SLM4 / YBR077C Overview
- Standard Name
- SLM4 1
- Systematic Name
- YBR077C
- SGD ID
- SGD:S000000281
- Aliases
- EGO3 4 , NIR1 2 , GSE1 3
- Feature Type
- ORF , Verified
- Description
- Subunit of EGO/GSE complex; vacuolar/endosomal membrane-associated EGO/GSE complex regulates exit from rapamycin-induced growth arrest, stimulating microautophagy and sorting of Gap1p from endosome to plasma membrane; essential for integrity and function of EGO; targeted to vacuole via AP-3 pathway; gene exhibits synthetic genetic interaction with MSS4 1 2 3 4 5 6
- Name Description
- Synthetic Lethal with Mss4 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
- SLM4/YBR077C is located on the right arm of chromosome II, coding sequence is 489 nucleotides long with 2 nonsynonymous SNPs
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.
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 SLM4 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 the EGO complex involved in signal transduction and microautophagy; localizes to the vacuole membrane and late endosome membrane
View computational annotations
Molecular Function
- Manually Curated
- enables molecular function unknown (ND)
Biological Process
- Manually Curated
- involved in microautophagy (IMP)
- involved in signal transduction (IMP)
Cellular Component
- Manually Curated
- located in fungal-type vacuole membrane (IDA)
- located in late endosome membrane (IDA)
- part of Ragulator complex (IDA, IPI)
- High-Throughput
- located in cytoplasm (HDA)
- located in fungal-type vacuole membrane (HDA)
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
- SLM4/YBR077C is a non-essential gene in reference strain S288C; null mutants are viable but display decreased autophagy and reticulophagy, decreased nutrient uptake, decreased utilization of carbon and nitrogen sources, decreased fermentative growth rate, and auxotrophy for certain nutrients. Stress resistance phenotypes are complex and context-dependent: null mutants show decreased acquired and innate thermotolerance (though innate thermotolerance is increased in some conditions), increased heat sensitivity, increased cold sensitivity, decreased hydrostatic pressure resistance, decreased oxidative stress resistance, decreased starvation resistance, and variable resistance to chemicals (both increased and decreased depending on the compound), though killer toxin resistance is increased and overall stress resistance is increased in some conditions. Null mutants display abnormal and increased accumulation of certain chemical compounds, increased chitin deposition, decreased protein/peptide modification, and abnormal vacuolar morphology. Lifespan effects include abnormal replicative lifespan, increased chronological lifespan, and increased sporulation efficiency. Additional phenotypes include decreased competitive fitness, decreased resistance to enzymatic treatment, decreased transposable element transposition, and decreased metal resistance. Overexpression of SLM4 results in increased colony sectoring.
Classical Genetics
- null
- acquired thermotolerance: decreased
- auxotrophy
- chemical compound accumulation: abnormal
- chemical compound accumulation: increased
- chitin deposition: increased
- chronological lifespan: increased
- cold sensitivity: increased
- competitive fitness: decreased
- fermentative growth: decreased rate
- heat sensitivity: increased
- hydrostatic pressure resistance: decreased
- innate thermotolerance: decreased
- innate thermotolerance: increased
- killer toxin resistance: increased
- oxidative stress resistance: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: decreased
- reticulophagy: decreased
- sporulation efficiency: increased
- starvation resistance: decreased
- stress resistance: increased
- toxin resistance: decreased
- transposable element transposition: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- viable
- unspecified
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.
191 total interactions for 113 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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