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DNMT3B DNA methyltransferase 3 beta [ Homo sapiens (human) ]

Gene ID: 1789, updated on 12-Jan-2019

Summary

Official Symbol
DNMT3Bprovided by HGNC
Official Full Name
DNA methyltransferase 3 betaprovided by HGNC
Primary source
HGNC:HGNC:2979
See related
Ensembl:ENSG00000088305 MIM:602900
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ICF; ICF1; M.HsaIIIB
Summary
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]
Expression
Broad expression in testis (RPKM 3.4), skin (RPKM 1.5) and 25 other tissues See more
Orthologs

Genomic context

See DNMT3B in Genome Data Viewer
Location:
20q11.21
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (32762385..32809356)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (31350191..31397162)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene BCL2 antagonist/killer 1 pseudogene 1 Neighboring gene COMM domain containing 7 Neighboring gene microtubule associated protein RP/EB family member 1 Neighboring gene EF-hand calcium binding domain 8

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency
MedGen: C4551557 OMIM: 242860 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Genome-wide association study of inattention and hyperactivity-impulsivity measured as quantitative traits.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates DNMT1, DNMT3A, and DNMT3B both at the mRNA and protein levels in primary tumors PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cysteine and methionine metabolism, organism-specific biosystem (from KEGG)
    Cysteine and methionine metabolism, organism-specific biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • Cysteine and methionine metabolism, conserved biosystem (from KEGG)
    Cysteine and methionine metabolism, conserved biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • DNA methylation, organism-specific biosystem (from REACTOME)
    DNA methylation, organism-specific biosystemMethylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine ...
  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Hematopoietic Stem Cell Gene Regulation by GABP alpha/beta Complex, organism-specific biosystem (from WikiPathways)
    Hematopoietic Stem Cell Gene Regulation by GABP alpha/beta Complex, organism-specific biosystemGABP alpha/beta complex mediates the maintenance of hematopoietic stem cells (HSCs) through control of proteins necessary for epigenetic modification and transcription regulation. The activation of k...
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Methionine degradation, organism-specific biosystem (from KEGG)
    Methionine degradation, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • Methionine degradation, conserved biosystem (from KEGG)
    Methionine degradation, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • Negative epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
    Negative epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughl...
  • NoRC negatively regulates rRNA expression, organism-specific biosystem (from REACTOME)
    NoRC negatively regulates rRNA expression, organism-specific biosystemOnly about half of the rRNA gene copies in a cell are expressed. The remaining copies are silenced by modifications to histones and DNA (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and P...
  • One Carbon Metabolism, organism-specific biosystem (from WikiPathways)
    One Carbon Metabolism, organism-specific biosystemThis one-carbon metabolism pathway is centered around folate. Folate has two key carbon-carbon double bonds. Saturating one of them yields dihydrofolate (DHF) and adding an additional molecule of hyd...
  • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
    PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA (cytosine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA (cytosine-5-)-methyltransferase activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA (cytosine-5-)-methyltransferase activity TAS
Traceable Author Statement
more info
PubMed 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-methyltransferase activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-methyltransferase activity TAS
Traceable Author Statement
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
C-5 methylation of cytosine IEA
Inferred from Electronic Annotation
more info
 
DNA methylation NAS
Non-traceable Author Statement
more info
PubMed 
DNA methylation TAS
Traceable Author Statement
more info
PubMed 
cellular response to dexamethasone stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to hyperoxia IEA
Inferred from Electronic Annotation
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
negative regulation of histone H3-K9 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
response to activity IEA
Inferred from Electronic Annotation
more info
 
response to caffeine IEA
Inferred from Electronic Annotation
more info
 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to ionizing radiation IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
response to vitamin A IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA (cytosine-5)-methyltransferase 3B
Names
DNA (cytosine-5-)-methyltransferase 3 beta
DNA MTase HsaIIIB
DNA cytosine-5--methyltransferase 3 beta
DNA methyltransferase HsaIIIB
NP_001193984.1
NP_001193985.1
NP_008823.1
NP_787044.1
NP_787045.1
NP_787046.1
XP_011526955.1
XP_011526956.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007290.1 RefSeqGene

    Range
    5001..51972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_56

mRNA and Protein(s)

  1. NM_001207055.1NP_001193984.1  DNA (cytosine-5)-methyltransferase 3B isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks several in-frame exons compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF156487, AF176228, AF331857, AK299915
    Consensus CDS
    CCDS56183.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000403169.2, ENST00000443239.7
    Conserved Domains (3) summary
    cd05835
    Location:181267
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:512674
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:369488
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  2. NM_001207056.1NP_001193985.1  DNA (cytosine-5)-methyltransferase 3B isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks several in-frame exons compared to variant 1. The resulting isoform (8) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF156487, AF176228, AF331857, AK299821, AK299915
    Consensus CDS
    CCDS56184.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000412305.1, ENST00000456297.6
    Conserved Domains (3) summary
    cd05835
    Location:147233
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:478640
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:335454
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  3. NM_006892.3NP_008823.1  DNA (cytosine-5)-methyltransferase 3B isoform 1

    See identical proteins and their annotated locations for NP_008823.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF156487, AF331857
    Consensus CDS
    CCDS13205.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000328547.2, ENST00000328111.6
    Conserved Domains (3) summary
    cd05835
    Location:223309
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:574756
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:431550
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  4. NM_175848.1NP_787044.1  DNA (cytosine-5)-methyltransferase 3B isoform 2

    See identical proteins and their annotated locations for NP_787044.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. Isoform 2 is shorter than isoform 1.
    Source sequence(s)
    AF156487, AF176228, AF331857
    Consensus CDS
    CCDS13206.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000313397.4, ENST00000353855.6
    Conserved Domains (3) summary
    cd05835
    Location:223309
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:554736
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:411530
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  5. NM_175849.1NP_787045.1  DNA (cytosine-5)-methyltransferase 3B isoform 3

    See identical proteins and their annotated locations for NP_787045.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks three exons in the coding region but maintains the reading frame, compared to variant 1. Isoform 3 is shorter than isoform 1.
    Source sequence(s)
    AF156487, AF176228, AF331857
    Consensus CDS
    CCDS13207.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000337764.2, ENST00000348286.6
    Conserved Domains (3) summary
    cd05835
    Location:223309
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:554716
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:411530
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  6. NM_175850.2NP_787046.1  DNA (cytosine-5)-methyltransferase 3B isoform 6

    See identical proteins and their annotated locations for NP_787046.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate exon in the 5' UTR and coding region that introduces an upstream start codon, compared to variant 1. Variant 6 also lacks an in-frame exon in the coding region, compared to variant 1. Isoform 6 is shorter and has a unique N-terminus, compared to isoform 1.
    Source sequence(s)
    AF156487, AF176228, AF331857
    Consensus CDS
    CCDS13204.1
    UniProtKB/Swiss-Prot
    Q9UBC3
    Related
    ENSP00000201963.3, ENST00000201963.3
    Conserved Domains (3) summary
    cd05835
    Location:235321
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:566748
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:423542
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    32762385..32809356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528654.2XP_011526956.1  DNA (cytosine-5)-methyltransferase 3B isoform X2

    Conserved Domains (3) summary
    cd05835
    Location:193279
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:524686
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:381500
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
  2. XM_011528653.2XP_011526955.1  DNA (cytosine-5)-methyltransferase 3B isoform X1

    See identical proteins and their annotated locations for XP_011526955.1

    Conserved Domains (3) summary
    cd05835
    Location:235321
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    COG0270
    Location:566728
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:423542
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

RNA

  1. XR_936512.2 RNA Sequence

  2. XR_936511.2 RNA Sequence

  3. XR_936510.2 RNA Sequence

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