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 |
|---|---|---|---|---|---|---|---|---|
| 2678-YDL234C_NumOfGenes_2 | YDL234C | GYP7 | NA | GTPase-activating protein for yeast Rab family members; members include Ypt7p (most effective), Ypt1p, Ypt31p, and Ypt32p (in vitro); involved in vesicle mediated protein trafficking; contains a PH-like domain | Core | NA | NA | NA |
| 2679-YDL235C | YDL235C | YPD1 | NA | Osmotic stress-responsive phosphorelay intermediate sensor protein; phosphorylated by the plasma membrane sensor Sln1p in response to osmotic stress and then in turn phosphorylates the response regulators Ssk1p in the cytosol and Skn7p in the nucleus | Accessory | Ancestral | NA | NA |
| 2680-YDL236W | YDL236W | PHO13 | 4-nitrophenylphosphatase | Conserved phosphatase acting as a metabolite repair enzyme; shows specific dephosphorylating activity on two side-products of central carbohydrate metabolism, 2-phosphoglycolate and 4-phosphoerythronate; alkaline phosphatase specific for p-nitrophenyl phosphate; also has protein phosphatase activity; human ortholog PGP shows similar substrate specificity, deletion causes similar metabolite accumulation phenotypes, suggesting conserved role in eliminating glycolytic byproducts | Accessory | Ancestral | NA | NA |
| 2681-YDL237W | YDL237W | AIM6 | LRC1 | Protein of unknown function; required for respiratory growth; YDL237W is not an essential gene | Accessory | Ancestral | NA | NA |
| 2682-YDL238C | YDL238C | GUD1 | guanine deaminase | Guanine deaminase; a catabolic enzyme of the guanine salvage pathway producing xanthine and ammonia from guanine; activity is low in exponentially-growing cultures but expression is increased in post-diauxic and stationary-phase cultures | Accessory | Ancestral | NA | NA |
| 2683-YDL239C | YDL239C | ADY3 | NA | Protein required for spore wall formation; subunit of the leading edge protein (LEP) complex (Ssp1-Ady3-Don1-Irc10) that forms a ring-like structure at the leading edge of the prospore membrane during meiosis II; mediates assembly of the LEP complex, formation of the ring-like structure via interaction with spindle pole body components and prospore membrane maturation; potentially phosphorylated by Cdc28p; ADY3 has a paralog, CNM67, that arose from the whole | Accessory | Ancestral | NA | NA |
| 2684-YDL240C-A | YDL240C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; identified by sequence comparison with hemiascomycetous yeast species | Core | NA | NA | NA |
| 2685-YDL240W | YDL240W | LRG1 | NA | GTPase-activating protein (GAP); contains Rho1p-specific GAP activity, interacting with activated forms of Rho1p; functions along with Sac7p as a negative regulator of the Pkc1p-mediated cell wall integrity signaling pathway; negative regulator of cell wall 1,3-beta-glucan biosynthesis; required for efficient cell fusion; contains a RhoGAP domain and three Lin-11-Isl1-Mec-3 (LIM) domains | Accessory | Ancestral | NA | NA |
| 2686-YDL241W | YDL241W | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; YDL241W is not an essential gene | Accessory | Unknown | NA | NA |
| 2687-YDL242W_NumOfGenes_2 | YDL242W | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains | Accessory | Unknown | NA | NA |
| 2688-YDL243C | YDL243C | AAD4 | putative aryl-alcohol dehydrogenase | Putative aryl-alcohol dehydrogenase; involved in oxidative stress response; similar to P. chrysosporium aryl-alcohol dehydrogenase; expression induced in cells treated with the mycotoxin patulin; members of the AAD gene family comprise three pairs (AAD3 + AAD15, AAD6/AAD16 + AAD4, AAD10 + AAD14) whose two genes are more related to one another than to other members of the family | Accessory | Ancestral | NA | NA |
| 2689-YDL247W_NumOfGenes_2 | YDL247W | MPH2 | alpha-glucoside permease | Alpha-glucoside permease; transports maltose, maltotriose, alpha-methylglucoside, and turanose; almost identical to Mph3p; encoded in a subtelomeric position in a region likely to have undergone duplication | Accessory | Ancestral | NA | NA |
| 2690-YDL247W-A | YDL247W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; identified by sequence comparison with hemiascomycetous yeast species | Accessory | Ancestral | NA | NA |
| 2691-YDR001C | YDR001C | NTH1 | alpha,alpha-trehalase NTH1 | Neutral trehalase, degrades trehalose; required for thermotolerance and may mediate resistance to other cellular stresses; phosphorylated and activated by Cdc28p at the G1/S phase transition to coordinately regulate carbohydrate metabolism and the cell cycle; inhibited by Dcs1p; NTH1 has a paralog, NTH2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2692-YDR002W | YDR002W | YRB1 | Ran GTPase-binding protein YRB1|STP52|SFO1|HTN1|CST20 | Ran GTPase binding protein; involved in nuclear protein import and RNA export, ubiquitin-mediated protein degradation during the cell cycle; shuttles between the nucleus and cytoplasm; is essential; homolog of human RanBP1 | Core | NA | NA | NA |