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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

Microbiology & Infectious Diseases Congress
  See 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)
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 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 immunodeficiency, centromere instability and facial anomalies syndrome, and early-onset schizophrenia, and among its related super-pathways are Sulfur amino acid metabolism and One carbon pool by folate. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NT_011362.10  NC_018931.2  
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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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

Explore proteomics data for DNMT3B at MOPED 

Post-translational modifications:

  • UniProtKB: Sumoylated
  • View modification sites using PhosphoSitePlus
  • 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 MOPED1, PaxDb2 and MAXQB3 :    About this image 

    DNMT3B Protein Expression
    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  

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000792heterochromatin ----
    GO:0005634nucleus IDA--
    GO:0005720nuclear heterochromatin IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0043231intracellular membrane-bounded organelle IDA--

    DNMT3B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    5/6 InterPro protein domains (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 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 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


    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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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): 5/7 molecular function terms (GO ID links to tree view) (see all 7):    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 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 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

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

       inGenious Targeting Laboratory - Custom generated mouse model solutions for DNMT3B 
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for DNMT3B 

    miRNA
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    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)

    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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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for DNMT3B About   (see all 6)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Cysteine and methionine metabolism
    Cysteine and methionine metabolism0.37
    Methionine metabolism0.32
    2One Carbon Metabolism
    One Carbon Metabolism0.53
    3Metabolism
    Metabolic pathways0.40
    4DNA Methylation and Transcriptional Repression
    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

    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


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


    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-923794 I2D: score=3 STRING: ENSP00000263360
    EZH2Q159101, 3, ENSP000003201474EBI-80125,EBI-530054 I2D: score=3 STRING: ENSP00000320147
    About this table

    Gene Ontology (GO): 5/10 biological process terms (GO ID links to tree view) (see all 10):    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:0010628positive regulation of gene expression IMP18413740

    DNMT3B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 #
    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--

    10/11 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)

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

    (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,
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    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 ENST00000443239
    ENST00000456297 ENST00000201963(uc002wyf.3) ENST00000344505 ENST00000375623

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

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    Additional mRNA 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):

    BQ277772 NM_006892 BM834719 CD654323 NM_175849 AI954642 AL120820 CR609754 
    AF129269 BU850032 CK825649 AA565566 NM_175850 AF129267 AI114879 NM_175848 
    AF331857 AF176228 AF129268 AA206264 BE046956 BU854958 CD654631 BF820890 

    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)      DNMT3B embryonic expression: see
    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 
     5/15 selected tissues (see all 15) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 23 entries
             VUB03_DM1
             ESI-051   
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
             brain/midbrain   
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Definitive Hematopoietic Stem Cells Definitive Yolk Sac
             cd34+ cells   
     
     Epiblast (Early Embryonic Tissues)    fully expand to see all 2 entries
             Epiblast Cells Epiblast
             Epiblast Stem Cell line 5
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Telencephalon

    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

    Primer
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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

    This gene was present in the common ancestor of chordates.

    Orthologs for DNMT3B gene from 4/12 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 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
    Uncharacterized protein
    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)
    About This Section
    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) 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

    10/1325 SNPs in DNMT3B are shown (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--------
    VAR_0115074
    Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)4--see VAR_0115072 V A 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
    SABiosciences Cancer Mutation PCR Assays
    2 SABiosciences qBiomarker Copy Number PCR Arrays 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
    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

  • 20/69 diseases for DNMT3B (see all 69):    About MalaCards
    immunodeficiency, centromere instability and facial anomalies syndrome    early-onset schizophrenia    mutagen sensitivity    malignant pleural mesothelioma
    purpura    adenoid cystic carcinoma    nasopharyngitis    t cell deficiency
    adenoiditis    stomach cancer    endometrial adenocarcinoma    hematopoietic stem cell transplantation
    squamous cell carcinoma of the head and neck    adenomyosis    myelodysplastic syndromes    germ cell tumors
    acute leukemia    neuroendocrine tumor    oral lichen planus    lung cancer

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

    DNMT3B for disorders           About GeneDecksing

    10/35 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)
    About This Section

    PubMed articles for DNMT3B gene, integrated from 9 sources (see all 389):
    (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. DNMT3B Promoter Polymorphism and Risk of Gastric Canc er. (PubMed id 19517237)1, 4, 9 Hu J....Xu H. (2009)
    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. (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. (2007)
    9. Polymorphisms in the DNA methyltransferase 3b gene and prostate cancer risk. (PubMed id 16012746)1, 4, 9 Singal R....Schlesselman J.J. (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. (1999)

    (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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, In Situ Hybridization Assays from
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    About This Section

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