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 |
|---|---|---|---|---|---|---|---|---|
| 7433-YPL085W | YPL085W | SEC16 | LPF1 | COPII vesicle coat protein required for ER transport vesicle budding; essential factor in endoplasmic reticulum exit site (ERES) formation, as well as in COPII-mediated ER-to-Golgi traffic; bound to periphery of ER membranes and may act to stabilize initial COPII complexes; interacts with Sec23p, Sec24p and Sec31p | Core | NA | NA | NA |
| 7434-YPL086C | YPL086C | ELP3 | Elongator subunit ELP3|KAT9|KTI8|TOT3|HPA1 | Subunit of Elongator complex; Elongator is required for modification of wobble nucleosides in tRNA; exhibits histone acetyltransferase activity that is directed to histones H3 and H4; disruption confers resistance to K. lactis zymotoxin; human homolog ELP3 can partially complement yeast elp3 null mutant | Core | NA | NA | NA |
| 7435-YPL087W | YPL087W | YDC1 | alkaline dihydroceramidase | Alkaline dihydroceramidase, involved in sphingolipid metabolism; preferentially hydrolyzes dihydroceramide to a free fatty acid and dihydrosphingosine; has a minor reverse activity; YDC1 has a paralog, YPC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7436-YPL088W | YPL088W | NA | aldo-keto reductase superfamily protein | Putative aryl alcohol dehydrogenase; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance | Core | NA | NA | NA |
| 7437-YPL089C | YPL089C | RLM1 | NA | MADS-box transcription factor; component of the protein kinase C-mediated MAP kinase pathway involved in the maintenance of cell integrity; phosphorylated and activated by the MAP-kinase Slt2p; RLM1 has a paralog, SMP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7438-YPL090C | YPL090C | RPS6A | eS6|ribosomal 40S subunit protein S6A|S6e|rp9|YS4|S6A|S10A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S6, no bacterial homolog; phosphorylated on S233 by Ypk3p in a TORC1-dependent manner, and on S232 in a TORC1/2-dependent manner by Ypk1/2/3p; RPS6A has a paralog, RPS6B, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 7439-YPL091W | YPL091W | GLR1 | glutathione-disulfide reductase GLR1|LPG17 | Cytosolic and mitochondrial glutathione oxidoreductase; converts oxidized glutathione to reduced glutathione; cytosolic Glr1p is the main determinant of the glutathione redox state of the mitochondrial intermembrane space; mitochondrial Glr1p has a role in resistance to hyperoxia; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7440-YPL092W | YPL092W | SSU1 | LPG16 | Plasma membrane sulfite pump involved in sulfite metabolism; required for efficient sulfite efflux; major facilitator superfamily protein | Core | NA | NA | NA |
| 7441-YPL093W | YPL093W | NOG1 | putative GTPase NOG1 | Putative GTPase; associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins | Core | NA | NA | NA |
| 7442-YPL094C | YPL094C | SEC62 | Sec63 complex subunit SEC62|LPG14 | Essential subunit of Sec63 complex; with Sec61 complex, Kar2p/BiP and Lhs1p forms a channel competent for SRP-dependent and post-translational SRP-independent protein targeting and import into the ER; cotranslationally N-acetylated by NatA; other members are Sec63p, Sec66p, and Sec72p | Core | NA | NA | NA |
| 7443-YPL095C | YPL095C | EEB1 | medium-chain fatty acid ethyl ester synthase/esterase | Acyl-coenzymeA:ethanol O-acyltransferase; responsible for the major part of medium-chain fatty acid ethyl ester biosynthesis during fermentation; possesses short-chain esterase activity; may be involved in lipid metabolism and detoxification; EEB1 has a paralog, EHT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7444-YPL096C-A | YPL096C-A | ERI1 | RIN1 | Endoplasmic reticulum membrane protein that binds and inhibits Ras2p; binds to and inhibits GTP-bound Ras2p at the endoplasmic reticulum (ER); component of the GPI-GnT complex which catalyzes the first step in GPI-anchor biosynthesis; probable homolog of mammalian PIG-Y protein | Core | NA | NA | NA |
| 7445-YPL096W | YPL096W | PNG1 | peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase | Conserved peptide N-glycanase; deglycosylating enzyme that cleaves N-glycans that are attached to misfolded ERAD substrate glycoproteins prior to proteasome-dependent degradation; localizes to the cytoplasm and nucleus; activity is enhanced by interaction with Rad23p; human ortholog NGLY1 is associated with a syndrome characterized by developmental delays, epilepsy, absence of tears and liver disease | Core | NA | NA | NA |
| 7446-YPL097W | YPL097W | MSY1 | tyrosine--tRNA ligase MSY1 | Mitochondrial tyrosyl-tRNA synthetase | Core | NA | NA | NA |
| 7447-YPL098C | YPL098C | MGR2 | NA | Subunit of the TIM23 translocase complex; acts to couple Tim21p with the core Tim23 translocase; provides quality control for insertion of membrane proteins by regulating their release into the inner membrane by the TIM23 complex; absolutely required for mitochondrial import of presequence-containing proteins at elevated temperature; required for viability of cells lacking the mitochondrial genome (petite-negative phenotype) | Core | NA | NA | NA |