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 |
|---|---|---|---|---|---|---|---|---|
| 4463-YHR201C | YHR201C | PPX1 | exopolyphosphatase | Exopolyphosphatase; hydrolyzes inorganic polyphosphate (poly P) into Pi residues; located in the cytosol, plasma membrane, and mitochondrial matrix | Core | NA | NA | NA |
| 4464-YHR202W | YHR202W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole, while HA-tagged protein is found in the soluble fraction, suggesting cytoplasmic localization | Core | NA | NA | NA |
| 4465-YHR204W | YHR204W | MNL1 | alpha-1,2-mannosidase MNL1|HTM1 | Alpha-1,2-specific exomannosidase of the endoplasmic reticulum; involved in glycan trimming of both folded and misfolded glycoproteins; complexes with Pdi1p, and trims a mannose from Man8GlcNac2 glycans to generate Man7GlcNac2, an oligosaccharide signal on glycoproteins destined for ER-associated protein degradation; requires Pdi1p for stability and substrate recognition; human homolog EDEM1 can complement yeast null mutant | Core | NA | NA | NA |
| 4466-YHR205W | YHR205W | SCH9 | serine/threonine protein kinase SCH9|HRM2|KOM1 | AGC family protein kinase; functional ortholog of mammalian S6 kinase; phosphorylated by Tor1p and required for TORC1-mediated regulation of ribosome biogenesis, translation initiation, and entry into G0 phase; involved in transactivation of osmostress-responsive genes; regulates G1 progression, cAPK activity and nitrogen activation of the FGM pathway; integrates nutrient signals and stress signals from sphingolipids to regulate lifespan | Core | NA | NA | NA |
| 4467-YHR206W | YHR206W | SKN7 | kinase-regulated stress-responsive transcription factor SKN7|POS9|BRY1 | Nuclear response regulator and transcription factor; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; part of a branched two-component signaling system; required for optimal induction of heat-shock genes in response to oxidative stress; involved in osmoregulation; relocalizes to the cytosol in response to hypoxia; SKN7 has a paralog, HMS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4468-YHR207C | YHR207C | SET5 | S-adenosylmethionine-dependent methyltransferase | Methyltransferase involved in methylation of histone H4 Lys5, -8, -12; S-adenosylmethionine-dependent; zinc-finger protein, contains one canonical and two unusual fingers in unusual arrangements; deletion enhances replication of positive-strand RNA virus | Accessory | Ancestral | NA | NA |
| 4469-YHR208W | YHR208W | BAT1 | branched-chain-amino-acid transaminase BAT1|TWT1|ECA39 | Mitochondrial branched-chain amino acid (BCAA) aminotransferase; preferentially involved in BCAA biosynthesis; homolog of murine ECA39; highly expressed during logarithmic phase and repressed during stationary phase; BAT1 has a paralog, BAT2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4470-YHR209W | YHR209W | CRG1 | S-adenosylmethionine-dependent methyltransferase | S-AdoMet-dependent methyltransferase involved in lipid homeostasis; mediates resistance to a drug cantharidin | Accessory | Ancestral | NA | NA |
| 4471-YHR210C | YHR210C | NA | aldose 1-epimerase superfamily protein | Putative aldose 1-epimerase superfamily protein; non-essential gene; highly expressed under anaeorbic conditions | Accessory | Ancestral | NA | NA |
| 4472-YHR211W_NumOfGenes_3 | YHR211W | FLO5 | flocculin FLO5 | Lectin-like cell wall protein (flocculin) involved in flocculation; binds mannose chains on the surface of other cells, confers floc-forming ability that is chymotrypsin resistant but heat labile; important for co-flocculation with other yeasts, mediating interaction with specific species; FLO5 has a paralog, FLO1, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 4473-YHR213W_NumOfGenes_5 | YHR213W | NA | NA | Pseudogenic fragment with similarity to flocculins; YHR213W has a paralog, YAR062W, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 4474-YHR213W-A | YHR213W-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 4475-YHR213W-B_NumOfGenes_2 | YHR213W-B | NA | NA | Pseudogenic fragment with similarity to flocculins; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; YHR213W-B has a paralog, YAR064W, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 4476-YHR214C-D_NumOfGenes_2 | YHR214C-D | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; SWAT-GFP and mCherry fusion proteins localize to the nucleus and endoplasmic reticulum respectively; YHR214C-D has a paralog, YAR069C, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 4477-YHR215W_NumOfGenes_2 | YHR215W | PHO12 | acid phosphatase PHO12|PHO10 | One of three repressible acid phosphatases; glycoprotein that is transported to the cell surface by the secretory pathway; pregulated by phosphate starvation; PHO12 has a paralog, PHO11, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |