene

  1. Cloning, expression and chromosome locations of the human DNMT3 gene family. (PMID: 10433969) Xie S. … Li E. (Gene 1999) 2 3 4 23
  2. A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. (PMID: 12138111) Chen T. … Li E. (J. Biol. Chem. 2002) 3 4 23
  3. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. (PMID: 16682412) Li H. … Pfeifer G.P. (J. Biol. Chem. 2006) 3 4 23
  4. The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. (PMID: 10325416) Robertson K.D. … Jones P.A. (Nucleic Acids Res. 1999) 3 4 23
  5. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. (PMID: 17713477) Jia D. … Cheng X. (Nature 2007) 3 4 23

Products for DNMT3A Gene

Sources for DNMT3A Gene

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