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

Gene ID: 445396, updated on 12-Sep-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 act upstream of or within mRNA processing. Predicted to be active in nucleus. Orthologous to human RBBP6 (RB binding protein 6, ubiquitin ligase). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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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 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. 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
  3. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
  4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (7) 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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