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    rbbp6 retinoblastoma binding protein 6 [ Danio rerio (zebrafish) ]

    Gene ID: 445396, updated on 9-Dec-2024

    Summary

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    Official Symbol
    rbbp6provided by ZNC
    Official Full Name
    retinoblastoma binding protein 6provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040930-5
    See related
    Ensembl:ENSDARG00000037919 AllianceGenome:ZFIN:ZDB-GENE-040930-5
    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
    rbbp6l; im:7158869
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination and ubiquitin-dependent protein catabolic process. Predicted to be active in nucleus. Orthologous to human RBBP6 (RB binding protein 6, ubiquitin ligase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See rbbp6 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (35406146..35421194)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (35276639..35291686)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene protein kinase C, beta b Neighboring gene calcium channel, voltage-dependent, gamma subunit 3b Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1b Neighboring gene trinucleotide repeat containing adaptor 6A

    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. Retinoblastoma binding protein 6 and crystallin lambda 1 are cadmium-responsive genes in zebrafish embryos and adults retinae. Scudiero R, et al. C R Biol, 2017 Apr. PMID 28385620
    2. Generation and characterization of a novel gne Knockout Model in Zebrafish. Livne H, et al. Front Cell Dev Biol, 2022. PMID 36353515, Free PMC Article
    3. Identification of 315 genes essential for early zebrafish development. Amsterdam A, et al. Proc Natl Acad Sci U S A, 2004 Aug 31. PMID 15256591, Free PMC Article
    4. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process 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
    E3 ubiquitin-protein ligase RBBP6
    NP_001003873.1
    NP_001180603.1
    XP_005164074.1
    XP_005164075.1
    XP_005164076.1
    XP_005164077.1
    XP_021326039.1
    XP_068072769.1

    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_001003873.2 → NP_001003873.1  E3 ubiquitin-protein ligase RBBP6 isoform 2

      See identical proteins and their annotated locations for NP_001003873.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks most 3' exons and has an alternate 3' segment, as compared to variant 1. The resulting isoform 2 is much shorter than isoform 1.
      Source sequence(s)
      BX255942
      UniProtKB/TrEMBL
      A8WG97, Q6DRF1
      Related
      ENSDARP00000055265.7, ENSDART00000055266.9
      Conserved Domains (1) summary
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain

    2. NM_001193674.1 → NP_001180603.1  E3 ubiquitin-protein ligase RBBP6 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the full-length transcript and encodes isoform 1.
      Source sequence(s)
      BX255942
      UniProtKB/TrEMBL
      A0A8M1NUN3, E7EXE9
      Related
      ENSDARP00000093768.6, ENSDART00000102994.6
      Conserved Domains (4) summary
      COG5222
      Location:2 → 386
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      cd00162
      Location:257 → 300
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:153 → 173
      zf-CCHC_2; Zinc knuckle

    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_007114.7 Reference GRCz11 Primary Assembly

      Range
      35406146..35421194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005164019.5 → XP_005164076.1  E3 ubiquitin-protein ligase RBBP6 isoform X4

      UniProtKB/TrEMBL
      A0A8M2BB84, I3IS00
      Related
      ENSDARP00000125662.1, ENSDART00000150918.2
      Conserved Domains (4) summary
      COG5222
      Location:2 → 386
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      cd00162
      Location:257 → 300
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:153 → 173
      zf-CCHC_2; Zinc knuckle

    2. XM_005164018.5 → XP_005164075.1  E3 ubiquitin-protein ligase RBBP6 isoform X2

      UniProtKB/TrEMBL
      A0A8M2BBH7
      Conserved Domains (4) summary
      COG5222
      Location:2 → 386
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      cd00162
      Location:257 → 300
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:153 → 173
      zf-CCHC_2; Zinc knuckle

    3. XM_021470364.2 → XP_021326039.1  E3 ubiquitin-protein ligase RBBP6 isoform X5

      UniProtKB/TrEMBL
      A0A8M9PME0
      Conserved Domains (4) summary
      pfam10243
      Location:1341 → 1538
      MIP-T3; Microtubule-binding protein MIP-T3
      cl26464
      Location:327 → 511
      Atrophin-1; Atrophin-1 family
      cl26511
      Location:996 → 1421
      Neuromodulin_N; Gap junction protein N-terminal region
      cl26688
      Location:2 → 386
      DWNN; DWNN domain

    4. XM_005164017.5 → XP_005164074.1  E3 ubiquitin-protein ligase RBBP6 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BB64
      Conserved Domains (4) summary
      COG5222
      Location:2 → 385
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      cd00162
      Location:256 → 299
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:153 → 173
      zf-CCHC_2; Zinc knuckle

    5. XM_005164020.5 → XP_005164077.1  E3 ubiquitin-protein ligase RBBP6 isoform X3

      UniProtKB/TrEMBL
      A0A8M2BBF1
      Conserved Domains (4) summary
      COG5222
      Location:2 → 385
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      cd00162
      Location:256 → 299
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:153 → 173
      zf-CCHC_2; Zinc knuckle

    6. XM_068216668.1 → XP_068072769.1  E3 ubiquitin-protein ligase RBBP6 isoform X6

    Nucleotide Protein
    Heading Accession and Version

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