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 |
|---|---|---|---|---|---|---|---|---|
| 5543-YLR084C | YLR084C | RAX2 | NA | N-glycosylated protein; involved in the maintenance of bud site selection during bipolar budding; localization requires Rax1p; RAX2 mRNA stability is regulated by Mpt5p | Accessory | Ancestral | NA | NA |
| 5544-YLR085C | YLR085C | ARP6 | NA | Actin-related protein that binds nucleosomes; a component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A | Accessory | Ancestral | NA | NA |
| 5545-YLR086W | YLR086W | SMC4 | condensin subunit SMC4 | Subunit of the condensin complex; condensin reorganizes chromosomes during both mitosis and meiosis; forms a subcomplex with Smc2p that has ATP-hydrolyzing and DNA-binding activity, but other condensin subunits are required for chromatin binding; required for tRNA gene clustering at the nucleolus; potential Cdc28p substrate | Core | NA | NA | NA |
| 5546-YLR087C | YLR087C | CSF1 | NA | Protein required for fermentation at low temperature; plays a role in the maturation of secretory proteins; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5547-YLR088W | YLR088W | GAA1 | GPI-anchor transamidase subunit GAA1|END2 | Subunit of the GPI:protein transamidase complex; removes the GPI-anchoring signal and attaches GPI (glycosylphosphatidylinositol) to proteins in the ER; human homolog GPAA1 can complement growth defects of yeast thermosensitive mutant at restrictive temperature | Core | NA | NA | NA |
| 5548-YLR089C | YLR089C | ALT1 | alanine transaminase ALT1 | Alanine transaminase (glutamic pyruvic transaminase); involved in alanine biosynthesis and catabolism; TOR1-independent role in determining chronological lifespan; expression is induced in the presence of alanine; repression is mediated by Nrg1p; ALT1 has a paralog, ALT2, that arose from the whole genome duplication; Alt2p is catalytically inactive | Core | NA | NA | NA |
| 5549-YLR090W | YLR090W | XDJ1 | NA | Chaperone with a role in facilitating mitochondrial protein import; ascomycete-specific member of the DnaJ-like family, closely related to Ydj1p; predicted to be C-terminally prenylated; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5550-YLR091W | YLR091W | GEP5 | RRG5 | Protein of unknown function; required for mitochondrial genome maintenance; detected in highly purified mitochondria in high-throughput studies; null mutant has decreased levels of cardiolipin and phosphatidylethanolamine | Core | NA | NA | NA |
| 5551-YLR092W | YLR092W | SUL2 | sulfate permease | High affinity sulfate permease; sulfate uptake is mediated by specific sulfate transporters Sul1p and Sul2p, which control the concentration of endogenous activated sulfate intermediates | Core | NA | NA | NA |
| 5552-YLR093C | YLR093C | NYV1 | MAM2 | v-SNARE component of the vacuolar SNARE complex; involved in vesicle fusion; inhibits ATP-dependent Ca(2+) transport activity of Pmc1p in the vacuolar membrane | Core | NA | NA | NA |
| 5553-YLR094C | YLR094C | GIS3 | NA | Protein of unknown function | Core | NA | NA | NA |
| 5554-YLR095C | YLR095C | IOC2 | NA | Subunit of the Isw1b complex; exhibits nucleosome-stimulated ATPase activity and acts within coding regions to coordinate transcription elongation with termination and processing; contains a PHD finger motif; other complex members are Isw1p and Ioc4p | Core | NA | NA | NA |
| 5555-YLR096W | YLR096W | KIN2 | serine/threonine protein kinase KIN2 | Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane; KIN2 has a paralog, KIN1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5556-YLR097C | YLR097C | HRT3 | SCF ubiquitin ligase complex subunit HRT3 | Putative SCF-ubiquitin ligase F-box protein; based on both genetic and physical interactions and sequence similarity; identified in association with Cdc53p, Skp1p and Ubi4 in large and small-scale studies | Core | NA | NA | NA |
| 5557-YLR098C | YLR098C | CHA4 | SIL3|SIL2 | DNA binding transcriptional activator; mediates serine/threonine activation of the catabolic L-serine (L-threonine) deaminase (CHA1); Zinc-finger protein with Zn[2]-Cys[6] fungal-type binuclear cluster domain | Core | NA | NA | NA |