RRP4 / YHR069C Overview
- Standard Name
- RRP4 1
- Systematic Name
- YHR069C
- SGD ID
- SGD:S000001111
- Feature Type
- ORF , Verified
- Description
- Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain RNA binding domains; mutations in the human ortholog, EXOSC2, cause SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies) syndrome, an RNA exosomopathy 2 3 4 5 6 7
- Name Description
- Ribosomal RNA Processing 1
- Comparative Info
-
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Summary
- Rrp4p is 359 amino acids long with ribosomal L27 protein-like, nucleic-acid binding, and KH domains; subunit of the exosome; shares several domains with proteins involved in DNA recombination, DNA repair, and DNA replication; undergoes various post-translational modifications including acetylation and phosphorylation on 14 residues
- Length (a.a.)
- 359
- Mol. Weight (Da)
- 39422.8
- Isoelectric Point
- 6.18
- Median Abundance (molecules/cell)
- 5006 +/- 740
- Half-life (hr)
- 9.9
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all RRP4 alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- Subunit of both nuclear and cytoplasmic exosome (RNase complex); involved in exonucleolytic trimming of tricistronic pre-ribosomal RNA (SSU-rRNA, 5.8S rRNA, LSU-rRNA) to generate mature 3'-ends of 5.8S transcripts and nuclear polyadenylation-dependent RNA degradation; contributes to U4 small nuclear RNA (snRNA) and small nucleolar RNA 3'-end processing
View computational annotations
Molecular Function
- Manually Curated
- enables molecular function unknown (ND)
Biological Process
- Manually Curated
- involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (IMP)
- involved in nuclear mRNA surveillance (IGI)
- involved in nuclear polyadenylation-dependent rRNA catabolic process (IMP)
- involved in nuclear-transcribed mRNA catabolic process (IMP)
- involved in poly(A)-dependent snoRNA 3'-end processing (IMP)
- involved in TRAMP-dependent tRNA surveillance pathway (IDA)
- involved in U4 snRNA 3'-end processing (IMP)
Cellular Component
- Manually Curated
- part of cytoplasmic exosome (RNase complex) (IDA)
- part of nuclear exosome (RNase complex) (IDA)
Complex
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
- Summary
- Essential gene; ts mutant is sensitive to benomyl and nocodazole at the permissive temperature; ts mutation and repression cause accumulation of unprocessed RNAs; in large-scale studies, ts mutant shows chromosome instability at the semi-permissive temperature; diploid heterozygous null mutant is haploinsufficient, sensitive to heat and oxidative stress, and has reduced competitive fitness
Classical Genetics
- null
- repressible
- conditional
- reduction of function
Disease
Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.
- Summary
- Yeast RRP4 is homologous to human EXOSC2, and has been used to study both multiple myeloma and SHRF (short stature, hearing loss, retinitis pigmentosa, and distinctive facies) which is an RNA exosomopathy linked to missense mutations in genes encoding structural subunits of the evolutionarily-conserved 10-subunit RNA exosome exoribonuclease complex
Manually Curated
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
- Summary
- Interacts physically with proteins involed in rRNA processing and RNA catabolism; interacts genetically with genes involved in transcription and rRNA processing
480 total interactions for 326 unique genes
Physical Interactions
- Affinity Capture-MS: 164
- Affinity Capture-RNA: 4
- Affinity Capture-Western: 22
- Co-purification: 4
- PCA: 2
- Proximity Label-MS: 1
- Reconstituted Complex: 4
- Two-hybrid: 5
Genetic Interactions
- Dosage Rescue: 1
- Negative Genetic: 211
- Phenotypic Enhancement: 2
- Phenotypic Suppression: 1
- Positive Genetic: 49
- Synthetic Growth Defect: 7
- Synthetic Lethality: 3
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Regulators
- 2
- Targets
- 0
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2009-09-09
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.