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 |
|---|---|---|---|---|---|---|---|---|
| 5693-YLR236C | YLR236C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF YLR235C | Accessory | Ancestral | NA | NA |
| 5694-YLR237W | YLR237W | THI7 | thiamine transporter THI7|THI10 | Plasma membrane transporter responsible for the uptake of thiamine; contributes to uptake of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside (acadesine); member of the major facilitator superfamily of transporters; mutation of human ortholog causes thiamine-responsive megaloblastic anemia | Core | NA | NA | NA |
| 5695-YLR238W | YLR238W | FAR10 | NA | Protein involved in recovery from arrest in response to pheromone; acts in a cell cycle arrest recovery pathway independent from Far1p; interacts with Far3p, Far7p, Far8p, Far9p, and Far11p; potential Cdc28p substrate; FAR10 has a paralog, VPS64, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5696-YLR239C | YLR239C | LIP2 | lipoyl(octanoyl) transferase LIP2 | Lipoyl ligase; involved in the modification of mitochondrial enzymes by the attachment of lipoic acid groups | Core | NA | NA | NA |
| 5697-YLR240W | YLR240W | VPS34 | phosphatidylinositol 3-kinase VPS34|VPS7|STT8|VPT29|VPL7|PEP15|END12 | Phosphatidylinositol (PI) 3-kinase that synthesizes PI-3-phosphate; forms membrane-associated signal transduction complex with Vps15p to regulate protein sorting; activated by the GTP-bound form of Gpa1p; a fraction is localized, with Vps15p, to nuclear pores at nucleus-vacuole junctions and may facilitate transcription elongation for genes positioned at the nuclear periphery | Core | NA | NA | NA |
| 5698-YLR241W | YLR241W | CSC1 | NA | Calcium permeable gated cation channel; may be involved in detoxification; similar to Arabidopsis CSC1 | Core | NA | NA | NA |
| 5699-YLR242C | YLR242C | ARV1 | sterol homeostasis protein ARV1 | Cortical ER protein; implicated in the membrane insertion of tail-anchored C-terminal single transmembrane domain proteins; may function in transport of glycosylphosphatidylinositol intermediates into the ER lumen; required for normal intracellular sterol distribution; human ARV1, required for normal cholesterol and bile acid homeostasis, can complement yeast arv1 null mutant; human variant causing early onset epileptic encephalopathy is unable to rescue the yeast null | Core | NA | NA | NA |
| 5700-YLR243W | YLR243W | GPN3 | putative signal sequence-binding GTPase GPN3 | Putative GTPase with a role in biogenesis of RNA pol II and polIII; may be involved in assembly of RNA polymerases II and III and in their transport into the nucleus; may have a role in sister chromatid cohesion; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively; contains a Gly-Pro-Asn motif in the G domain; similar to Npa3p and Gpn2p | Core | NA | NA | NA |
| 5701-YLR244C | YLR244C | MAP1 | methionine aminopeptidase MAP1 | Methionine aminopeptidase; catalyzes the cotranslational removal of N-terminal methionine from nascent polypeptides; function is partially redundant with that of Map2p | Core | NA | NA | NA |
| 5702-YLR245C | YLR245C | CDD1 | cytidine deaminase | Cytidine deaminase; catalyzes the modification of cytidine to uridine in vitro but native RNA substrates have not been identified, localizes to both the nucleus and cytoplasm | Core | NA | NA | NA |
| 5703-YLR246W | YLR246W | ERF2 | palmitoyltransferase ERF2 | Subunit of a palmitoyltransferase; this complex adds a palmitoyl lipid moiety to heterolipidated substrates such as Ras1p and Ras2p through a thioester linkage; mutants partially mislocalize Ras2p to the vacuole; palmitoyltransferase is composed of Erf2p and Shr5p | Core | NA | NA | NA |
| 5704-YLR247C | YLR247C | IRC20 | E3 ubiquitin-protein ligase IRC20 | E3 ubiquitin ligase and putative helicase; involved in synthesis-dependent strand annealing-mediated homologous recombination; ensures precise end-joining along with Srs2p in the Yku70p/Yku80p/Lig4p-dependent nonhomologous end joining (NHEJ) pathway; localizes to both the mitochondrion and the nucleus; contains a Snf2/Swi2 family ATPase/helicase and a RING finger domain; interacts with Cdc48p and Smt3p; null mutant displays increased levels of spontaneous Rad52p foci | Core | NA | NA | NA |
| 5705-YLR248W | YLR248W | RCK2 | serine/threonine protein kinase RCK2|CMK3|CLK1 | Protein kinase involved in response to oxidative and osmotic stress; identified as suppressor of S. pombe cell cycle checkpoint mutations; similar to CaM (calmodulin) kinases; RCK2 has a paralog, RCK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5706-YLR249W | YLR249W | YEF3 | translation elongation factor EF-3|EF-3|eEF3|TEF3 | Translation elongation factor 3; contains two ABC cassettes; binds and hydrolyzes ATP; YEF3 has a paralog, HEF3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5707-YLR250W | YLR250W | SSP120 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |