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 |
|---|---|---|---|---|---|---|---|---|
| 6833-YOL034W | YOL034W | SMC5 | DNA repair ATPase SMC5 | Subunit of the SMC5-SMC6 complex; the SMC5-SMC6 complex plays a key role in the removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair; binds single-stranded DNA and has ATPase activity; supports nucleolar function; S. pombe homolog forms a heterodimer with S. pombe Rad18p that is involved in DNA repair | Core | NA | NA | NA |
| 6834-YOL036W_NumOfGenes_3 | YOL036W | NA | NA | Protein of unknown function; potential Cdc28p substrate; YOL036W has a paralog, YIR016W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6835-YOL038C-A | YOL038C-A | NA | NA | Putative protein of unknown function; identified by SAGE analysis | Accessory | Unknown | NA | NA |
| 6836-YOL038W | YOL038W | PRE6 | proteasome core particle subunit alpha 4 | Alpha 4 subunit of the 20S proteasome; may replace alpha 3 subunit (Pre9p) under stress conditions to create a more active proteasomal isoform; GFP-fusion protein relocates from cytosol to the mitochondrial surface upon oxidative stress | Core | NA | NA | NA |
| 6837-YOL039W | YOL039W | RPP2A | P2A|ribosomal protein P2A|RPLA2|RPL44 | Ribosomal protein P2 alpha; a component of the ribosomal stalk, which is involved in the interaction between translational elongation factors and the ribosome; free (non-ribosomal) P2 stimulates the phosphorylation of the eIF2 alpha subunit (Sui2p) by Gcn2p; regulates the accumulation of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm | Core | NA | NA | NA |
| 6838-YOL040C | YOL040C | RPS15 | uS19|ribosomal 40S subunit protein S15|S19|rp52|S21|S15|RPS21 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S15 and bacterial S19 | Core | NA | NA | NA |
| 6839-YOL041C | YOL041C | NOP12 | NA | Nucleolar protein involved in pre-25S rRNA processing; also involved in biogenesis of large 60S ribosomal subunit; contains an RNA recognition motif (RRM); binds to Ebp2; similar to Nop13p and Nsr1p | Core | NA | NA | NA |
| 6840-YOL042W | YOL042W | NGL1 | RNA exonuclease | Putative endonuclease; has a domain similar to a magnesium-dependent endonuclease motif in mRNA deadenylase Ccr4p; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6841-YOL043C | YOL043C | NTG2 | bifunctional N-glycosylase/AP lyase NTG2|SCR2 | DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase; involved in base excision repair, localizes to the nucleus; sumoylated; NTG2 has a paralog, NTG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6842-YOL044W | YOL044W | PEX15 | PAS21 | Tail-anchored type II integral peroxisomal membrane protein; required for peroxisome biogenesis; cells lacking Pex15p mislocalize peroxisomal matrix proteins to cytosol; overexpression results in impaired peroxisome assembly | Core | NA | NA | NA |
| 6843-YOL045W_NumOfGenes_2 | YOL045W | PSK2 | serine/threonine protein kinase PSK2 | PAS-domain containing serine/threonine protein kinase; regulates sugar flux and translation in response to an unknown metabolite by phosphorylating Ugp1p and Gsy2p (sugar flux) and Caf20p, Tif11p and Sro9p (translation); PSK2 has a paralog, PSK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6844-YOL047C | YOL047C | LDS2 | NA | Protein Involved in spore wall assembly; localizes to lipid droplets found on or outside of the prospore membrane; shares similarity with Lds1p and Rrt8p, and a strain mutant for all 3 genes exhibits reduced dityrosine fluorescence relative to the single mutants; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 6845-YOL048C | YOL048C | RRT8 | NA | Protein involved in spore wall assembly; shares similarity with Lds1p and Lds2p and a strain mutant for all 3 genes exhibits reduced dityrosine fluorescence relative to the single mutants; identified in a screen for mutants with increased levels of rDNA transcription; green fluorescent protein (GFP)-fusion protein localizes to lipid particles; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6846-YOL049W | YOL049W | GSH2 | glutathione synthase | Glutathione synthetase; catalyzes the ATP-dependent synthesis of glutathione (GSH) from gamma-glutamylcysteine and glycine; induced by oxidative stress and heat shock | Core | NA | NA | NA |
| 6847-YOL051W_NumOfGenes_2 | YOL051W | GAL11 | MED15|ABE1|SPT13|SDS4|RAR3 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; affects transcription by acting as target of activators and repressors; forms part of the tail domain of mediator | Core | NA | NA | NA |