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 |
|---|---|---|---|---|---|---|---|---|
| 3638-YFR051C | YFR051C | RET2 | coatomer subunit delta | Delta subunit of the coatomer complex (COPI); COPI coats Golgi-derived transport vesicles; involved in retrograde transport between Golgi and ER | Accessory | Ancestral | NA | NA |
| 3639-YFR052C-A | YFR052C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF HXK1/YFR053C | Accessory | Ancestral | NA | NA |
| 3640-YFR052W | YFR052W | RPN12 | proteasome regulatory particle lid subunit RPN12|NIN1 | Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3641-YFR053C | YFR053C | HXK1 | hexokinase 1 | Hexokinase isoenzyme 1; a cytosolic protein that catalyzes phosphorylation of glucose during glucose metabolism; expression is highest during growth on non-glucose carbon sources; glucose-induced repression involves hexokinase Hxk2p; HXK1 has a paralog, HXK2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3642-YFR054C | YFR054C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains | Accessory | Unknown | NA | NA |
| 3643-YFR055W | YFR055W | IRC7 | cysteine-S-conjugate beta-lyase IRC7 | Beta-lyase involved in the production of thiols; null mutant displays increased levels of spontaneous Rad52p foci; expression induced by nitrogen limitation in a GLN3, GAT1-dependent manner and by copper levels in a Mac1-dependent manner | Accessory | Ancestral | NA | NA |
| 3644-YFR056C | YFR056C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized gene YFR055W | Accessory | Ancestral | NA | NA |
| 3645-YFR057W | YFR057W | NA | NA | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 3646-YGL001C | YGL001C | ERG26 | sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) | C-3 sterol dehydrogenase; catalyzes the second of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; human homolog NSDHL implicated in CK syndrome, and can complement yeast null mutant; molecular target of natural product and antifungal compound FR171456 | Core | NA | NA | NA |
| 3647-YGL002W | YGL002W | ERP6 | NA | Member of the p24 family involved in ER to Golgi transport; similar to Emp24p and Erv25p; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; ERP6 has a paralog, ERP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3648-YGL003C | YGL003C | CDH1 | HCT1 | Activator of anaphase-promoting complex/cyclosome (APC/C); antagonist of the spindle assembly checkpoint; directs ubiquitination of cyclins resulting in mitotic exit; targets the APC/C to specific substrates including: Cdc20p, Ase1p, Cin8p, Fin1p and Clb5p; partially active in metaphase, and fully active in anaphase; cell-cycle regulated | Core | NA | NA | NA |
| 3649-YGL004C | YGL004C | RPN14 | NA | Evolutionarily conserved 19S regulatory particle assembly-chaperone; proteasome-interacting protein involved in the assembly of the base subcomplex of the 19S proteasome regulatory particle (RP); null mutants accumulate ubiquitinated Gcn4p and display decreased 26S proteasome stability; interacts with Rpt5p | Core | NA | NA | NA |
| 3650-YGL005C | YGL005C | COG7 | Golgi transport complex subunit COG7|COD5 | Component of the conserved oligomeric Golgi complex; a cytosolic tethering complex (Cog1p through Cog8p) that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments | Core | NA | NA | NA |
| 3651-YGL006W | YGL006W | PMC1 | calcium-transporting ATPase PMC1 | Vacuolar Ca2+ ATPase involved in depleting cytosol of Ca2+ ions; prevents growth inhibition by activation of calcineurin in the presence of elevated concentrations of calcium; similar to mammalian PMCA1a | Core | NA | NA | NA |
| 3652-YGL006W-A | YGL006W-A | NA | NA | Putative protein of unknown function; identified by SAGE | Accessory | Unknown | NA | NA |