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 |
|---|---|---|---|---|---|---|---|---|
| 4493-YIL012W | YIL012W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4494-YIL013C | YIL013C | PDR11 | ATP-binding cassette multidrug transporter PDR11 | ATP-binding cassette (ABC) transporter; multidrug transporter involved in multiple drug resistance; mediates sterol uptake when sterol biosynthesis is compromised; regulated by Pdr1p; required for anaerobic growth; PDR11 has a paralog, AUS1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4495-YIL014C-A | YIL014C-A | NA | YIL015C-A | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 4496-YIL014W | YIL014W | MNT3 | alpha-1,3-mannosyltransferase MNT3 | Alpha-1,3-mannosyltransferase; adds the fourth and fifth alpha-1,3-linked mannose residues to O-linked glycans during protein O-glycosylation | Accessory | Ancestral | NA | NA |
| 4497-YIL015W | YIL015W | BAR1 | aspartyl protease BAR1|SST1 | Aspartyl protease; secreted into the periplasmic space of mating type a cell; helps cells find mating partners; cleaves and inactivates alpha factor allowing cells to recover from alpha-factor-induced cell cycle arrest | Core | NA | NA | NA |
| 4498-YIL016W | YIL016W | SNL1 | NA | Ribosome-associated protein; proposed to act in protein synthesis and nuclear pore complex biogenesis and maintenance as well as protein folding; has similarity to the mammalian BAG-1 protein | Core | NA | NA | NA |
| 4499-YIL017C | YIL017C | VID28 | glucose-induced degradation complex subunit VID28|YIL017W|GID5 | GID Complex subunit, serves as adaptor for regulatory subunit Vid24p; protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); localized to the nucleus and the cytoplasm | Core | NA | NA | NA |
| 4500-YIL018W_NumOfGenes_2 | YIL018W | RPL2B | uL2|ribosomal 60S subunit protein L2B|L2|rp8|YL6|L5B|L2B|LOT2|RPL5A | Ribosomal 60S subunit protein L2B; homologous to mammalian ribosomal protein L2 and bacterial L2; RPL2B has a paralog, RPL2A, that arose from the whole genome duplication; expression is upregulated at low temperatures | Core | NA | NA | NA |
| 4501-YIL019W | YIL019W | FAF1 | NA | Protein required for pre-rRNA processing; also required for 40S ribosomal subunit assembly | Core | NA | NA | NA |
| 4502-YIL020C | YIL020C | HIS6 | 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase HIS6 | Enzyme that catalyzes the fourth step in the histidine pathway; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; mutations cause histidine auxotrophy and sensitivity to Cu, Co, and Ni salts | Core | NA | NA | NA |
| 4503-YIL020C-A | YIL020C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps origin of replication ARS918, partially overlaps ORF RPB3/YIL021W | Accessory | Ancestral | NA | NA |
| 4504-YIL021W_NumOfGenes_2 | YIL021W | RPB3 | DNA-directed RNA polymerase II core subunit RPB3|B44 | RNA polymerase II third largest subunit B44; part of central core; similar to prokaryotic alpha subunit | Core | NA | NA | NA |
| 4505-YIL022W | YIL022W | TIM44 | protein translocase subunit TIM44|MPI1|MIM44|ISP45 | Essential component of the TIM23 complex; tethers the import motor and regulatory factors (PAM complex) to the translocation channel (Tim23p-Tim17p core complex); TIM23 complex is short for the translocase of the inner mitochondrial membrane | Core | NA | NA | NA |
| 4506-YIL023C | YIL023C | YKE4 | Zn(2+) transporter YKE4 | Zinc transporter; localizes to the ER; null mutant is sensitive to calcofluor white, leads to zinc accumulation in cytosol; ortholog of the mouse KE4 and member of the ZIP (ZRT, IRT-like Protein) family | Core | NA | NA | NA |
| 4507-YIL024C | YIL024C | NA | NA | Putative protein of unknown function; non-essential gene; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p | Core | NA | NA | NA |