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 |
|---|---|---|---|---|---|---|---|---|
| 4043-YGR144W | YGR144W | THI4 | thiamine thiazole synthase|MOL1|ESP35 | Thiazole synthase; abundant protein involved in the formation of the thiazole moiety of thiamine during thiamine biosynthesis; acts more as a co-substrate rather than an enzyme by providing the sulphur source for thiazole formation; undergoes a single turnover only; required for mitochondrial genome stability in response to DNA damaging agents | Core | NA | NA | NA |
| 4044-YGR145W | YGR145W | ENP2 | ribosome biosynthesis protein ENP2 | Component of the SSU; required for pre-18S rRNA processing, biogenesis of the small ribosomal subunit; interacts with U3 snoRNA, Mpp10p and Bfr2p; contains WD repeats, and has homology to Spb1p | Core | NA | NA | NA |
| 4045-YGR146C | YGR146C | ECL1 | NA | Protein of unknown function; mitochondrial-dependent role in the extension of chronological lifespan; overexpression increases oxygen consumption and respiratory activity while deletion results in reduced oxygen consumption under conditions of caloric restriction; induced by iron homeostasis transcription factor Aft2p; multicopy suppressor of temperature sensitive hsf1 mutant; induced by treatment with 8-methoxypsoralen and UVA irradiation | Core | NA | NA | NA |
| 4046-YGR146C-A | YGR146C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 4047-YGR147C | YGR147C | NAT2 | NA | Protein of unknown function; has an apparent role in acetylation of N-terminal methionine residues | Core | NA | NA | NA |
| 4048-YGR148C | YGR148C | RPL24B | eL24|ribosomal 60S subunit protein L24B|L24e|rp29|YL21|L30B|L24B|RPL30B | Ribosomal 60S subunit protein L24B; not essential for translation but may be required for normal translation rate; homologous to mammalian ribosomal protein L24, no bacterial homolog; RPL24B has a paralog, RPL24A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4049-YGR149W | YGR149W | GPC1 | NA | Glycerophosphocholine acyltransferase (GPCAT); involved in in phosphatidylcholine (PC) synthesis; uses acetyl-CoA to acylate glycero-3-phosphocholine to yield lyso-PC; also catalyzes acylation of glycerophosphoethanolamine with acyl-CoA; predicted to be an integal membrane protein | Core | NA | NA | NA |
| 4050-YGR150C | YGR150C | CCM1 | DMR1|RRG2 | Mitochondrial 15S rRNA-binding protein; required for intron removal of COB and COX1 pre-mRNAs; has separable roles in stabilizing mitochondrial 15S rRNA and in maturation of the COB and COX1 mRNAs; contains pentatricopeptide repeat (PPR) motifs; mutant is respiratory deficient and has defective plasma membrane electron transport | Core | NA | NA | NA |
| 4051-YGR152C_NumOfGenes_2 | YGR152C | RSR1 | Ras family GTPase RSR1|BUD1 | GTP-binding protein of the Ras superfamily; required for bud site selection, morphological changes in response to mating pheromone, and efficient cell fusion; localized to the plasma membrane; significantly similar to mammalian Rap GTPases | Core | NA | NA | NA |
| 4052-YGR153W | YGR153W | NA | TOS10 | Putative protein of unknown function | Core | NA | NA | NA |
| 4053-YGR154C | YGR154C | GTO1 | omega-class glutathione transferase | Omega-class glutathione transferase; induced under oxidative stress; putative peroxisomal localization | Core | NA | NA | NA |
| 4054-YGR155W | YGR155W | CYS4 | cystathionine beta-synthase CYS4|VMA41|STR4|NHS5 | Cystathionine beta-synthase; catalyzes synthesis of cystathionine from serine and homocysteine, the first committed step in cysteine biosynthesis; responsible for hydrogen sulfide generation; advances passage through START by promoting cell growth which requires catalytic activity, and reducing critical cell size independent of catalytic activity; mutations in human ortholog CBS cause homocystinuria; human CBS can complement yeast null mutant | Core | NA | NA | NA |
| 4055-YGR156W | YGR156W | PTI1 | cleavage polyadenylation factor subunit PTI1 | Essential component of CPF (cleavage and polyadenylation factor); involved in 3' end formation of snoRNA and mRNA; interacts directly with Pta1p; relocalizes to the cytosol in response to hypoxia; similar to mammalian Cleavage-Stimulation Factor CstF-64 | Core | NA | NA | NA |
| 4056-YGR157W | YGR157W | CHO2 | phosphatidylethanolamine N-methyltransferase|PEM1 | Phosphatidylethanolamine methyltransferase (PEMT); catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis | Core | NA | NA | NA |
| 4057-YGR158C | YGR158C | MTR3 | exosome non-catalytic core subunit MTR3 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hMtr3p (EXOSC6) | Core | NA | NA | NA |