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 |
|---|---|---|---|---|---|---|---|---|
| 5528-YLR068W | YLR068W | FYV7 | NA | Essential protein required for maturation of 18S rRNA; required for survival upon exposure to K1 killer toxin | Core | NA | NA | NA |
| 5529-YLR069C | YLR069C | MEF1 | NA | Mitochondrial elongation factor involved in translational elongation | Core | NA | NA | NA |
| 5530-YLR070C | YLR070C | XYL2 | D-xylulose reductase XYL2 | Xylitol dehydrogenase; converts xylitol to D-xylulose; expression induced by xylose, even though this pentose sugar is not well utilized by S. cerevisiae; null mutant has cell wall defect | Core | NA | NA | NA |
| 5531-YLR071C | YLR071C | RGR1 | MED14 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for glucose repression, HO repression, RME1 repression and sporulation | Core | NA | NA | NA |
| 5532-YLR072W | YLR072W | LAM6 | LTC1 | Sterol transporter that transfers sterols between membranes; may regulate and coordinate formation of contact sites between organelles; localizes to ER-mitochondrial contact sites in a Tom70p- and Tom71p-dependent manner; mitochondrial localization requires GRAM domain; also localizes to ER-vacuole contact sites, in a Vac8p-dependent manner; has GRAM and StART-like (VASt) domains; one of six StART-like domain-containing proteins in yeast; conserved across eukaryotes | Core | NA | NA | NA |
| 5533-YLR073C | YLR073C | RFU1 | NA | Protein that inhibits Doa4p deubiquitinating activity; contributes to ubiquitin homeostasis by regulating the conversion of free ubiquitin chains to ubiquitin monomers by Doa4p; GFP-fusion protein localizes to endosomes | Core | NA | NA | NA |
| 5534-YLR074C_NumOfGenes_2 | YLR074C | BUD20 | NA | C2H2-type zinc finger protein required for ribosome assembly; shuttling factor which associates with pre-60S particles in the nucleus, accompanying them to the cytoplasm; cytoplasmic dissociation of Bud20p requires Drg1p; N-terminus harbors a nuclear localization signal (NLS) and a nuclear export signal (NES); cytoplasmic Bud20p is reimported by Kap123-dependent pathway; involved in bud-site selection; diploid mutants display a random budding pattern; similar to human ZNF593 | Core | NA | NA | NA |
| 5535-YLR075W_NumOfGenes_3 | YLR075W | RPL10 | uL16|ribosomal 60S subunit protein L10|L16|L10|QSR1|GRC5 | Ribosomal 60S subunit protein L10; homologous to mammalian ribosomal protein L10 and bacterial L16; responsible for joining the 40S and 60S subunits; regulates translation initiation; similar to members of the QM gene family; protein abundance increases under DNA replication stress; mutations in human homolog implicated in T-cell acute lymphoblastic leukemia and also autism spectrum disorders (ASD); human RPL10 can complement yeast null mutant | Core | NA | NA | NA |
| 5536-YLR077W_NumOfGenes_2 | YLR077W | FMP25 | BCA1 | Protein required for assembly of respiratory complex III; mitochondrial inner membrane protein; required for an early step in assembly of respiratory complex III (cytochrome bc1 complex); mRNA is targeted to mitochondria | Core | NA | NA | NA |
| 5537-YLR078C_NumOfGenes_2 | YLR078C | BOS1 | SEC32 | v-SNARE (vesicle specific SNAP receptor); localized to the endoplasmic reticulum membrane and necessary for vesicular transport from the ER to the Golgi; required for efficient nuclear fusion during mating | Accessory | Ancestral | NA | NA |
| 5538-YLR079W | YLR079W | SIC1 | BYC1|cyclin-dependent protein serine/threonine kinase inhibiting protein SIC1|SDB25 | Cyclin-dependent kinase inhibitor (CKI); inhibitor of Cdc28-Clb kinase complexes that controls G1/S phase transition, preventing premature S phase and ensuring genomic integrity; phosphorylated by Clb5/6-Cdk1 and Cln1/2-Cdk1 kinase which regulate timing of Sic1p degradation; phosphorylation targets Sic1p for SCF(CDC4)-dependent turnover; functional homolog of mammalian Kip1 | Accessory | Ancestral | NA | NA |
| 5539-YLR080W | YLR080W | EMP46 | NA | Integral membrane component of ER-derived COPII-coated vesicles; functions in ER to Golgi transport; EMP46 has a paralog, EMP47, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5540-YLR081W | YLR081W | GAL2 | galactose permease GAL2 | Galactose permease; required for utilization of galactose; also able to transport glucose | Accessory | Ancestral | NA | NA |
| 5541-YLR082C_NumOfGenes_2 | YLR082C | SRL2 | NA | Protein of unknown function; overexpression suppresses the lethality caused by a rad53 null mutation | Accessory | Ancestral | NA | NA |
| 5542-YLR083C | YLR083C | EMP70 | TMN1|p24a | Protein with a role in cellular adhesion and filamentous growth; also endosome-to-vacuole sorting; similar to Tmn3p; member of Transmembrane Nine family of proteins with 9 transmembrane segments; EMP70 has a paralog, TMN2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |