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:0000037627
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:000002412
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000177cytoplasmic exosome (RNase complex)ISOSGD:S000002269GO_REF:000002410
GO:0005829cytosolIDAPMID:168233722317
GO:0000178exosome (RNase complex)IDAPMID:2350358814
GO:0000176nuclear exosome (RNase complex)ISOSGD:S000002269GO_REF:000002413
GO:0005730nucleolusIEASL-0188GO_REF:0000039345
GO:0005634nucleusIDAPMID:168233722730
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrrp42ΔNullPMID:204732891309
Microscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002421inviable after spore germination, single or double cell division, abnormal cell shapeMicroscopyrrp42ΔNullPECO:0000005, PECO:0000137PMID:2369780614
penetrance FYPO_EXT:0000001
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
142318744232200
242322984234086

UTRs

Region Start End Reference
three_prime_UTR42329504234086PMID:21511999
five_prime_UTR42318744231952PMID: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
PF01138 Pfam IPR001247 Exoribonuclease, phosphorolytic domain 1 31 161 6
PTHR11097:SF4 HMMPANTHER 1 287 1
PTHR11097 HMMPANTHER 1 287 3
SSF54211 SuperFamily IPR020568 4 166 29
SSF54211 SuperFamily IPR020568 211 228 29
SSF55666 SuperFamily IPR015847 208 284 5
Low complexity (SEG) seg 144 155

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)DuringConditionScaleEvidenceReference
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)DuringConditionScaleEvidenceReference
0.97during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
3.4during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
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)
SPD / RIKEN14/14F01Orfeome Localization Data
EntrezGene2540116exosome subunit Rrp42 (predicted)
WikiGene2540116exosome subunit Rrp42 (predicted)
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
RefSeq mRNANM_001023779972h- exosome subunit Rrp42 (predicted) (SPBC16G5.10), mRNA
RefSeq mRNANM_001023780972h- BAG family molecular chaperone regulator Bag101 (bag101), mRNA
European Nucleotide ArchiveCAA19030ENA Protein Mapping
UniParcUPI0000134939UniProt Archive

Literature for rrp42

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014