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 |
|---|---|---|---|---|---|---|---|---|
| 2303-YCL016C | YCL016C | DCC1 | NA | Subunit of a complex with Ctf8p and Ctf18p; shares some components with Replication Factor C; required for sister chromatid cohesion and telomere length maintenance | Core | NA | NA | NA |
| 2304-YCL017C | YCL017C | NFS1 | SPL1 | Cysteine desulfurase; involved in iron-sulfur cluster (Fe/S) biogenesis and in thio-modification of mitochondrial and cytoplasmic tRNAs; essential protein located predominantly in mitochondria | Core | NA | NA | NA |
| 2305-YCL018W | YCL018W | LEU2 | 3-isopropylmalate dehydrogenase | Beta-isopropylmalate dehydrogenase (IMDH); catalyzes the third step in the leucine biosynthesis pathway; can additionally catalyze the conversion of beta-ethylmalate into alpha-ketovalerate | Accessory | Ancestral | NA | NA |
| 2306-YCL021W-A_NumOfGenes_2 | YCL021W-A | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the vacuole | Accessory | Ancestral | NA | NA |
| 2307-YCL022C_NumOfGenes_2 | YCL022C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps verified gene KCC4/YCL024W | Accessory | Ancestral | NA | NA |
| 2308-YCL023C | YCL023C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified ORF KCC4 | Core | NA | NA | NA |
| 2309-YCL025C | YCL025C | AGP1 | amino acid transporter AGP1|YCC5 | Low-affinity amino acid permease with broad substrate range; involved in uptake of asparagine, glutamine, and other amino acids; expression regulated by SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p); AGP1 has a paralog, GNP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2310-YCL026C-A | YCL026C-A | FRM2 | type II nitroreductase|YCLX08C | Type II nitroreductase, using NADH as reductant; mutants are defective in fatty acid mediated repression of genes involved in fatty acid biosynthesis indicative of a role in lipid signaling; involved in the oxidative stress response; transcription induction by cadmium and selenite indicates a possible role in the metal stress response; expression induced in cells treated with the mycotoxin patulin | Core | NA | NA | NA |
| 2311-YCL026C-B | YCL026C-B | HBN1 | putative nitroreductase|YCL027C-A | Protein of unknown function; similar to bacterial nitroreductases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; protein becomes insoluble upon intracellular iron depletion; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2312-YCL027W | YCL027W | FUS1 | NA | Membrane protein localized to the shmoo tip; required for cell fusion; expression regulated by mating pheromone; proposed to coordinate signaling, fusion, and polarization events required for fusion; potential Cdc28p substrate | Core | NA | NA | NA |
| 2313-YCL028W | YCL028W | RNQ1 | prion domain-containing protein RNQ1|[PIN(+)] | [PIN(+)] prion; an infectious protein conformation that is generally an ordered protein aggregate | Core | NA | NA | NA |
| 2314-YCL029C | YCL029C | BIK1 | PAC14|ARM5 | Microtubule-associated protein; component of the interface between microtubules and kinetochore, involved in sister chromatid separation; essential in polyploid cells but not in haploid or diploid cells; ortholog of mammalian CLIP-170 | Core | NA | NA | NA |
| 2315-YCL030C | YCL030C | HIS4 | trifunctional histidinol dehydrogenase/phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase | Multifunctional enzyme containing phosphoribosyl-ATP pyrophosphatase; phosphoribosyl-AMP cyclohydrolase, and histidinol dehydrogenase activities; catalyzes the second, third, ninth and tenth steps in histidine biosynthesis | Core | NA | NA | NA |
| 2316-YCL031C | YCL031C | RRP7 | NA | Essential protein involved in rRNA processing and ribosome biogenesis; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2317-YCL032W | YCL032W | STE50 | NA | Adaptor protein for various signaling pathways; involved in mating response, invasive/filamentous growth, osmotolerance; acts as an adaptor that links G protein-associated Cdc42p-Ste20p complex to the effector Ste11p to modulate signal transduction | Core | NA | NA | NA |