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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

DNMT3B Gene

protein-coding   GIFtS: 72
GCID: GC20P031350

DNA (cytosine-5-)-methyltransferase 3 beta

 Explore 74 diseases affiliated with
DNMT3B via our new
 Human Malady Compendium 
Biological research products
for DNMT3B
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
DNA (Cytosine-5-)-Methyltransferase 3 Beta1 2     ICF2 5
M.HsaIIIB2 3     ICF12
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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for DNMT3B:
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)

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:
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


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.1  NT_011362.10  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for DNMT3B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

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
Subcellular location: Nucleus
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

Post-translational modifications:

  • Sumoylated1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UBC3

  • 4/13 DME Specific Peptides for DNMT3B (Q9UBC3) (see all 13)
     FENVVAM  HYTDVSNM  SNSIKQGK  DGYQSYCT 

    DNMT3B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    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   ENSP00000201963   ENSP00000403169  
     ENSP00000412305   ENSP00000345105   ENSP00000364774  

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    Novus Biologicals DNMT3B Protein
    Novus Biologicals DNMT3B Lysate
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for DNMT3B

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000775chromosome, centromeric region ----
    GO:0000792heterochromatin ----
    GO:0005634nucleus IDA--
    GO:0005720nuclear heterochromatin IEA--
    GO:0005730NOT nucleolus IDA--


    DNMT3B for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for DNMT3B


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    DNMT3B for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR025811 C5_MeTrfase_3
     IPR018117 C5_DNA_meth_AS
     IPR001525 C5_MeTfrase
     IPR025766 ADD
     IPR000313 PWWP

    Graphical View of Domain Structure for InterPro Entry Q9UBC3

    ProtoNet protein and cluster: Q9UBC3

    2 Blocks protein families:
    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 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


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         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
    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

    miRNA
    Products:
        
    miRTarBase miRNAs that target DNMT3B:
    hsa-mir-369-5p (MIRT005961), hsa-mir-29c (MIRT003025), hsa-mir-148a (MIRT000955), hsa-mir-29a (MIRT003027), hsa-mir-29b (MIRT003026)

    OriGene 3'-UTR Clone (see all 4): DNMT3B
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat DNMT3B
    8/48 QIAGEN miScript miRNA 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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    Clone
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    Gene Ontology (GO): 5/9 molecular function terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003714transcription corepressor activity IMP18567530
    GO:0003886DNA (cytosine-5-)-methyltransferase activity TAS10433969
    GO:0005515protein binding IPI--
    GO:0008168methyltransferase activity ----


    DNMT3B for ontologies           About GeneDecksing


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

    Animal Models:
         Mouse knock-outs for DNMT3B: Dnmt3btm5.2Enl Dnmt3btm2Enl
         15 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Dnmt3b):
     cardiovascular system  cellular  craniofacial  embryogenesis  growth/size 
     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


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/6 super-pathways (see all 6About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Methionine metabolism
    Methionine metabolism1.00
    Methionine metabolism1.00
    2Selected targets of Oct-3/4
    Selected targets of Oct-3/41.00
    3One Carbon Metabolism
    One Carbon Metabolism1.00
    4DNA Methylation and Transcriptional Repression
    DNA Methylation and Transcriptional Repression1.00
    5Metabolism
    Metabolic pathways0.38

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    2 EMD Millipore Pathways for DNMT3B
        Selected targets of Oct-3/4
    Methionine metabolism

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

    1 GeneGo (Thomson Reuters) Pathway for DNMT3B
        Methionine metabolism

    1 BioSystems Pathway for DNMT3B 
        One Carbon Metabolism


    2         Kegg Pathways  (Kegg details for DNMT3B):
        Cysteine and methionine metabolism
    Metabolic pathways


    DNMT3B for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for DNMT3B

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

    5/75 Interacting proteins for DNMT3B (Q9UBC31, 2, 3 ENSP000003285474) via UniProtKB, MINT, STRING, and/or I2D (see all 75)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UHRF1Q96T882, 3MINT-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-1177693 I2D: score=3 STRING: ENSP00000263360
    EZH2Q159101, 3, ENSP000003201474EBI-80125,EBI-746496 I2D: score=3 STRING: ENSP00000320147
    About this table

    Gene Ontology (GO): 5/20 biological process terms (GO ID links to tree view) (see all 20):    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 ----


    DNMT3B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    DNMT3B for compounds           About GeneDecksing

    EMD Millipore small molecules for DNMT3B:
    Small Molecule - inhibitor
    Browse drugs & compounds from Enzo Life Sciences

    Compounds for DNMT3B available from Tocris Bioscience    About this table
    CompoundAction CAS #
    RG 108Non-nucleoside DNA methyltransferase inhibitor[48208-26-0]
    ZebularineDNA methyltransferase and cytidine deaminase inhibitor[3690-10-6]
    DecitabineDNA methyltransferase inhibitor[2353-33-5]
    5-AzacytidineDNA methyltransferase inhibitor[320-67-2]

    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--
    10/11 Novoseek 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)

    Search CenterWatch for drugs/clinical trials and news about DNMT3B / DNM3B 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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 Clusters for DNMT3B:

    DNA (cytosine-5-)-methyltransferase 3 beta
    Hs.643024  [show with all ESTs], Hs.713611  [show with all ESTs]
    Unigene Representative Sequences: BQ222535, DQ321787
    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 ENST00000201963(uc002wyf.3)
    ENST00000443239 ENST00000456297 ENST00000344505 ENST00000375623

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    8/48 QIAGEN miScript miRNA 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
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    Inhib. RNA
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat DNMT3B
    Clone
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    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for DNMT3B (see all 10)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DNMT3B 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat DNMT3B
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    Additional cDNA sequence: 

    AB208880.1 AF129267.1 AF129268.1 AF129269.1 AF156487.1 AF156488.1 AF176228.1 AF331857.1 
    AK001191.1 AK295176.1 AK299776.1 AK299821.1 AK299915.1 AK300857.1 DQ321787.1 

    14 DOTS entries:

    DT.113253  DT.113255  DT.100781518  DT.120812129  DT.100781515  DT.100781514  DT.40118740  DT.100730319 
    DT.102842807  DT.97812649  DT.100730272  DT.102842808  DT.91846915  DT.102842804 

    24/103 AceView cDNA sequences (see all 103):

    AF176228 CK825649 BE046956 BQ277772 AF129268 AA565566 NM_006892 AF129269 
    AF331857 NM_175849 BU850032 BU854958 CD654323 AA206264 CR609754 AL120820 
    AI114879 AF129267 AI954642 NM_175850 NM_175848 BM834719 AI332472 BM677321 

    GeneLoc Exon Structure

    5/17 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    DNMT3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TAGCTACAGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    DNMT3B expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Neural TubeMesencephalic Ventricular ZoneNeural Tube
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10/18 LifeMap Cells (see all 18
    NameCategory
    Induced pluripotent stem cell line 201B6 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    BG01V (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    CA1 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    CA2 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    VUB02 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    VUB03_DM1 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    VUB04_CF (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    VUB07 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    VUB09_FSHD (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    FES22 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass

    See DNMT3B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DNMT3B

    SOURCE GeneReport for Unigene clusters: Hs.643024 Hs.713611

    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

        SABiosciences Expression via Pathway-Focused 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

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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

    This gene was present in the common ancestor of animals.

    Orthologs for DNMT3B gene from 5/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dnmt3b1 , 5 DNA methyltransferase 3B1, 5 83.47(n)1
    85.26(a)1
      2 (75.79 cM)5
    134361  NM_001122997.11  NP_001116469.11 
     1536494505 
    chicken
    (Gallus gallus)
    Aves DNMT3B1 DNA (cytosine-5-)-methyltransferase 3 beta 68.34(n)
    65.85(a)
      419287  NM_001024828.1  NP_001019999.1 
    lizard
    (Anolis carolinensis)
    Reptilia DNMT3B6
    --
    81(a)
    1 ↔ 1
    GL343873.1(121908-140319)
    zebrafish
    (Danio rerio)
    Actinopterygii AF135438.12   -- 77.26(n)   30659  AF135438.1 
    honey bee
    (Apis mellifera)
    Insecta --
    --
    --
    23(a)
    19(a)
    many ↔ many
    many ↔ many
    Group2.1(246578-252516)
    Group2.1(246777-305645)


    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)
    About This Section
    Paralogs for DNMT3B gene
    DNMT3A2  DNMT3L2  
    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, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1062 NCBI SNPs in DNMT3B are shown (see all 1062    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs731121161,2
    C,F,--28137809(+) CGGACC/GCTGCT 5 -- int11Minor allele frequency- G:0.03NA 120
    rs731121191,2
    C,--28137947(+) AGGGGG/AACGCG 5 -- int12Minor allele frequency- A:0.04NA 122
    rs775903001,2
    C,F,--28137951(+) GGACGC/AGCTGG 5 -- int11Minor allele frequency- A:0.17WA 118
    rs731121211,2
    C,--28138021(+) TTGCTA/CATGGG 5 -- int10--------
    rs1115931831,2
    --28138425(+) ACTCCC/TGTGTG 5 -- int11Minor allele frequency- T:0.50CSA 2
    rs803103111,2
    F,--28138587(+) ACAAGT/CTGTAA 5 -- int11Minor allele frequency- C:0.03EA 120
    rs751389391,2
    F,--28138633(+) AGGATC/TTCACC 5 -- int11Minor allele frequency- T:0.04NA 120
    rs732581221,2
    C,--28138761(+) AGCTGG/CGAAGT 5 -- int11Minor allele frequency- C:0.50WA 2
    rs595074941,2
    C,F,--28139018(+) GCCATT/CGTTGG 5 -- int14Minor allele frequency- C:0.12WA CSA NA 242
    rs75088301,2
    H--28139834(+) AGCCAC/AGTGGG 5 -- int14Minor allele frequency- A:0.00NS EA 420

    HapMap Linkage Disequilibrium report for DNMT3B (31350191 - 31397162 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for DNMT3B
         1 CNV: 5133
    Human Gene Mutation Database (HGMD): DNMT3B

    Locus Specific Mutation Databases (LSDB): DNMT3B

    SABiosciences Cancer Mutation PCR Assays
    2 SABiosciences qBiomarker Copy Number PCR Arrays containing DNMT3B:
    Oncogenes & Tumor Suppressor Genes 384HC
    Pancreatic Cancer
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat 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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    DNMT3B for disorders           About GeneDecksing

    OMIM gene information: 602900   
    OMIM disorders: 242860  
    UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
  • Defects in DNMT3B are a cause of immunodeficiency-centromeric instability-facial anomalies syndrome type 1
  • (ICF1) [MIM:242860]. A rare disorder characterized by a variable immunodeficiency, 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

    20/74 diseases for DNMT3B (see all 74):    About MalaCards
    immunodeficiency    diffuse large b-cell lymphoma    b-cell lymphomas    mutagen sensitivity
    testicular germ cell tumor    malignant pleural mesothelioma    germ cell tumor    x inactivation
    adenoid cystic carcinoma    squamous cell carcinoma of the head and neck    systemic lupus erythematosus    squamous cell carcinoma
    lupus erythematosus    myelodysplastic syndrome    transitional cell carcinoma    acute lymphoblastic leukemia
    chronic lymphocytic leukemia    lymphoblastic leukemia    acute myeloid leukemia    carcinoma

    1 disease from the University of Copenhagen DISEASES database for DNMT3B:
    Cancer

    10/35 Novoseek 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)
    About This Section

    PubMed articles for DNMT3B gene, integrated from 9 sources (see all 369):
    (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. (1999)
    2. DNMT3B polymorphisms and risk of primary lung cancer. (PubMed id 15528220)1, 4, 9 Lee S.J....Park J.Y. (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. (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. (1999)
    5. Genetic variation in ICF syndrome: evidence for genetic heterogeneity. (PubMed id 11102980)1, 2, 9 Wijmenga C.... Pearson P.L. (2000)
    6. Polymorphisms in the DNA methyltransferase 3b gene and prostate cancer risk. (PubMed id 16012746)1, 4, 9 Singal R....Schlesselman J.J. (2005)
    7. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. (PubMed id 10555141)1, 2, 9 Okano M.... Li E. (1999)
    8. DNA methyltransferase 3B acts as a co-repressor of the human polycomb protein hPc2 to repress fibroblast growth factor receptor 3 transcription. (PubMed id 18567530)1, 2, 9 Kim S.-H.... Kim T.-Y. (2008)
    9. Single nucleotide polymorphism in DNA methyltransferase 3B promoter and its association with gastric cardiac adenocarcinoma in North China. (PubMed id 15962389)1, 4, 9 Wang Y.M....Zhang J.H. (2005)
    10. DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. (PubMed id 15580563)1, 2, 9 Jiang Y.L.... Viegas-Pequignot E. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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
    Entrez Gene: 1789 HGNC: 2979 AceView: DNMT3B Ensembl:ENSG00000088305 euGenes: HUgn1789
    ECgene: DNMT3B Kegg: 1789 H-InvDB: DNMT3B

    (According to HUGE)
    About This Section
      --

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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    About This Section

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