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 |
|---|---|---|---|---|---|---|---|---|
| 6053-YML128C | YML128C | MSC1 | NA | Protein of unknown function; mutant is defective in directing meiotic recombination events to homologous chromatids; the authentic, non-tagged protein is detected in highly purified mitochondria and is phosphorylated | Core | NA | NA | NA |
| 6054-YML129C | YML129C | COX14 | NA | Mitochondrial cytochrome c oxidase (complex IV) assembly factor; also involved in translational regulation of Cox1p and prevention of Cox1p aggregation before assembly; associates with complex IV assembly intermediates and complex III/complex IV supercomplexes; located in the mitochondrial membrane | Core | NA | NA | NA |
| 6055-YML130C | YML130C | ERO1 | ER oxidoreductin | Thiol oxidase required for oxidative protein folding in the ER; essential for maintaining ER redox balance; feedback regulated via reduction and oxidation of regulatory bonds; reduced Pdi1p activates Ero1p by direct reduction of Ero1p regulatory bonds; depletion of thiol substrates and accumulation of oxidized Pdi1p results in inactivation of Ero1p by both Pdi1p-mediated oxidation and autonomous oxidation of Ero1p regulatory bonds; ero1-1 mutation complemented by human ERO1L | Core | NA | NA | NA |
| 6056-YML131W | YML131W | NA | NA | Protein of unknown function; similar to medium chain dehydrogenase/reductases; expression induced by stresses including osmotic shock, DNA damaging agents, and other chemicals; GFP-fusion protein localizes to the cytoplasm; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6057-YMR001C | YMR001C | CDC5 | polo kinase CDC5|PKX2|MSD2 | Polo-like kinase; controls targeting and activation of Rho1p at cell division site via Rho1p guanine nucleotide exchange factors; regulates Spc72p; also functions in adaptation to DNA damage during meiosis; regulates the shape of the nucleus and expansion of the nuclear envelope during mitosis; similar to Xenopus Plx1 and S. pombe Plo1p; human homologs PLK1, PLK3 can each complement yeast cdc5 thermosensitive mutants | Core | NA | NA | NA |
| 6058-YMR001C-A | YMR001C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6059-YMR002W | YMR002W | MIX17 | MIC17 | Mitochondrial intermembrane space protein; required for normal oxygen consumption; contains twin cysteine-x9-cysteine motifs; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6060-YMR003W | YMR003W | AIM34 | NA | Protein of unknown function; GFP-fusion protein localizes to the mitochondria; null mutant is viable and displays reduced frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 6061-YMR004W | YMR004W | MVP1 | NA | Protein required for sorting proteins to the vacuole; Mvp1p and Vps1p act in concert to promote membrane traffic to the vacuole; participates in transcription initiation and/or early elongation of specific genes; interacts with "foot domain" of RNA polymerase II; deletion results in abnormal CTD-Ser5 phosphorylation of RNA polymerase II at specific promoter regions; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6062-YMR005W | YMR005W | TAF4 | TafII48|MPT1|TSG2|TAF48 | TFIID subunit (48 kDa); involved in RNA polymerase II transcription initiation; potential Cdc28p substrate | Core | NA | NA | NA |
| 6063-YMR006C | YMR006C | PLB2 | lysophospholipase | Phospholipase B (lysophospholipase) involved in lipid metabolism; displays transacylase activity in vitro; overproduction confers resistance to lysophosphatidylcholine | Core | NA | NA | NA |
| 6064-YMR007W | YMR007W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR007W is not an essential gene | Core | NA | NA | NA |
| 6065-YMR008C | YMR008C | PLB1 | lysophospholipase | Phospholipase B (lysophospholipase) involved in lipid metabolism; required for efficient acyl chain remodeling of newly synthesized phosphatidylethanolamine-derived phosphatidylcholine; required for deacylation of phosphatidylcholine and phosphatidylethanolamine but not phosphatidylinositol; PLB1 has a paralog, PLB3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6066-YMR009W | YMR009W | ADI1 | acireductone dioxygenase (Ni2+-requiring) | Acireductone dioxygenease involved in methionine salvage pathway; transcribed as polycistronic mRNA with YMR010W and regulated post-transcriptionally by RNase III (Rnt1p) cleavage; ADI1 mRNA is induced in heat shock conditions; human ortholog ADI1 can complement yeast adi1 mutant | Core | NA | NA | NA |
| 6067-YMR010W | YMR010W | ANY1 | NA | Putative protein of unknown function; null allele suppresses the lethality of neo1 and dop1 null alleles, as well as the growth defect of a mon2 null allele, and the cold sensitivity of a drs2 null; proposed function as a phospholipid scramblase that reduces membrane asymmetry; PQ loop family member; localizes to the cytoplasm and endoplasmic reticulum in HTP studies; non-essential gene | Core | NA | NA | NA |