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 |
|---|---|---|---|---|---|---|---|---|
| 7088-YOR124C | YOR124C | UBP2 | ubiquitin-specific protease UBP2 | Ubiquitin-specific protease; removes ubiquitin from ubiquitinated proteins; controls K63 homeostasis during oxidative stress; deubiquitinates Rsp5p and is required for MVB sorting of membrane proteins; can cleave polyubiquitin and has isopeptidase activity | Core | NA | NA | NA |
| 7089-YOR125C | YOR125C | CAT5 | putative monooxygenase CAT5|COQ7 | Protein required for ubiquinone (Coenzyme Q) biosynthesis; localizes to the matrix face of the mitochondrial inner membrane in a large complex with ubiquinone biosynthetic enzymes; required for gluconeogenic gene activation | Core | NA | NA | NA |
| 7090-YOR126C | YOR126C | IAH1 | isoamyl acetate-hydrolyzing esterase | Isoamyl acetate-hydrolyzing esterase; required in balance with alcohol acetyltransferase to maintain optimal amounts of isoamyl acetate, which is particularly important in sake brewing | Core | NA | NA | NA |
| 7091-YOR127W | YOR127W | RGA1 | THE1|DBM1 | GTPase-activating protein for polarity-establishment protein Cdc42p; implicated in control of septin organization, pheromone response, and haploid invasive growth; relocalizes from bud neck to cytoplasm upon DNA replication stress; RGA1 has a paralog, RGA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7092-YOR128C | YOR128C | ADE2 | phosphoribosylaminoimidazole carboxylase ADE2 | Phosphoribosylaminoimidazole carboxylase; catalyzes a step in the 'de novo' purine nucleotide biosynthetic pathway; red pigment accumulates in mutant cells deprived of adenine | Core | NA | NA | NA |
| 7093-YOR129C | YOR129C | AFI1 | NA | Arf3p polarization-specific docking factor; required for the polarized distribution of the ADP-ribosylation factor, Arf3p; participates in polarity development and maintenance of a normal haploid budding pattern; interacts with Cnm7p | Core | NA | NA | NA |
| 7094-YOR130C | YOR130C | ORT1 | ARG11 | Ornithine transporter of the mitochondrial inner membrane; exports ornithine from mitochondria as part of arginine biosynthesis; functionally complemented by human ortholog, SLC25A15, which is associated with hyperammonaemia-hyperornithinaemia-homocitrullinuria (HHH) syndrome, but HHH-associated variants fail to complement | Core | NA | NA | NA |
| 7095-YOR131C | YOR131C | NA | putative haloacid dehalogenase-like hydrolase | Putative haloacid dehalogenase-like hydrolase; non-essential gene; overexpression causes a cell cycle delay or arrest; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7096-YOR132W | YOR132W | VPS17 | retromer subunit VPS17|VPT3|PEP21 | Subunit of the membrane-associated retromer complex; essential for endosome-to-Golgi retrograde protein transport; peripheral membrane protein that assembles onto the membrane with Vps5p to promote vesicle formation; required for recruiting the retromer complex to the endosome membranes | Core | NA | NA | NA |
| 7097-YOR134W | YOR134W | BAG7 | NA | Rho GTPase activating protein (RhoGAP); stimulates the intrinsic GTPase activity of Rho1p, which plays a bud growth by regulating actin cytoskeleton organization and cell wall biosynthesis, resulting in the downregulation of Rho1p; structurally and functionally related to Sac7p; BAG7 has a paralog, SAC7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7098-YOR135C | YOR135C | IRC14 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YOR136W; null mutant displays increased levels of spontaneous Rad52 foci | Accessory | Ancestral | NA | NA |
| 7099-YOR136W | YOR136W | IDH2 | isocitrate dehydrogenase (NAD(+)) IDH2 | Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase; complex catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle; phosphorylated | Core | NA | NA | NA |
| 7100-YOR137C | YOR137C | SIA1 | NA | Protein of unassigned function; involved in activation of the Pma1p plasma membrane H+-ATPase by glucose; contains peptide signal for membrane localization | Core | NA | NA | NA |
| 7101-YOR138C | YOR138C | RUP1 | NA | Protein that regulates ubiquitination of Rsp5p; has a WW domain consensus motif of PPPSY (residues 131-135) that mediates binding of Rsp5p to Ubp2p; contains an UBA domain; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 7102-YOR140W_NumOfGenes_2 | YOR140W | SFL1 | NA | Transcriptional repressor and activator; involved in repression of flocculation-related genes, and activation of stress responsive genes; has direct role in INO1 transcriptional memory; negatively regulated by cAMP-dependent protein kinase A subunit Tpk2p; premature stop codon (C1430T, Q477-stop) in SK1 background is linked to the aggressively invasive phenotype of SK1 relative to BY4741 (S288C) | Accessory | Ancestral | NA | NA |