SCS2 / YER120W Overview
- Standard Name
- SCS2 1
- Systematic Name
- YER120W
- SGD ID
- SGD:S000000922
- Feature Type
- ORF , Verified
- Description
- Integral ER membrane protein, regulates phospholipid metabolism; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect the ER to the plasma membrane (PM); regulates PI4P levels by controlling access of Sac1p to PM substrate PI4P; interacts with FFAT motifs in Opi1p, Swh1p, Osh2p and Osh3p; role in NVJ integrity and micronucleophagy; role in telomeric silencing; VAMP-associated protein (VAP) homolog; SCS2 has a paralog, SCS22, that arose from the whole genome duplication 2 3 4 5 7 8 9 10
- Name Description
- Suppressor of Choline Sensitivity 6
- Paralog
- SCS22 7
- 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
- SCS2 is located on the right arm of chromosome V between AVT6 vacuolar aspartate and glutamate exporter and uncharacterized gene YER121W; coding sequence is 735 nucleotides long with 3 SNPs, one of which causes a Phe/Cys polymorphism at residue 242; SCS2 has paralog SCS22 from the whole genome duplication
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
- Scs2p is 244 amino acids long, of average half-life, and moderate in abundance; undergoes various post-translational modifications, including acetylation, phosphorylation, succinylation, sumoylation, and ubiquitinylation on 16 sites
- Length (a.a.)
- 244
- Mol. Weight (Da)
- 26915.7
- Isoelectric Point
- 4.55
- Median Abundance (molecules/cell)
- 14184 +/- 9151
- Half-life (hr)
- 10.7
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 SCS2 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
- Phosphatidylinositol- and FFAT-motif binding protein involved in endoplasmic reticulum (ER) inheritance, ER polarization and ER membrane organization; regulates nuclear import of transcription factors and intracellular lipid transport; also involved in phospholipid biosynthesis and telomeric chromatin silencing; localizes to the nuclear envelope, nucleus-vacuolar junctions, the ER, and bud tips and necks
View computational annotations
Molecular Function
- Manually Curated
- enables FFAT motif binding (IPI, IMP)
- enables phosphatidylinositol binding (IDA)
Biological Process
- Manually Curated
- involved in endoplasmic reticulum inheritance (IGI, IMP)
- involved in endoplasmic reticulum membrane organization (IGI)
- involved in endoplasmic reticulum polarization (IDA)
- involved in negative regulation of protein import into nucleus (IPI, IMP)
- involved in phospholipid biosynthetic process (IMP, IGI)
- involved in regulation of intracellular lipid transport (IMP)
- involved in regulation of phosphatidylinositol dephosphorylation (IGI)
- acts upstream of or within reticulophagy (IGI)
- involved in subtelomeric heterochromatin formation (IGI, IMP)
Cellular Component
- Manually Curated
- located in cellular bud neck (IPI)
- located in cellular bud tip (IDA)
- located in endoplasmic reticulum (IDA, HDA)
- located in endoplasmic reticulum membrane (IDA)
- located in nuclear envelope (IDA)
- located in nuclear membrane (IDA)
- located in nucleus-vacuole junction (IDA)
- located in plasma membrane (IDA)
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 has inositol auxotrophy and cold sensitivity; null mutation also leads to highly elongated cells and reduced telomeric silencing; overexpression causes slow growth
Classical Genetics
- null
- autophagy: decreased
- auxotrophy
- cell shape: abnormal
- cold sensitivity: increased
- endomembrane system morphology: abnormal
- endoplasmic reticulum morphology: abnormal
- micronucleophagy: decreased
- protein/peptide distribution: abnormal
- resistance to chemicals: decreased
- silencing: decreased
- viability: decreased
- viable
- overexpression
- reduction of function
- null
- bud morphology: abnormal
- competitive fitness: decreased
- endocytosis: decreased
- haploinsufficient
- protein/peptide accumulation: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- silencing: decreased
- sporulation: decreased
- starvation resistance: decreased
- vacuolar morphology: abnormal
- viable
- overexpression
Large-scale Survey
Disease
Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.
- Summary
- Yeast SCS2 is homologous to human VAPB, and has been used to study mutations found in patients with amyotrophic lateral sclerosis type 8
Manually Curated
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
- Scs2p interacts physically with proteins involved in lipid metabolism; SCS2 interacts genetically with gene involved in mitosis; The scs2 null mutant is viable; the null mutant of paralog scs22 is viable; the scs2 scs22 double mutant has not been annotated for phenotype.
663 total interactions for 382 unique genes
Physical Interactions
- Affinity Capture-MS: 103
- Affinity Capture-RNA: 5
- Affinity Capture-Western: 11
- Co-crystal Structure: 1
- Co-localization: 2
- Co-purification: 2
- PCA: 17
- Protein-peptide: 1
- Proximity Label-MS: 1
- Reconstituted Complex: 6
- Two-hybrid: 2
Genetic Interactions
- Dosage Growth Defect: 1
- Dosage Lethality: 2
- Dosage Rescue: 24
- Negative Genetic: 358
- Phenotypic Enhancement: 5
- Phenotypic Suppression: 13
- Positive Genetic: 57
- Synthetic Growth Defect: 39
- Synthetic Lethality: 6
- Synthetic Rescue: 7
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
- 7
- 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: 2007-06-01
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.