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 |
|---|---|---|---|---|---|---|---|---|
| 4088-YGR187C | YGR187C | HGH1 | NA | Nonessential protein of unknown function; predicted to be involved in ribosome biogenesis; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; similar to mammalian BRP16 (Brain protein 16); relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4089-YGR188C | YGR188C | BUB1 | protein kinase BUB1 | Protein kinase involved in the cell cycle checkpoint into anaphase; in complex with Mad1p and Bub3p, prevents progression into anaphase in presence of spindle damage; Cdc28p-mediated phosphorylation at Bub1p-T566 is important for degradation in anaphase and adaptation of checkpoint to prolonged mitotic arrest; associates with centromere DNA via Skp1p; involved in Sgo1p relocalization in response to sister kinetochore tension; paralog MAD3 arose from whole genome duplication | Core | NA | NA | NA |
| 4090-YGR189C | YGR189C | CRH1 | transglycosylase | Chitin transglycosylase; functions in the transfer of chitin to beta(1-6) and beta(1-3) glucans in the cell wall; similar and functionally redundant to Utr2; localizes to sites of polarized growth; expression induced by cell wall stress | Accessory | Ancestral | NA | NA |
| 4091-YGR190C | YGR190C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene HIP1/YGR191W | Accessory | Ancestral | NA | NA |
| 4092-YGR191W | YGR191W | HIP1 | histidine permease | High-affinity histidine permease; also involved in the transport of manganese ions | Core | NA | NA | NA |
| 4093-YGR192C_NumOfGenes_2 | YGR192C | TDH3 | glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) TDH3|GAPDH|GPD|SSS2|HSP36|HSP35|GLD1 | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isozyme 3; involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell wall; GAPDH-derived antimicrobial peptides secreted by S. cerevisiae are active against a wide variety of wine-related yeasts and bacteria; binds AU-rich RNA | Core | NA | NA | NA |
| 4094-YGR193C | YGR193C | PDX1 | NA | E3-binding protein of the mitochondrial pyruvate dehydrogenase complex; plays a structural role in the complex by binding and positioning dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide acetyltransferase (E2) core | Core | NA | NA | NA |
| 4095-YGR194C_NumOfGenes_2 | YGR194C | XKS1 | xylulokinase | Xylulokinase; converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains | Core | NA | NA | NA |
| 4096-YGR195W | YGR195W | SKI6 | exosome non-catalytic core subunit SKI6|RRP41|ECM20 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp41p (EXOSC4) | Core | NA | NA | NA |
| 4097-YGR196C | YGR196C | FYV8 | NA | Protein of unknown function; required for survival upon exposure to K1 killer toxin | Core | NA | NA | NA |
| 4098-YGR197C | YGR197C | SNG1 | NA | Protein involved in resistance to nitrosoguanidine and 6-azauracil; expression is regulated by transcription factors involved in multidrug resistance; SNG1 has a paralog, YJR015W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4099-YGR198W | YGR198W | YPP1 | NA | Cargo-transport protein involved in endocytosis; interacts with phosphatidylinositol-4-kinase Stt4p; is required, along with Efr3p, for the assembly and recruitment of multiple copies of the kinase into phosphoinositide kinase (PIK) patches at the plasma membrane; positively regulates Stt4p; GFP-fusion protein localizes to the cytoplasm; YGR198W is an essential gene | Core | NA | NA | NA |
| 4100-YGR199W | YGR199W | PMT6 | dolichyl-phosphate-mannose-protein mannosyltransferase PMT6 | Protein O-mannosyltransferase; transfers mannose from dolichyl phosphate-D-mannose to protein serine/threonine residues of secretory proteins; reaction is essential for cell wall rigidity; member of a family of mannosyltransferases | Core | NA | NA | NA |
| 4101-YGR200C | YGR200C | ELP2 | Elongator subunit ELP2|KTI3|TOT2 | Subunit of Elongator complex; binds to microtubules via conserved alkaline residues; has two seven-bladed WD40 β propellers; Elongator complex is required for modification of wobble nucleosides in tRNA; target of Kluyveromyces lactis zymocin | Core | NA | NA | NA |
| 4102-YGR201C | YGR201C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |