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 |
|---|---|---|---|---|---|---|---|---|
| 2753-YDR064W | YDR064W | RPS13 | uS15|ribosomal 40S subunit protein S13|YS15|S27a|S15|S13|RPS13C|RPS13B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S13 and bacterial S15 | Core | NA | NA | NA |
| 2754-YDR065W | YDR065W | RRG1 | NA | Protein of unknown function; required for vacuolar acidification and mitochondrial genome maintenance; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 2755-YDR066C | YDR066C | RTR2 | putative protein-serine/threonine phosphatase | Protein of unknown function; exhibits genetic interactions with Rtr1p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YDR066C is not an essential gene; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress; RTR2 has a paralog, RTR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2756-YDR067C | YDR067C | OCA6 | protein-tyrosine-phosphatase | Cytoplasmic protein required for replication of Brome mosaic virus; S. cerevisiae is a model system for studying positive-strand RNA virus replication; null mutation confers sensitivity to tunicamycin and DTT | Core | NA | NA | NA |
| 2757-YDR068W | YDR068W | DOS2 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 2758-YDR069C | YDR069C | DOA4 | ubiquitin-specific protease DOA4|UBP4|SSV7|NPI2|MUT4|DOS1 | Ubiquitin hydrolase; deubiquitinates intralumenal vesicle (ILVs) cargo proteins; required for recycling ubiquitin from proteasome-bound ubiquitinated intermediates, acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins destined for the vacuole; DOA4 has a paralog, UBP5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2759-YDR070C | YDR070C | FMP16 | NA | Protein of unknown function; may be involved in responding to conditions of stress; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2760-YDR071C | YDR071C | PAA1 | polyamine acetyltransferase | Polyamine acetyltransferase; acetylates polyamines (e.g. putrescine, spermidine, spermine) and also aralkylamines (e.g. tryptamine, phenylethylamine); may be involved in transcription and/or DNA replication | Core | NA | NA | NA |
| 2761-YDR072C | YDR072C | IPT1 | MIC2|inositolphosphotransferase|KTI6|SYR4 | Inositolphosphotransferase; involved in synthesis of mannose-(inositol-P)2-ceramide (M(IP)2C), the most abundant sphingolipid; can mutate to resistance to the antifungals syringomycin E and DmAMP1 and to K. lactis zymocin | Core | NA | NA | NA |
| 2762-YDR073W | YDR073W | SNF11 | NA | Subunit of the SWI/SNF chromatin remodeling complex; involved in transcriptional regulation; interacts with a highly conserved 40-residue sequence of Snf2p; relocates to the cytosol under hypoxic conditions | Core | NA | NA | NA |
| 2763-YDR074W | YDR074W | TPS2 | trehalose-phosphatase TPS2|PFK3|HOG2 | Phosphatase subunit of the trehalose-6-P synthase/phosphatase complex; involved in synthesis of the storage carbohydrate trehalose; expression is induced by stress conditions and repressed by the Ras-cAMP pathway; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2764-YDR075W | YDR075W | PPH3 | phosphoprotein phosphatase PP4 catalytic subunit PPH3 | Catalytic subunit of protein phosphatase PP4 complex; Pph3p and Psy2p form active complex, Psy4p may provide substrate specificity; regulates recovery from the DNA damage checkpoint, the gene conversion- and single-strand annealing-mediated pathways of meiotic double-strand break repair and efficient Non-Homologous End-Joining (NHEJ) pathway; involved in activation of Gln3p to alleviate nitrogen catabolite repression; Pph3p and Psy2p localize to foci on meiotic chromosomes | Core | NA | NA | NA |
| 2765-YDR076W | YDR076W | RAD55 | putative DNA-dependent ATPase RAD55 | Protein that stimulates strand exchange; stimulates strand exchange by stabilizing the binding of Rad51p to single-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; forms heterodimer with Rad57p | Core | NA | NA | NA |
| 2766-YDR077W | YDR077W | SED1 | NA | Major stress-induced structural GPI-cell wall glycoprotein; associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites; SED1 has a paralog, SPI1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2767-YDR078C | YDR078C | SHU2 | NA | Component of Shu complex (aka PCSS complex); Shu complex also includes Psy3, Csm2, Shu1, and promotes error-free DNA repair, Shu complex mediates inhibition of Srs2p function; promotes formation of Rad51p filaments; important for both mitotic and meiotic homologous recombination, and contains a conserved SWIM domain that is necessary for both | Core | NA | NA | NA |