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Aliases for DNMT3B Gene

Aliases for DNMT3B Gene

  • DNA (Cytosine-5-)-Methyltransferase 3 Beta 2 3
  • DNA Methyltransferase HsaIIIB 3 4
  • DNA MTase HsaIIIB 3 4
  • EC 2.1.1.37 4 64
  • M.HsaIIIB 3 4
  • ICF1 3 6
  • DNA (Cytosine-5)-Methyltransferase 3B 3
  • Dnmt3b 4
  • ICF 3

External Ids for DNMT3B Gene

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 MicroRNAs in cancer and Metabolism. GO annotations related to this gene include transcription corepressor activity and DNA-methyltransferase activity. An important paralog of this gene is DNMT3A.

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

  • 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

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

Genomics for DNMT3B Gene

Genomic Location for DNMT3B Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DNMT3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DNMT3B Gene

Regulatory Elements for DNMT3B Gene

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

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

Other Protein References for DNMT3B Gene

Domains for DNMT3B Gene

UniProtKB/Swiss-Prot:

DNM3B_HUMAN
Domain:
  • The PWWP domain is essential for targeting to pericentric heterochromatin:
    • Q9UBC3
  • Contains 1 ADD domain.:
    • Q9UBC3
  • Contains 1 PWWP domain.:
    • Q9UBC3
  • Contains 1 SAM-dependent MTase C5-type domain.:
    • Q9UBC3
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.:
    • Q9UBC3
Similarity:
  • Contains 1 GATA-type zinc finger.:
    • Q9UBC3
  • Contains 1 PHD-type zinc finger.:
    • Q9UBC3
genes like me logo Genes that share domains with DNMT3B: view

No data available for Gene Families for DNMT3B Gene

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:0003677 DNA binding --
GO:0003714 transcription corepressor activity IMP 18567530
GO:0003886 DNA (cytosine-5-)-methyltransferase activity TAS 10433969
GO:0005515 protein binding IPI 11735126
GO:0008168 methyltransferase activity --
genes like me logo Genes that share ontologies with DNMT3B: view
genes like me logo Genes that share phenotypes with DNMT3B: view

Animal Models for DNMT3B Gene

MGI Knock Outs for DNMT3B:

No data available for Transcription Factor Targeting 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

Gene Ontology (GO) - Cellular Components for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin --
GO:0005634 nucleus IDA 17303076
GO:0005654 nucleoplasm TAS --
GO:0005720 nuclear heterochromatin IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with DNMT3B: view

Pathways for DNMT3B Gene

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

Pathways by source for DNMT3B Gene

1 GeneGo (Thomson Reuters Life Sciences Research) pathway for DNMT3B Gene
1 Qiagen pathway for DNMT3B Gene

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:0006306 DNA methylation TAS 10433969
GO:0006346 methylation-dependent chromatin silencing IEA --
GO:0006349 regulation of gene expression by genetic imprinting IEA --
GO:0010212 response to ionizing radiation IEA --
genes like me logo Genes that share ontologies with DNMT3B: view

Compounds for DNMT3B Gene

(9) ApexBio Compounds for DNMT3B Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor. Incorporates into DNA forming covalent adducts with cellular DNMT1, depleting enzyme activity. [320-67-2]
Decitabine (NSC127716, 5AZA-CdR) Decitabine is a kind of deoxycytidine analog and an inducer of cellular differentiation. [2353-33-5]
Lomeguatrib Inhibitor of O6-methylguanine-DNA methyltransferase (MGMT); (IC50 = 0.009 uM in cell-free extracts from HeLa S3 cells); [192441-08-0]
Nanaomycin A Selective DNMT3B inhibitor, regulates DNA methylation. [52934-83-5]
Nanaomycin C amide of nanaomycin A [58286-55-8]
RG 108 RG108 is a DNA methyltransferase (DMNT) inhibitor that enhanced reprogramming of OK-transduced MEFs in the presence of BIX. [48208-26-0]
SGI-110 SGI-110 is a second generation DNA-hypomethyating agent. [929901-49-5]
Thioguanine Thioguanine is a purine antimetabolite widely used in the treatment of acute lymphoblastic leukemia, autoimmune disorders (e.g., Crohns disease, rheumatoid arthritis) and organ transplant recipients. [154-42-7]
Zebularine Zebularine, a chemically stable cytidine analog containing a 2-(1H)-pyridimidinone ring, is an effective DNA methylation inhibitor which can act with DNA methyltransferases to form a covalent complex. It has been shown to cause demethylation and reactivat [3690-10-6]

(5) Tocris Compounds for DNMT3B Gene

Compound Action Cas Number
3-Deazaneplanocin A hydrochloride Histone methyltransferase inhibitor [120964-45-6]
BIX 01294 G9a-like protein and G9a histone lysine methyltransferase inhibitor [935693-62-2]
SGC 0946 Highly potent and selective DOT1L inhibitor; cell permeable
UNC 0638 Selective G9a and GLP histone lysine methyltransferase inhibitor [1255517-77-1]
UNC 0646 Potent and selective G9a/GLP inhibitor [1320288-17-2]

(3) HMDB Compounds for DNMT3B Gene

Compound Synonyms Cas Number PubMed IDs
5-Methylcytosine
  • 4-Amino-5-methyl-2-pyrimidinol
554-01-8
S-Adenosylhomocysteine
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
979-92-0
S-Adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
29908-03-0

(11) Novoseek inferred chemical compound relationships for DNMT3B Gene

Compound -log(P) Hits PubMed IDs
5-aza-2deoxycytidine 87 17
5-methylcytosine 74.1 1
cytosine 72.2 3
zebularine 59.5 1
arsenite 26.8 1
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 differential expression in normal tissues according to GTEx for DNMT3B Gene

This gene is overexpressed in Testis (5.3) and Pancreas (5.0).

Integrated Proteomics: protein expression 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 expressions with DNMT3B: view

Orthologs for DNMT3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for DNMT3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DNMT3B 36
  • 99.49 (n)
  • 99.88 (a)
DNMT3B 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DNMT3B 37
  • 91 (a)
OneToOne
LOC100848415 36
  • 88.65 (n)
  • 92.46 (a)
dog
(Canis familiaris)
Mammalia DNMT3B 36
  • 88.31 (n)
  • 92.74 (a)
DNMT3B 37
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dnmt3b 36
  • 82.7 (n)
  • 84.32 (a)
Dnmt3b 16
Dnmt3b 37
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DNMT3B 37
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DNMT3B 37
  • 66 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Dnmt3b 36
  • 83.59 (n)
  • 85.41 (a)
chicken
(Gallus gallus)
Aves DNMT3B 36
  • 69.95 (n)
  • 69.9 (a)
DNMT3B 37
  • 56 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DNMT3B 37
  • 81 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii -- 36
dnmt4 36
  • 66.36 (n)
  • 67.96 (a)
dnmt4 37
  • 55 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 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

Selected 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 MAF
rs15475 -- 32,809,006(-) TGGAA(A/T)AAAAA utr-variant-3-prime
rs630087 -- 32,794,365(-) TTTGG(G/T)ttttt intron-variant
rs660291 -- 32,800,043(+) ACGCA(C/T)GTGAT intron-variant
rs709046 -- 32,803,423(+) GTTGG(C/T)CACCT intron-variant
rs730823 -- 32,780,365(+) GACGC(C/T)GGCGG reference, synonymous-codon

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

Relevant External Links for DNMT3B Gene

HapMap Linkage Disequilibrium report
DNMT3B
Human Gene Mutation Database (HGMD)
DNMT3B
Locus Specific Mutation Databases (LSDB)
DNMT3B

Disorders for DNMT3B Gene

(1) OMIM Diseases for DNMT3B Gene (602900)

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.

(5) University of Copenhagen DISEASES for DNMT3B Gene

(35) Novoseek inferred disease relationships for DNMT3B Gene

Disease -log(P) Hits PubMed IDs
icf syndrome 95.5 29
cancer 58.1 40
tumors 49.5 35
immunodeficiency 45.6 24
colon cancer 39.3 7

Relevant External Links for DNMT3B

Genetic Association Database (GAD)
DNMT3B
Human Genome Epidemiology (HuGE) Navigator
DNMT3B
genes like me logo Genes that share disorders with DNMT3B: view

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
  2. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. (PMID: 10555141) Okano M. … Li E. (Cell 1999) 3 4 23
  3. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. (PMID: 10588719) Hansen R.S. … Gartler S.M. (Proc. Natl. Acad. Sci. U.S.A. 1999) 3 4 23
  4. Genetic variation in ICF syndrome: evidence for genetic heterogeneity. (PMID: 11102980) Wijmenga C. … Pearson P.L. (Hum. Mutat. 2000) 3 4 23
  5. A novel polymorphism in human cytosine DNA-methyltransferase-3B promoter is associated with an increased risk of lung cancer. (PMID: 12208751) Shen H. … Wei Q. (Cancer Res. 2002) 3 23 49

Products for DNMT3B Gene

Sources for DNMT3B Gene

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