FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Rrp40
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General Information
Symbol
Dmel\Rrp40
Species
D. melanogaster
Name
Ribosomal RNA processing 40
Annotation Symbol
CG31938
Feature Type
protein_coding_gene
FlyBase ID
FBgn0260648
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Ribosomal RNA processing 40 (Rrp40) encodes a protein involved in gene expression regulation. [Date last reviewed: 2019-07-11] (FlyBase Gene Snapshot)
All Summaries
Also Known As

dRrp40

Key Links
Genomic Location
Cytogenetic map
22B1-22B1
Sequence location
Recombination map
2-3
RefSeq locus
NT_033779 REGION:1728732..1729762
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (16 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables RNA binding
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000481223
(GO Reference Genome Project, 2011-)
Biological Process (11 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
involved_in brain development
inferred from mutant phenotype
(Morton et al., 2020)
involved_in mushroom body development
inferred from mutant phenotype
(Morton et al., 2020)
involved_in regulation of embryonic development
inferred from mutant phenotype
(Morton et al., 2020)
involved_in regulation of gene expression
inferred from mutant phenotype
(Kiss and Andrulis, 2010)
Terms Based on Predictions or Assertions (7 terms)
CV Term
Evidence
References
involved_in CUT catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000481223
(GO Reference Genome Project, 2011-)
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
inferred from biological aspect of ancestor with PANTHER:PTN000481223
(GO Reference Genome Project, 2011-)
involved_in nuclear polyadenylation-dependent rRNA catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000481224
(GO Reference Genome Project, 2011-)
involved_in nuclear-transcribed mRNA catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000481224
(GO Reference Genome Project, 2011-)
involved_in poly(A)-dependent snoRNA 3'-end processing
inferred from biological aspect of ancestor with PANTHER:PTN000481223
(GO Reference Genome Project, 2011-)
involved_in TRAMP-dependent tRNA surveillance pathway
inferred from biological aspect of ancestor with PANTHER:PTN000481224
(GO Reference Genome Project, 2011-)
involved_in U4 snRNA 3'-end processing
inferred from biological aspect of ancestor with PANTHER:PTN000481223
(GO Reference Genome Project, 2011-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Graham et al., 2006)
part_of exosome (RNase complex)
inferred from mutant phenotype
(Morton et al., 2020)
inferred from direct assay
(Forler et al., 2003)
part_of nuclear exosome (RNase complex)
inferred from direct assay
(Andrulis et al., 2002)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of cytoplasmic exosome (RNase complex)
inferred from biological aspect of ancestor with PANTHER:PTN000481224
(GO Reference Genome Project, 2011-)
part_of exosome (RNase complex)
inferred from electronic annotation with InterPro:IPR026699
(InterPro Project Members, 2004-)
part_of nuclear exosome (RNase complex)
inferred from biological aspect of ancestor with PANTHER:PTN000481224
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with SGD:S000005502
(Andrulis et al., 2002)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the RRP40 family. (Q8IPX7)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Ribosomal RNA processing 40 (Rrp40) encodes a protein involved in gene expression regulation. [Date last reviewed: 2019-07-11]
Gene Group (FlyBase)
NUCLEAR EXOSOME COMPLEX -
The nuclear exosome is a 3'-5' exonuclease complex that is involved in the processing and degradation many types of RNAs, including mRNA, rRNA, snRNA, snoRNA and tRNA. In yeast and humans, the exosome has a barrel structure, the core of which is formed by a ring of six RNase PH domain subunits and a cap of three S1/KH-domain subunits. (Adapted from FBrf0210381 and PMID:27345150).
CYTOPLASMIC EXOSOME COMPLEX -
The cytoplasmic exosome is a 3'-5' exonuclease complex involved in the processing and degradation many types of RNA which include the removal of unstable and aberrant transcripts. In yeast and humans, the exosome has a barrel structure, the core of which is formed by a ring of six RNase PH domain subunits and a cap of three S1/KH-domain subunits. (Adapted from FBrf0210381 and PMID:27345150).
Protein Function (UniProtKB)
Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events (By similarity). In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts such as antisense RNA species, and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm (By similarity). In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs (By similarity). The catalytic inactive RNA exosome core complex of 9 subunits is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes (By similarity). Required generally for normal embryonic and neuronal development (PubMed:32645003). Also plays a critical role in the maintenance of neuronal function in mature flies by controlling the levels of specific mRNAs such as the synaptic regulator Arc1 (PubMed:32645003).
(UniProt, Q8IPX7)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Rrp40 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q8IPX7)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Rrp40-RA
FBtr0077883
NM_164435
844
232
Rrp40-RB
FBtr0345430
NM_001298636
1031
232
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Rrp40-PA
FBpp0077551
25.0
232
8.46
Q8IPX7
NP_722725
AAN10459
Rrp40-PB
FBpp0311555
25.0
232
8.46
Q8IPX7
NP_001285565
AHN54080
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

232 aa isoforms: Rrp40-PA, Rrp40-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the RNA exosome complex (PubMed:12490954). Specifically part of the catalytically inactive RNA exosome core complex (By similarity).

(UniProt, Q8IPX7)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rrp40 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.19

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Graham et al., 2006)
part_of exosome (RNase complex)
inferred from mutant phenotype
(Morton et al., 2020)
inferred from direct assay
(Forler et al., 2003)
part_of nuclear exosome (RNase complex)
inferred from direct assay
(Andrulis et al., 2002)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rrp40 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rrp40
Transgenic constructs containing regulatory region of Rrp40
Aberrations (Deficiencies and Duplications) ( 3 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\EXOSC3
14 of 14
Yes
Yes
2  
Hsap\EXOSC2
2 of 14
No
No
3  
Hsap\EXOSC1
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Exosc3
14 of 14
Yes
Yes
Rnor\Exosc2
2 of 14
No
No
Rnor\Exosc1
1 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Exosc3
13 of 14
Yes
Yes
Mmus\Exosc2
2 of 14
No
No
Mmus\Exosc1
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\exosc3
7 of 13
Yes
Yes
Xtro\nipal3
6 of 13
No
Yes
Xtro\exosc1
1 of 13
No
No
Xtro\LOC100489782
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\exosc3
13 of 14
Yes
Yes
Drer\exosc2
2 of 14
No
No
Drer\wu:fc33b09
2 of 14
No
Yes
Drer\exosc1
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\exos-3
14 of 14
Yes
Yes
Cele\exos-2
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP010247
12 of 12
Yes
Yes
Agam\AgaP_AGAP011211
2 of 12
No
No
Agam\AgaP_AGAP008063
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (4)
Atha\AT2G25355
13 of 13
Yes
Yes
Atha\AT4G32175
13 of 13
Yes
Yes
Atha\RRP4
2 of 13
No
No
Atha\AT5G38890
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\RRP40
13 of 13
Yes
Yes
Scer\RRP4
2 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\SPAC22A12.12c
12 of 12
Yes
Yes
Spom\SPAC2F7.14c
2 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Rrp40. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
Rrp4
4 of 13
Csl4
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 3 )
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
EXOSC3; exosome component 3
model of  pontocerebellar hypoplasia type 1B
IEA
(FlyBase, 2019-)
Modifiers Based on Experimental Evidence ( 2 )
Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
Homo sapiens (Human)
Gene name
Score
OMIM
OMIM Phenotype
DO term
Complementation?
Transgene?
EXOSC3; exosome component 3
14 of 14
EXOSOME COMPONENT 3; EXOSC3
 
Functional Complementation Data
Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
Interactions
Summary of Physical Interactions
Summary of Genetic Interactions
Interaction Browsers
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Component of the RNA exosome complex (PubMed:12490954). Specifically part of the catalytically inactive RNA exosome core complex (By similarity).
(UniProt, Q8IPX7 )
Linkouts
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
FlyBase
External Links
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-3
Cytogenetic map
22B1-22B1
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
22B1-22B1
Limits computationally determined from genome sequence between P{PZ}l(2)0411104111 and P{lacW}CG17646k11021
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

2-3

(FlyBase, 2016)

2-3.0

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (9)
Genomic Clones (13)
 

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (3)
 

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced
BDGP DGC clones
Other clones
Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       

      • New stable cell line derived from S2-unspecified : Stable S2 cell lines were created expressing copper-inducible epitope-tagged exosome subunits to examine the subcellular distribution of exosome complex components. Stable lines were created containing the following exosome subunits; Dis3, Rrp6, Mtr3, Rrp42, Rrp4, Ski6, Rrp46, Rrp40, and Csl4.

        (Graham et al., 2006)
      Other Comments

      Identification: as a protein that copurifies with Spt6 protein.

      (Andrulis et al., 2002)

      New annotation (CG31938) in release 3 of the genome annotation.

      (FlyBase Genome Annotators, 2002-2003)
      Relationship to Other Genes
      Source for database merge of

      Source for merge of: Rrp40 CG31938

      (Graham et al., 2006)
      Additional comments
      Nomenclature History
      Source for database identify of
      Nomenclature comments
      Etymology
      Synonyms and Secondary IDs (4)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      External Crossreferences and Linkouts ( 35 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
      UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      Other crossreferences
      AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      Flygut - An atlas of the Drosophila adult midgut
      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      References (53)