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

    Gene ID: 1789, updated on 23-Apr-2017
    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; Vega:OTTHUMG00000032226
    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]
    Orthologs
    Location:
    20q11.21
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency
    MedGen: C0398788 OMIM: 242860 GeneReviews: Not available
    Compare labs

    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

    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

    • 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
    Products Interactant Other Gene Complex Source Pubs Description

    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-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 from RNA polymerase II promoter 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 drug 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
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    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

    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, OTTHUMP00000273326, ENST00000443239.7, OTTHUMT00000470233
      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, OTTHUMP00000273327, ENST00000456297.6, OTTHUMT00000470234
      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, OTTHUMP00000030604, ENST00000328111.6, OTTHUMT00000078643
      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, OTTHUMP00000030605, ENST00000353855.6, OTTHUMT00000078644
      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, OTTHUMP00000030606, ENST00000348286.6, OTTHUMT00000078645
      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, OTTHUMP00000164397, ENST00000201963.3, OTTHUMT00000257075
      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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p7 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

    Alternate CHM1_1.1

    Genomic

    1. NC_018931.2 Alternate CHM1_1.1

      Range
      31253633..31300607
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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