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 |
|---|---|---|---|---|---|---|---|---|
| 6308-YMR240C | YMR240C | CUS1 | U2 snRNP complex subunit CUS1 | Protein required for assembly of U2 snRNP into the spliceosome; forms a complex with Hsh49p and Hsh155p | Core | NA | NA | NA |
| 6309-YMR241W | YMR241W | YHM2 | NA | Citrate and oxoglutarate carrier protein; exports citrate from and imports oxoglutarate into the mitochondrion, causing net export of NADPH reducing equivalents; also associates with mt nucleoids and has a role in replication and segregation of the mt genome | Core | NA | NA | NA |
| 6310-YMR242C | YMR242C | RPL20A | eL20|ribosomal 60S subunit protein L20A|L20e|L20A|L18A|RPL18A2 | Ribosomal 60S subunit protein L20A; homologous to mammalian ribosomal protein L18A, no bacterial homolog; RPL20A has a paralog, RPL20B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6311-YMR242W-A | YMR242W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6312-YMR243C | YMR243C | ZRC1 | Zn(2+) transporter ZRC1|OSR1 | Vacuolar membrane zinc transporter; transports zinc from cytosol to vacuole for storage; also has role in resistance to zinc shock resulting from sudden influx of zinc into cytoplasm; human ortholog SLC30A10 functions as a Mn transporter and mutations in SLC30A10 cause neurotoxic accumulation of Mn in liver and brain; ZRC1 has a paralog, COT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6313-YMR244C-A_NumOfGenes_2 | YMR244C-A | COA6 | NA | Protein involved in cytochrome c oxidase (Complex IV) assembly; involved in delivery of copper to Complex IV; also required for efficient formation of respiratory supercomplexes comprised of Complexes III and IV; localizes to the mitochondrial intermembrane space; ortholog implicated in cardiac defects in zebrafish and human; transcription is induced in response to the DNA-damaging agent MMS; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6314-YMR244W | YMR244W | NA | NA | Putative protein of unknown function; SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to just the vacuole | Core | NA | NA | NA |
| 6315-YMR246W | YMR246W | FAA4 | long-chain fatty acid-CoA ligase FAA4 | Long chain fatty acyl-CoA synthetase; activates fatty acids with a preference for C12:0-C16:0 chain lengths; role in the competitive import of long-chain fatty acids and sphingoid long-chain bases; role in stationary phase survival; localizes to lipid particles and the plasma membrane; role in sphingolipid-to-glycerolipid metabolism; forms cytoplasmic foci upon replication stress; faa1 faa4 double null complemented by any of human ACSBG1, ACSL1, 3, 4, 5, 6, SLC27A2, or 4 | Core | NA | NA | NA |
| 6316-YMR247C | YMR247C | RKR1 | ubiquitin-protein ligase RKR1|LTN1 | RING domain E3 ubiquitin ligase; involved in ubiquitin-mediated degradation of non-stop proteins and translationally stalled ER membrane proteins; component of ribosome-bound RQC (ribosome quality control) complex; degrades products of mRNAs lacking a termination codon regardless of a poly(A) tail; functional connections to chromatin modification; homolog of mouse Listerin, mutations in which reported to cause neurodegeneration | Core | NA | NA | NA |
| 6317-YMR247W-A | YMR247W-A | NA | NA | Putative protein of unknown function; SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to just the vacuole | Core | NA | NA | NA |
| 6318-YMR250W | YMR250W | GAD1 | glutamate decarboxylase GAD1 | Glutamate decarboxylase; converts glutamate into gamma-aminobutyric acid (GABA) during glutamate catabolism; involved in response to oxidative stress | Core | NA | NA | NA |
| 6319-YMR251W | YMR251W | GTO3 | omega-class glutathione transferase | Omega class glutathione transferase; putative cytosolic localization | Core | NA | NA | NA |
| 6320-YMR251W-A | YMR251W-A | HOR7 | NA | Protein of unknown function; overexpression suppresses Ca2+ sensitivity of mutants lacking inositol phosphorylceramide mannosyltransferases Csg1p and Csh1p; transcription is induced under hyperosmotic stress and repressed by alpha factor; HOR7 has a paralog, DDR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6321-YMR252C | YMR252C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YMR252C is not an essential gene | Core | NA | NA | NA |
| 6322-YMR253C | YMR253C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YMR253C is not an essential gene | Core | NA | NA | NA |