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 |
|---|---|---|---|---|---|---|---|---|
| 7448-YPL099C | YPL099C | INA17 | AIM43|FMP14 | F1F0 ATPase synthase peripheral stalk assembly factor; subunit of the matrix-exposed inner mitochondrial membrane localized INA complex (Ina22p-Ina17p) involved in assembly of the F1F0 peripheral stalk; co-purifies with Ina22p and ATP synthase subunits; null mutant displays elevated frequency of mitochondrial genome loss and has a respiratory growth defect | Core | NA | NA | NA |
| 7449-YPL100W | YPL100W | ATG21 | HSV1|MAI1 | Phosphoinositide binding protein; required for vesicle formation in the cytoplasm-to-vacuole targeting (Cvt) pathway; binds both phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol 3-phosphate; WD-40 repeat protein | Core | NA | NA | NA |
| 7450-YPL101W_NumOfGenes_2 | YPL101W | ELP4 | Elongator subunit ELP4|KTI9|TOT7|HAP1 | Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex; which is required for modification of wobble nucleosides in tRNA; required for Elongator structural integrity; null mutation is functionally complemented by human ELP4 | Core | NA | NA | NA |
| 7451-YPL102C | YPL102C | 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; deletion mutation enhances replication of Brome mosaic virus in S. cerevisiae, but this is likely due to effects on the overlapping gene ELP4 | Core | NA | NA | NA |
| 7452-YPL103C_NumOfGenes_2 | YPL103C | FMP30 | N-acetylphosphatidylethanolamine-hydrolyzing phospholipase D | Protein with a role in maintaining mitochondrial morphology; also involved in maintaining normal cardiolipin levels; mitochondrial inner membrane protein; proposed to be involved in N-acylethanolamine metabolism; related to mammalian N-acylPE-specific phospholipase D | Core | NA | NA | NA |
| 7453-YPL104W_NumOfGenes_2 | YPL104W | MSD1 | aspartate--tRNA ligase MSD1|LPG5 | Mitochondrial aspartyl-tRNA synthetase; required for acylation of aspartyl-tRNA; yeast and bacterial aspartyl-, asparaginyl-, and lysyl-tRNA synthetases contain regions with high sequence similarity, suggesting a common ancestral gene | Core | NA | NA | NA |
| 7454-YPL105C_NumOfGenes_2 | YPL105C | SYH1 | MYR1 | Protein of unknown function that influences nuclear pore distribution; co-purifies with ribosomes; contains a GYF domain, which bind proline-rich sequences; deletion extends chronological lifespan; SYH1 has a paralog, SMY2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7455-YPL106C_NumOfGenes_2 | YPL106C | SSE1 | adenyl-nucleotide exchange factor SSE1|MSI3|LPG3 | ATPase component of heat shock protein Hsp90 chaperone complex; serves as nucleotide exchange factor to load ATP onto the SSA class of cytosolic Hsp70s; plays a role in prion propagation and determining prion variants; binds unfolded proteins; member of Hsp110 subclass of HSP70 proteins; deletion results in spindle elongation in S phase; SSE1 has a paralog, SSE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7456-YPL107W_NumOfGenes_2 | YPL107W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YPL107W is not an essential gene | Core | NA | NA | NA |
| 7457-YPL108W_NumOfGenes_2 | YPL108W | NA | NA | Cytoplasmic protein of unknown function; non-essential gene that is induced in a GDH1 deleted strain with altered redox metabolism; GFP-fusion protein is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 7458-YPL109C_NumOfGenes_2 | YPL109C | NA | NA | UbiB family protein; contains transmembrane domain and mitochondrial targeting sequence; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 7459-YPL110C | YPL110C | GDE1 | glycerophosphocholine phosphodiesterase | Glycerophosphocholine (GroPCho) phosphodiesterase; hydrolyzes GroPCho to choline and glycerolphosphate, for use as a phosphate source and as a precursor for phosphocholine synthesis; may interact with ribosomes | Core | NA | NA | NA |
| 7460-YPL111W | YPL111W | CAR1 | arginase|cargA|LPH15 | Arginase, catabolizes arginine to ornithine and urea; expression responds to both induction by arginine and nitrogen catabolite repression; disruption decreases production of carcinogen ethyl carbamate during wine fermentation and also enhances freeze tolerance | Core | NA | NA | NA |
| 7461-YPL112C | YPL112C | PEX25 | NA | Peripheral peroxisomal membrane peroxin; required for the regulation of peroxisome size and maintenance, recruits GTPase Rho1p to peroxisomes, induced by oleate, interacts with Pex27p; PEX25 has a paralog, PEX27, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7462-YPL113C_NumOfGenes_2 | YPL113C | NA | glyoxylate reductase | Glyoxylate reductase; acts on glyoxylate and hydroxypyruvate substrates; YPL113C is not an essential gene | Core | NA | NA | NA |