LOC1 / YFR001W Overview
- Standard Name
- LOC1 1
- Systematic Name
- YFR001W
- SGD ID
- SGD:S000001897
- Feature Type
- ORF , Verified
- Description
- RNA binding chaperone with ATP-independent RNA annealing activity; Nucleolar protein involved in asymmetric localization of ASH1 mRNA; binds cooperatively with She2p to the E3 zip-code element in the 3'-UTR; ribosomal 60S biogenesis factor required for Rpl43p loading; 66S pre-ribosomal particle component involved in pre-rRNA processing and 60S nuclear export; Ty1 host factor; has intrinsically disordered RNA binding (PUN) motifs; relocalizes to the cytoplasm upon DNA replication stress 1 2 3 4 5 6 7 8
- Name Description
- LOCalization of mRNA 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.
- Summary
- LOC1/YFR001W is located on the right arm of chromosome VI, coding sequence is 615 nucleotides long
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 | CGD Synteny Browser
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
- Relocalizes from nucleus to cytoplasm upon DNA replication stress
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 LOC1 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
- Nucleolar RNA binding chaperone with ATP-independent RNA annealing activity; part of the large subunit precursor to the preribosome; involved in rRNA processing, biogenesis of the large subunit, and export of the LSU from the nucleus; binds mRNA and has roles in mRNA localization and regulation of translation as part of a chaperone complex
View computational annotations
Molecular Function
- Manually Curated
- enables mRNA binding (IDA)
- enables ribosome binding (IDA)
- enables RNA folding chaperone (IDA)
- enables RNA strand annealing activity (IDA)
Biological Process
- Manually Curated
- involved in endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (IMP)
- involved in endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (IMP)
- involved in endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (IMP)
- involved in intracellular mRNA localization (IMP)
- involved in negative regulation of translation (IDA)
- involved in ribosomal large subunit biogenesis (IMP, IPI)
- involved in ribosomal large subunit export from nucleus (IMP)
Cellular Component
- Manually Curated
- located in nucleolus (IDA)
- part of preribosome, large subunit precursor (IDA)
- part of protein folding chaperone complex (IMP)
- High-Throughput
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
- LOC1/YFR001W is a non-essential gene in reference strain S288C; null mutants are viable but grow slowly with decreased fermentative growth rate, decreased vegetative growth, increased G1 phase duration, haploinsufficiency, and decreased competitive fitness. Null mutants exhibit abnormal, decreased, and increased accumulation of different chemical compounds, decreased and increased RNA accumulation, abnormal RNA localization, decreased protein/peptide accumulation, abnormal budding pattern, abnormal cell shape, decreased cell size, abnormal vacuolar morphology, decreased endocytosis, and decreased peroxisomal transport. Stress resistance phenotypes are highly context-dependent: null mutants show increased heat sensitivity, decreased desiccation resistance, decreased freeze-thaw resistance, decreased metal resistance, variable overall stress resistance (both increased and decreased depending on conditions), and variable resistance to chemicals (both increased and decreased depending on the compound), while resistance to enzymatic treatment and toxin resistance are increased. Null mutants display absent or decreased utilization of nitrogen sources, decreased mitotic recombination, decreased transposable element transposition, increased chronological lifespan, and variable replicative lifespan (both increased and decreased depending on conditions). Overexpression of LOC1 results in increased filamentous growth.
Classical Genetics
- null
- chronological lifespan: increased
- growth in exponential phase: decreased rate
- heat sensitivity: increased
- protein/peptide accumulation: decreased
- replicative lifespan: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- RNA accumulation: decreased
- RNA accumulation: increased
- RNA localization: abnormal
- transposable element transposition: decreased
- vegetative growth: decreased
- vegetative growth: decreased rate
- null
- budding pattern: abnormal
- cell cycle progression in G1 phase: increased duration
- cell shape: abnormal
- cell size: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- fermentative growth: decreased rate
- freeze-thaw resistance: decreased
- haploinsufficient
- heat sensitivity: increased
- metal resistance: decreased
- mitotic recombination: decreased
- peroxisomal transport: decreased
- replicative lifespan: decreased
- replicative lifespan: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: increased
- stress resistance: decreased
- stress resistance: increased
- toxin resistance: increased
- transposable element transposition: decreased
- utilization of nitrogen source: absent
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased
- vegetative growth: decreased rate
- viable
- overexpression
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.
347 total interactions for 195 unique genes
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.
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.
All Curated Literature
All manually curated literature for the specified gene, shown as a count of references by year of publication followed by the most recent papers. Click "Literature Details" or "See all" to view all literature information for this locus, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review).
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