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 |
|---|---|---|---|---|---|---|---|---|
| 6158-YMR100W | YMR100W | MUB1 | NA | MYND domain-containing protein; component of the Mub1p-Ubr2p-Rad6p ubiquitin ligase complex, required for ubiquitination and degradation of Rpn4p; interacts with Ubr2p (E3) and indirectly with Rad6p (E2); short-lived protein degraded in a Ubr2p/Rad6p dependent manner; proposed to function as both a partner and substrate of the Ubr2p/Rad6p ubiquitin ligase; similar to the A. nidulans samB gene | Core | NA | NA | NA |
| 6159-YMR101C | YMR101C | SRT1 | ditrans,polycis-polyprenyl diphosphate synthase | Forms the dehydrodolichyl diphosphate syntase (DDS) complex with NUS1; involved in synthesis of long-chain dolichols (19-22 isoprene units; as opposed to Rer2p which synthesizes shorter-chain dolichols); localizes to lipid bodies; transcription is induced during stationary phase | Core | NA | NA | NA |
| 6160-YMR102C | YMR102C | NA | NA | Protein of unknown function; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance; mutant shows increased resistance to azoles; not an essential gene; YMR102C has a paralog, DGR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6161-YMR103C | YMR103C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR103C is not an essential gene | Core | NA | NA | NA |
| 6162-YMR104C | YMR104C | YPK2 | putative protein kinase YPK2|YKR2 | Protein kinase similar to S/T protein kinase Ypk1p; functionally redundant with YPK1 at the genetic level; participates in a signaling pathway required for optimal cell wall integrity; involved in the TORC-dependent phosphorylation of ribosomal proteins Rps6a/b (S6); human homolog SGK2 can complement a ypk1 ypk2 double mutant | Core | NA | NA | NA |
| 6163-YMR105C | YMR105C | PGM2 | phosphoglucomutase PGM2|GAL5 | Phosphoglucomutase; catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism; functions as the acceptor for a Glc-phosphotransferase; protein abundance increases in response to DNA replication stress; PGM2 has a paralog, PGM1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6164-YMR105W-A | YMR105W-A | NA | NA | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 6165-YMR106C | YMR106C | YKU80 | ATP-dependent DNA helicase YKU80|HDF2 | Subunit of telomeric Ku complex (Yku70p-Yku80p); involved in telomere length maintenance, structure and telomere position effect; required for localization of telomerase ribonucleoprotein via interaction with TLC1 guide RNA; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair; colocalizes with quiescent cell telomere hyperclusters | Accessory | Ancestral | NA | NA |
| 6166-YMR107W | YMR107W | SPG4 | NA | Protein required for high temperature survival during stationary phase; not required for growth on nonfermentable carbon sources | Accessory | Ancestral | NA | NA |
| 6167-YMR108W | YMR108W | ILV2 | acetolactate synthase catalytic subunit|THI1|SMR1 | Acetolactate synthase; catalyses the first common step in isoleucine and valine biosynthesis and is the target of several classes of inhibitors, localizes to the mitochondria; expression of the gene is under general amino acid control | Core | NA | NA | NA |
| 6168-YMR109W | YMR109W | MYO5 | myosin 5 | One of two type I myosin motors; contains proline-rich tail homology 2 (TH2) and SH3 domains; MYO5 deletion has little effect on growth, but myo3 myo5 double deletion causes severe defects in growth and actin cytoskeleton organization; MYO5 has a paralog, MYO3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6169-YMR110C | YMR110C | HFD1 | hexadecenal dehydrogenase | Dehydrogenase involved in ubiquinone and sphingolipid metabolism; oxidizes 4-hydroxybenzaldehyde into 4-hydroxybenzoic acid in ubiquinone biosynthesis; converts hexadecenal to hexadecenoic acid in sphingosine 1-phosphate breakdown pathway; located in the mitochondrial outer membrane and also in lipid particles; human homolog ALDH3A2, a fatty aldehyde dehydrogenase (FALDH) mutated in neurocutaneous disorder Sjogren-Larsson syndrome, can complement yeast hfd1 mutant | Core | NA | NA | NA |
| 6170-YMR111C | YMR111C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YMR111C is not an essential gene; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 6171-YMR112C | YMR112C | MED11 | NA | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential protein | Core | NA | NA | NA |
| 6172-YMR113W | YMR113W | FOL3 | dihydrofolate synthase | Dihydrofolate synthetase, involved in folic acid biosynthesis; catalyzes conversion of dihydropteroate to dihydrofolate in folate coenzyme biosynthesis; FOL3 has a paralog, RMA1, that arose from the whole genome duplication | Core | NA | NA | NA |