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 |
|---|---|---|---|---|---|---|---|---|
| 6473-YNL080C | YNL080C | EOS1 | NA | Protein involved in N-glycosylation; deletion mutation confers sensitivity to exidative stress and shows synthetic lethality with mutations in the spindle checkpoint genes BUB3 and MAD1; YNL080C is not an essential gene | Core | NA | NA | NA |
| 6474-YNL081C | YNL081C | SWS2 | putative mitochondrial 37S ribosomal protein SWS2 | Putative mitochondrial ribosomal protein of the small subunit; has similarity to E. coli S13 ribosomal protein; participates in controlling sporulation efficiency; localizes to vacuole in response to H2O2 | Core | NA | NA | NA |
| 6475-YNL082W | YNL082W | PMS1 | ATP-binding mismatch repair protein | ATP-binding protein required for mismatch repair; required for both mitosis and meiosis; functions as a heterodimer with Mlh1p; binds double- and single-stranded DNA via its N-terminal domain, similar to E. coli MutL | Core | NA | NA | NA |
| 6476-YNL083W | YNL083W | SAL1 | Ca(2+)-binding ATP:ADP antiporter SAL1 | ADP/ATP transporter; member of the Ca2+-binding subfamily of mitochondrial carriers, with two EF-hand motifs; transport activity of either Sal1p or Pet9p is critical for viability; polymorphic in different S. cerevisiae strains | Core | NA | NA | NA |
| 6477-YNL084C | YNL084C | END3 | NA | EH domain-containing protein involved in endocytosis; actin cytoskeletal organization and cell wall morphogenesis; forms a complex with Sla1p and Pan1p | Core | NA | NA | NA |
| 6478-YNL085W | YNL085W | MKT1 | NA | Protein similar to nucleases that forms a complex with Pbp1p; complex may mediate posttranscriptional regulation of HO; involved in propagation of M2 dsRNA satellite of L-A virus; allelic variation affects mitochondrial genome stability, drug resistance, and more; forms cytoplasmic foci upon DNA replication stress; localization to P-bodies under ethanol stress differs between strains | Core | NA | NA | NA |
| 6479-YNL086W | YNL086W | SNN1 | BLS1 | Subunit of the BLOC-1 complex involved in endosomal maturation; interacts with Msb3p; green fluorescent protein (GFP)-fusion protein localizes to endosomes | Core | NA | NA | NA |
| 6480-YNL087W | YNL087W | TCB2 | tricalbin | ER protein involved in ER-plasma membrane tethering; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to plasma membrane (PM) and regulate PM phosphatidylinositol-4-phosphate (PI4P) levels by controlling access of Sac1p phosphatase to its substrate PI4P in the PM; contains 3 calcium and lipid binding domains; mRNA is targeted to bud; TCB2 has a paralog, TCB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6481-YNL088W | YNL088W | TOP2 | DNA topoisomerase 2|TRF3|TOR3 | Topoisomerase II; relieves torsional strain in DNA by cleaving and re-sealing phosphodiester backbone of both positively and negatively supercoiled DNA; cleaves complementary strands; localizes to axial cores in meiosis; required for replication slow zone (RSZ) breakage following Mec1p inactivation; human homolog TOP2A implicated in cancers, and can complement yeast null mutant | Core | NA | NA | NA |
| 6482-YNL090W_NumOfGenes_2 | YNL090W | RHO2 | Rho family GTPase RHO2 | Non-essential small GTPase of the Rho/Rac family of Ras-like proteins; involved in the establishment of cell polarity and in microtubule assembly | Core | NA | NA | NA |
| 6483-YNL091W | YNL091W | NST1 | NA | Protein of unknown function; mediates sensitivity to salt stress; interacts physically with the splicing factor Msl1p and also displays genetic interaction with MSL1 | Core | NA | NA | NA |
| 6484-YNL092W | YNL092W | NA | S-adenosylmethionine-dependent methyltransferase | S-adenosylmethionine-dependent protein methyltransferase; capable of automethylation; member of the seven beta-strand family; YNL092W is not an essential gene | Core | NA | NA | NA |
| 6485-YNL093W | YNL093W | YPT53 | Rab family GTPase YPT53 | Stress-induced Rab family GTPase; required for vacuolar protein sorting and endocytosis; involved in ionic stress tolerance; similar to Vps21p and Ypt52p; functional homolog of Vps21p; mammalian Rab5 homolog; YPT53 has a paralog, VPS21, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6486-YNL094W | YNL094W | APP1 | phosphatidate phosphatase APP1 | Phosphatidate phosphatase, converts phosphatidate to diacylglycerol; App1p, Pah1p, Dpp1p, and Lpp1p are responsible for all the phosphatidate phosphatase activity; component of cortical actin patches; interacts with components of endocytic pathway | Core | NA | NA | NA |
| 6487-YNL095C | YNL095C | NA | NA | Putative protein of unknown function; predicted to contain a transmembrane domain; not an essential gene; YNL095C has a paralog, ECM3, that arose from the whole genome duplication | Core | NA | NA | NA |