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

    Gene ID: 321084, updated on 2-Nov-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
    Enables DNA-methyltransferase activity. Acts upstream of or within determination of heart left/right asymmetry. Predicted to be active 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 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) and DNMT3L (DNA methyltransferase 3 like). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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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
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (23356242..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 uncharacterized LOC137496344 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. In vivo DNA methylation editing in zebrafish. Liang F, et al. Epigenetics, 2023 Dec. PMID 36945831, Free PMC Article
    2. Tributyltin causes generational neurodevelopmental toxicity and the protective effect of folic acid in zebrafish. Cai H, et al. J Environ Sci (China), 2024 Mar. PMID 37980044
    3. Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b. Smith TH, et al. Dev Genes Evol, 2011 Mar. PMID 21258815
    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. Expression patterns of dnmt3aa, dnmt3ab, and dnmt4 during development and fin regeneration in zebrafish. Takayama K, et al. Gene Expr Patterns, 2014 Mar. PMID 24509247

    See all (49) 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
    XP_068078968.1
    XP_068078969.1

    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: GCF_000002035.6-RS_2024_08

    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
      23356242..23381199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005166992.5 → 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_005166994.5 → 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_005166996.5 → 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

    4. XM_005166993.5 → 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

    5. XM_068222868.1 → XP_068078969.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X3

    6. XM_068222867.1 → XP_068078968.1  DNA (cytosine-5-)-methyltransferase 3 beta, duplicate a isoform X1

    Nucleotide Protein
    Heading Accession and Version

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