rrp40 (SPAC22A12.12c)


Gene Standard Namerrp40 Characterisation Statuspublished
Systematic IDSPAC22A12.12c Feature Typeprotein coding
Synonyms Name Description
Productexosome subunit Rrp40 Product Size240aa, 26.73 kDa
Genomic Location Chromosome I, 1180072-1178856 (1217nt); CDS:1179931-1179209 (723nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003723RNA bindingIEAUniProtKB-KW:KW-0694GO_REF:0000037628
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000467exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)ISOSGD:S000005502GO_REF:000002415
GO:0034661ncRNA catabolic processISOSGD:S000005502GO_REF:000002419
GO:0070651nonfunctional rRNA decayISOSGD:S000005502GO_REF:000002413
GO:0071042nuclear polyadenylation-dependent mRNA catabolic processISOSGD:S000005502GO_REF:000002412
GO:0071035nuclear polyadenylation-dependent rRNA catabolic processISOSGD:S000005502GO_REF:000002412
GO:0071038nuclear polyadenylation-dependent tRNA catabolic processISOSGD:S000005502GO_REF:000002412
GO:0070478nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decayISOSGD:S000005502GO_REF:000002413
GO:0070481nuclear-transcribed mRNA catabolic process, non-stop decayISOSGD:S000005502GO_REF:000002413
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000177cytoplasmic exosome (RNase complex)ISOSGD:S000005502GO_REF:000002410
GO:0000178exosome (RNase complex)IDAPMID:2350358814
GO:0000176nuclear exosome (RNase complex)ISOSGD:S000005502GO_REF:000002413
GO:0005730nucleolusIEASL-0188GO_REF:0000039355
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrrp40ΔNullPMID:204732891331
Microscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:23697806638
FYPO:0002379inviable after spore germination, without cell division, with elongated germ tube57
penetrance FYPO_EXT:0000003Microscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000310inviable after spore germination, without cell division, with normal germ tube morphology303
penetrance FYPO_EXT:0000001Microscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
111800721178856

UTRs

Region Coordinates Reference
five_prime_UTR1180072..1179932PMID:21511999
three_prime_UTR1179208..1178856PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PTHR21321 HMMPANTHER IPR026699 Exosome complex RNA-binding protein 1/RRP40/RRP4 13 240 2
PTHR21321:SF3 HMMPANTHER 13 240 1
SSF54791 SuperFamily IPR004088 K Homology domain, type 1 162 239 9
SSF50249 SuperFamily IPR012340 Nucleic acid-binding, OB-fold 70 163 57

View domain organization at Pfam

Protein Properties

Ave. residue weight 111.36 Da
Charge 2.50
Isoelectric point 7.85
Molecular weight 26.73 kDa
Number of residues 240
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
4196.15during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
1232during GO:0072690PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
4440.94during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
2.4during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
0.35during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4569
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3393
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
dis33'-5' exoribonuclease subunit Dis3 (predicted) Affinity Capture-MSPMID:23755256
Affinity Capture-MSPMID:23503588
rrp43exosome subunit Rrp43 Affinity Capture-MSPMID:23503588
External References
Database Identifier Description
NBRP SPAC22A12.12c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC22A12.12c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC22A12.12c BioGRID Interaction Datasets
Expression Viewer SPAC22A12.12c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC22A12.12c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC22A12.12c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC22A12.12c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC22A12.12c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC22A12.12c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC22A12.12c Cell Cycle Data
GEO SPAC22A12.12c GEO profiles
PInt SPAC22A12.12c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC22A12.12c Peptides identified in tandem mass spectrometry proteomics experiments
WikiGene2541837exosome subunit Rrp40 (predicted)
EntrezGene2541837exosome subunit Rrp40 (predicted)
SPD / RIKEN08/08E12Orfeome Localization Data
UniProtKB/SwissProtO13903Exosome complex component rrp40
ModBaseO13903Database of comparative protein structure models
STRINGO13903Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593242exosome subunit Rrp40 (predicted)
RefSeq mRNANM_001018639972h- exosome subunit Rrp40 (predicted) (SPAC22A12.12c), mRNA
European Nucleotide ArchiveCAB16582ENA Protein Mapping
European Nucleotide ArchiveCAB16582.1ENA Protein Mapping
UniParcUPI000006BDFBUniProt Archive

Literature for rrp40

Search: Europe PMC or PubMed

Release Version: PomBase:22_45 - 08 Aug 2014