RAT1 / YOR048C Overview
- Standard Name
- RAT1 1
- Systematic Name
- YOR048C
- SGD ID
- SGD:S000005574
- Aliases
- HKE1 7 , TAP1 1 , XRN2 12
- Feature Type
- ORF , Verified
- Description
- Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism, including rRNA and snoRNA processing, as well as poly (A+) dependent and independent mRNA transcription termination; required for cotranscriptional pre-rRNA cleavage; displaces Cdk1p from elongating transcripts, especially as RNAPII reaches the poly(A) site, negatively regulates phosphorylation of the CTD of RNAPII, and inhibits RNAPII transcriptional elongation 1 2 3 4 5 6
- Name Description
- Ribonucleic Acid Trafficking 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.
- Length (a.a.)
- 1006
- Mol. Weight (Da)
- 115928.3
- Isoelectric Point
- 6.8
- Median Abundance (molecules/cell)
- 3466 +/- 778
- Half-life (hr)
- 8.0
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 RAT1 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
- Nuclear 5' to 3' RNA exoribonuclease; functions in both exosome-dependent and poly(A)-coupled RNAPII transcriptional termination; functions in mRNA surveillance, and processing of both rRNA and snoRNA; inhibits RNAPII transcriptional elongation, and phosphorylation of the CTD of RNAPII
View computational annotations
Molecular Function
- Manually Curated
- enables 5'-3' RNA exonuclease activity (IDA)
- enables mRNA binding (HDA)
Biological Process
- Manually Curated
- involved in cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (IDA)
- acts upstream of or within mRNA splicing, via spliceosome (IMP)
- involved in NAD-cap decapping (IDA)
- involved in negative regulation of transcription elongation by RNA polymerase II (IMP, IGI)
- involved in nuclear mRNA surveillance (IGI, IMP)
- involved in nuclear polyadenylation-dependent rRNA catabolic process (IMP)
- involved in rRNA processing (IMP, IGI)
- involved in sno(s)RNA processing (IGI, IMP)
- involved in termination of RNA polymerase II transcription, exosome-dependent (IGI, IMP)
- involved in termination of RNA polymerase II transcription, poly(A)-coupled (IMP)
Cellular Component
- Manually Curated
- located in mitochondrion (HDA)
- located in nucleus (HDA, 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; null mutant accumulates poly(A)+ RNA in the nucleus, and conditional mutant accumulates unprocessed forms of pre-rRNA and snoRNAs; conditional mutant has an S phase delay, increased hydroxyurea sensitivity, and accumulates telomeric repeat-containing RNA (TERRA) and shortened telomeres; null mutant displays chromosomal instability and decreased competitive fitness in rich media; conditional mutant has increased phosphorylation of the C-terminal domain (CTD) of RNAPII, and elevated recruitment of Ctk1p to active chromatin; overexpression causes slow growth and elevated invasive growth
Classical Genetics
- null
- repressible
- conditional
- null
- overexpression
- repressible
- reduction of function
- conditional
Large-scale Survey
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.
744 total interactions for 632 unique genes
Physical Interactions
- Affinity Capture-MS: 207
- Affinity Capture-RNA: 12
- Affinity Capture-Western: 15
- Biochemical Activity: 1
- Co-localization: 1
- Co-purification: 1
- Proximity Label-MS: 1
- Reconstituted Complex: 2
Genetic Interactions
- Dosage Growth Defect: 1
- Dosage Rescue: 5
- Negative Genetic: 364
- Phenotypic Enhancement: 13
- Phenotypic Suppression: 7
- Positive Genetic: 88
- Synthetic Growth Defect: 7
- Synthetic Lethality: 5
- Synthetic Rescue: 14
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
- 3
- 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: 2000-04-12
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.