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Aliases for DNMT3A Gene

Aliases for DNMT3A Gene

  • DNA (Cytosine-5-)-Methyltransferase 3 Alpha 2 3 5
  • DNA MTase HsaIIIA 3 4
  • EC 2.1.1.37 4 63
  • M.HsaIIIA 3 4
  • DNA Cytosine Methyltransferase 3A2 3
  • DNA Methyltransferase HsaIIIA 4
  • DNMT3A2 3
  • Dnmt3a 4
  • TBRS 3

External Ids for DNMT3A Gene

Previous GeneCards Identifiers for DNMT3A Gene

  • GC02M025377
  • GC02M025548
  • GC02M025430
  • GC02M025367
  • GC02M025455

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. [provided by RefSeq, Mar 2016]

GeneCards Summary for DNMT3A Gene

DNMT3A (DNA (Cytosine-5-)-Methyltransferase 3 Alpha) is a Protein Coding gene. Diseases associated with DNMT3A include tatton-brown-rahman syndrome and tall stature-intellectual disability-facial dysmorphism syndrome. Among its related pathways are Gene Expression and Metabolism. GO annotations related to this gene include identical protein binding and methyltransferase activity. An important paralog of this gene is LOC102724184.

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

  • Protein arginine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the arginine residues on histones and other proteins. The dysregulation of this methylation is critical in the development of certain cancers.

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

Regulatory Elements for DNMT3A Gene

Promoters for DNMT3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around DNMT3A on UCSC Golden Path with GeneCards custom track

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

Genomic Location for DNMT3A Gene

Chromosome:
2
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

Genes around DNMT3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DNMT3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DNMT3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DNMT3A Gene

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.
  • Ubiquitination at Lys 200 and Lys 367
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for DNMT3A (DNMT3A)

Domains & Families for DNMT3A Gene

Gene Families for DNMT3A Gene

Protein Domains for DNMT3A Gene

Suggested Antigen Peptide Sequences for DNMT3A Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y6K1

UniProtKB/Swiss-Prot:

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

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:0009008 DNA-methyltransferase activity TAS --
genes like me logo Genes that share ontologies with DNMT3A: view
genes like me logo Genes that share phenotypes with DNMT3A: view

Human Phenotype Ontology for DNMT3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DNMT3A Gene

MGI Knock Outs for DNMT3A:

Animal Model Products

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targets 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
mitochondrion 2
cytoskeleton 1
cytosol 1
golgi apparatus 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for DNMT3A Gene

Pathways & Interactions for DNMT3A Gene

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

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:0006346 methylation-dependent chromatin silencing IEA --
GO:0006349 regulation of gene expression by genetic imprinting TAS 12138111
GO:0007568 aging IEA --
genes like me logo Genes that share ontologies with DNMT3A: view

No data available for SIGNOR curated interactions for DNMT3A Gene

Drugs & Compounds for DNMT3A Gene

(13) Drugs for DNMT3A Gene - From: Novoseek, ApexBio, Tocris, DGIdb, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
Thioguanine Approved Pharma Purine antimetabolite 77
Decitabine Approved, Investigational Pharma DNA methyltransferase inhibitor 208
Zebularine Experimental Pharma DNA methylation inhibitor, DNA methyltransferase and cytidine deaminase inhibitor 0
s-adenosylhomocysteine Experimental Pharma 0

(4) Additional Compounds for DNMT3A Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-methylcytosine
  • 4-Amino-5-methyl-2-(1H)-Pyrimidinone
  • 4-Amino-5-methyl-2-pyrimidinol
  • 5-Methyl-Cytosine
  • 5-Methylcytosine
  • 5-Methylcytosine>96
554-01-8
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:

Flow Cytometry Products

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

Protein differential expression in normal tissues from HIPED for DNMT3A Gene

This gene is overexpressed in Urine (35.0) and Peripheral blood mononuclear cells (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with DNMT3A: view

Protein tissue co-expression partners for DNMT3A Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for DNMT3A Gene

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 35
  • 99.81 (n)
  • 100 (a)
DNMT3A 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DNMT3A 36
  • 87 (a)
OneToOne
DNMT3A 35
  • 93.14 (n)
  • 97.03 (a)
dog
(Canis familiaris)
Mammalia LOC482996 35
  • 93.86 (n)
  • 98.76 (a)
DNMT3A 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dnmt3a 16
Dnmt3a 35
  • 90.68 (n)
  • 96.37 (a)
Dnmt3a 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 92 (a)
OneToMany
-- 36
  • 94 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 88 (a)
OneToMany
-- 36
  • 99 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Dnmt3a 35
  • 90.6 (n)
  • 96.15 (a)
chicken
(Gallus gallus)
Aves DNMT3A 35
  • 82.04 (n)
  • 89.15 (a)
DNMT3A 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DNMT3A 36
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100496503 35
  • 75.29 (n)
  • 81.47 (a)
zebrafish
(Danio rerio)
Actinopterygii dnmt3aa 36
  • 60 (a)
OneToMany
dnmt3ab 36
  • 67 (a)
OneToMany
dnmt3ab 35
  • 75.28 (n)
  • 84.65 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7801 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 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

(2) 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
VAR_067234 A patient with chronic myelomonocytic leukemia
VAR_067236 A patient with chronic myelomonocytic leukemia
VAR_067237 A patient with chronic myelomonocytic leukemia
VAR_067238 A patient with chronic myelomonocytic leukemia
VAR_071463 Tatton-Brown-Rahman syndrome (TBRS)

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

Variation tolerance for DNMT3A Gene

Residual Variation Intolerance Score: 2.11% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.22; 24.46% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DNMT3A Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DNMT3A Gene

Disorders for DNMT3A Gene

MalaCards: The human disease database

(14) MalaCards diseases for DNMT3A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

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.

Relevant External Links for DNMT3A

Genetic Association Database (GAD)
DNMT3A
Human Genome Epidemiology (HuGE) Navigator
DNMT3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DNMT3A
genes like me logo Genes that share disorders with DNMT3A: view

No data available for Genatlas for DNMT3A Gene

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 67
  2. Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion. (PMID: 20227382) Purdy M.M. … Reich N.O. (Arch. Biochem. Biophys. 2010) 3 23
  3. Depletion of DNMT3A suppressed cell proliferation and restored PTEN in hepatocellular carcinoma cell. (PMID: 20467490) Zhao Z. … Fan H. (J. Biomed. Biotechnol. 2010) 3 23
  4. MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1. (PMID: 19211935) Garzon R. … Marcucci G. (Blood 2009) 3 23
  5. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. (PMID: 19246518) El-Maarri O. … ChAcdin F. (Hum. Mol. Genet. 2009) 3 23

Products for DNMT3A Gene

Sources for DNMT3A Gene

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