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 |
|---|---|---|---|---|---|---|---|---|
| 7373-YPL024W | YPL024W | RMI1 | NCE4 | Subunit of the RecQ (Sgs1p) - Topo III (Top3p) complex; stimulates superhelical relaxing, DNA catenation/decatenation and ssDNA binding activities of Top3p; involved in response to DNA damage; functions in S phase-mediated cohesion establishment via a pathway involving the Ctf18-RFC complex and Mrc1p; stimulates Top3p DNA catenation/decatenation activity; null mutants display increased rates of recombination and delayed S phase | Core | NA | NA | NA |
| 7374-YPL025C | YPL025C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 7375-YPL026C | YPL026C | SKS1 | putative serine/threonine protein kinase SKS1|SHA3 | Putative serine/threonine protein kinase; involved in the adaptation to low concentrations of glucose independent of the SNF3 regulated pathway; SKS1 has a paralog, VHS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7376-YPL027W | YPL027W | SMA1 | NA | Protein of unknown function involved in prospore membrane assembly; involved in the assembly of the prospore membrane during sporulation; interacts with Spo14p | Core | NA | NA | NA |
| 7377-YPL028W | YPL028W | ERG10 | acetyl-CoA C-acetyltransferase|TSM0115|LPB3 | Acetyl-CoA C-acetyltransferase (acetoacetyl-CoA thiolase); cytosolic enzyme that transfers an acetyl group from one acetyl-CoA molecule to another, forming acetoacetyl-CoA; involved in the first step in mevalonate biosynthesis; human ACAT1 functionally complements the growth defect caused by repression of ERG10 expression | Core | NA | NA | NA |
| 7378-YPL029W | YPL029W | SUV3 | ATP-dependent RNA helicase SUV3|LPB2 | ATP-dependent RNA helicase; component of the mitochondrial degradosome along with the RNase Dss1p; the degradosome associates with the ribosome and mediates RNA turnover; also required during splicing of the COX1 AI5_beta intron; expression of a processed form of human homolog SUPV3L1 carrying an N-terminal deletion of 46 amino acids rescues yeast suv3 null mutant | Core | NA | NA | NA |
| 7379-YPL030W | YPL030W | TRM44 | tRNA (uracil) methyltransferase | tRNA(Ser) Um(44) 2'-O-methyltransferase; involved in maintaining levels of the tRNA-Ser species tS(CGA) and tS(UGA); conserved among metazoans and fungi but there does not appear to be a homolog in plants; TRM44 is a non-essential gene | Accessory | Ancestral | NA | NA |
| 7380-YPL031C | YPL031C | PHO85 | cyclin-dependent serine/threonine-protein kinase PHO85|phoU|LDB15 | Cyclin-dependent kinase; has ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle; human lissencephaly-associated homolog CDK5 functionally complements null mutation | Accessory | Ancestral | NA | NA |
| 7381-YPL032C | YPL032C | SVL3 | NA | Protein of unknown function; mutant phenotype suggests a potential role in vacuolar function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; relocalizes from bud neck to cytoplasm upon DNA replication stress; SVL3 has a paralog, PAM1, that arose from the whole genome duplication | Accessory | Unknown | NA | NA |
| 7382-YPL033C | YPL033C | SRL4 | NA | Protein of unknown function; involved in regulation of dNTP production; null mutant suppresses the lethality of lcd1 and rad53 mutations; expression is induced by Kar4p | Core | NA | NA | NA |
| 7383-YPL034W | YPL034W | NA | NA | Putative protein of unknown function; YPL034W is not essential gene | Core | NA | NA | NA |
| 7384-YPL035C | YPL035C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized gene YPL034W; YPL035C is not an essential gene | Accessory | Ancestral | NA | NA |
| 7385-YPL036W | YPL036W | PMA2 | H(+)-exporting P2-type ATPase PMA2 | Plasma membrane H+-ATPase; isoform of Pma1p, involved in pumping protons out of the cell; regulator of cytoplasmic pH and plasma membrane potential | Core | NA | NA | NA |
| 7386-YPL037C | YPL037C | EGD1 | NA | Subunit beta1 of the nascent polypeptide-associated complex (NAC); involved in protein targeting, associated with cytoplasmic ribosomes; enhances DNA binding of the Gal4p activator; homolog of human BTF3b; EGD1 has a paralog, BTT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7387-YPL038W | YPL038W | MET31 | NA | Zinc-finger DNA-binding transcription factor; targets strong transcriptional activator Met4p to promoters of sulfur metabolic genes; involved in transcriptional regulation of the methionine biosynthetic genes; feedforward loop controlling expression of MET32 and the lack of such a loop for MET31 may account for the differential actions of Met31p and Met32p; MET31 has a paralog, MET32, that arose from the whole genome duplication | Core | NA | NA | NA |