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 |
|---|---|---|---|---|---|---|---|---|
| 6203-YMR141C | YMR141C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR141C is not an essential gene | Core | NA | NA | NA |
| 6204-YMR142C_NumOfGenes_2 | YMR142C | RPL13B | eL13|ribosomal 60S subunit protein L13B|L13e|L13B | Ribosomal 60S subunit protein L13B; not essential for viability; homologous to mammalian ribosomal protein L13, no bacterial homolog; RPL13B has a paralog, RPL13A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6205-YMR143W | YMR143W | RPS16A | uS9|ribosomal 40S subunit protein S16A|S9|rp61R|S16A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S16 and bacterial S9; RPS16A has a paralog, RPS16B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6206-YMR144W | YMR144W | FDO1 | NA | Protein involved in directionality of mating type switching; acts with Fkh1p to control which donor mating-type locus is inserted into MAT locus during mating type switching; localized to the nucleus; not an essential gene | Core | NA | NA | NA |
| 6207-YMR145C | YMR145C | NDE1 | NADH-ubiquinone reductase (H(+)-translocating) NDE1|NDH1 | Mitochondrial external NADH dehydrogenase; type II NAD(P)H:quinone oxidoreductase that catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p provide cytosolic NADH to the mitochondrial respiratory chain; NDE1 has a paralog, NDE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6208-YMR146C | YMR146C | TIF34 | translation initiation factor eIF3 subunit i | eIF3i subunit of the eukaryotic translation initiation factor 3 (eIF3); subunit of the core complex of eIF3; essential for translation; stimulates rate of ribosomal scanning during translation reinitiation; eIF3 is also involved in programmed stop codon readthrough | Core | NA | NA | NA |
| 6209-YMR147W | YMR147W | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the cell periphery | Core | NA | NA | NA |
| 6210-YMR148W | YMR148W | OSW5 | NA | Protein of unknown function with possible role in spore wall assembly; predicted to contain an N-terminal transmembrane domain; osw5 null mutant spores exhibit increased spore wall permeability and sensitivity to beta-glucanase digestion | Core | NA | NA | NA |
| 6211-YMR149W | YMR149W | SWP1 | dolichyl-diphosphooligosaccharide-protein glycotransferase | Delta subunit of the oligosaccharyl transferase glycoprotein complex; complex is required for N-linked glycosylation of proteins in the endoplasmic reticulum | Core | NA | NA | NA |
| 6212-YMR150C | YMR150C | IMP1 | endopeptidase catalytic subunit IMP1|PET-TS2858 | Catalytic subunit of mitochondrial inner membrane peptidase complex; required for maturation of mitochondrial proteins of the intermembrane space; complex contains two catalytic subunits (Imp1p and Imp2p that differ in substrate specificty) and Som1p | Core | NA | NA | NA |
| 6213-YMR151W | YMR151W | YIM2 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; 5% of ORF overlaps the verified gene IMP1 | Core | NA | NA | NA |
| 6214-YMR152W | YMR152W | YIM1 | NA | Protein of unknown function; null mutant displays sensitivity to DNA damaging agents; may have a role in lipid metabolism, based on localization to lipid droplets; 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 |
| 6215-YMR153W_NumOfGenes_2 | YMR153W | NUP53 | FG-nucleoporin NUP53 | FG-nucleoporin component of central core of nuclear pore complex (NPC); also part of the NPC nuclear basket; contributes directly to nucleocytoplasmic transport; involved in regulation of transcription and mitosis; induces membrane tubulation, which may contribute to nuclear pore assembly; NUP53 has a paralog, ASM4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6216-YMR154C | YMR154C | RIM13 | CPL1 | Calpain-like cysteine protease; involved in proteolytic activation of Rim101p in response to alkaline pH; localizes to punctate structures in alkaline conditions and in vps4 mutant; has similarity to A. nidulans palB | Core | NA | NA | NA |
| 6217-YMR155W | YMR155W | NA | NA | Putative protein of unknown function; identified as interacting with Hsp82p in a high-throughput two-hybrid screen | Core | NA | NA | NA |