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 |
|---|---|---|---|---|---|---|---|---|
| 2348-YCL064C | YCL064C | CHA1 | L-serine/L-threonine ammonia-lyase CHA1 | Catabolic L-serine (L-threonine) deaminase; catalyzes the degradation of both L-serine and L-threonine; required to use serine or threonine as the sole nitrogen source, transcriptionally induced by serine and threonine | Core | NA | NA | NA |
| 2349-YCL067C_NumOfGenes_3 | YCL067C | HMLALPHA2 | homeodomain mating type protein alpha2|ALPHA2 | Silenced copy of ALPHA2 at HML; homeobox-domain protein that associates with Mcm1p in haploid cells to repress a-specific gene expression and interacts with a1p in diploid cells to repress haploid-specific gene expression | Core | NA | NA | NA |
| 2350-YCR001W | YCR001W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YCR001W is not an essential gene | Accessory | Unknown | NA | NA |
| 2351-YCR002C | YCR002C | CDC10 | septin CDC10 | Component of the septin ring, required for cytokinesis; septins are GTP-binding proteins that assemble into rod-like hetero-oligomers that can associate to form filaments; septin rings at the mother-bud neck act as scaffolds for recruiting cell division factors and as barriers to prevent diffusion of specific proteins between mother and daughter cells; N-terminus interacts with phosphatidylinositol-4,5-bisphosphate; protein abundance increases under DNA damage stress | Accessory | Ancestral | NA | NA |
| 2352-YCR003W | YCR003W | MRPL32 | mitochondrial 54S ribosomal protein YmL32|YmL32 | Mitochondrial ribosomal protein of the large subunit; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 2353-YCR004C | YCR004C | YCP4 | flavodoxin-like fold family protein | Protein of unknown function; has sequence and structural similarity to flavodoxins; predicted to be palmitoylated; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 2354-YCR005C | YCR005C | CIT2 | citrate (Si)-synthase CIT2 | Citrate synthase, peroxisomal isozyme involved in glyoxylate cycle; catalyzes condensation of acetyl coenzyme A and oxaloacetate to form citrate; expression is controlled by Rtg1p and Rtg2p transcription factors; SCF-Ucc1 regulates level of Cit2p to maintain citrate homeostasis; oxaloacetate-dependent positive feedback loop inhibits Cit2p ubiquitination; CIT2 has a paralog, CIT1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2355-YCR006C | YCR006C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YCR006C is not an essential gene | Accessory | Ancestral | NA | NA |
| 2356-YCR007C | YCR007C | NA | DUP240 family protein | Putative integral membrane protein; member of DUP240 gene family; SWAT-GFP and mCherry fusion proteins localize to the cell periphery and vacuole; YCR007C is not an essential gene | Core | NA | NA | NA |
| 2357-YCR008W | YCR008W | SAT4 | serine/threonine protein kinase SAT4|HAL4 | Ser/Thr protein kinase involved in salt tolerance; funtions in regulation of Trk1p-Trk2p potassium transporter; overexpression affects the Fe-S and lipoamide containing proteins in the mitochondrion; required for lipoylation of Lat1p, Kgd2p and Gcv3p; partially redundant with Hal5p; has similarity to Npr1p; localizes to the cytoplasm and mitochondrion | Accessory | Ancestral | NA | NA |
| 2358-YCR009C | YCR009C | RVS161 | amphiphysin-like protein RVS161|SPE161|FUS7|END6 | Amphiphysin-like lipid raft protein; N-BAR domain protein that interacts with Rvs167p and regulates polarization of the actin cytoskeleton, endocytosis, cell polarity, cell fusion and viability following starvation or osmotic stress | Accessory | Ancestral | NA | NA |
| 2359-YCR010C | YCR010C | ADY2 | ATO1 | Acetate transporter required for normal sporulation; phosphorylated in mitochondria; ADY2 has a paralog, ATO2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2360-YCR011C | YCR011C | ADP1 | putative ATP-dependent permease ADP1 | Putative ATP-dependent permease of the ABC transporter family | Core | NA | NA | NA |
| 2361-YCR012W_NumOfGenes_2 | YCR012W | PGK1 | phosphoglycerate kinase | 3-phosphoglycerate kinase; catalyzes transfer of high-energy phosphoryl groups from the acyl phosphate of 1,3-bisphosphoglycerate to ADP to produce ATP; key enzyme in glycolysis and gluconeogenesis | Core | NA | NA | NA |
| 2362-YCR014C | YCR014C | POL4 | DNA-directed DNA polymerase IV|POLX | DNA polymerase IV; undergoes pair-wise interactions with Dnl4p-Lif1p and Rad27p to mediate repair of DNA double-strand breaks by non-homologous end joining (NHEJ); homologous to mammalian DNA polymerase beta | Core | NA | NA | NA |