SNF5 / YBR289W Overview
- Standard Name
- SNF5 1
- Systematic Name
- YBR289W
- SGD ID
- SGD:S000000493
- Aliases
- HAF4 60 , SWI10 14 , TYE4 61 62
- Feature Type
- ORF , Verified
- Description
- Subunit of the SWI/SNF chromatin remodeling complex; involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2p and Snf6p; relocates to the cytosol under hypoxic conditions 2 3 5
- Name Description
- Sucrose NonFermenting 4
- 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
- Snf5p is 905 amino acids long, low in abundance; contains multiple polyglutamine repeats (QQQ...), 151 of the 905 residues are glutamine; acetylated on K350, ubiquitinylated on K154 and K447, phosphorylated on 9 residues
- Length (a.a.)
- 905
- Mol. Weight (Da)
- 102547.0
- Isoelectric Point
- 8.49
- Median Abundance (molecules/cell)
- 1956 +/- 832
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 SNF5 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
- DNA-binding and transcription-factor-binding subunit of the SWI/SNF chromatin remodelling complex, which disrupts chromatin structure to enhance binding of transcription factors; involved in carbon catabolite activation of RNA Pol II transcription, double-strand break repair, and activation of invasive growth in response to glucose limitation; localizes to the nucleus and to the cytosol during response to hypoxia
View computational annotations
Molecular Function
- Manually Curated
Biological Process
- Manually Curated
- involved in carbon catabolite activation of transcription (IGI)
- involved in chromatin remodeling (IGI, IMP)
- involved in double-strand break repair via homologous recombination (IMP)
- involved in positive regulation of invasive growth in response to glucose limitation (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP, IGI)
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
- Non-essential gene; null mutant displays slow growth, UV sensitivity, defects in using glutamate as nitrogen source, increased cell size, small nucleolus, overexpanded ER with disorganized cytosolic structures, decreased competitive growth, decreased chronological lifespan, abnormal sporulation, decreased respiratory growth, and sensitivity to hydroxyurea, methyl methanesulfonate, azoles, various antifungals, various metals, heat, Congo Red, sorbate, boric acid, caffeine, cycloheximide
Classical Genetics
- null
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- metal resistance: decreased
- resistance to chemicals: decreased
- resistance to enzymatic treatment: decreased
- toxin resistance: decreased
- transposable element transposition: decreased
- UV resistance: decreased
- vegetative growth: decreased
- reduction of function
- null
- acid pH resistance: decreased
- alkaline pH resistance: decreased
- cell size: increased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- endoplasmic reticulum morphology: abnormal
- freeze-thaw resistance: decreased
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- killer toxin resistance: increased
- liquid culture appearance: abnormal
- metal resistance: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: absent
- respiratory growth: decreased rate
- size of nucleolus: decreased
- sporulation: abnormal
- starvation resistance: decreased
- toxin resistance: decreased
- utilization of nitrogen source: decreased rate
- 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.
- Summary
- Snf5p interacts physically with proteins involved in transcription; SNF5 interacts genetically with genes involved in transcription
690 total interactions for 519 unique genes
Physical Interactions
- Affinity Capture-MS: 106
- Affinity Capture-RNA: 8
- Affinity Capture-Western: 32
- Co-crystal Structure: 2
- Co-localization: 2
- Co-purification: 5
- PCA: 1
- Reconstituted Complex: 12
- Two-hybrid: 3
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Lethality: 2
- Dosage Rescue: 1
- Negative Genetic: 290
- Phenotypic Enhancement: 3
- Phenotypic Suppression: 6
- Positive Genetic: 186
- Synthetic Growth Defect: 16
- Synthetic Lethality: 11
- Synthetic Rescue: 2
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.
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: 2006-03-27
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.