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DNMT3B Gene

protein-coding   GIFtS: 72
GCID: GC20P031350

DNA (Cytosine-5-)-Methyltransferase 3 Beta

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(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 Beta1 2     ICF12 5
M.HsaIIIB2 3     ICF2
DNA Methyltransferase HsaIIIB2 3     DNA (Cytosine-5)-Methyltransferase 3B2
DNA MTase HsaIIIB2 3     Dnmt3b3
EC 2.1.1.373 8     

External Ids:    HGNC: 29791   Entrez Gene: 17892   Ensembl: ENSG000000883057   OMIM: 6029005   UniProtKB: Q9UBC33   

Export aliases for DNMT3B gene to outside databases

Previous GC identifers: GC20P031108 GC20P032018 GC20P032065 GC20P030813 GC20P028137


(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 DNMT3B 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 which is thought to function in de novo methylation,
rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is
developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial
anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length
sequences of variants 4 and 5 have not been determined. (provided by RefSeq, May 2011)

GeneCards Summary for DNMT3B Gene:
DNMT3B (DNA (cytosine-5-)-methyltransferase 3 beta) is a protein-coding gene. Diseases associated with DNMT3B include early-onset schizophrenia, and immunodeficiency-centromeric instability-facial anomalies syndrome 1. GO annotations related to this gene include transcription corepressor activity and DNA-methyltransferase activity. An important paralog of this gene is DNMT3L.

UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
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. May preferentially
methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by
associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By
similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1
gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are
probably not functional due to the deletion of two conserved methyltransferase motifs. Function as
transcriptional corepressor by associating with ZHX1

summary for DNMT3B 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 DNMT3B 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:
NC_000020.11  NC_018931.2  NT_011362.11  
Regulatory elements:
   Regulatory transcription factor binding sites in the DNMT3B gene promoter:
         Lmo2   Olf-1   MyoD   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDNMT3B promoter sequence
   Search Chromatin IP Primers for DNMT3B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DNMT3B


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

Entrez Gene cytogenetic band: 20q11.2   Ensembl cytogenetic band:  20q11.21   HGNC cytogenetic band: 20q11.2

DNMT3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DNMT3B gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P031350:  view genomic region     (about GC identifiers)

Start:
31,350,191 bp from pter      End:
31,397,162 bp from pter
Size:
46,972 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 (See protein sequence)
Recommended Name: DNA (cytosine-5)-methyltransferase 3B  
Size: 853 amino acids; 95751 Da
Subunit: Interacts with BAZ2A/TIP5, SUV39H1 and CBX4. Interacts with UHRF1 (By similarity). Interacts with DNMT1
and DNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1. Interacts with the PRC2/EED-EZH2 complex
2 PDB 3D structures from and Proteopedia for DNMT3B:
3FLG (3D)        3QKJ (3D)    
Secondary accessions: A2A2E2 B4DSM8 B4DSU1 E1P5M6 E1P5M7 E7EN63 E9PBF2 Q9UBD4 Q9UJQ5 Q9UKA6
Q9UNE5 Q9Y5R9 Q9Y5S0
Alternative splicing: 8 isoforms:  Q9UBC3-1   Q9UBC3-2   Q9UBC3-3   Q9UBC3-4   Q9UBC3-5   Q9UBC3-6   Q9UBC3-7   Q9UBC3-8   
(No experimental confirmation available)

Explore the universe of human proteins at neXtProt for DNMT3B: NX_Q9UBC3

Explore proteomics data for DNMT3B at MOPED

Post-translational modifications: 

  • Sumoylated1
  • Citrullinated by PADI4 (By similarity)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for DNMT3B (Q9UBC3) (see all 13)
     FENVVAM  HYTDVSNM  SNSIKQGK  DGYQSYCT 


    See DNMT3B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_001193984.1  NP_001193985.1  NP_008823.1  NP_787044.1  NP_787045.1  NP_787046.1  

    ENSEMBL proteins: 
     ENSP00000328547   ENSP00000313397   ENSP00000337764   ENSP00000403169   ENSP00000412305  
     ENSP00000201963   ENSP00000345105   ENSP00000364774  
    Reactome Protein details: Q9UBC3

    DNMT3B Human Recombinant Protein Products:

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    OriGene Purified Protein for DNMT3B
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    OriGene MassSpec for DNMT3B
    OriGene Custom Protein Services for DNMT3B
    GenScript Custom Purified and Recombinant Proteins Services for DNMT3B
    Novus Biologicals DNMT3B Proteins
    Novus Biologicals DNMT3B Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for DNMT3B

    DNMT3B Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of DNMT3B
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    Novus Biologicals DNMT3B Antibodies
    Abcam antibodies for DNMT3B
    Cloud-Clone Corp. Antibodies for DNMT3B
    ThermoFisher Antibody for DNMT3B
    LSBio Antibodies in human, mouse, rat for DNMT3B

    DNMT3B Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for DNMT3B
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for DNMT3B
    Cloud-Clone Corp. CLIAs for DNMT3B


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 6):
     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 Q9UBC3

    ProtoNet protein and cluster: Q9UBC3

    2 Blocks protein domains:
    IPB000313 PWWP domain
    IPB001525 C-5 cytosine-specific DNA methylase


    UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
    Domain: The PWWP domain is essential for targeting to pericentric heterochromatin
    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


    DNMT3B for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DNM3B_HUMAN, Q9UBC3
    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. May preferentially
    methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by
    associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By
    similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1
    gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are
    probably not functional due to the deletion of two conserved methyltransferase motifs. Function as
    transcriptional corepressor by associating with ZHX1
    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 DNMT3B:
    DNA (cytosine -5)-methyltransferase 3 beta ,abundantly expressed in ES cells in testis and thymus but barely
    detectable in differentiated cells and adult tissues,with at least two alternatively spliced isoforms 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 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003714transcription corepressor activity IMP18567530
    GO:0003886DNA (cytosine-5-)-methyltransferase activity TAS10433969
    GO:0005515protein binding IPI11735126
    GO:0008168methyltransferase activity ----
         
    DNMT3B for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for DNMT3B:
     Increased G1 DNA content  Increased cell death HMECs cel  Increased cell death in breast 

         15 MGI mutant phenotypes (inferred from 10 alleles(MGI details for Dnmt3b):
     cardiovascular system  cellular  craniofacial  embryogenesis  growth/size/body 
     hematopoietic system  immune system  liver/biliary system  mortality/aging  nervous system 
     no phenotypic analysis  reproductive system  skeleton  tumorigenesis  vision/eye 

    DNMT3B for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for DNMT3B: Dnmt3btm5.2Enl Dnmt3btm2Enl

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DNMT3B
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for DNMT3B

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for DNMT3B
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for DNMT3B

    miRNA
    Products:
        
    miRTarBase miRNAs that target DNMT3B:
    hsa-mir-29c-3p (MIRT003025), hsa-mir-375 (MIRT019897), hsa-mir-335-5p (MIRT018547), hsa-mir-29b-3p (MIRT003026), hsa-mir-369-5p (MIRT005961), hsa-mir-148a-3p (MIRT000955), hsa-mir-29a-3p (MIRT003027), hsa-mir-93-5p (MIRT048777)

    Block miRNA regulation of human, mouse, rat DNMT3B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DNMT3B (see all 48):
    hsa-miR-429 hsa-miR-4328 hsa-miR-29a hsa-miR-3921 hsa-miR-124 hsa-miR-3613-3p hsa-miR-29a* hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidDNMT3B 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for DNMT3B
    Predesigned siRNA for gene silencing in human, mouse, rat DNMT3B

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for DNMT3B

    Clone
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    OriGene clones in human, mouse for DNMT3B (see all 26)
    OriGene ORF clones in mouse, rat for DNMT3B
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): DNMT3B (NM_006892)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for DNMT3B
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DNMT3B

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for DNMT3B 
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    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DNMT3B


    (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
    DNM3B_HUMAN, Q9UBC3: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000792heterochromatin ----
    GO:0005634nucleus IDA--
    GO:0005720nuclear heterochromatin IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IEA--

    DNMT3B for ontologies           About GeneDecksing


    (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 DNMT3B About   (see all 6)  
    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
    5Selected targets of Oct 3 4
    Selected targets of Oct 3 4

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for DNMT3B
        DNA Methylation and Transcriptional Repression

    1 GeneGo (Thomson Reuters) Pathway for DNMT3B
        Methionine metabolism

    2 BioSystems Pathways for DNMT3B
        One Carbon Metabolism
    Trans-sulfuration and one carbon metabolism

    2 Reactome Pathways for DNMT3B
        PRC2 methylates histones and DNA
    NoRC negatively regulates rRNA expression


    3 Kegg Pathways  (Kegg details for DNMT3B):
        Cysteine and methionine metabolism
    Metabolic pathways
    MicroRNAs in cancer


    DNMT3B for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DNMT3B: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Cell Lineage Identification in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              Polycomb & Trithorax Complexes in human mouse rat
              Embryonic Stem Cells in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for DNMT3B

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

    Selected Interacting proteins for DNMT3B (Q9UBC31, 2, 3 ENSP000003285474) via UniProtKB, MINT, STRING, and/or I2D (see all 91)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UHRF1Q96T881, 2, 3EBI-80125,EBI-1548946 MINT-7296336 MINT-7296510 MINT-7296314 MINT-7296421 MINT-7296305 MINT-7296379 MINT-7296468 I2D: score=2 
    DNMT3AQ9Y6K12, 3, ENSP000002647094MINT-7296314 MINT-6178415 MINT-6178447 MINT-7296379 MINT-6178404 I2D: score=2 STRING: ENSP00000264709
    UBE2IP632791, 3, ENSP000003248974EBI-80125,EBI-80168 I2D: score=4 STRING: ENSP00000324897
    EEDO755301, 3, ENSP000002633604EBI-80125,EBI-923794 I2D: score=3 STRING: ENSP00000263360
    EZH2Q159101, 3, ENSP000003201474EBI-80125,EBI-530054 I2D: score=3 STRING: ENSP00000320147
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA17303076
    GO:0006306DNA methylation TAS10433969
    GO:0006346methylation-dependent chromatin silencing IEA--
    GO:0006349regulation of gene expression by genetic imprinting IEA--
    GO:0010212response to ionizing radiation IEA--

    DNMT3B for ontologies           About GeneDecksing



    (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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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
    9 ApexBio Compounds for DNMT3B     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 DNMT3B 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 DNMT3B    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--

    Selected Novoseek inferred chemical compound relationships for DNMT3B gene (see all 11)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    5-aza-2'deoxycytidine 87 24 19306077 (4), 20372798 (2), 16977793 (1), 12665573 (1) (see all 13)
    5-methylcytosine 74.1 1 12242669 (1)
    cytosine 72.2 4 17178860 (1), 12177302 (1), 11531283 (1)
    zebularine 59.5 1 16807237 (1)
    arsenite 26.8 1 19679824 (1)
    folate 20.5 1 19451595 (1)
    tamoxifen 6.37 7 19019622 (5), 14555514 (1)
    homocysteine 0 2 17688412 (2)
    oligonucleotide 0 2 15362956 (1), 11741835 (1)
    zinc 0 2 19128516 (1), 10857753 (1)



    DNMT3B for compounds           About GeneDecksing



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
    About This Section

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    REFSEQ mRNAs for DNMT3B gene (6 alternative transcripts): 
    NM_001207055.1  NM_001207056.1  NM_006892.3  NM_175848.1  NM_175849.1  NM_175850.2  

    Unigene Cluster for DNMT3B:

    DNA (cytosine-5-)-methyltransferase 3 beta
    Hs.643024  [show with all ESTs]
    Unigene Representative Sequence: BQ222535
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000328111(uc010ztx.1 uc010zty.1 uc002wyc.3 uc002wyd.3 uc002wye.3 uc010ztz.2 uc010zua.2 uc010gee.3 uc010gef.3 uc002wyg.3)
    ENST00000353855(uc010geg.3 uc010geh.3) ENST00000348286 ENST00000443239
    ENST00000456297 ENST00000201963(uc002wyf.3) ENST00000344505 ENST00000375623

    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat DNMT3B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DNMT3B (see all 48):
    hsa-miR-429 hsa-miR-4328 hsa-miR-29a hsa-miR-3921 hsa-miR-124 hsa-miR-3613-3p hsa-miR-29a* hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidDNMT3B 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat DNMT3B
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    OriGene ORF clones in mouse, rat for DNMT3B
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): DNMT3B (NM_006892)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for DNMT3B
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DNMT3B
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for DNMT3B
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat DNMT3B
      QuantiTect SYBR Green Assays in human, mouse, rat DNMT3B
      QuantiFast Probe-based Assays in human, mouse, rat DNMT3B

    Additional mRNA sequence: L32168.1 

    3 DOTS entries:

    DT.113253  DT.100781518  DT.113255 

    Selected AceView cDNA sequences (see all 103):

    BE046956 AA565566 BU850032 BM834719 BU854958 BQ277772 NM_175848 AF331857 
    AA206264 CR609754 NM_175850 NM_006892 AL120820 NM_175849 CK825649 AI114879 
    AF129268 CD654323 AF129267 AF176228 AI954642 AF129269 AA477705 BF434659 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3B (see all 17)    About this scheme

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

    ExUns: 16b · 16c ^ 17 ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b · 24c
    SP1:                                                                                                      
    SP2:                                                                                                      
    SP3:                                                                                                      
    SP4:                                                                          -                           
    SP5:                                                                                                      


    ECgene alternative splicing isoforms for DNMT3B

    (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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    DNMT3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGCTACAGG
    DNMT3B Expression
    About this image


    DNMT3B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 11) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 18 entries
             VUB03_DM1
     
     Epiblast (Early Embryonic Tissues)    fully expand to see all 3 entries
             Epiblast Cells Epiblast
             Epiblast Stem Cell line 5
             Epiblast-like cells
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Mesencephalic Ventricular Zone
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Thymus (Hematopoietic System)
             Thymus
    DNMT3B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DNMT3B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.643024

    UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
    Tissue specificity: Ubiquitous; highly expressed in fetal liver, heart, kidney, placenta, and at lower levels in
    spleen, colon, brain, liver, small intestine, lung, peripheral blood mononuclear cells, and skeletal muscle.
    Isoform 1 is expressed in all tissues except brain, skeletal muscle and PBMC, 3 is ubiquitous, 4 is expressed in
    all tissues except brain, skeletal muscle, lung and prostate and 5 is detectable only in testis and at very low
    level in brain and prostate

        Pathway & Disease-focused RT2 Profiler PCR Arrays including DNMT3B: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Cell Lineage Identification in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              Polycomb & Trithorax Complexes in human mouse rat
              Embryonic Stem Cells in human mouse rat

    Primer
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DNMT3B

    (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 DNMT3B gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dnmt3b1 , 5 DNA methyltransferase 3B1, 5 82.7(n)1
    84.32(a)1
      2 (75.79 cM)5
    134361  NM_001122997.21  NP_001116469.11 
     1536494505 
    chicken
    (Gallus gallus)
    Aves DNMT3B1 DNA (cytosine-5-)-methyltransferase 3 beta 69.95(n)
    69.9(a)
      419287  NM_001024828.1  NP_001019999.1 
    lizard
    (Anolis carolinensis)
    Reptilia DNMT3B6
    DNA (cytosine-5-)-methyltransferase 3 beta
    81(a)
    1 ↔ 1
    GL343873.1(121908-140377)
    zebrafish
    (Danio rerio)
    Actinopterygii AF135438.12   -- 77.26(n)   30659  AF135438.1 


    ENSEMBL Gene Tree for DNMT3B (if available)
    TreeFam Gene Tree for DNMT3B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DNMT3B gene
    DNMT3L2  DNMT3A2  
    1 SIMAP similar gene for DNMT3B using alignment to 3 protein entries:     DNM3B_HUMAN (see all proteins):
    DNMT3A

    DNMT3B for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for DNMT3B
    PGOHUM00000240078


    (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)
    About This Section

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    Selected SNPs for DNMT3B (see all 1325)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0115084
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115082 V G mis40--------
    VAR_0115064
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115062 A V mis40--------
    rs1469816241,2,4
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115072 mis40--------
    VAR_0225804
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0225802 L P mis40--------
    VAR_0115094
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115092 A P mis40--------
    VAR_0115104
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115102 H R mis40--------
    rs60588731,2
    C--28140685(+) TTTTTC/TTTTTT 5 -- int1 trp30--------
    rs2002498091,2
    --28143228(+) GCAAT-/TCTCTGA 5 -- int10--------
    rs1129523061,2
    C--28143230(+) CAATT-/CC    
       T
    /CTC
    CTGAC
    10 -- cds11CSA 2
    rs49112541,2
    C,F,A--28144700(+) GACAGA/CATCTC 5 -- int17Minor allele frequency- C:0.29NA WA CSA EA 366

    HapMap Linkage Disequilibrium report for DNMT3B (31350191 - 31397162 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for DNMT3B:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833956CNV Loss17160897
    nsv833957CNV Gain+Loss17160897

    Human Gene Mutation Database (HGMD): DNMT3B
    Locus Specific Mutation Databases (LSDB): DNMT3B

    Site Specific Mutation Identification with PCR Assays
    2 Copy Number PCR Panels containing DNMT3B:
    Oncogenes & Tumor Suppressor Genes 384HC
    Pancreatic Cancer
    SeqTarget long-range PCR primers for resequencing DNMT3B
    DNA2.0 Custom Variant and Variant Library Synthesis for DNMT3B

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

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    OMIM gene information: 602900   
    OMIM disorders: 242860  
    UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
  • Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860]: A rare disorder
    characterized by a variable immunodeficiency resulting in recurrent infections, facial anomalies, and branching
    of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and
    psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome
    in some, but not all, patients. Note=The disease is caused by mutations affecting the gene represented in this
    entry

  • Selected diseases for DNMT3B (see all 77):    
    About MalaCards
    early-onset schizophrenia    immunodeficiency-centromeric instability-facial anomalies syndrome 1    mutagen sensitivity    adenomyosis
    oral lichen planus    malignant pleural mesothelioma    purpura    adenoid cystic carcinoma
    t cell deficiency    nasopharyngitis    lichen planus    stomach cancer
    hematopoietic stem cell transplantation    adenoiditis    endometrial adenocarcinoma    testicular germ cell tumor
    squamous cell carcinoma of the head and neck    pancreatic ductal adenocarcinoma    myelodysplastic syndromes    seminoma

    5 diseases from the University of Copenhagen DISEASES database for DNMT3B:
    Malignant glioma     Leukemia     Carcinoma     Colorectal cancer
    Lung cancer

    DNMT3B for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014

    Selected Novoseek inferred disease relationships for DNMT3B gene (see all 35)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    icf syndrome 95.5 37 18762900 (3), 18029387 (3), 15326630 (2), 10588719 (2) (see all 21)
    cancer 58.1 58 15721400 (4), 15661247 (4), 12015329 (3), 18455294 (2) (see all 27)
    tumors 49.5 54 17067458 (2), 18097598 (2), 18563322 (2), 15661247 (2) (see all 31)
    immunodeficiency 45.6 31 20211012 (2), 10588719 (2), 18432406 (2), 11087891 (1) (see all 21)
    colon cancer 39.3 8 19723660 (2), 15547111 (1), 19156137 (1), 12496760 (1) (see all 6)
    purpura thrombocytopenic idiopathic 38.2 2 18437543 (2)
    colorectal cancer 35.7 19 19470733 (4), 16702365 (3), 18662374 (2), 18089774 (1) (see all 8)
    hepatocellular carcinoma 31.9 19 16318277 (5), 19567080 (3), 19465161 (2), 18023104 (2) (see all 7)
    gastric cancer 31.3 22 16211278 (5), 20127025 (3), 19517237 (3), 11146446 (2) (see all 5)
    endometrial cancer 29.5 11 15661247 (4), 19306077 (2), 19107573 (1)

    Genetic Association Database (GAD): DNMT3B
    Human Genome Epidemiology (HuGE) Navigator: DNMT3B (50 documents)

    Export disorders for DNMT3B 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)
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    PubMed articles for DNMT3B gene, integrated from 10 sources (see all 396):
    (articles sorted by number of sources associating them with DNMT3B)
        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. DNMT3B polymorphisms and risk of primary lung cancer. (PubMed id 15528220)1, 4, 9 Lee S.J....Park J.Y. (Carcinogenesis 2005)
    3. No evidence of correlation between the single nucleotide polymorphism of DNMT3B promoter and gastric cancer risk in a Japanese population. (PubMed id 16211278)1, 4, 9 Aung P.P....Yasui W. (Oncol. Rep. 2005)
    4. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. (PubMed id 10588719)1, 2, 9 Hansen R.S.... Gartler S.M. (Proc. Natl. Acad. Sci. U.S.A. 1999)
    5. Genetic variation in ICF syndrome: evidence for genetic heterogeneity. (PubMed id 11102980)1, 2, 9 Wijmenga C.... Pearson P.L. (Hum. Mutat. 2000)
    6. DNMT3B promoter polymorphism and risk of gastric cancer. (PubMed id 19517237)1, 4, 9 Hu J....Xu H. (Dig. Dis. Sci. 2010)
    7. Promoter polymorphisms of DNMT3B and the risk of colorectal cancer in Chinese: a case-control study. (PubMed id 18662374)1, 4, 9 Fan H....Zhao Z. (amp 2008)
    8. DNA methyltransferase 3B promoter polymorphism and its susceptibility to primary hepatocellular carcinoma in the Chinese Han nationality population: a case-control study. (PubMed id 18023104)1, 4, 9 Wu Y. and Lin J.S. (World J. Gastroenterol. 2007)
    9. Polymorphisms in the DNA methyltransferase 3b gene and prostate cancer risk. (PubMed id 16012746)1, 4, 9 Singal R....Schlesselman J.J. (Oncol. Rep. 2005)
    10. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. (PubMed id 10555141)1, 2, 9 Okano M.... Li E. (Cell 1999)

    (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)
    About This Section

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    Entrez Gene: 1789 HGNC: 2979 AceView: DNMT3B Ensembl:ENSG00000088305 euGenes: HUgn1789
    ECgene: DNMT3B Kegg: 1789 H-InvDB: DNMT3B

    (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 DNMT3B Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for DNMT3B Genetics and Cytogenetics in Oncology and Haematology
    DNMT3Bbasehttp://bioinf.uta.fi/DNMT3Bbase/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for DNMT3B gene:
    Search GeneIP for patents involving DNMT3B

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



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