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 IDTerm NameEvidenceWith/FromReferenceCount
GO:00001753'-5'-exoribonuclease activityISOSGD:S000002269GO_REF:000002416
GO:0003723RNA bindingIEAUniProtKB-KW:KW-0694GO_REF:0000037648
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:S000002269GO_REF:000002415
GO:0034661ncRNA catabolic processISOSGD:S000002269GO_REF:000002419
GO:0070651nonfunctional rRNA decayISOSGD:S000002269GO_REF:000002413
GO:0071042nuclear polyadenylation-dependent mRNA catabolic processISOSGD:S000002269GO_REF:000002412
GO:0071035nuclear polyadenylation-dependent rRNA catabolic processISOSGD:S000002269GO_REF:000002412
GO:0071038nuclear polyadenylation-dependent tRNA catabolic processISOSGD:S000002269GO_REF:000002412
GO:0070478nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decayISOSGD:S000002269GO_REF:000002413
GO:0070481nuclear-transcribed mRNA catabolic process, non-stop decayISOSGD:S000002269GO_REF:000002413
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000177cytoplasmic exosome (RNase complex)ISOSGD:S000002269GO_REF:000002410
GO:0005829cytosolIDAPMID:168233722319
GO:0000178exosome (RNase complex)IDAPMID:2350358814
GO:0000176nuclear exosome (RNase complex)ISOSGD:S000002269GO_REF:000002413
GO:0005730nucleolusIEASL-0188GO_REF:0000039357
GO:0005634nucleusIDAPMID:168233722737
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:236978061337
Microscopyrrp42ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002421inviable after spore germination, single or double cell division, abnormal cell shape16
penetrance FYPO_EXT:0000001Microscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
142318744232200
242322984234086
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
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
27743during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
25554during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
29320during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
25296during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
25979during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
2644.33during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
4856.3during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3.4during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.97during 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 fungi4599
conserved in eukaryotes4514
conserved in metazoa3428
conserved in vertebrates3402
conserved in eukaryotes only2498
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 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
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_46 - 30 Aug 2014