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 |
|---|---|---|---|---|---|---|---|---|
| 6548-YNL156C | YNL156C | NSG2 | NA | Protein involved in regulation of sterol biosynthesis; specifically stabilizes Hmg2p, one of two HMG-CoA isoenzymes that catalyze the rate-limiting step in sterol biosynthesis; homolog of mammalian INSIG proteins; NSG2 has a paralog, NSG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6549-YNL157W | YNL157W | IGO1 | phosphatase regulator | Protein required for initiation of G0 program; prevents degradation of nutrient-regulated mRNAs via the 5'-3' mRNA decay pathway; phosphorylated by Rim15p; GFP protein localizes to the cytoplasm and nucleus; IGO1 has a paralog, IGO2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6550-YNL158W | YNL158W | PGA1 | NA | Essential component of GPI-mannosyltransferase II; complex is responsible for second mannose addition to GPI precursors as a partner of Gpi18p; required for maturation of Gas1p and Pho8p; has synthetic genetic interactions with secretory pathway genes | Core | NA | NA | NA |
| 6551-YNL159C | YNL159C | ASI2 | NA | Subunit of the inner nuclear membrane Asi ubiquitin ligase complex; the Asi complex targets both misfolded proteins of the inner nuclear membrane-associated degradation (INMAD) pathway and inner for ubiquitin-mediated degradation; acts with Asi1p and Asi3p to ensure the fidelity of SPS-sensor signaling by targeting latent unprocessed forms of Stp1p and Stp2p, maintaining the repressed state of gene expression in the absence of inducing amino acids | Core | NA | NA | NA |
| 6552-YNL160W | YNL160W | YGP1 | NA | Cell wall-related secretory glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in adaptation prior to stationary phase entry; YGP1 has a paralog, SPS100, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6553-YNL161W | YNL161W | CBK1 | serine/threonine protein kinase CBK1 | Serine/threonine protein kinase of the the RAM signaling network; Ndr/LATS family member; binds regulatory subunit Mob2p; involved in regulation of cellular morphogenesis, polarized growth, and septum destruction; phosphorylation by Cbk1p regulates localization and activity of Ace2p transcription factor and Ssd1p translational repressor; Cbk1p activity is regulated by both phosphorylation and specific localization; relocalizes to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 6554-YNL162W | YNL162W | RPL42A | eL42|ribosomal 60S subunit protein L42A|L44e|YL27|L42A|L41A | Ribosomal 60S subunit protein L42A; homologous to mammalian ribosomal protein L36A, no bacterial homolog; RPL42A has a paralog, RPL42B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6555-YNL162W-A | YNL162W-A | NA | NA | Putative protein of unknown function; identified by homology | Core | NA | NA | NA |
| 6556-YNL163C | YNL163C | RIA1 | GTPase RIA1|EFL1 | Cytoplasmic GTPase/eEF2-like factor involved in ribosomal biogenesis; with Sdo1p, a guanine nucleotide exchange factor (GEF), promotes release of Tif6p from 60S ribosomal subunits in the cytoplasm so that they can assemble with 40S subunits to generate mature ribosomes; required for quality control check of newly made large ribosomal subunits before they are released into the pool of translating ribosomes | Core | NA | NA | NA |
| 6557-YNL164C | YNL164C | IBD2 | NA | Component of the BUB2-dependent spindle checkpoint pathway; interacts with Bfa1p and functions upstream of Bub2p and Bfa1p | Core | NA | NA | NA |
| 6558-YNL165W | YNL165W | NA | NA | Putative protein of unknown function; YNL165W is not an essential gene | Core | NA | NA | NA |
| 6559-YNL166C | YNL166C | BNI5 | NA | Linker protein responsible for recruitment of myosin to the bud neck; interacts with the C-terminal extensions of septins Cdc11p and Shs1p and binds Myo1p to promote cytokinesis | Core | NA | NA | NA |
| 6560-YNL167C | YNL167C | SKO1 | ACR1 | Basic leucine zipper transcription factor of the ATF/CREB family; forms a complex with Tup1p and Cyc8p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses | Core | NA | NA | NA |
| 6561-YNL168C | YNL168C | FMP41 | NA | Putative protein of unknown function; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6562-YNL169C | YNL169C | PSD1 | phosphatidylserine decarboxylase 1 | Phosphatidylserine decarboxylase of the mitochondrial inner membrane; converts phosphatidylserine to phosphatidylethanolamine; regulates mitochondrial fusion and morphology by affecting lipid mixing in the mitochondrial membrane and by influencing the ratio of long to short forms of Mgm1p; partly exposed to the mitochondrial intermembrane space; autocatalytically processed | Core | NA | NA | NA |