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 |
|---|---|---|---|---|---|---|---|---|
| 7688-YPR064W | YPR064W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YPR064W is not an essential gene | Core | NA | NA | NA |
| 7689-YPR065W | YPR065W | ROX1 | REO1 | Heme-dependent repressor of hypoxic genes; mediates aerobic transcriptional repression of hypoxia induced genes such as COX5b and CYC7; repressor function regulated through decreased promoter occupancy in response to oxidative stress; contains an HMG domain that is responsible for DNA bending activity; involved in the hyperosmotic stress resistance | Core | NA | NA | NA |
| 7690-YPR066W | YPR066W | UBA3 | NEDD8-activating protein UBA3 | Protein that activates Rub1p (NEDD8) before neddylation; acts together with Ula1p; may play a role in protein degradation; GFP-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 7691-YPR067W | YPR067W | ISA2 | NA | Protein required for maturation of mitochondrial [4Fe-4S] proteins; functions in a complex with Isa1p and possibly Iba57p; localizes to the mitochondrial intermembrane space, overexpression of ISA2 suppresses grx5 mutations | Core | NA | NA | NA |
| 7692-YPR068C | YPR068C | HOS1 | histone deacetylase|CST3 | Class I histone deacetylase (HDAC) family member; deacetylates Smc3p on lysine residues at anaphase onset; has sequence similarity to Hda1p, Rpd3p, Hos2p, and Hos3p; interacts with the Tup1p-Ssn6p corepressor complex | Core | NA | NA | NA |
| 7693-YPR069C | YPR069C | SPE3 | spermidine synthase | Spermidine synthase; involved in biosynthesis of spermidine and also in biosynthesis of pantothenic acid; spermidine is required for growth of wild-type cells | Core | NA | NA | NA |
| 7694-YPR070W | YPR070W | MED1 | NA | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation | Core | NA | NA | NA |
| 7695-YPR071W | YPR071W | NA | NA | Putative membrane protein; YPR071W is not an essential gene; YPR071W has a paralog, YIL029C, that arose from a single-locus duplication | Accessory | Ancestral | NA | NA |
| 7696-YPR072W | YPR072W | NOT5 | CCR4-NOT core subunit NOT5 | Component of the CCR4-NOT core complex, involved in mRNA decapping; involved intranscription initiation and elongation and in mRNA degradation; conserved lysine in human homolog of Not5p and Not3p is mutated in cancers | Core | NA | NA | NA |
| 7697-YPR073C | YPR073C | LTP1 | tyrosine protein phosphatase LTP1 | Protein phosphotyrosine phosphatase of unknown cellular role; activated by adenine | Core | NA | NA | NA |
| 7698-YPR074C | YPR074C | TKL1 | transketolase TKL1 | Transketolase; catalyzes conversion of xylulose-5-phosphate and ribose-5-phosphate to sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate in the pentose phosphate pathway; needed for synthesis of aromatic amino acids; TKL1 has a paralog, TKL2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7699-YPR074W-A | YPR074W-A | NA | NA | Hypothetical protein identified by homology | Core | NA | NA | NA |
| 7700-YPR075C_NumOfGenes_2 | YPR075C | OPY2 | NA | Integral membrane protein that acts as a membrane anchor for Ste50p; involved in the signaling branch of the high-osmolarity glycerol (HOG) pathway and as a regulator of the filamentous growth pathway; overproduction blocks cell cycle arrest in the presence of mating pheromone; relocalizes from vacuole to plasma membrane upon DNA replication stress | Core | NA | NA | NA |
| 7701-YPR078C_NumOfGenes_2 | YPR078C | NA | NA | Putative protein of unknown function; possible role in DNA metabolism and/or in genome stability; expression is heat-inducible | Core | NA | NA | NA |
| 7702-YPR079W | YPR079W | MRL1 | NA | Membrane protein; has similarity to mammalian mannose-6-phosphate receptors; possibly functions as a sorting receptor in the delivery of vacuolar hydrolases; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |