LOC1 / YFR001W Overview
- Standard Name
- LOC1 1
- Systematic Name
- YFR001W
- SGD ID
- SGD:S000001897
- Feature Type
- ORF , Verified
- Description
- Nucleolar protein involved in the asymmetric localization of ASH1 mRNA; binds cooperatively with She2p to the E3 zip-code element in the 3'-UTR of the mRNA; constituent of 66S pre-ribosomal particles involved in pre-rRNA processing and nuclear export of the 60S subunit; may facilitate Rpl43p loading; required post-transcriptionally for efficient retrotransposition; absence results in decreased Ty1 Gag:GFP protein levels; relocalizes from nucleus to cytoplasm upon DNA replication stress 1 2 3 4 5 6 7
- 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.
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
- Relocalizes from nucleus to cytoplasm upon DNA replication stress
- Length (a.a.)
- 204
- Mol. Weight (Da)
- 23622.0
- Isoelectric Point
- 11.07
- Median Abundance (molecules/cell)
- 3874 +/- 881
- Half-life (hr)
- 9.4
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 protein that is 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; also 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)
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 (IPI, IMP)
- involved in ribosomal large subunit export from nucleus (IMP)
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.
Classical Genetics
- null
- chronological lifespan: increased
- heat sensitivity: increased
- protein/peptide accumulation: decreased
- replicative lifespan: increased
- resistance to chemicals: decreased
- 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.
336 total interactions for 188 unique genes
Physical Interactions
- Affinity Capture-MS: 179
- Affinity Capture-RNA: 15
- Affinity Capture-Western: 43
- Co-crystal Structure: 7
- Co-localization: 3
- Co-purification: 1
- PCA: 8
- Protein-RNA: 2
- Proximity Label-MS: 1
- Reconstituted Complex: 9
- Two-hybrid: 33
Genetic Interactions
- Dosage Rescue: 2
- Negative Genetic: 21
- Phenotypic Enhancement: 2
- Phenotypic Suppression: 1
- Positive Genetic: 1
- Synthetic Growth Defect: 7
- Synthetic Rescue: 1
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
- 5
- 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.
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.