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 |
|---|---|---|---|---|---|---|---|---|
| 1853-YAR019W-A | YAR019W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF CDC15/YAR019C | Core | NA | NA | NA |
| 1854-YAR023C_NumOfGenes_2 | YAR023C | NA | DUP240 family protein | Putative integral membrane protein; member of DUP240 gene family | Core | NA | NA | NA |
| 1855-YAR027W | YAR027W | UIP3 | DUP240 family protein UIP3 | Putative integral membrane protein of unknown function; interacts with Ulp1p at the nuclear periphery; member of DUP240 gene family | Accessory | Ancestral | NA | NA |
| 1856-YAR028W_NumOfGenes_2 | YAR028W | NA | DUP240 family protein | Putative integral membrane protein; member of DUP240 gene family; GFP-fusion protein is induced in response to the DNA-damaging agent MMS | Accessory | Ancestral | NA | NA |
| 1857-YAR029W | YAR029W | NA | DUP240 family protein | Member of DUP240 gene family but contains no transmembrane domains; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Accessory | Ancestral | NA | NA |
| 1858-YAR030C | YAR030C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YAR029W and the verified gene PRM9 | Accessory | Unknown | NA | NA |
| 1859-YAR031W | YAR031W | PRM9 | pheromone-regulated DUP240 family protein PRM9 | Pheromone-regulated protein; contains 3 predicted transmembrane segments and an FF sequence, a motif involved in COPII binding; member of DUP240 gene family; PRM9 has a paralog, PRM8, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 1860-YAR035C-A | YAR035C-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; predicted to have a role in cell budding based on computational "guilt by association" analysis | Accessory | Unknown | NA | NA |
| 1861-YAR035W_NumOfGenes_2 | YAR035W | YAT1 | carnitine O-acetyltransferase YAT1 | Outer mitochondrial carnitine acetyltransferase; minor ethanol-inducible enzyme involved in transport of activated acyl groups from the cytoplasm into the mitochondrial matrix; phosphorylated | Accessory | Ancestral | NA | NA |
| 1862-YAR042W | YAR042W | SWH1 | oxysterol-binding protein related protein SWH1|OSH1|YAR044W | Protein similar to mammalian oxysterol-binding protein; contains ankyrin repeats and FFAT motif; interacts with ER anchor Scs2p at the nucleus-vacuole junction; regulated by sterol binding; SWH1 has a paralog, OSH2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 1863-YAR047C | YAR047C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Introgression | S. paradoxus | NA |
| 1864-YAR050W_NumOfGenes_3 | YAR050W | FLO1 | flocculin FLO1|FLO4|FLO2 | Lectin-like protein involved in flocculation; cell wall protein that binds mannose chains on the surface of other cells, confers floc-forming ability that is chymotrypsin sensitive and heat resistant; important for co-flocculation with other yeasts, mediating interaction with specific species; FLO1 has a paralog, FLO5, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 1865-YAR053W | YAR053W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 1866-YAR060C_NumOfGenes_2 | YAR060C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YAR060C has a paralog, YHR212C, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 1867-YAR066W_NumOfGenes_3 | YAR066W | NA | NA | Putative GPI protein; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively; YAR066W has a paralog, YHR214W, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |