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 |
|---|---|---|---|---|---|---|---|---|
| 5333-YKR041W | YKR041W | NA | NA | Protein of unknown function; localizes to the mitotic spindle; overexpression of YKR041W affects endocytic protein trafficking | Accessory | Ancestral | NA | NA |
| 5334-YKR042W | YKR042W | UTH1 | SUN family protein UTH1 | Mitochondrial inner membrane protein; role in mitophagy is disputed; implicated in cell wall biogenesis, the oxidative stress response, life span during starvation, and cell death; SUN family member; UTH1 has a paralog, NCA3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5335-YKR043C | YKR043C | SHB17 | sedoheptulose-bisphosphatase | Sedoheptulose bisphosphatase involved in riboneogenesis; dephosphorylates sedoheptulose 1,7-bisphosphate, which is converted via the nonoxidative pentose phosphate pathway to ribose-5-phosphate; facilitates the conversion of glycolytic intermediates to pentose phosphate units; also has fructose 1,6-bisphosphatase activity but this is probably not biologically relevant, since deletion does not affect FBP levels; GFP-fusion protein localizes to the cytoplasm and nucleus | Accessory | Ancestral | NA | NA |
| 5336-YKR044W | YKR044W | UIP5 | NA | Protein of unknown function that interacts with Ulp1p; a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates | Accessory | Ancestral | NA | NA |
| 5337-YKR045C | YKR045C | NA | NA | Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
| 5338-YKR046C | YKR046C | PET10 | NA | Protein of unknown function that localizes to lipid particles; localization suggests a role in lipid metabolism; expression pattern suggests a role in respiratory growth; computational analysis of large-scale protein-protein interaction data suggests a role in ATP/ADP exchange | Accessory | Ancestral | NA | NA |
| 5339-YKR047W | YKR047W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene NAP1 | Accessory | Ancestral | NA | NA |
| 5340-YKR048C | YKR048C | NAP1 | histone chaperone NAP1 | Histone chaperone; involved in histone exchange by removing and replacing histone H2A-H2B dimers or histone variant dimers from assembled nucleosomes; involved in the transport of H2A and H2B histones to the nucleus; required for the regulation of microtubule dynamics during mitosis; interacts with mitotic cyclin Clb2p; controls bud morphogenesis; phosphorylated by CK2; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5341-YKR049C | YKR049C | FMP46 | putative redox protein | Putative redox protein containing a thioredoxin fold; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5342-YKR050W | YKR050W | TRK2 | RPD2 | Component of the Trk1p-Trk2p potassium transport system; contributes to K(+) supply and maintenance of plasma-membrane potential; TRK2 has a paralog, TRK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5343-YKR051W | YKR051W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5344-YKR052C | YKR052C | MRS4 | Fe(2+) transporter | Iron transporter of the mitochondrial carrier family; mediates Fe2+ transport across the inner mitochondrial membrane; active under low-iron conditions; may transport other cations; protein abundance increases in response to DNA replication stress; MRS4 has a paralog, MRS3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5345-YKR053C | YKR053C | YSR3 | sphinganine kinase YSR3|LBP2 | Dihydrosphingosine 1-phosphate phosphatase; membrane protein involved in sphingolipid metabolism; YSR3 has a paralog, LCB3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5346-YKR054C | YKR054C | DYN1 | dynein heavy chain|PAC6|DHC1 | Cytoplasmic heavy chain dynein; microtubule motor protein; member of the AAA+ protein family, required for anaphase spindle elongation; involved in spindle assembly, chromosome movement, and spindle orientation during cell division, targeted to microtubule tips by Pac1p; motility along microtubules inhibited by She1p | Core | NA | NA | NA |
| 5347-YKR055W | YKR055W | RHO4 | Rho family GTPase RHO4 | Non-essential small GTPase; member of the Rho/Rac subfamily of Ras-like proteins; likely to be involved in the establishment of cell polarity; has long N-terminal extension that plays an important role in Rho4p function and is shared with Rho4 homologs in other yeasts and filamentous fungi | Core | NA | NA | NA |