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    mbd3b methyl-CpG binding domain protein 3b [ Danio rerio (zebrafish) ]

    Gene ID: 321217, updated on 9-Dec-2024

    Summary

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    Official Symbol
    mbd3bprovided by ZNC
    Official Full Name
    methyl-CpG binding domain protein 3bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-9792
    See related
    Ensembl:ENSDARG00000061810 AllianceGenome:ZFIN:ZDB-GENE-030131-9792
    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
    cb99; cb357; mdb3b; sb:cb99; sb:cb357; wu:fc41c05; zgc:111851
    Summary
    Predicted to enable methyl-CpG binding activity. Acts upstream of or within several processes, including Kupffer's vesicle development; determination of heart left/right asymmetry; and hemopoiesis. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including Kupffer's vesicle; central nervous system; forerunner cell group; midbrain neural keel; and retina. Orthologous to human MBD3 (methyl-CpG binding domain protein 3). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See mbd3b in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (20292526..20312798, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (20267548..20284466, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene unc-13 homolog A (C. elegans) Neighboring gene si:dkey-110c1.10 Neighboring gene transcription factor 3b Neighboring gene zinc finger and BTB domain containing 7a

    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. The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Hendrich B, et al. Trends Genet, 2003 May. PMID 12711219
    2. Specific NuRD components are required for fin regeneration in zebrafish. Pfefferli C, et al. BMC Biol, 2014 Apr 29. PMID 24779377, Free PMC Article
    3. TEADs, Yap, Taz, Vgll4s transcription factors control the establishment of Left-Right asymmetry in zebrafish. Fillatre J, et al. Elife, 2019 Sep 12. PMID 31513014, Free PMC Article
    4. Foxq2 determines blue cone identity in zebrafish. Ogawa Y, et al. Sci Adv, 2021 Oct 8. PMID 34613771, Free PMC Article
    5. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. Brocal I, et al. BMC Genomics, 2016 Mar 24. PMID 27009152, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC111851

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyl-CpG binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA methylation-dependent constitutive heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 definitive hemopoiesis 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 hematopoietic progenitor cell differentiation 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
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    methyl-CpG-binding domain protein 3b

    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_212580.1 → NP_997745.1  methyl-CpG-binding domain protein 3b

      See identical proteins and their annotated locations for NP_997745.1

      Status: PROVISIONAL

      Source sequence(s)
      AY238338
      UniProtKB/TrEMBL
      Q7ZZR0
      Related
      ENSDARP00000048774.6, ENSDART00000048775.9
      Conserved Domains (3) summary
      pfam14048
      Location:121 → 211
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:51 → 116
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
      cl00110
      Location:5 → 46
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    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_007133.7 Reference GRCz11 Primary Assembly

      Range
      20292526..20312798 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068216256.1 → XP_068072357.1  methyl-CpG-binding domain protein 3b isoform X3

    2. XM_005170433.5 → XP_005170490.1  methyl-CpG-binding domain protein 3b isoform X2

      UniProtKB/TrEMBL
      A0A8M2BHS2
      Conserved Domains (3) summary
      pfam14048
      Location:143 → 233
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:73 → 138
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
      cl00110
      Location:28 → 68
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    3. XM_005170432.5 → XP_005170489.1  methyl-CpG-binding domain protein 3b isoform X1

      UniProtKB/TrEMBL
      A0A2R8QPC3, A0A8M2BI62
      Related
      ENSDARP00000156475.1, ENSDART00000182125.1
      Conserved Domains (3) summary
      pfam14048
      Location:144 → 234
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:74 → 139
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
      cl00110
      Location:29 → 69
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395103.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      355568..372612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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