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 activity17
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
GO Cellular Component
Term NameCount
cytoplasmic exosome (RNase complex)10
Annotation ExtensionEvidenceWith/FromReference
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
exosome (RNase complex)14
Annotation ExtensionEvidenceWith/FromReference
nuclear exosome (RNase complex)13
Annotation ExtensionEvidenceWith/FromReference
nucleolus365
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationrrp42Δ1452

Cell Phenotype

Term NameGenotypesCount
inviable after spore germination, single or double cell division, abnormal cell shaperrp42Δ24
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons4231874..4232200, 4232298..4234086
Intron4232201..4232297
mRNA4231874..4234086
5' UTR4231874..4231952PMID:21511999
CDS4231953..4232200, 4232298..4232949
3' UTR4232950..4234086PMID: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 HMMPANTHER 1 282 3
PTHR11097:SF8 HMMPANTHER 1 282 1
SSF55666 SuperFamily IPR015847 Exoribonuclease, phosphorolytic domain 2 208 284 5
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

View domain organization at Pfam

Protein Properties

Ave. residue weight 107.07 Da
Charge -16.00
Codon Adaptation Index 0.39
Isoelectric point 4.17
Molecular weight 32.01 kDa
Number of residues 299
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for rrp42 (SPBC16G5.10)

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3.4during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.97during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2505
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC16G5.10 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bydis33'-5' exoribonuclease subunit Dis3 Affinity Capture-MSPMID:23503588
affinity captured bypir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
affinity captured byred1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
affinity captured byrrp43exosome 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)
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
Cyclebase SPBC16G5.10.1 Cell Cycle Data
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 mRNANM_001023779972h- exosome subunit Rrp42 (predicted) (SPBC16G5.10), mRNA
European Nucleotide ArchiveCAA19030.1ENA Protein Mapping
UniParcUPI0000134939UniProt Archive

Literature for rrp42

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016