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dnmt3ba DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a [ Danio rerio (zebrafish) ]

Gene ID: 321084, updated on 5-May-2024

Summary

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Official Symbol
dnmt3baprovided by ZNC
Official Full Name
DNA (cytosine-5-)-methyltransferase 3 beta, duplicate aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-050314-4
See related
Ensembl:ENSDARG00000052402 AllianceGenome:ZFIN:ZDB-GENE-050314-4
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
cb91; dnmt7; dnmt3b; dnmt3b2; dnmt3bl; sb:cb91; wu:fb16h07
Summary
Predicted to enable DNA (cytosine-5-)-methyltransferase activity; DNA binding activity; and metal ion binding activity. Acts upstream of or within DNA methylation. Predicted to be located in nucleus. Is expressed in several structures, including cardiovascular system; eye; immature eye; midbrain; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in several diseases, including acute myeloid leukemia; autoimmune disease (multiple); carcinoma (multiple); immunodeficiency-centromeric instability-facial anomalies syndrome 1; and thymoma. Orthologous to several human genes including DNMT3L (DNA methyltransferase 3 like). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

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See dnmt3ba in Genome Data Viewer
Location:
chromosome: 8
Exon count:
26
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (23356180..23381199)
105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (23334952..23359960)

Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene PTK6 protein tyrosine kinase 6a Neighboring gene nucleolar protein 4-like a Neighboring gene si:dkey-16n15.3 Neighboring gene microtubule-associated protein, RP/EB family, member 1a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b. Smith TH, et al. Dev Genes Evol, 2011 Mar. PMID 21258815
  2. 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
  3. Critical window of exposure of CMIT/MIT with respect to developmental effects on zebrafish embryos: Multi-level endpoint and proteomics analysis. Chatterjee N, et al. Environ Pollut, 2021 Jan 1. PMID 33120346
  4. Environmental chemicals differentially affect epigenetic-related mechanisms in the zebrafish liver (ZF-L) cell line and in zebrafish embryos. Blanc M, et al. Aquat Toxicol, 2019 Oct. PMID 31442592
  5. An embryonic 100μg/L lead exposure results in sex-specific expression changes in genes associated with the neurological system in female or cancer in male adult zebrafish brains. Lee J, et al. Neurotoxicol Teratol, 2018 Jan-Feb. PMID 29074346

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Developmental remodelling of non-CG methylation at satellite DNA repeats.
    Title: Developmental remodelling of non-CG methylation at satellite DNA repeats.
  2. dnmt7 specifically methylates no tail gene in the genome
    Title: Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 determination of heart left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  

General protein information

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Preferred Names
DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a
Names
DNA (cytosine-5-)-methyltransferase 3 beta, like
DNA (cytosine-5-)-methyltransferase 7
NP_001018312.2
XP_005167049.1
XP_005167050.1
XP_005167051.1
XP_005167053.1

NCBI Reference Sequences (RefSeq)

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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_001020476.2 → NP_001018312.2  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a

    Status: VALIDATED

    Source sequence(s)
    BX005340, CR762393
    UniProtKB/TrEMBL
    A0A2R9YJL5, A0A8M1N5U2
    Related
    ENSDARP00000079796.6, ENSDART00000085361.6
    Conserved Domains (4) summary
    cd05835
    Location:858 → 941
    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 ...
    pfam00307
    Location:16 → 91
    CH; Calponin homology (CH) domain
    cl17173
    Location:1178 → 1446
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    cl22851
    Location:1034 → 1153
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007119.7 Reference GRCz11 Primary Assembly

    Range
    23356180..23381199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005166992.4 → XP_005167049.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X1

    See identical proteins and their annotated locations for XP_005167049.1

    UniProtKB/TrEMBL
    A0A8M2BEF6, E7F6H4
    Related
    ENSDARP00000108732.1, ENSDART00000125729.4
    Conserved Domains (4) summary
    cd05835
    Location:902 → 985
    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 ...
    pfam00307
    Location:16 → 91
    CH; Calponin homology (CH) domain
    cl17173
    Location:1222 → 1490
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    cl22851
    Location:1078 → 1197
    PHD_SF; PHD finger superfamily

  2. XM_005166994.4 → XP_005167051.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X2

    UniProtKB/TrEMBL
    A0A8M2BEG2
    Conserved Domains (4) summary
    cd05835
    Location:879 → 962
    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 ...
    pfam00307
    Location:16 → 91
    CH; Calponin homology (CH) domain
    cl17173
    Location:1199 → 1467
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    cl22851
    Location:1055 → 1174
    PHD_SF; PHD finger superfamily

  3. XM_005166993.4 → XP_005167050.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X1

    See identical proteins and their annotated locations for XP_005167050.1

    UniProtKB/TrEMBL
    A0A8M2BEF6, E7F6H4
    Conserved Domains (4) summary
    cd05835
    Location:902 → 985
    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 ...
    pfam00307
    Location:16 → 91
    CH; Calponin homology (CH) domain
    cl17173
    Location:1222 → 1490
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    cl22851
    Location:1078 → 1197
    PHD_SF; PHD finger superfamily

  4. XM_005166996.4 → XP_005167053.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X3

    UniProtKB/TrEMBL
    A0A8M2BEH1, B0S581, F1R009
    Related
    ENSDARP00000118153.1, ENSDART00000145062.3
    Conserved Domains (4) summary
    cd05835
    Location:835 → 918
    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 ...
    pfam00307
    Location:16 → 91
    CH; Calponin homology (CH) domain
    cl17173
    Location:1155 → 1423
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    cl22851
    Location:1011 → 1130
    PHD_SF; PHD finger superfamily
Nucleotide Protein
Heading Accession and Version

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