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 |
|---|---|---|---|---|---|---|---|---|
| 7778-YPR160W_NumOfGenes_3 | YPR160W | GPH1 | glycogen phosphorylase | Glycogen phosphorylase required for the mobilization of glycogen; non-essential; regulated by cyclic AMP-mediated phosphorylation; phosphorylation by Cdc28p may coordinately regulate carbohydrate metabolism and the cell cycle; expression is regulated by stress-response elements and by the HOG MAP kinase pathway | Core | NA | NA | NA |
| 7779-YPR161C | YPR161C | SGV1 | cyclin-dependent serine/threonine protein kinase SGV1|BUR1 | Cyclin (Bur2p)-dependent protein kinase; part of the BUR kinase complex which functions in transcriptional regulation; phosphorylates the carboxy-terminal domain (CTD) of Rpo21p and the C-terminal repeat domain of Spt5p; recruits Spt6p to the CTD at the onset of transcription; regulated by Cak1p; similar to metazoan CDK9 proteins | Core | NA | NA | NA |
| 7780-YPR162C | YPR162C | ORC4 | origin recognition complex subunit 4 | Subunit of the origin recognition complex (ORC); ORC directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; ORC4 has a paralog, RIF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7781-YPR163C | YPR163C | TIF3 | eIF4B|STM1|RBL3 | Translation initiation factor eIF-4B; contains an RNA recognition motif and binds to single-stranded RNA; has RNA annealing activity; interacts with Rps20p at the head of the 40S ribosomal subunit and alters the structure of the mRNA entry channel | Core | NA | NA | NA |
| 7782-YPR164W | YPR164W | MMS1 | SLM6|RTT108 | Subunit of E3 ubiquitin ligase complex involved in replication repair; stabilizes protein components of the replication fork such as the fork-pausing complex and leading strand polymerase, preventing fork collapse and promoting efficient recovery during replication stress; regulates Ty1 transposition; involved with Rtt101p in nonfunctional rRNA decay | Core | NA | NA | NA |
| 7783-YPR165W | YPR165W | RHO1 | Rho family GTPase RHO1 | GTP-binding protein of the rho subfamily of Ras-like proteins; involved in establishment of cell polarity; regulates protein kinase C (Pkc1p) and the cell wall synthesizing enzyme 1,3-beta-glucan synthase (Fks1p and Gsc2p) | Core | NA | NA | NA |
| 7784-YPR166C | YPR166C | MRP2 | mitochondrial 37S ribosomal protein MRP2 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 7785-YPR167C | YPR167C | MET16 | phosphoadenylyl-sulfate reductase (thioredoxin) | 3'-phosphoadenylsulfate reductase; reduces 3'-phosphoadenylyl sulfate to adenosine-3',5'-bisphosphate and free sulfite using reduced thioredoxin as cosubstrate, involved in sulfate assimilation and methionine metabolism | Core | NA | NA | NA |
| 7786-YPR168W | YPR168W | NUT2 | mediator complex subunit NUT2|MED10 | Subunit of the RNA polymerase II mediator complex; conserved from yeast to human; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for transcriptional activation and has a role in basal transcription; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7787-YPR169W | YPR169W | JIP5 | NA | Protein required for biogenesis of the large ribosomal subunit; required for biogenesis of the large ribosomal subunit; interacts with proteins involved in RNA processing, ribosome biogenesis, ubiquitination and demethylation; similar to WDR55, a human WD repeat protein; essential gene | Core | NA | NA | NA |
| 7788-YPR170C | YPR170C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORFs YPR169W-A and YPR170W-B | Core | NA | NA | NA |
| 7789-YPR170W-B_NumOfGenes_3 | YPR170W-B | NA | NA | Putative protein of unknown function; conserved in fungi; SWAT-GFP fusion protein localizes to the vacuole membrane; partially overlaps the dubious genes YPR169W-A, YPR170W-A and YRP170C | Core | NA | NA | NA |
| 7790-YPR171W | YPR171W | BSP1 | NA | Adapter that links synaptojanins to the cortical actin cytoskeleton; the synaptojanins are Inp52p and Inp53p | Core | NA | NA | NA |
| 7791-YPR172W | YPR172W | NA | pyridoxal 5'-phosphate synthase | Protein of unknown function; predicted to encode a pyridoxal 5'-phosphate synthase based on sequence similarity but purified protein does not possess this activity, nor does it bind flavin mononucleotide (FMN); transcriptionally activated by Yrm1p along with genes involved in multidrug resistance; YPR172W has a paralog, YLR456W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7792-YPR173C | YPR173C | VPS4 | AAA family ATPase VPS4|DID6|VPT10|VPL4|GRD13|END13|CSC1 | AAA-ATPase involved in multivesicular body (MVB) protein sorting; ATP-bound Vps4p localizes to endosomes and catalyzes ESCRT-III disassembly and membrane release; ATPase activity is activated by Vta1p; regulates cellular sterol metabolism | Core | NA | NA | NA |