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 |
|---|---|---|---|---|---|---|---|---|
| 3563-YFL040W_NumOfGenes_2 | YFL040W | NA | NA | Putative transporter; member of the sugar porter family; YFL040W is not an essential gene; may have a role in intracellular sterol transport | Core | NA | NA | NA |
| 3564-YFL041W_NumOfGenes_2 | YFL041W | FET5 | ferroxidase FET5 | Multicopper oxidase; integral membrane protein with similarity to Fet3p; may have a role in iron transport | Core | NA | NA | NA |
| 3565-YFL041W-A | YFL041W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 3566-YFL042C_NumOfGenes_2 | YFL042C | LAM5 | LTC2|YFL043C | Putative sterol transfer protein; one of six StART-like domain-containing proteins in yeast that may be involved in sterol transfer between intracellular membranes; conserved across eukaryotes; has both GRAM and StART-like (VASt) domains; localizes to membrane contact sites throughout the cell, including nucleus-vacuole junctions and ER-mitochondrial contact sites | Core | NA | NA | NA |
| 3567-YFL044C_NumOfGenes_2 | YFL044C | OTU1 | ubiquitin-specific protease OTU1|YOD1 | Deubiquitylation enzyme that binds to the chaperone-ATPase Cdc48p; may contribute to regulation of protein degradation by deubiquitylating substrates that have been ubiquitylated by Ufd2p; member of the Ovarian Tumor (OTU) family; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3568-YFL045C_NumOfGenes_2 | YFL045C | SEC53 | phosphomannomutase SEC53|ALG4 | Phosphomannomutase; involved in synthesis of GDP-mannose and dolichol-phosphate-mannose; required for folding and glycosylation of secretory proteins in the ER lumen | Core | NA | NA | NA |
| 3569-YFL046W_NumOfGenes_2 | YFL046W | FMP32 | NA | Putative assembly factor for cytochrome c oxidase; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; has similarity to human MCUR1/CCDC90A | Core | NA | NA | NA |
| 3570-YFL047W_NumOfGenes_2 | YFL047W | RGD2 | NA | GTPase-activating protein (RhoGAP) for Cdc42p and Rho5p; relocalizes from bud neck to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3571-YFL048C_NumOfGenes_2 | YFL048C | EMP47 | NA | Integral membrane component of ER-derived COPII-coated vesicles; functionS in ER to Golgi transport; EMP47 has a paralog, EMP46, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3572-YFL049W_NumOfGenes_2 | YFL049W | SWP82 | NA | Member of the SWI/SNF chromatin remodeling complex; has an as yet unidentified role in the complex; has identifiable counterparts in closely related yeast species; abundantly expressed in many growth conditions; paralog of Npl6p; relocates to the cytosol under hypoxic conditions | Core | NA | NA | NA |
| 3573-YFL050C | YFL050C | ALR2 | putative Mg(2+) transporter ALR2 | Probable Mg(2+) transporter; overexpression confers increased tolerance to Al(3+) and Ga(3+) ions; plays a role in regulating Ty1 transposition | Accessory | Ancestral | NA | NA |
| 3574-YFL051C_NumOfGenes_2 | YFL051C | NA | NA | Putative protein of unknown function; SWAT-GFP fusion protein localizes to the cell periphery while mCherry fusion protein localizes to both the cell periphery and vacuole; YFL051C is not an essential gene | Accessory | Ancestral | NA | NA |
| 3575-YFL052W_NumOfGenes_2 | YFL052W | ZNF1 | DNA-binding domain containing protein|ROP1 | Zinc cluster transcription factor that regulates respiratory growth; binds to promoters of genes involved in respiration, gluconeogenesis, and the glyoxylate shunt; required for normal carbon source utilization and stress response | Accessory | Ancestral | NA | NA |
| 3576-YFL053W_NumOfGenes_2 | YFL053W | DAK2 | dihydroxyacetone kinase | Dihydroxyacetone kinase; required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation | Accessory | Ancestral | NA | NA |
| 3577-YFL054C_NumOfGenes_2 | YFL054C | AQY3 | NA | Putative channel-like protein; similar to Fps1p; mediates passive diffusion of glycerol in the presence of ethanol | Accessory | Ancestral | NA | NA |