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DNMT3A Gene

protein-coding   GIFtS: 72
GCID: GC02M025455

DNA (Cytosine-5-)-Methyltransferase 3 Alpha

  See DNMT3A-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
DNA (Cytosine-5-)-Methyltransferase 3 Alpha1 2     DNA (Cytosine-5)-Methyltransferase 3A2
M.HsaIIIA2 3     DNA Cytosine Methyltransferase 3A22
DNA MTase HsaIIIA2 3     Dnmt3a3
EC 2.1.1.373 8     DNA Methyltransferase HsaIIIA3
DNMT3A22     

External Ids:    HGNC: 29781   Entrez Gene: 17882   Ensembl: ENSG000001197727   OMIM: 6027695   UniProtKB: Q9Y6K13   

Export aliases for DNMT3A gene to outside databases

Previous GC identifers: GC02M025377 GC02M025548 GC02M025430 GC02M025367 GC02M025194


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 tatton-brown-rahman syndrome, and lymphosarcoma. GO annotations related to this gene include chromatin binding and unmethylated CpG binding. An important paralog of this gene is DNMT3L.

UniProtKB/Swiss-Prot: DNM3A_HUMAN, Q9Y6K1
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

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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the DNMT3A gene promoter:
         p53   YY1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): DNMT3A promoter sequence
   Search Chromatin IP Primers for DNMT3A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DNMT3A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p23   Ensembl cytogenetic band:  2p23.3   HGNC cytogenetic band: 2p23

DNMT3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DNMT3A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M025455:  view genomic region     (about GC identifiers)

Start:
25,455,845 bp from pter      End:
25,565,459 bp from pter
Size:
109,615 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DNM3A_HUMAN, Q9Y6K1 (See protein sequence)
Recommended Name: DNA (cytosine-5)-methyltransferase 3A  
Size: 912 amino acids; 101858 Da
Subunit: 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)
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Sequence caution: Sequence=AAL57039.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAN40037.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
5 PDB 3D structures from and Proteopedia for DNMT3A:
2QRV (3D)        3A1A (3D)        3A1B (3D)        3LLR (3D)        3SVM (3D)    
Secondary accessions: E9PEB8 Q86TE8 Q86XF5 Q8IZV0 Q8WXU9
Alternative promoter usage, Alternative splicing: 3 isoforms:  Q9Y6K1-1   Q9Y6K1-2   Q9Y6K1-3   (Produced by alternative splicing)

Explore the universe of human proteins at neXtProt for DNMT3A: NX_Q9Y6K1

Explore proteomics data for DNMT3A at MOPED

Post-translational modifications: 

  • Sumoylated; sumoylation disrupts the ability to interact with histone deacetylases (HDAC1 and HDAC2) and repress
    transcription (By similarity)1
  • Ubiquitination2 at Lys200, Lys367
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for DNMT3A (Q9Y6K1) (see all 21)
     FENVVAM  EEASPPA  NPYKEVYT  VATTPEPV 


    See DNMT3A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_072046.2  NP_715640.2  NP_783328.1  NP_783329.1  

    ENSEMBL proteins: 
     ENSP00000370122   ENSP00000324375   ENSP00000264709   ENSP00000370132   ENSP00000384237  
     ENSP00000384852  
    Reactome Protein details: Q9Y6K1

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    5 InterPro protein domains:
     IPR025811 C5_MeTrfase_3
     IPR018117 C5_DNA_meth_AS
     IPR001525 C5_MeTfrase
     IPR025766 ADD
     IPR000313 PWWP_dom

    Graphical View of Domain Structure for InterPro Entry Q9Y6K1

    ProtoNet protein and cluster: Q9Y6K1

    1 Blocks protein domain: IPB000313 PWWP domain

    UniProtKB/Swiss-Prot: DNM3A_HUMAN, Q9Y6K1
    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)
    Similarity: Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family
    Similarity: Contains 1 ADD domain
    Similarity: Contains 1 GATA-type zinc finger
    Similarity: Contains 1 PHD-type zinc finger
    Similarity: Contains 1 PWWP domain
    Similarity: Contains 1 SAM-dependent MTase C5-type domain


    Find genes that share domains with DNMT3A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DNM3A_HUMAN, Q9Y6K1
    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
    Catalytic activity: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
    Enzyme regulation: Activated by binding to the regulatory factor DNMT3L (By similarity)

         Genatlas biochemistry entry for DNMT3A:
    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)

         Enzyme Number (IUBMB): EC 2.1.1.371 2

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA12138111
    GO:0003682chromatin binding IEA--
    GO:0003886DNA (cytosine-5-)-methyltransferase activity IDA12138111
    GO:0005515protein binding IPI16357870
    GO:0008168methyltransferase activity ----
         
    Find genes that share ontologies with DNMT3A           About GenesLikeMe


    Phenotypes:
         11 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Dnmt3a):
     behavior/neurological  cellular  embryogenesis  endocrine/exocrine gland  growth/size/body 
     homeostasis/metabolism  mortality/aging  muscle  nervous system  no phenotypic analysis 
     reproductive system 

    Find genes that share phenotypes with DNMT3A           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for DNMT3A: Dnmt3atm1.1Jae Dnmt3atm3.2Enl Dnmt3atm2Enl

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DNMT3A
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    miRTarBase miRNAs that target DNMT3A:
    hsa-mir-101-3p (MIRT007188), hsa-mir-29c-3p (MIRT003028), hsa-mir-194-5p (MIRT005897), hsa-mir-29a-3p (MIRT003021), hsa-mir-143-3p (MIRT000716), hsa-mir-29b-3p (MIRT003029), hsa-mir-369-5p (MIRT005960), hsa-mir-193b-3p (MIRT016379), hsa-mir-18a-3p (MIRT040898)

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    Selected qRT-PCR Assays for microRNAs that regulate DNMT3A (see all 44):
    hsa-miR-194* hsa-miR-4307 hsa-miR-3607-3p hsa-miR-19b-2* hsa-miR-429 hsa-miR-199a-3p hsa-miR-29a hsa-let-7a-2*
    SwitchGear 3'UTR luciferase reporter plasmidDNMT3A 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DNM3A_HUMAN, Q9Y6K1: Nucleus. Cytoplasm. Note=Accumulates in the major satellite repeats at pericentric
    heterochromatin (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1
    golgi apparatus1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000775chromosome, centromeric region IEA--
    GO:0000791euchromatin IDA12138111
    GO:0000792heterochromatin ----
    GO:0005634nucleus IDA--
    GO:0005720nuclear heterochromatin IEA--

    Find genes that share ontologies with DNMT3A           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for DNMT3A About   (see all 8)  
    See pathways by source

    SuperPathContained pathways About
    1One carbon pool by folate
    One Carbon Metabolism0.53
    Methionine metabolism0.35
    Trans-sulfuration and one carbon metabolism0.43
    2Metabolism
    Metabolic pathways0.38
    3Sulfur amino acid metabolism
    Cysteine and methionine metabolism0.35
    4Macrophage Differentiation and Growth Inhibition by METS
    DNA Methylation and Transcriptional Repression0.30
    5Validated targets of C-MYC transcriptional repression
    Validated targets of C-MYC transcriptional repression


    Find genes that share SuperPaths with DNMT3A           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for DNMT3A
        DNA Methylation and Transcriptional Repression

    1 Cell Signaling Technology (CST) Pathway for DNMT3A
        Chromatin Regulation / Acetylation

    1 GeneGo (Thomson Reuters) Pathway for DNMT3A
        Methionine metabolism

    3 BioSystems Pathways for DNMT3A
        One Carbon Metabolism
    Validated targets of C-MYC transcriptional repression
    Trans-sulfuration and one carbon metabolism


    1 Reactome Pathway for DNMT3A
        PRC2 methylates histones and DNA


    3 Kegg Pathways  (Kegg details for DNMT3A):
        Cysteine and methionine metabolism
    Metabolic pathways
    MicroRNAs in cancer

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DNMT3A: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Polycomb & Trithorax Complexes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for DNMT3A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for DNMT3A (Q9Y6K11, 2, 3 ENSP000002647094) via UniProtKB, MINT, STRING, and/or I2D (see all 78)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    H3F3BP842431, 2, 3EBI-923653,EBI-120658 MINT-7297055 MINT-7297159 MINT-7297230 MINT-7297026 MINT-7297142 MINT-7297083 MINT-7297041 I2D: score=2 
    HIST1H3EP684313, ENSP000003535814I2D: score=2 STRING: ENSP00000353581
    H3F3AP842431, 2, 3, ENSP000003557784EBI-923653,EBI-120658 MINT-7297055 MINT-7297159 MINT-7297230 MINT-7297026 MINT-7297142 MINT-7297083 MINT-7297041 I2D: score=2 STRING: ENSP00000355778
    HIST1H3AP684313, ENSP000003502754I2D: score=2 STRING: ENSP00000350275
    HIST1H3BP684313I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0006306DNA methylation IDA12138111
    GO:0006346methylation-dependent chromatin silencing IEA--
    GO:0006349regulation of gene expression by genetic imprinting TAS12138111
    GO:0007283spermatogenesis IEA--

    Find genes that share ontologies with DNMT3A           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    9 ApexBio Compounds for DNMT3A     About this table
    CompoundAction CAS #
    5-AzacytidineDNA 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]
    LomeguatribInhibitor of O6-methylguanine-DNA methyltransferase (MGMT); (IC50 = 0.009 uM in cell-free extracts from HeLa S3 cells); [192441-08-0]
    Nanaomycin ASelective DNMT3B inhibitor, regulates DNA methylation[52934-83-5]
    Nanaomycin Camide of nanaomycin A[58286-55-8]
    RG 108RG108 is a DNA methyltransferase (DMNT) inhibitor that enhanced reprogramming of OK-transduced MEFs in the presence of BIX. [48208-26-0]
    SGI-110SGI-110 is a second generation DNA-hypomethyating agent[929901-49-5]
    ThioguanineThioguanine is a purine antimetabolite widely used in the treatment of acute lymphoblastic leukemia, autoimmune disorders (e.g., Crohn's disease, rheumatoid arthritis) and organ transplant recipients[154-42-7]
    ZebularineZebularine, 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 reactivation of a silenced and hypermethylated p16 gene[3690-10-6]

    Compounds for DNMT3A available from Tocris Bioscience    About this table
    CompoundAction CAS #
    UNC 0638Selective G9a and GLP histone lysine methyltransferase inhibitor[1255517-77-1]
    BIX 01294G9a-like protein and G9a histone lysine methyltransferase inhibitor[935693-62-2]
    SGC 0946Highly potent and selective DOT1L inhibitor; cell permeable--
    3-Deazaneplanocin A hydrochlorideHistone methyltransferase inhibitor[120964-45-6]
    UNC 0646Potent and selective G9a/GLP inhibitor[1320288-17-2]

    3 HMDB Compounds for DNMT3A    About this table
    CompoundSynonyms CAS #PubMed Ids
    5-Methylcytosine4-Amino-5-methyl-2-pyrimidinol (see all 5)554-01-8--
    S-Adenosylhomocysteine(S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine (see all 19)979-92-0--
    S-Adenosylmethionine(3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine (see all 16)29908-03-0--

    8 Novoseek inferred chemical compound relationships for DNMT3A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    5-aza-2'deoxycytidine 79.8 13 20372798 (2), 12665573 (1), 17556066 (1), 17998942 (1) (see all 7)
    5-methylcytosine 72.4 1 12242669 (1)
    cytosine 66.3 12 19921333 (3), 15799776 (2), 19450891 (1), 12138111 (1) (see all 7)
    s-adenosylmethionine 53.2 16 15671018 (3), 16829525 (2), 17107663 (1)
    azathioprine 16 1 15547111 (1)
    zinc 3.22 6 15362956 (1), 19139273 (1), 10857753 (1)
    folate 2.03 1 19451595 (1)
    oligonucleotide 0 2 15362956 (1), 15854647 (1)



    Find genes that share compounds with DNMT3A           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for DNMT3A gene (4 alternative transcripts): 
    NM_022552.4  NM_153759.3  NM_175629.2  NM_175630.1  

    Unigene Cluster for DNMT3A:

    DNA (cytosine-5-)-methyltransferase 3 alpha
    Hs.515840  [show with all ESTs]
    Unigene Representative Sequence: AB208833
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380746(uc002rgb.3) ENST00000321117(uc002rgc.3) ENST00000264709(uc002rgd.3)
    ENST00000380756(uc010eyi.3) ENST00000402667 ENST00000474887 ENST00000482935
    ENST00000491288 ENST00000466601 ENST00000461228 ENST00000474807 ENST00000484184
    ENST00000470983 ENST00000496570 ENST00000406659(uc002rgf.3)
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    Additional mRNA sequence: 

    AB208833.1 AF067972.2 AF331856.1 AF480163.1 AK025230.1 BC018214.1 BC023612.2 BC032392.1 
    BC043617.1 BC051864.1 

    15 DOTS entries:

    DT.95110184  DT.114106  DT.100749646  DT.92430946  DT.40285287  DT.100749645  DT.100662074  DT.99928292 
    DT.102823845  DT.121026073  DT.121026102  DT.100749647  DT.92430938  DT.97780601  DT.99954735 

    Selected AceView cDNA sequences (see all 207):

    W67657 BE466006 BF223723 BC023612 BQ434593 AI655929 AW078997 AI861939 
    AI971537 BC032392 AI634419 AW594007 AA364876 AA969118 AI670957 BM669897 
    BM480043 BC043617 BG056010 CB852889 AF331856 NM_153759 AI651158 AI392759 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3A (see all 11)    About this scheme

    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:                                -                                                                                                                           

    ExUns: 17 ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26
    SP1:                          -     -                                                         
    SP2:                          -                                                               
    SP3:                                                                                          
    SP4:                                                                                          
    SP5:                                                                                          


    ECgene alternative splicing isoforms for DNMT3A

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    DNMT3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAATAACCCT
    DNMT3A Expression
    About this image


    DNMT3A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Mature Endothelial Cells Blood Brain Barrier
             Cerebellum
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Epiblast (Early Embryonic Tissues)    fully expand to see all 2 entries
             Epiblast Cells Epiblast
             Epiblast-like cells
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    DNMT3A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DNMT3A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.515840

    UniProtKB/Swiss-Prot: DNM3A_HUMAN, Q9Y6K1
    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

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DNMT3A: 
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of chordates.

    Orthologs for DNMT3A gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dnmt3a1 , 5 DNA methyltransferase 3A1, 5 90.68(n)1
    96.37(a)1
      12 (1.99 cM)5
    134351  NM_007872.41  NP_031898.11 
     38060075 
    chicken
    (Gallus gallus)
    Aves DNMT3A1 DNA (cytosine-5-)-methyltransferase 3 alpha 82.04(n)
    89.15(a)
      421991  NM_001024832.1  NP_001020003.1 
    lizard
    (Anolis carolinensis)
    Reptilia DNMT3A6
    Uncharacterized protein
    82(a)
    1 ↔ 1
    GL343593.1(257019-350250)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia AL969565.22   -- 78.29(n)    AL969565.2 
    zebrafish
    (Danio rerio)
    Actinopterygii dnmt3ab1 DNA (cytosine-5-)-methyltransferase 3 alpha b 75.28(n)
    84.65(a)
      553189  NM_001018140.1  NP_001018150.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DNMT3A gene
    DNMT3L2  DNMT3B2  
    2 SIMAP similar genes for DNMT3A using alignment to 4 protein entries:     DNM3A_HUMAN (see all proteins):
    DNMT3B    DNMT3L

    Find genes that share paralogs with DNMT3A           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for DNMT3A
    PGOHUM00000240077


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for DNMT3A (see all 1932)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0672344
    A patient with chronic myelomonocytic leukemia4--see VAR_0672342 G D mis40--------
    VAR_0672374
    A patient with chronic myelomonocytic leukemia4--see VAR_0672372 R H mis40--------
    VAR_0672384
    A patient with chronic myelomonocytic leukemia4--see VAR_0672382 R P mis40--------
    VAR_0672364
    A patient with chronic myelomonocytic leukemia4--see VAR_0672362 R C mis40--------
    rs7522081,2
    C,F,A,H--25455389(-) AGGACC/TGGCCG 3 -- ds500122Minor allele frequency- T:0.21MN NS EA NA WA CSA 2502
    rs1892322811,2
    --25455486(+) CTGGCC/TGCCCA 3 -- ds50010--------
    rs1504884711,2
    C--25455759(+) GGGGCC/TGGGAG 3 -- ds50010--------
    rs1808110741,2
    --25455940(+) GCCCTC/TGAATT 3 -- ut310--------
    rs1864971511,2
    --25456119(+) ACCTGG/TCTCCC 3 -- ut310--------
    rs1454211721,2
    --25456170(+) GCCCAC/TCGTGA 3 -- ut310--------

    HapMap Linkage Disequilibrium report for DNMT3A (25455845 - 25565459 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for DNMT3A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv828653CNV Loss20364138
    esv27729CNV Loss19812545
    esv33372CNV Loss17666407
    esv988737CNV Loss20482838
    esv2573580CNV Loss19546169
    nsv455908CNV Loss19166990
    dgv57n68CNV Loss17160897

    Human Gene Mutation Database (HGMD): DNMT3A
    2 Site Specific Mutation Identification with PCR Assays for DNMT3A:
    Cosmic IdAA Change
    87007p.P904L
    53042p.R882C
    2 Site Specific Cancer Mutation PCR Panels containing DNMT3A:
    Acute Myeloid Leukemia
    Myelodysplastic Syndromes
    SeqTarget long-range PCR primers for resequencing DNMT3A
    DNA2.0 Custom Variant and Variant Library Synthesis for DNMT3A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 602769    OMIM disorders: --

    5 diseases for DNMT3A:    
    About MalaCards
    tatton-brown-rahman syndrome    lymphosarcoma    chronic myelomonocytic leukemia    juvenile myelomonocytic leukemia
    acute myeloid leukemia

    1 disease from the University of Copenhagen DISEASES database for DNMT3A:
    Leukemia

    Find genes that share disorders with DNMT3A           About GenesLikeMe

    Selected Novoseek inferred disease relationships for DNMT3A gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cancer 42.6 9 12015329 (2), 16682412 (1), 14555514 (1), 19139273 (1) (see all 7)
    tumors 37.1 13 16870044 (1), 17408664 (1), 18253830 (1), 11496321 (1) (see all 12)
    hepatocellular carcinoma 28.3 5 20467490 (2), 17549390 (1), 19139273 (1)
    colon cancer 20 2 15547111 (2)
    ovarian cancer 19.7 2 11531283 (2)
    carcinoma 14 4 17998942 (4)
    cancer lung 6.39 1 16870044 (1)
    endometrial cancer 3.64 1 17556066 (1)
    hepatitis chronic 3.6 4 17549390 (2), 11230735 (1)
    colorectal cancer 3.21 1 19454286 (1)

    Genetic Association Database (GAD): DNMT3A
    Human Genome Epidemiology (HuGE) Navigator: DNMT3A (14 documents)

    Export disorders for DNMT3A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

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    PubMed articles for DNMT3A gene, integrated from 10 sources (see all 308):
    (articles sorted by number of sources associating them with DNMT3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning, expression and chromosome locations of the human DNMT3 gene family. (PubMed id 10433969)1, 2, 3, 9 Xie S....Li E. (Gene 1999)
    2. A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. (PubMed id 12138111)1, 2, 9 Chen T.... Li E. (J. Biol. Chem. 2002)
    3. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. (PubMed id 17713477)1, 2, 9 Jia D.... Cheng X. (Nature 2007)
    4. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. (PubMed id 19834512)1, 2, 9 Otani J.... Shirakawa M. (EMBO Rep. 2009)
    5. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. (PubMed id 16682412)1, 2, 9 Li H.... Pfeifer G.P. (J. Biol. Chem. 2006)
    6. The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. (PubMed id 10325416)1, 2, 9 Robertson K.D.... Jones P.A. (Nucleic Acids Res. 1999)
    7. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. (PubMed id 19246518)1, 4, 9 El-Maarri O....ChAcdin F. (Hum. Mol. Genet. 2009)
    8. Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. (PubMed id 12145218)1, 2, 9 Kim G.-D.... Pradhan S. (EMBO J. 2002)
    9. Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. (PubMed id 21828135)1, 2 Jankowska A.M.... Maciejewski J.P. (Blood 2011)
    10. MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. (PubMed id 22086334)1, 2 Chang Y....Cheng X. (Nat. Commun. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1788 HGNC: 2978 AceView: DNMT3A Ensembl:ENSG00000119772 euGenes: HUgn1788
    ECgene: DNMT3A Kegg: 1788 H-InvDB: DNMT3A

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for DNMT3A Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for DNMT3A Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for DNMT3A gene:
    Search GeneIP for patents involving DNMT3A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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