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dnmt3bb.1 DNA (cytosine-5-)-methyltransferase 3 beta, duplicate b.1 [ Danio rerio (zebrafish) ]

Gene ID: 317744, updated on 19-May-2025
Official Symbol
dnmt3bb.1provided by ZNC
Official Full Name
DNA (cytosine-5-)-methyltransferase 3 beta, duplicate b.1provided by ZNC
Primary source
ZFIN:ZDB-GENE-050314-1
See related
Ensembl:ENSDARG00000036791 AllianceGenome:ZFIN:ZDB-GENE-050314-1
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
cb633; dnmt4; dnmt3b
Summary
Predicted to enable DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates and DNA binding activity. Acts upstream of or within several processes, including Kupffer's vesicle development; hematopoietic stem cell homeostasis; and negative regulation of gene expression via chromosomal CpG island methylation. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; hematopoietic system; immature eye; mesoderm; and nervous system. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); facioscapulohumeral muscular dystrophy 4; immunodeficiency-centromeric instability-facial anomalies syndrome 1; and thymoma. Orthologous to human DNMT3B (DNA methyltransferase 3 beta). [provided by Alliance of Genome Resources, May 2025]
Orthologs
all
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Location:
chromosome: 23
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 23 NC_133198.1 (19910883..20001322, complement)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 23 NC_007134.7 (17010906..17101228, complement)

Chromosome 23 - NC_133198.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC141380474 Neighboring gene DNA (cytosine-5-)-methyltransferase beta, duplicate b.3 Neighboring gene DNA (cytosine-5-)-methyltransferase 3 beta, duplicate b.2 Neighboring gene uncharacterized LOC141380473 Neighboring gene uncharacterized LOC141380470 Neighboring gene COMM domain containing 7 Neighboring gene nucleolar protein 4-like b

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Related articles in PubMed

  1. miR-29b-3p Inhibitor Alleviates Hypomethylation-Related Aberrations Through a Feedback Loop Between miR-29b-3p and DNA Methylation in Cardiomyocytes. Wu F, et al. Front Cell Dev Biol, 2022. PMID 35478963, Free PMC Article
  2. Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b. Smith TH, et al. Dev Genes Evol, 2011 Mar. PMID 21258815
  3. An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation. Dobrzycki T, et al. Biol Open, 2018 Apr 9. PMID 29535102, Free PMC Article
  4. Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development. Campos C, et al. Gene, 2012 May 25. PMID 22450363
  5. PM2.5-induced extensive DNA methylation changes in the heart of zebrafish embryos and the protective effect of folic acid. Jiang Y, et al. Environ Pollut, 2019 Dec. PMID 31614245

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

Homology

Clone Names

  • MGC152725

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA (cytosine-5-)-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within Kupffer's vesicle development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within determination of heart left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within determination of left/right symmetry IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within hematopoietic stem cell homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of hematopoietic stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
DNA (cytosine-5)-methyltransferase 3B
Names
DNA (cytosine-5-)-methyltransferase 4
dnmt3b1
NP_001020621.1
XP_005162085.1
XP_009294991.1
XP_009294992.1
XP_073794105.1
XP_073794107.1
XP_073794108.1
XP_073794109.1

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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.

mRNA and Protein(s)

  1. NM_001025450.1 → NP_001020621.1  DNA (cytosine-5)-methyltransferase 3B

    See identical proteins and their annotated locations for NP_001020621.1

    Status: PROVISIONAL

    Source sequence(s)
    AB196915
    UniProtKB/TrEMBL
    A0A8M1N716, Q588C6
    Related
    ENSDARP00000053417.5, ENSDART00000053418.6
    Conserved Domains (3) summary
    cd05835
    Location:203 → 289
    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:537 → 699
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:394 → 513
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

  1. NC_133198.1 Reference GRCz12tu Primary Assembly

    Range
    19910883..20001322 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_073938008.1 → XP_073794109.1  DNA (cytosine-5)-methyltransferase 3B isoform X7

  2. XM_073938004.1 → XP_073794105.1  DNA (cytosine-5)-methyltransferase 3B isoform X3

  3. XM_073938007.1 → XP_073794108.1  DNA (cytosine-5)-methyltransferase 3B isoform X6

  4. XM_009296716.5 → XP_009294991.1  DNA (cytosine-5)-methyltransferase 3B isoform X2

    UniProtKB/TrEMBL
    A0A8M3AY81
    Conserved Domains (3) summary
    cd05835
    Location:155 → 241
    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:489 → 651
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:346 → 465
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

  5. XM_073938006.1 → XP_073794107.1  DNA (cytosine-5)-methyltransferase 3B isoform X5

  6. XM_005162028.6 → XP_005162085.1  DNA (cytosine-5)-methyltransferase 3B isoform X1

    UniProtKB/TrEMBL
    A0A8M2B8X0
    Conserved Domains (3) summary
    cd05835
    Location:203 → 289
    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:537 → 696
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:394 → 513
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

  7. XM_009296717.5 → XP_009294992.1  DNA (cytosine-5)-methyltransferase 3B isoform X4

    UniProtKB/TrEMBL
    A0A8M3AV60
    Conserved Domains (3) summary
    cd05835
    Location:203 → 289
    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:537 → 699
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd11728
    Location:394 → 513
    ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)
Nucleotide Protein Strain
Heading Accession and Version

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