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 |
|---|---|---|---|---|---|---|---|---|
| 2318-YCL033C | YCL033C | MXR2 | MSRB | Methionine-R-sulfoxide reductase; involved in the response to oxidative stress; protects iron-sulfur clusters from oxidative inactivation along with MXR1; involved in the regulation of lifespan | Core | NA | NA | NA |
| 2319-YCL034W | YCL034W | LSB5 | NA | Protein involved in membrane-trafficking events at plasma membrane; interacts with actin regulators Sla1p and Las17p, ubiquitin, Arf3p to couple actin dynamics to membrane trafficking processes; similar structure to GGA family of proteins with N-terminal VHS domain and GAT domain; binds Las17p, which is homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly, actin polymerization; may mediate disassembly of Pan1 complex from endocytic coat | Core | NA | NA | NA |
| 2320-YCL035C | YCL035C | GRX1 | dithiol glutaredoxin GRX1 | Glutathione-dependent disulfide oxidoreductase; hydroperoxide and superoxide-radical responsive, heat-stable, with active site cysteine pair; protects cells from oxidative damage; GRX1 has a paralog, GRX2, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2321-YCL036W | YCL036W | GFD2 | YCD6 | Protein of unknown function; identified as a high-copy suppressor of a dbp5 mutation; GFD2 has a paralog, YDR514C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2322-YCL037C | YCL037C | SRO9 | NA | Cytoplasmic RNA-binding protein; shuttles between nucleus and cytoplasm and is exported from the nucleus in an mRNA export-dependent manner; associates with translating ribosomes; involved in heme regulation of Hap1p as a component of the HMC complex, also involved in the organization of actin filaments; contains a La motif; SRO9 has a paralog, SLF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2323-YCL038C | YCL038C | ATG22 | AUT4 | Vacuolar integral membrane protein required for efflux of amino acids; required for efflux of amino acids during autophagic body breakdown in the vacuole; null mutation causes a gradual loss of viability during starvation | Core | NA | NA | NA |
| 2324-YCL039W | YCL039W | GID7 | glucose-induced degradation complex subunit GID7|MOH2 | Subunit of GID Complex that binds directly to central component Vid30p; GID complex is involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; Gid7p contains six WD40 repeats; computational analysis suggests that Gid7p and Moh1p have similar functions | Core | NA | NA | NA |
| 2325-YCL040W | YCL040W | GLK1 | glucokinase|HOR3 | Glucokinase; catalyzes the phosphorylation of glucose at C6 in the first irreversible step of glucose metabolism; one of three glucose phosphorylating enzymes; expression regulated by non-fermentable carbon sources; GLK1 has a paralog, EMI2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2326-YCL041C | YCL041C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps both the verified gene PDI1/YCL043C and the uncharacterized gene YCL042W | Accessory | Ancestral | NA | NA |
| 2327-YCL042W | YCL042W | NA | NA | Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
| 2328-YCL043C | YCL043C | PDI1 | protein disulfide isomerase PDI1|TRG1|MFP1 | Protein disulfide isomerase; multifunctional oxidoreductase of the ER lumen, essential for disulfide bond formation in secretory and cell-surface proteins, processing of non-native disulfide bonds; Ero1p activator; complexes with exomannosidase, Mnl1p to facilitate the recognition of misfolded glycoproteins and the trimming of glycan Man8GlcNAc2 to Man7GlcNAc2 on substrates, thereby accelerating ERAD; PDI1 has a paralog, EUG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2329-YCL044C | YCL044C | MGR1 | NA | Subunit of the mitochondrial (mt) i-AAA protease supercomplex; i-AAA degrades misfolded mitochondrial proteins; forms a subcomplex with Mgr3p that binds to substrates to facilitate proteolysis; required for growth of cells lacking mtDNA | Core | NA | NA | NA |
| 2330-YCL045C_NumOfGenes_2 | YCL045C | EMC1 | NA | Member of conserved endoplasmic reticulum membrane complex; involved in efficient folding of proteins in the ER; null mutant displays induction of the unfolded protein response; interacts with Gal80p; homologous to worm H17B01.4/EMC-1, fly CG2943, and human KIAA0090 | Core | NA | NA | NA |
| 2331-YCL047C | YCL047C | POF1 | nicotinamide-nucleotide adenylyltransferase | Nicotinamide mononucleotide-specific adenylyltransferase (NMNAT); catalyzes the conversion of nicotinamide mononucleotide (NMN) to nicotinamide adenine dinucleotide (NAD+); role in the nicotinamide riboside (NR) salvage pathway of NAD+ biosynthesis; involved in NR and NAD+ homeostasis; ATPase involved in protein quality control and filamentation pathways; interacts physically with Kss1p and suppresses the filamentation defect of a kss1 deletion | Core | NA | NA | NA |
| 2332-YCL048W | YCL048W | SPS22 | NA | Protein of unknown function; SPS22 has a paralog, SPS2, that arose from the whole genome duplication; redundant with Sps2p for the organization of the beta-glucan layer of the spore wall | Core | NA | NA | NA |