rrp42 (SPBC16G5.10)

Gene Standard Namerrp42 Characterisation Statuspublished
Systematic IDSPBC16G5.10 Feature Typeprotein coding
Synonyms Name Description
Productexosome subunit Rrp42 Product Size299aa, 32.01 kDa
Genomic Location Chromosome II, 4231874-4234086 (2213nt); CDS:4231953-4232949 (997nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
3'-5'-exoribonuclease activity16
Annotation ExtensionEvidenceWith/FromReference
RNA binding646
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
GO Cellular Component
Term NameCount
cytoplasmic exosome (RNase complex)10
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
exosome (RNase complex)14
Annotation ExtensionEvidenceWith/FromReference
nuclear exosome (RNase complex)13
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:236978061338

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002421inviable after spore germination, single or double cell division, abnormal cell shape17
penetrance FYPO_EXT:0000001Microscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:23697806
Ensembl transcript structure with UTRs, exons and introns


Exon Start End


Region Coordinates Reference
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
PF01138 Pfam IPR001247 Exoribonuclease, phosphorolytic domain 1 31 161 6
PTHR11097 HMMPANTHER 1 287 3
PTHR11097:SF4 HMMPANTHER 1 287 1
SSF54211 SuperFamily IPR020568 Ribosomal protein S5 domain 2-type fold 4 166 29
SSF54211 SuperFamily IPR020568 Ribosomal protein S5 domain 2-type fold 211 228 29
SSF55666 SuperFamily IPR015847 Exoribonuclease, phosphorolytic domain 2 208 284 5

View domain organization at Pfam

Protein Properties

Ave. residue weight 107.07 Da
Charge -16.00
Isoelectric point 4.17
Molecular weight 32.01 kDa
Number of residues 299
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
27743during GO:0000080PECO:0000126,
single_cellmass spectrometry evidencePMID:24763107
25554during GO:0000084PECO:0000126,
single_cellmass spectrometry evidencePMID:24763107
29320during GO:0000085PECO:0000126,
single_cellmass spectrometry evidencePMID:24763107
25296during GO:0000087PECO:0000126,
single_cellmass spectrometry evidencePMID:24763107
2644.33during GO:0072690PECO:0000005,
population_wideexperimental evidencePMID:23101633
25979during GO:0072690PECO:0000126,
single_cellmass spectrometry evidencePMID:24763107
4856.3during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3.4during GO:0072690PECO:0000005,
population_wideexperimental evidencePMID:23101633
0.97during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
population_wideexperimental evidencePMID:23101633
Species Distribution
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in eukaryotes only2497

Manually curated orthologous groups


Orthologs in Compara

Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
pir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
dis33'-5' exoribonuclease subunit Dis3 Affinity Capture-MSPMID:23755256
Affinity Capture-MSPMID:23503588
red1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
Affinity Capture-MSPMID:24210919
rrp43exosome subunit Rrp43 Affinity Capture-MSPMID:23503588
External References
Database Identifier Description
NBRP SPBC16G5.10 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC16G5.10 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC16G5.10 BioGRID Interaction Datasets
Expression Viewer SPBC16G5.10 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC16G5.10 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC16G5.10 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC16G5.10 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC16G5.10 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC16G5.10 Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC16G5.10 Cell Cycle Data
GEO SPBC16G5.10 GEO profiles
PInt SPBC16G5.10 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC16G5.10 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC16G5.10 Fission yeast phenotypic data & analysis
SPD / RIKEN14/14F01Orfeome Localization Data
UniProtKB/SwissProtO60124Exosome complex component rrp42
ModBaseO60124Database of comparative protein structure models
STRINGO60124Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596759exosome subunit Rrp42 (predicted)
RefSeq PeptideNP_596760BAG family molecular chaperone regulator Bag101 (predicted)
RefSeq mRNANM_001023779972h- exosome subunit Rrp42 (predicted) (SPBC16G5.10), mRNA
RefSeq mRNANM_001023780972h- BAG family molecular chaperone regulator Bag101 (predicted) (bag101), mRNA
European Nucleotide ArchiveCAA19030.1ENA Protein Mapping
UniParcUPI0000134939UniProt Archive

Literature for rrp42

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014