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 |
|---|---|---|---|---|---|---|---|---|
| 7628-YPR004C | YPR004C | AIM45 | NA | Putative ortholog of mammalian ETF-alpha; interacts with frataxin, Yfh1p; null mutant displays elevated frequency of mitochondrial genome loss; may have a role in oxidative stress response; ETF-alpha is an electron transfer flavoprotein complex subunit | Core | NA | NA | NA |
| 7629-YPR005C | YPR005C | HAL1 | NA | Cytoplasmic protein involved in halotolerance; decreases intracellular Na+ (via Ena1p) and increases intracellular K+ by decreasing efflux; expression repressed by Ssn6p-Tup1p and Sko1p and induced by NaCl, KCl, and sorbitol through Gcn4p | Accessory | Ancestral | NA | NA |
| 7630-YPR006C | YPR006C | ICL2 | methylisocitrate lyase ICL2 | 2-methylisocitrate lyase of the mitochondrial matrix; functions in the methylcitrate cycle to catalyze the conversion of 2-methylisocitrate to succinate and pyruvate; ICL2 transcription is repressed by glucose and induced by ethanol | Core | NA | NA | NA |
| 7631-YPR007C | YPR007C | REC8 | SPO69 | Meiosis-specific component of the sister chromatid cohesion complex; alpha-kleisin family member that maintains cohesion between sister chromatids during meiosis I; maintains cohesion between centromeres of sister chromatids until meiosis II; independent of its role in sister chromatid cohesion, Rec8p promotes allelic collisions and prevents nonspecific chromosome interactions; homolog of S. pombe Rec8p | Core | NA | NA | NA |
| 7632-YPR008W | YPR008W | HAA1 | NA | Transcriptional activator involved in adaptation to weak acid stress; activates transcription of TPO2, YRO2, and other genes encoding membrane stress proteins; HAA1 has a paralog, CUP2, that arose from the whole genome duplication; relocalizes from cytoplasm to nucleus upon DNA replication stress | Core | NA | NA | NA |
| 7633-YPR009W | YPR009W | SUT2 | NA | Zn2Cys6 family transcription factor; positively regulates sterol uptake under anaerobic conditions with SUT1; represses filamentation-inducing genes during non-starvation conditions; positively regulates mating along with SUT1 by repressing the expression of genes (PRR2, NCE102 and RHO5) which function as mating inhibitors; multicopy suppressor of mutations that cause low activity of the cAMP/PKA pathway; SUT2 has a paralog, SUT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7634-YPR010C | YPR010C | RPA135 | DNA-directed RNA polymerase I core subunit RPA135|A135|SRP3|RRN2|RPA2 | RNA polymerase I second largest subunit A135 | Core | NA | NA | NA |
| 7635-YPR010C-A | YPR010C-A | NA | NA | Putative protein of unknown function; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the cytosol; conserved among Saccharomyces sensu stricto species | Core | NA | NA | NA |
| 7636-YPR011C | YPR011C | NA | NA | Mitochondrial transporter; major substrates are adenosine 5'-phosphosulfate (APS) and 3'-phospho-adenosine 5'-phosphosulfate (PAPS); member of the mitochondrial carrier family; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 7637-YPR012W | YPR012W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YPR012W is not an essential gene | Core | NA | NA | NA |
| 7638-YPR013C | YPR013C | CMR3 | NA | Putative zinc finger protein; YPR013C is not an essential gene | Core | NA | NA | NA |
| 7639-YPR014C | YPR014C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YPR014C is not an essential gene | Core | NA | NA | NA |
| 7640-YPR015C | YPR015C | NA | NA | Putative zinc finger transcription factor; binds DNA in sequence-specific manner; overexpression causes a cell cycle delay or arrest | Core | NA | NA | NA |
| 7641-YPR016C | YPR016C | TIF6 | translation initiation factor 6|CDC95 | Constituent of 66S pre-ribosomal particles; has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits | Core | NA | NA | NA |
| 7642-YPR016W-A | YPR016W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |