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 NameCount
RNA binding646
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
GO Cellular Component
Term NameCount
cytoplasmic exosome (RNase complex)10
Annotation ExtensionEvidenceWith/FromReference
exosome (RNase complex)14
Annotation ExtensionEvidenceWith/FromReference
nuclear exosome (RNase complex)13
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:236978061338
Microscopyrrp40ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyrrp40ΔNullPECO:0000005, PECO:0000137PMID:23697806686
FYPO:0002379inviable after spore germination, without cell division, with elongated germ tube58
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:SF1 HMMPANTHER 14 240 1
PTHR21321 HMMPANTHER IPR026699 Exosome complex RNA-binding protein 1/RRP40/RRP4 14 240 2
SSF54791 SuperFamily 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)ExtensionConditionScaleEvidenceReference
4196.15during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
1232during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
4440.94during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.4during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.35during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
red1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
dis33'-5' exoribonuclease subunit Dis3 Affinity Capture-MSPMID:23755256
Affinity Capture-MSPMID:23503588
pir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
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
SYSGRO SPAC22A12.12c Fission yeast phenotypic data & analysis
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 ArchiveCAB16582.1ENA Protein Mapping
UniParcUPI000006BDFBUniProt Archive

Literature for rrp40

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014