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 |
|---|---|---|---|---|---|---|---|---|
| 5963-YML046W | YML046W | PRP39 | NA | U1 snRNP protein involved in splicing; contains multiple tetriatricopeptide repeats | Core | NA | NA | NA |
| 5964-YML047C | YML047C | PRM6 | pheromone-regulated K(+) transporter PRM6|KCH2 | Potassium transporter that mediates K+ influx; activates high-affinity Ca2+ influx system (HACS) during mating pheromone response; expression up-regulated in response to alpha factor; regulated by Ste12p during mating; localized to sites of polarized growth; member of a fungal-specific gene family; PRM6 has a paralog, KCH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5965-YML047W-A | YML047W-A | NA | YML048W-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF PRM6/YML047C | Accessory | Ancestral | NA | NA |
| 5966-YML048W | YML048W | GSF2 | ECM6 | Endoplasmic reticulum (ER) localized integral membrane protein; may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression | Core | NA | NA | NA |
| 5967-YML049C | YML049C | RSE1 | U2 snRNP complex subunit RSE1 | Protein involved in pre-mRNA splicing; component of the pre-spliceosome; associates with U2 snRNA; involved in ER to Golgi transport | Core | NA | NA | NA |
| 5968-YML050W | YML050W | AIM32 | NA | Protein of unknown function; null mutant is viable and displays elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 5969-YML051W | YML051W | GAL80 | transcription regulator GAL80 | Transcriptional regulator involved in the repression of GAL genes; involved in the repression of GAL genes in the absence of galactose; inhibits transcriptional activation by Gal4p; inhibition relieved by Gal3p or Gal1p binding | Core | NA | NA | NA |
| 5970-YML052W | YML052W | SUR7 | NA | Plasma membrane protein, component of eisosomes; long-lived protein that remains stable in eisosomes of mother cells while other eisosome proteins, Pil1p and Lsp1p, turn over; may function to anchor the eisosome in place; sporulation and plasma membrane sphingolipid content are altered in mutants; localizes to furrow-like invaginations (MCC patches) | Core | NA | NA | NA |
| 5971-YML053C | YML053C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus; overexpression causes a cell cycle delay or arrest; YML053C is not an essential gene | Core | NA | NA | NA |
| 5972-YML054C | YML054C | CYB2 | FCB2 | Cytochrome b2 (L-lactate cytochrome-c oxidoreductase); component of the mitochondrial intermembrane space, required for lactate utilization; expression is repressed by glucose and anaerobic conditions | Core | NA | NA | NA |
| 5973-YML054C-A | YML054C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5974-YML055W | YML055W | SPC2 | signal peptidase complex subunit SPC2|SPY1 | Subunit of signal peptidase complex; complex catalyzes cleavage of N-terminal signal sequences of proteins targeted to the secretory pathway; homologous to mammalian SPC25; other members of the complex are Spc1p, Spc1p, and Sec11p | Core | NA | NA | NA |
| 5975-YML056C | YML056C | IMD4 | IMP dehydrogenase IMD4 | Inosine monophosphate dehydrogenase; catalyzes the rate-limiting step in the de novo synthesis of GTP; member of a four-gene family in S. cerevisiae, constitutively expressed; IMD4 has a paralog, IMD3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5976-YML057C-A | YML057C-A | NA | YML058C-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene CMP2/YML057W | Accessory | Ancestral | NA | NA |
| 5977-YML057W | YML057W | CMP2 | calcineurin catalytic subunit A|CNA2 | Calcineurin A; one isoform (the other is Cna1p) of the catalytic subunit of calcineurin, a Ca++/calmodulin-regulated protein phosphatase which regulates Crz1p (a stress-response transcription factor), the other calcineurin subunit is CNB1; regulates the function of Aly1p alpha-arrestin; CMP2 has a paralog, CNA1, that arose from the whole genome duplication | Core | NA | NA | NA |