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 |
|---|---|---|---|---|---|---|---|---|
| 1928-YBL057C_NumOfGenes_2 | YBL057C | PTH2 | aminoacyl-tRNA hydrolase | One of two mitochondrially-localized peptidyl-tRNA hydrolases; negatively regulates the ubiquitin-proteasome pathway via interactions with ubiquitin-like ubiquitin-associated proteins; dispensable for cell growth; see also PTH1 | Core | NA | NA | NA |
| 1929-YBL058W_NumOfGenes_2 | YBL058W | SHP1 | protein phosphatase regulator SHP1|UBX1 | UBX domain-containing substrate adaptor for Cdc48p; ubiquitin regulatory X domain-containing protein that acts as a substrate recruiting cofactor for Cdc48p; positively regulates Glc7p PPase activity to promote growth and mitotic progression in complex with Cdc48p; ubiquitinated protein interactor involved in ER-associated degradation (ERAD); regulated by nuclear Ub-dependent degradation (INMAD pathway) independent of the Asi and Doa10 complexes; homolog of human p47 (NSFL1C) | Core | NA | NA | NA |
| 1930-YBL059C-A_NumOfGenes_2 | YBL059C-A | CMC2 | NA | Protein involved in respiratory chain complex assembly or maintenance; protein of the mitochondrial intermembrane space; contains twin Cx9C motifs that can form coiled coil-helix-coiled-coil helix fold | Core | NA | NA | NA |
| 1931-YBL059W | YBL059W | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YBL059W has a paralog, YER093C-A, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 1932-YBL060W_NumOfGenes_2 | YBL060W | YEL1 | Arf family guanine nucleotide exchange factor YEL1 | Guanine nucleotide exchange factor specific for Arf3p; localized to the bud neck and tip; required for localization of Arf3p to the bud neck and tip | Core | NA | NA | NA |
| 1933-YBL061C_NumOfGenes_3 | YBL061C | SKT5 | CSD4|CHS4|CAL2 | Activator of Chs3p (chitin synthase III) during vegetative growth; recruits Chs3p to the bud neck via interaction with Bni4p; SKT5 has a paralog, SHC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1934-YBL063W_NumOfGenes_2 | YBL063W | KIP1 | CIN9 | Kinesin-related motor protein; required for mitotic spindle assembly, chromosome segregation, and 2 micron plasmid partitioning; functionally redundant with Cin8p for chromosomal but not plasmid functions | Core | NA | NA | NA |
| 1935-YBL064C | YBL064C | PRX1 | thioredoxin peroxidase PRX1 | Mitochondrial peroxiredoxin with thioredoxin peroxidase activity; has a role in reduction of hydroperoxides; reactivation requires Trr2p and glutathione; induced during respiratory growth and oxidative stress; phosphorylated; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 1936-YBL065W | YBL065W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified ORF SEF1/YBL066C; YBL065W is a non-essential gene | Core | NA | NA | NA |
| 1937-YBL066C | YBL066C | SEF1 | NA | Putative transcription factor; has homolog in Kluyveromyces lactis | Core | NA | NA | NA |
| 1938-YBL067C | YBL067C | UBP13 | ubiquitin-specific protease UBP13 | Ubiquitin-specific protease that cleaves Ub-protein fusions; UBP13 has a paralog, UBP9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1939-YBL068W | YBL068W | PRS4 | ribose phosphate diphosphokinase subunit PRS4 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, synthesizes PRPP; which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes; PRS4 has a paralog, PRS2, that arose from the whole genome duplication; a missense mutation in the conserved residue R196 of its human homolog PRPS1 is pathogenic | Core | NA | NA | NA |
| 1940-YBL069W_NumOfGenes_2 | YBL069W | AST1 | NA | Lipid raft associated protein; interacts with the plasma membrane ATPase Pma1p and has a role in its targeting to the plasma membrane by influencing its incorporation into lipid rafts; sometimes classified in the medium-chain dehydrogenase/reductases (MDRs) superfamily; AST1 has a paralog, AST2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1941-YBL070C | YBL070C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 1942-YBL071C | YBL071C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YBL071C is not an essential gene | Core | NA | NA | NA |