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 |
|---|---|---|---|---|---|---|---|---|
| 5438-YLL038C | YLL038C | ENT4 | NA | Protein of unknown function; contains an N-terminal epsin-like domain; proposed to be involved in the trafficking of Arn1p in the absence of ferrichrome | Core | NA | NA | NA |
| 5439-YLL039C | YLL039C | UBI4 | ubiquitin|UB14|SCD2 | Ubiquitin; becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5440-YLL040C | YLL040C | VPS13 | membrane morphogenesis protein VPS13|VPT2|SOI1 | Protein involved in prospore membrane morphogenesis; peripheral membrane protein that localizes to the prospore membrane and at numerous membrane contact sites; involved in sporulation, vacuolar protein sorting, prospore membrane formation during sporulation, and protein-Golgi retention; required for mitochondrial integrity; contains a PH-like domain; homologous to human CHAC and COH1 which are involved in Chorea-acanthocytosis and Cohen syndrome, respectively | Core | NA | NA | NA |
| 5441-YLL041C | YLL041C | SDH2 | succinate dehydrogenase iron-sulfur protein subunit SDH2|SDHB|ACN17 | Iron-sulfur protein subunit of succinate dehydrogenase; the complex couples the oxidation of succinate to the transfer of electrons to ubiquinone as part of the TCA cycle and the mitochondrial respiratory chain; other members are Sdh1p, Sdh3p, and Sdh4p | Core | NA | NA | NA |
| 5442-YLL042C | YLL042C | ATG10 | E2-like conjugating enzyme|APG10 | Conserved E2-like conjugating enzyme; mediates formation of the Atg12p-Atg5p conjugate, which is a critical step in autophagy | Core | NA | NA | NA |
| 5443-YLL043W | YLL043W | FPS1 | NA | Aquaglyceroporin, plasma membrane channel; involved in efflux of glycerol and xylitol, and in uptake of acetic acid, arsenite, and antimonite; key factor in maintaining redox balance by mediating passive diffusion of glycerol; phosphorylated by Hog1p MAPK under acetate stress; deletion improves xylose fermentation; regulated by Rgc1p and Ask10p, which are regulated by Hog1p phosphorylation under osmotic stress; phosphorylation by Ypk1p required to maintain an open state | Core | NA | NA | NA |
| 5444-YLL046C_NumOfGenes_2 | YLL046C | RNP1 | NA | Ribonucleoprotein that contains two RNA recognition motifs (RRM); RNP1 has a paralog, SBP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5445-YLL048C | YLL048C | YBT1 | bile acid-transporting ATPase YBT1|BAT1 | Transporter of the ATP-binding cassette (ABC) family; involved in bile acid transport; negative regulator of vacuole fusion; regulates release of lumenal Ca2+ stores; similar to mammalian bile transporters; YBT1 has a paralog, VMR1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5446-YLL049W | YLL049W | LDB18 | NA | Component of the dynactin complex; dynactin is required for dynein activity; null mutant exhibits defects in nuclear migration and spindle orientation and has reduced affinity for alcian blue dye; has homology to mammalian dynactin subunit p24 | Accessory | Ancestral | NA | NA |
| 5447-YLL050C | YLL050C | COF1 | cofilin | Cofilin, involved in pH-dependent actin filament depolarization; binds both actin monomers and filaments and severs filaments; involved in the selective sorting, export of the secretory cargo from the late golgi; genetically interacts with pmr1; thought to be regulated by phosphorylation at SER4; ubiquitous and essential in eukaryotes | Accessory | Ancestral | NA | NA |
| 5448-YLL051C | YLL051C | FRE6 | putative ferric-chelate reductase | Putative ferric reductase with similarity to Fre2p; expression induced by low iron levels | Accessory | Ancestral | NA | NA |
| 5449-YLL052C | YLL052C | AQY2 | NA | Water channel that mediates water transport across cell membranes; only expressed in proliferating cells; controlled by osmotic signals; may be involved in freeze tolerance; disrupted by a stop codon in many S. cerevisiae strains | Accessory | Ancestral | NA | NA |
| 5450-YLL053C | YLL053C | NA | NA | Putative protein; in the Sigma 1278B strain background YLL053C is contiguous with AQY2 which encodes an aquaporin | Accessory | Ancestral | NA | NA |
| 5451-YLL054C | YLL054C | NA | NA | Putative protein of unknown function with similarity to Pip2p; an oleate-specific transcriptional activator of peroxisome proliferation; YLL054C is not an essential gene | Accessory | Ancestral | NA | NA |
| 5452-YLL055W | YLL055W | YCT1 | NA | High-affinity cysteine-specific transporter; has similarity to the Dal5p family of transporters; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YCT1 is not an essential gene | Accessory | Ancestral | NA | NA |