Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 2108-YBR125C | YBR125C | PTC4 | type 2C protein phosphatase PTC4|GCT1 | Cytoplasmic type 2C protein phosphatase (PP2C); identified as a high-copy number suppressor of cnb1 mpk1 synthetic lethality; overexpression decreases high-osmolarity induced Hog1p phosphorylation and kinase activity | Core | NA | NA | NA |
| 2109-YBR126C | YBR126C | TPS1 | alpha,alpha-trehalose-phosphate synthase (UDP-forming) TPS1|TSS1|GLC6|GGS1|FDP1|CIF1|BYP1 | Synthase subunit of trehalose-6-P synthase/phosphatase complex; synthesizes the storage carbohydrate trehalose, which is critically important for survival of long-term desiccation; also found in a monomeric form; expression is induced by the stress response and repressed by the Ras-cAMP pathway; protein abundance increases in response to DNA replication stress and in response to prolonged exposure to boric acid | Core | NA | NA | NA |
| 2110-YBR126W-A_NumOfGenes_2 | YBR126W-A | MEO1 | NA | Putative protein of unknown function; identified by gene-trapping, microarray analysis, and genome-wide homology searches; mRNA identified as translated by ribosome profiling data; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; partially overlaps the dubious ORF YBR126W-B | Core | NA | NA | NA |
| 2111-YBR127C | YBR127C | VMA2 | H(+)-transporting V1 sector ATPase subunit B|ATPSV|VAT2 | Subunit B of V1 peripheral membrane domain of vacuolar H+-ATPase; electrogenic proton pump found throughout the endomembrane system; contains nucleotide binding sites; also detected in the cytoplasm; protein abundance increases in response to DNA replication stress; human homolog ATP6V1B1, implicated in autosomal-recessive distal renal tubular acidosis (RTA) with sensorineural deafness, complements yeast null mutant | Core | NA | NA | NA |
| 2112-YBR128C | YBR128C | ATG14 | APG14|CVT12 | Autophagy-specific subunit of phosphatidylinositol 3-kinase complex I; Atg14p targets complex I to the phagophore assembly site (PAS); required for localizing additional ATG proteins to the PAS; required for overflow degradation of misfolded proteins when ERAD is saturated; homolog of human Barkor; other members are Vps34, Vps15, and Vps30p | Core | NA | NA | NA |
| 2113-YBR129C | YBR129C | OPY1 | NA | Protein of unknown function; overproduction blocks cell cycle arrest in the presence of mating pheromone; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 2114-YBR130C | YBR130C | SHE3 | NA | Protein adaptor between Myo4p and the She2p-mRNA complex; part of the mRNA localization machinery that restricts accumulation of certain proteins to the bud; also required for cortical ER inheritance | Core | NA | NA | NA |
| 2115-YBR131W_NumOfGenes_2 | YBR131W | CCZ1 | CVT16 | Subunit of a heterodimeric guanine nucleotide exchange factor (GEF); subunit of the Mon1-Ccz1 GEF complex, which stimulates nucleotide exchange and activation of Ypt7p, a Rab family GTPase involved in membrane tethering and fusion events at the late endosome and vacuole; GEF activity is stimulated by membrane association and anionic phospholipids; involved in localizing Ypt7p to the vacuolar membrane; required for macroautophagy, the CVT pathway and mitophagy | Core | NA | NA | NA |
| 2116-YBR132C | YBR132C | AGP2 | NA | Plasma membrane regulator of polyamine and carnitine transport; has similarity to transporters but lacks transport activity; may act as a sensor that transduces environmental signals; has a positive or negative regulatory effect on transcription of many transporter genes | Core | NA | NA | NA |
| 2117-YBR133C | YBR133C | HSL7 | protein arginine N-methyltransferase | Protein arginine N-methyltransferase; exhibits septin and Hsl1p-dependent localization to the bud neck in budded cells and periodic Hsl1p-dependent phosphorylation; required with Hsl1p, and Elm1p for the mother-bud neck recruitment, phosphorylation, and degradation of Swe1p; interacts directly with Swe1p; relocalizes away from bud neck upon DNA replication stress; human homolog PRMT5 can complement yeast hsl7 mutant | Core | NA | NA | NA |
| 2118-YBR134W | YBR134W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 2119-YBR135W | YBR135W | CKS1 | cyclin-dependent protein kinase regulatory subunit CKS1 | Cyclin-dependent protein kinase regulatory subunit and adaptor; interacts with Cdc28p (aka Cdk1p); required for G1/S and G2/M phase transitions and budding; mediates phosphorylation and degradation of Sic1p; modulates proteolysis of M-phase targets through interactions with the proteasome; role in transcriptional regulation, recruiting proteasomal subunits to target gene promoters; human homologs CKS1B and CKS2 can each complement yeast cks1 null mutant | Core | NA | NA | NA |
| 2120-YBR136W | YBR136W | MEC1 | protein kinase MEC1|RAD31|SAD3|ESR1 | Genome integrity checkpoint protein and PI kinase superfamily member; Mec1p and Dun1p function in same pathway to regulate dNTP pools and telomere length; signal transducer required for cell cycle arrest and transcriptional responses to damaged or unreplicated DNA; facilitates replication fork progression and regulates P-body formation under replication stress; promotes interhomolog recombination by phosphorylating Hop1p; associates with shortened, dysfunctional telomeres | Core | NA | NA | NA |
| 2121-YBR137W | YBR137W | NA | NA | Protein with a role in ER delivery of tail-anchored membrane proteins; interacts with Sgt2p; binds to the TRC complex, which inserts proteins into the ER membrane; interacts with Msn5p karyopherin; YBR137W is not an essential gene | Core | NA | NA | NA |
| 2122-YBR138C | YBR138C | NA | HDR1 | Cytoplasmic protein of unknown function; APCC(Cdh1) substrate; potentially phosphorylated by Cdc28p; YBR138C is not an essential gene | Core | NA | NA | NA |