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 |
|---|---|---|---|---|---|---|---|---|
| 6983-YOR016C | YOR016C | ERP4 | NA | Member of the p24 family involved in ER to Golgi transport; similar to Emp24p and Erv25p; ERP4 has a paralog, ERP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6984-YOR017W | YOR017W | PET127 | NA | Protein with a role in 5'-end processing of mitochondrial RNAs; located in the mitochondrial membrane | Core | NA | NA | NA |
| 6985-YOR018W | YOR018W | ROD1 | ART4 | Alpha-arrestin involved in ubiquitin-dependent endocytosis; activating dephosphorylation relays glucose signaling to transporter endocytosis; calcineurin dephosphorylation is required for Rsp5p-dependent internalization of agonist-occupied Ste2p, as part of signal desensitization; recruits Rsp5p to Ste2p via its 2 PPXY motifs; protein abundance increases in response to DNA replication stress; ROD1 has a paralog, ROG3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6986-YOR019W | YOR019W | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; YOR019W has a paralog, JIP4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6987-YOR020C | YOR020C | HSP10 | CPN10 | Mitochondrial matrix co-chaperonin; inhibits the ATPase activity of Hsp60p, a mitochondrial chaperonin; involved in protein folding and sorting in the mitochondria; 10 kD heat shock protein with similarity to E. coli groES | Core | NA | NA | NA |
| 6988-YOR020W-A | YOR020W-A | NA | NA | Putative protein of unknown function; conserved in A. gossypii; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6989-YOR021C | YOR021C | SFM1 | protein-arginine N-methyltransferase SFM1 | SPOUT methyltransferase; catalyzes omega-monomethylation of Rps3p on Arg-146; not an essential gene; predicted to be involved in rRNA processing and ribosome biogenesis and in biopolymer catabolism | Core | NA | NA | NA |
| 6990-YOR022C | YOR022C | DDL1 | putative carboxylic ester hydrolase | DDHD domain-containing phospholipase A1; mitochondrial matrix enzyme with sn-1-specific activity, hydrolyzing cardiolipin, PE, PC, PG and PA; implicated in remodeling of mitochondrial phospholipids; antagonistically regulated by Aft1p and Aft2p; in humans, mutations in DDHD1 and DDHD2 genes cause specific types of hereditary spastic paraplegia, while DDL1-defective yeast share similar phenotypes such as mitochondrial dysfunction and defects in lipid metabolism | Core | NA | NA | NA |
| 6991-YOR023C | YOR023C | AHC1 | NA | Subunit of the Ada histone acetyltransferase complex; required for structural integrity of the complex; Ahc2p and Ahc1p are unique to the ADA complex and not shared with the related SAGA and SLIK complexes; Ahc2p may tether Ahc1p to the complex | Core | NA | NA | NA |
| 6992-YOR024W | YOR024W | NA | IRC12 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6993-YOR025W | YOR025W | HST3 | NAD-dependent histone deacetylase HST3 | Member of the Sir2 family of NAD(+)-dependent protein deacetylases; involved along with Hst4p in telomeric silencing, cell cycle progression, radiation resistance, genomic stability and short-chain fatty acid metabolism | Core | NA | NA | NA |
| 6994-YOR026W | YOR026W | BUB3 | PAC9 | Kinetochore checkpoint WD40 repeat protein; localizes to kinetochores during prophase and metaphase, delays anaphase in the presence of unattached kinetochores; forms complexes with Mad1p-Bub1p and with Cdc20p, binds Mad2p and Mad3p; functions at kinetochore to activate APC/C-Cdc20p for normal mitotic progression | Core | NA | NA | NA |
| 6995-YOR027W | YOR027W | STI1 | Hsp90 cochaperone STI1 | Hsp90 cochaperone; regulates spatial organization of amyloid-like proteins in the cytosol, thereby buffering the proteotoxicity caused by amyloid-like proteins; interacts with the Ssa group of the cytosolic Hsp70 chaperones and activates Ssa1p ATPase activity; interacts with Hsp90 chaperones and inhibits their ATPase activity; homolog of mammalian Hop | Core | NA | NA | NA |
| 6996-YOR028C | YOR028C | CIN5 | YAP4|HAL6 | Basic leucine zipper (bZIP) transcription factor of the yAP-1 family; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; mediates pleiotropic drug resistance and salt tolerance; nuclearly localized under oxidative stress and sequestered in the cytoplasm by Lot6p under reducing conditions; CIN5 has a paralog, YAP6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6997-YOR029W | YOR029W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YOR029W is not an essential gene | Accessory | Ancestral | NA | NA |