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 |
|---|---|---|---|---|---|---|---|---|
| 4688-YIR030W-A | YIR030W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF DAL7/YIR031C | Accessory | Ancestral | NA | NA |
| 4689-YIR031C | YIR031C | DAL7 | malate synthase DAL7|MSL2|MLS2 | Malate synthase; can accept butyryl-CoA as acyl-CoA donor in addition to traditional substrate acetyl-CoA; recycles glyoxylate generated during allantoin degradation; SWAT-GFP and mCherry fusion proteins localize to the cytosol; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation | Core | NA | NA | NA |
| 4690-YIR032C | YIR032C | DAL3 | ureidoglycolate hydrolase | Ureidoglycolate lyase; converts ureidoglycolate to glyoxylate and urea in the third step of allantoin degradation; expression is sensitive to nitrogen catabolite repression; this enzyme is sometimes referred to "ureidoglycolate hydrolase" but should not be confused with the Arabidopsis thaliana ureidoglycolate hydrolase enzyme which converts ureidoglycolate to glyoxylate, ammonia and carbon dioxide | Core | NA | NA | NA |
| 4691-YIR033W | YIR033W | MGA2 | NA | ER membrane protein involved in regulation of OLE1 transcription; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting; MGA2 has a paralog, SPT23, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4692-YIR034C | YIR034C | LYS1 | saccharopine dehydrogenase (NAD+, L-lysine-forming) | Saccharopine dehydrogenase (NAD+, L-lysine-forming); catalyzes the conversion of saccharopine to L-lysine, which is the final step in the lysine biosynthesis pathway; also has mRNA binding activity | Accessory | Ancestral | NA | NA |
| 4693-YIR035C | YIR035C | NA | sepiapterin reductase family protein | Putative cytoplasmic short-chain dehydrogenase/reductase | Core | NA | NA | NA |
| 4694-YIR036C | YIR036C | IRC24 | sepiapterin reductase family protein IRC24 | Putative benzil reductase;(GFP)-fusion protein localizes to the cytoplasm and is induced by the DNA-damaging agent MMS; sequence similarity with short-chain dehydrogenase/reductases; null mutant has increased spontaneous Rad52p foci | Core | NA | NA | NA |
| 4695-YIR036W-A | YIR036W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF IRC24/YIR036C | Accessory | Unknown | NA | NA |
| 4696-YIR037W | YIR037W | HYR1 | peroxiredoxin HYR1|ORP1|GPX3 | Thiol peroxidase; functions as a hydroperoxide receptor to sense intracellular hydroperoxide levels and transduce a redox signal to the Yap1p transcription factor; HYR1 has a paralog, GPX1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4697-YIR038C | YIR038C | GTT1 | bifunctional glutathione transferase/peroxidase | ER associated glutathione S-transferase; capable of homodimerization; glutathione transferase for Yvc1p vacuolar cation channel; expression induced during the diauxic shift and throughout stationary phase; functional overlap with Gtt2p, Grx1p, and Grx2p | Core | NA | NA | NA |
| 4698-YIR039C | YIR039C | YPS6 | aspartyl protease | Putative GPI-anchored aspartic protease; member of the yapsin family of proteases involved in cell wall growth and maintenance | Accessory | Ancestral | NA | NA |
| 4699-YIR042C | YIR042C | NA | NA | Putative protein of unknown function; YIR042C is a non-essential gene | Accessory | Ancestral | NA | NA |
| 4700-YIR043C | YIR043C | NA | YIR044C | Blocked reading frame; may encode a non-functional member of the conserved, often subtelomerically-encoded Cos protein family | Accessory | Ancestral | NA | NA |
| 4701-YJL001W | YJL001W | PRE3 | proteasome core particle subunit beta 1|CRL21 | Beta 1 subunit of the 20S proteasome; responsible for cleavage after acidic residues in peptides | Core | NA | NA | NA |
| 4702-YJL002C | YJL002C | OST1 | dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1|NLT1 | Alpha subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes asparagine-linked glycosylation of newly synthesized proteins | Core | NA | NA | NA |