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 |
|---|---|---|---|---|---|---|---|---|
| 5093-YKL024C | YKL024C | URA6 | bifunctional uridylate/adenylate kinase|SOC8 | Uridylate kinase; catalyzes the seventh enzymatic step in the de novo biosynthesis of pyrimidines, converting uridine monophosphate (UMP) into uridine-5'-diphosphate (UDP) | Core | NA | NA | NA |
| 5094-YKL025C | YKL025C | PAN3 | ECM35 | Essential subunit of the Pan2p-Pan3p poly(A)-ribonuclease complex; poly (A) mRNA binding subunit which recruits mRNA to the complex; the Pan2p-Pan3p complex controls poly(A) tail length and regulates the stoichiometry and activity of postreplication repair complexes | Core | NA | NA | NA |
| 5095-YKL026C | YKL026C | GPX1 | glutathione peroxidase GPX1 | Phospholipid hydroperoxide glutathione peroxidase; induced by glucose starvation that protects cells from phospholipid hydroperoxides and nonphospholipid peroxides during oxidative stress; GPX1 has a paralog, HYR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5096-YKL027W | YKL027W | TCD2 | tRNA threonylcarbamoyladenosine dehydratase | tRNA threonylcarbamoyladenosine dehydratase; required for the ct6A tRNA base modification, where an adenosine at position 37 is modified to form a cyclized active ester with an oxazolone ring; localized to the mitochondrial outer membrane; TCD2 has a paralog, TCD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5097-YKL028W | YKL028W | TFA1 | transcription factor TFIIE subunit TFA1 | TFIIE large subunit; involved in recruitment of RNA polymerase II to the promoter, activation of TFIIH, and promoter opening | Core | NA | NA | NA |
| 5098-YKL029C | YKL029C | MAE1 | malate dehydrogenase (oxaloacetate-decarboxylating) | Mitochondrial malic enzyme; catalyzes the oxidative decarboxylation of malate to pyruvate, which is a key intermediate in sugar metabolism and a precursor for synthesis of several amino acids | Core | NA | NA | NA |
| 5099-YKL030W | YKL030W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; partially overlaps the verified gene MAE1 | Accessory | Ancestral | NA | NA |
| 5100-YKL031W | YKL031W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species | Core | NA | NA | NA |
| 5101-YKL032C | YKL032C | IXR1 | DNA-binding transcription repressor IXR1|ORD1 | Transcriptional repressor that regulates hypoxic genes during normoxia; involved in the aerobic repression of genes such as COX5b, TIR1, and HEM13; binds DNA intrastrand cross-links formed by cisplatin; HMG (high mobility group box) domain containing protein which binds and bends cisplatin-modified DNA, blocking excision repair; IXR1 has a paralog, ABF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5102-YKL033W | YKL033W | TTI1 | FMP47 | Subunit of the ASTRA complex, involved in chromatin remodeling; telomere length regulator involved in the stability or biogenesis of PIKKs such as TORC1; similar to S. pombe Tti1p; detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5103-YKL033W-A | YKL033W-A | NA | putative hydrolase | Putative protein of unknown function; similar to uncharacterized proteins from other fungi | Core | NA | NA | NA |
| 5104-YKL034W | YKL034W | TUL1 | ubiquitin-protein ligase TUL1 | Subunit of the DSC ubiquitin ligase complex; golgi-localized RING-finger ubiquitin ligase (E3) involved in sorting polar transmembrane domain containing membrane proteins to multivesicular bodies for delivery to the vacuole; proposed involvement in the quality control of misfolded TMD containing proteins; ortholog of fission yeast dsc1 | Core | NA | NA | NA |
| 5105-YKL035W | YKL035W | UGP1 | UTP glucose-1-phosphate uridylyltransferase | UDP-glucose pyrophosphorylase (UGPase); catalyses the reversible formation of UDP-Glc from glucose 1-phosphate and UTP, involved in a wide variety of metabolic pathways, expression modulated by Pho85p through Pho4p; involved in PKA-mediated oxidative stress resistance and long-term survival in stationary phase; UGP1 has a paralog, YHL012W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5106-YKL036C | YKL036C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; partially overlaps the essential gene UGP1 gene and uncharacterized ORF YKL037W | Accessory | Ancestral | NA | NA |
| 5107-YKL037W | YKL037W | AIM26 | NA | Protein of unknown function; null mutant is viable and displays elevated frequency of mitochondrial genome loss; null mutation confers sensitivity to tunicamycin and DTT | Accessory | Ancestral | NA | NA |