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 binding582
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
nucleolus365
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationrrp40Δ1452

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cyclerrp40Δ882
inviable after spore germination, without cell division, with elongated germ tuberrp40Δ66
inviable after spore germination, without cell division, with normal germ tube morphologyrrp40Δ303
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1180072..1178856
mRNA1180072..1178856
5' UTR1180072..1179932PMID:21511999
CDS1179931..1179209
3' 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
PF15985 Pfam IPR004088 K Homology domain, type 1 160 207 2
PTHR21321:SF1 HMMPANTHER 14 240 1
PTHR21321 HMMPANTHER IPR026699 Exosome complex RNA-binding protein 1/RRP40/RRP4 14 240 2
SSF54791 SuperFamily IPR004088 K Homology domain, type 1 162 239 9
SSF50249 SuperFamily IPR012340 Nucleic acid-binding, OB-fold 70 163 57
Coil ncoils Predicted coiled-coil protein (DUF2205) 237 240 1057

View domain organization at Pfam

Protein Properties

Ave. residue weight 111.36 Da
Charge 2.50
Codon Adaptation Index 0.39
Isoelectric point 7.85
Molecular weight 26.73 kDa
Number of residues 240
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for rrp40 (SPAC22A12.12c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4196.15during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1232during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4440.94during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.4during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.35during 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
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPAC22A12.12c 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:23755256
affinity captured byrrp43exosome subunit Rrp43 Affinity Capture-MSPMID:23503588
affinity captured byred1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
affinity captured bypir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
binds activation domain construct withecm313-methyl-2-oxobutanoatehydroxymethyltransferase Ecm31 (predicted) Two-hybridPMID:26771498
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)
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
Cyclebase SPAC22A12.12c.1 Cell Cycle Data
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:30_60 - 12 May 2016