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exosc2 exosome component 2 [ Danio rerio (zebrafish) ]

Gene ID: 550234, updated on 2-Nov-2024

Summary

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Official Symbol
exosc2provided by ZNC
Official Full Name
exosome component 2provided by ZNC
Primary source
ZFIN:ZDB-GENE-050417-27
See related
Ensembl:ENSDARG00000028688 AllianceGenome:ZFIN:ZDB-GENE-050417-27
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
fa97b01; wu:fa97b01; zgc:110117
Summary
Predicted to enable RNA binding activity. Acts upstream of or within neural retina development; ribonucleotide metabolic process; and spinal cord development. Predicted to be part of cytoplasmic exosome (RNase complex) and nuclear exosome (RNase complex). Is expressed in immature eye; midbrain hindbrain boundary; and optic tectum. Human ortholog(s) of this gene implicated in short stature, hearing loss, retinitis pigmentosa, and distinctive facies. Orthologous to human EXOSC2 (exosome component 2). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See exosc2 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (72137331..72143289)
105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (71352825..71358783)

Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 1a, liver Neighboring gene SET and MYND domain containing 1a Neighboring gene sepiapterin reductase a Neighboring gene c-abl oncogene 1, non-receptor tyrosine kinase Neighboring gene RAB14, member RAS oncogene family, like

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. Exosc2 deficiency leads to developmental disorders by causing a nucleotide pool imbalance in zebrafish. Yatsuka H, et al. Biochem Biophys Res Commun, 2020 Dec 17. PMID 33333712
  2. Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition. Cabrera-Quio LE, et al. PLoS Genet, 2021 Feb. PMID 33600438, Free PMC Article
  3. The zebrafish mutation m865 affects formation of dopaminergic neurons and neuronal survival, and maps to a genetic interval containing the sepiapterin reductase locus. Ettl AK, et al. Anat Embryol (Berl), 2006 Dec. PMID 17024299
  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

What's a GeneRIF?
  1. Exosc2 deficiency leads to developmental disorders by causing a nucleotide pool imbalance in zebrafish.
    Title: Exosc2 deficiency leads to developmental disorders by causing a nucleotide pool imbalance in zebrafish.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in CUT catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in TRAMP-dependent tRNA surveillance pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in U4 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within neural retina development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear polyadenylation-dependent rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in poly(A)-dependent snoRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within rRNA processing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within ribonucleotide metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within spinal cord development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of cytoplasmic exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of exosome (RNase complex) IEA
Inferred from Electronic Annotation
more info
  
part_of nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
exosome complex component RRP4

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_001017572.2 → NP_001017572.2  exosome complex component RRP4

    Status: VALIDATED

    Source sequence(s)
    EH525603, EH545647
    UniProtKB/TrEMBL
    A0A8M1N4Y5, F8W3K6
    Related
    ENSDARP00000124376.1, ENSDART00000149195.2
    Conserved Domains (3) summary
    cd05789
    Location:77 → 168
    S1_Rrp4; S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...
    pfam14382
    Location:28 → 65
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    pfam15985
    Location:171 → 211
    KH_6; KH domain

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_007116.7 Reference GRCz11 Primary Assembly

    Range
    72137331..72143289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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