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Rrp40 Ribosomal RNA processing 40 [ Drosophila melanogaster (fruit fly) ]

Gene ID: 319033, updated on 11-Apr-2024

Summary

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Official Symbol
Rrp40provided by FlyBase
Official Full Name
Ribosomal RNA processing 40provided by FlyBase
Primary source
FLYBASE:FBgn0260648
Locus tag
Dmel_CG31938
See related
AllianceGenome:FB:FBgn0260648
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Drosophila melanogaster
Lineage
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as
CG31938; Dmel\CG31938; dRrp40
Summary
Predicted to enable RNA binding activity. Involved in several processes, including larval lymph gland hemopoiesis; mushroom body development; and regulation of embryonic development. Located in cytoplasm. Part of nuclear exosome (RNase complex). Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 1B. Orthologous to human EXOSC3 (exosome component 3). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See Rrp40 in Genome Data Viewer
Location:
22B1-22B1; 2-3 cM
Exon count:
1
Annotation release Status Assembly Chr Location
Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 2L NT_033779.5 (1728732..1729762)
Release 5.57 previous assembly Release 5 (GCF_000001215.2) 2L NT_033779.4 (1728732..1729762)

Chromosome 2L - NT_033779.5Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L48 Neighboring gene fritz Neighboring gene Replication in mitochondria 2 Neighboring gene Enolase Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Dis3- and exosome subunit-responsive 3' mRNA instability elements. Kiss DL, et al. Biochem Biophys Res Commun, 2012 Jul 6. PMID 22668878, Free PMC Article
  2. Core exosome-independent roles for Rrp6 in cell cycle progression. Graham AC, et al. Mol Biol Cell, 2009 Apr. PMID 19225159, Free PMC Article
  3. A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons. Morton DJ, et al. PLoS Genet, 2020 Jul. PMID 32645003, Free PMC Article
  4. Effects of codon usage on gene expression are promoter context dependent. Yang Q, et al. Nucleic Acids Res, 2021 Jan 25. PMID 33410890, Free PMC Article
  5. Transcription in the absence of histone H3.3. Hödl M, et al. Curr Biol, 2009 Jul 28. PMID 19523831

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons.
    Title: A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons.
Submit: New GeneRIF Correction

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by FlyBase

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 brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
  
involved_in larval lymph gland hemopoiesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mushroom body 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 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 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
  
involved_in regulation of embryonic development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of cytoplasmic exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of exosome (RNase complex) IDA
Inferred from Direct Assay
more info
 PubMed 
part_of exosome (RNase complex) IEA
Inferred from Electronic Annotation
more info
  
part_of exosome (RNase complex) IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nuclear exosome (RNase complex) IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nuclear exosome (RNase complex) ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
ribosomal RNA processing 40
Names
CG31938-PA
CG31938-PB
Rrp40-PA
Rrp40-PB

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NT_033779.5 Reference assembly

    Range
    1728732..1729762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001298636.1 → NP_001285565.1  ribosomal RNA processing 40, isoform B [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001285565.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8IPX7
    Conserved Domains (2) summary
    COG1097
    Location:5 → 213
    Rrp4; Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Translation, ribosomal structure and biogenesis]
    cd05790
    Location:63 → 148
    S1_Rrp40; Rrp40 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 ...

  2. NM_164435.3 → NP_722725.1  ribosomal RNA processing 40, isoform A [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_722725.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8IPX7
    Related
    FBpp0077551
    Conserved Domains (2) summary
    COG1097
    Location:5 → 213
    Rrp4; Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Translation, ribosomal structure and biogenesis]
    cd05790
    Location:63 → 148
    S1_Rrp40; Rrp40 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 ...
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IPX7.1 Q8IPX7

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