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Aliases for DNMT3B Gene

Aliases for DNMT3B Gene

  • DNA (Cytosine-5-)-Methyltransferase 3 Beta 2 3 5
  • DNA Methyltransferase HsaIIIB 3 4
  • DNA MTase HsaIIIB 3 4
  • EC 2.1.1.37 4 63
  • M.HsaIIIB 3 4
  • Dnmt3b 4
  • ICF1 3
  • ICF 3

External Ids for DNMT3B Gene

Previous GeneCards Identifiers for DNMT3B Gene

  • GC20P031108
  • GC20P032018
  • GC20P032065
  • GC20P030813
  • GC20P031350
  • GC20P028137

Summaries for DNMT3B Gene

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-centromeric instability-facial anomalies syndrome 1 and immunodeficiency, centromere instability and facial anomalies syndrome. Among its related pathways are Gene Expression and Metabolism. GO annotations related to this gene include transcription corepressor activity and unmethylated CpG binding. An important paralog of this gene is LOC102724184.

UniProtKB/Swiss-Prot for DNMT3B Gene

  • Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. 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.

Tocris Summary for DNMT3B Gene

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

Gene Wiki entry for DNMT3B Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DNMT3B Gene

Genomics for DNMT3B Gene

Regulatory Elements for DNMT3B Gene

Promoters for DNMT3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around DNMT3B on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the DNMT3B gene promoter:

Genomic Location for DNMT3B Gene

Chromosome:
20
Start:
32,762,385 bp from pter
End:
32,809,356 bp from pter
Size:
46,972 bases
Orientation:
Plus strand

Genomic View for DNMT3B Gene

Genes around DNMT3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DNMT3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DNMT3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DNMT3B Gene

Proteins for DNMT3B Gene

  • Protein details for DNMT3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBC3-DNM3B_HUMAN
    Recommended name:
    DNA (cytosine-5)-methyltransferase 3B
    Protein Accession:
    Q9UBC3
    Secondary Accessions:
    • A2A2E2
    • B4DSM8
    • B4DSU1
    • E1P5M6
    • E1P5M7
    • E7EN63
    • E9PBF2
    • Q9UBD4
    • Q9UJQ5
    • Q9UKA6
    • Q9UNE5
    • Q9Y5R9
    • Q9Y5S0

    Protein attributes for DNMT3B Gene

    Size:
    853 amino acids
    Molecular mass:
    95751 Da
    Quaternary structure:
    • 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.

    Three dimensional structures from OCA and Proteopedia for DNMT3B Gene

    Alternative splice isoforms for DNMT3B Gene

neXtProt entry for DNMT3B Gene

Proteomics data for DNMT3B Gene at MOPED

Post-translational modifications for DNMT3B Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for DNMT3B (DNMT3B)

Domains & Families for DNMT3B Gene

Gene Families for DNMT3B Gene

Suggested Antigen Peptide Sequences for DNMT3B Gene

Graphical View of Domain Structure for InterPro Entry

Q9UBC3

UniProtKB/Swiss-Prot:

DNM3B_HUMAN :
  • The PWWP domain is essential for targeting to pericentric heterochromatin.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.
  • Contains 1 GATA-type zinc finger.
Domain:
  • The PWWP domain is essential for targeting to pericentric heterochromatin.
  • Contains 1 ADD domain.
  • Contains 1 PWWP domain.
  • Contains 1 SAM-dependent MTase C5-type domain.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.
Similarity:
  • Contains 1 GATA-type zinc finger.
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with DNMT3B: view

Function for DNMT3B Gene

Molecular function for DNMT3B Gene

GENATLAS Biochemistry:
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)
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by binding to the regulatory factor DNMT3L.
UniProtKB/Swiss-Prot Function:
Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. 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.

Enzyme Numbers (IUBMB) for DNMT3B Gene

Gene Ontology (GO) - Molecular Function for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009008 DNA-methyltransferase activity TAS --
GO:0045322 unmethylated CpG binding IEA --
genes like me logo Genes that share ontologies with DNMT3B: view
genes like me logo Genes that share phenotypes with DNMT3B: view

Human Phenotype Ontology for DNMT3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DNMT3B Gene

MGI Knock Outs for DNMT3B:

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for DNMT3B Gene

Localization for DNMT3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DNMT3B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DNMT3B Gene COMPARTMENTS Subcellular localization image for DNMT3B gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for DNMT3B Gene

Pathways & Interactions for DNMT3B Gene

genes like me logo Genes that share pathways with DNMT3B: view

Gene Ontology (GO) - Biological Process for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 17303076
GO:0001666 response to hypoxia IEA --
GO:0006306 DNA methylation TAS 10433969
GO:0010424 DNA methylation on cytosine within a CG sequence IEA --
GO:0010628 positive regulation of gene expression IMP 18413740
genes like me logo Genes that share ontologies with DNMT3B: view

No data available for SIGNOR curated interactions for DNMT3B Gene

Drugs & Compounds for DNMT3B Gene

(14) Drugs for DNMT3B Gene - From: Novoseek, ApexBio, Tocris, and HMDB

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

(6) Additional Compounds for DNMT3B Gene - From: Novoseek and HMDB

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

(5) Tocris Compounds for DNMT3B Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor 320-67-2
Decitabine DNA methyltransferase inhibitor 2353-33-5
Lomeguatrib MGMT inhibitor 192441-08-0
RG 108 Non-nucleoside DNA methyltransferase inhibitor 48208-26-0
Zebularine DNA methyltransferase and cytidine deaminase inhibitor 3690-10-6

(7) ApexBio Compounds for DNMT3B Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor. 320-67-2
Decitabine (NSC127716, 5AZA-CdR) Deoxycytidine analog and cellular diifferentiation inducer 2353-33-5
Lomeguatrib MGMT inhibitor 192441-08-0
Nanaomycin A DNMT3B inhibitor 52934-83-5
RG 108 DNA methyltransferase inhibitor 48208-26-0
Thioguanine Purine antimetabolite 154-42-7
Zebularine DNA methylation inhibitor 3690-10-6
genes like me logo Genes that share compounds with DNMT3B: view

Transcripts for DNMT3B Gene

Unigene Clusters for DNMT3B Gene

DNA (cytosine-5-)-methyltransferase 3 beta:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3B Gene

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: - - - -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -
SP14: - - - -
SP15:
SP16: -
SP17:

ExUns: 16b · 16c ^ 17 ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b · 24c
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9: - - -
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for DNMT3B Gene

GeneLoc Exon Structure for
DNMT3B
ECgene alternative splicing isoforms for
DNMT3B

Expression for DNMT3B Gene

mRNA expression in normal human tissues for DNMT3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DNMT3B Gene

This gene is overexpressed in Testis (x5.3) and Pancreas (x5.0).

Protein differential expression in normal tissues from HIPED for DNMT3B Gene

This gene is overexpressed in Bone marrow stromal cell (28.2), Heart (20.7), and Lung (20.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for DNMT3B Gene



SOURCE GeneReport for Unigene cluster for DNMT3B Gene Hs.643024

mRNA Expression by UniProt/SwissProt for DNMT3B Gene

Q9UBC3-DNM3B_HUMAN
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.
genes like me logo Genes that share expression patterns with DNMT3B: view

Protein tissue co-expression partners for DNMT3B Gene

Primer Products

In Situ Assay Products

Orthologs for DNMT3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for DNMT3B Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC100848415 35
  • 88.65 (n)
  • 92.46 (a)
DNMT3B 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DNMT3B 35
  • 88.31 (n)
  • 92.74 (a)
DNMT3B 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dnmt3b 35
  • 82.7 (n)
  • 84.32 (a)
Dnmt3b 16
Dnmt3b 36
  • 81 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia DNMT3B 35
  • 99.49 (n)
  • 99.88 (a)
DNMT3B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Dnmt3b 35
  • 83.59 (n)
  • 85.41 (a)
oppossum
(Monodelphis domestica)
Mammalia DNMT3B 36
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DNMT3B 36
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves DNMT3B 35
  • 69.95 (n)
  • 69.9 (a)
DNMT3B 36
  • 56 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DNMT3B 36
  • 81 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii -- 35
dnmt4 35
  • 66.36 (n)
  • 67.96 (a)
dnmt4 36
  • 55 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 40 (a)
OneToMany
Species with no ortholog for DNMT3B:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DNMT3B Gene

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

Paralogs for DNMT3B Gene

Paralogs for DNMT3B Gene

(1) SIMAP similar genes for DNMT3B Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for DNMT3B Gene

genes like me logo Genes that share paralogs with DNMT3B: view

Variants for DNMT3B Gene

Sequence variations from dbSNP and Humsavar for DNMT3B Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs121908943 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) 32,800,200(+) ACGTC(A/G)CTTCT nc-transcript-variant, reference, missense
rs121908942 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) 32,800,916(+) GGAAA(A/G)GCCTG nc-transcript-variant, reference, missense
rs121908941 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) 32,802,416(+) CAAAG(G/T)TTCTG nc-transcript-variant, reference, missense
rs121908939 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) 32,807,791(+) CACAG(A/G)CGTGT nc-transcript-variant, reference, missense
rs121908940 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) 32,807,793(+) CAGAC(A/G/T)TGTCC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for DNMT3B Gene

Variant ID Type Subtype PubMed ID
nsv833956 CNV Loss 17160897
nsv833957 CNV Gain+Loss 17160897

Variation tolerance for DNMT3B Gene

Residual Variation Intolerance Score: 22.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.04; 50.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DNMT3B Gene

HapMap Linkage Disequilibrium report
DNMT3B
Human Gene Mutation Database (HGMD)
DNMT3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DNMT3B Gene

Disorders for DNMT3B Gene

MalaCards: The human disease database

(15) MalaCards diseases for DNMT3B Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency-centromeric instability-facial anomalies syndrome 1
  • common variable immunodeficiency
immunodeficiency, centromere instability and facial anomalies syndrome
  • icf syndrome
early-onset schizophrenia
  • early onset schizophrenia
testicular spermatocytic seminoma
  • spermatocytic seminoma
thrombocytopenic purpura, autoimmune
  • thrombocytopenia due to platelet alloimmunization
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

DNM3B_HUMAN
  • 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. {ECO:0000269 PubMed:10555141, ECO:0000269 PubMed:10588719, ECO:0000269 PubMed:10647011, ECO:0000269 PubMed:11102980, ECO:0000269 PubMed:15580563}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for DNMT3B

Genetic Association Database (GAD)
DNMT3B
Human Genome Epidemiology (HuGE) Navigator
DNMT3B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DNMT3B
genes like me logo Genes that share disorders with DNMT3B: view

No data available for Genatlas for DNMT3B Gene

Publications for DNMT3B Gene

  1. Cloning, expression and chromosome locations of the human DNMT3 gene family. (PMID: 10433969) Xie S. … Li E. (Gene 1999) 2 3 4 23 67
  2. DNMT3B promoter polymorphism and risk of gastric cancer. (PMID: 19517237) Hu J. … Xu H. (Dig. Dis. Sci. 2010) 3 23
  3. Association of the DNMT3B polymorphism with colorectal adenomatous polyps and adenocarcinoma. (PMID: 19626461) Guo X. … Wang S. (Mol. Biol. Rep. 2010) 3 23
  4. Increased CXCR4 expression in AsPC1 pancreatic carcinoma cells with RNA interference-mediated knockdown of DNMT1 and DNMT3B. (PMID: 19932585) Przybylski M. … Jagodzinski P.P. (Biomed. Pharmacother. 2010) 3 23
  5. Expression pattern and clinical significance of DNA methyltransferase 3B variants in gastric carcinoma. (PMID: 20127025) Su X. … Fan H. (Oncol. Rep. 2010) 3 23

Products for DNMT3B Gene

Sources for DNMT3B Gene

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