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 |
|---|---|---|---|---|---|---|---|---|
| 5108-YKL038W | YKL038W | RGT1 | NA | Glucose-responsive transcription factor; regulates expression of several glucose transporter (HXT) genes in response to glucose; binds to promoters and acts both as a transcriptional activator and repressor; recruits Tup1p/Cyc8p to target gene promoters; RGT1 has a paralog, EDS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5109-YKL039W | YKL039W | PTM1 | NA | Protein of unknown function; copurifies with late Golgi vesicles containing the v-SNARE Tlg2p; PTM1 has a paralog, YHL017W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5110-YKL040C | YKL040C | NFU1 | NUB1 | Protein involved in Fe-S cluster transfer to mitochondrial clients; protects [4Fe-4S] clusters from damage due to oxidative stress; acts along with Bol3 at a late step in the transfer of [4Fe-4S] clusters from the ISA complex to client proteins; Fe-S loaded homodimer at steady state; similar to NifU, a bacterial protein required for Fe/S cluster maturation; ortholog of the human NFU1, mutations of which are associated with Multiple Mitochondria Dysfunctions Syndrome (MMDS1) | Core | NA | NA | NA |
| 5111-YKL041W | YKL041W | VPS24 | ESCRT-III subunit protein VPS24|VPL26|DID3 | One of four subunits of the ESCRT-III complex; forms an endosomal sorting complex required for transport III (ESCRT-III) subcomplex with Did4p; involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway | Core | NA | NA | NA |
| 5112-YKL042W | YKL042W | SPC42 | NA | Central plaque component of spindle pole body (SPB); involved in SPB duplication, may facilitate attachment of the SPB to the nuclear membrane | Core | NA | NA | NA |
| 5113-YKL043W | YKL043W | PHD1 | NA | Transcriptional activator that enhances pseudohyphal growth; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate; PHD1 has a paralog, SOK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5114-YKL044W | YKL044W | MMO1 | NA | Protein of unknown function; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the mitochondria; mRNA identified as translated by ribosome profiling data; MMO1 is a non-essential gene | Core | NA | NA | NA |
| 5115-YKL045W | YKL045W | PRI2 | DNA primase subunit PRI2 | Subunit of DNA primase; DNA primase is required for DNA synthesis and double-strand break repair | Core | NA | NA | NA |
| 5116-YKL046C | YKL046C | DCW1 | putative mannan endo-1,6-alpha-mannosidase | Putative mannosidase; GPI-anchored membrane protein required for cell wall biosynthesis in bud formation;homologous to Dfg5p | Core | NA | NA | NA |
| 5117-YKL047W | YKL047W | ANR2 | NA | Protein of unknown function; may have a role in lipid metabolism, based on localization to lipid droplets; predicted to be palmitoylated | Core | NA | NA | NA |
| 5118-YKL048C | YKL048C | ELM1 | serine/threonine protein kinase ELM1|LDB9 | Serine/threonine protein kinase; regulates the orientation checkpoint, the morphogenesis checkpoint and the metabolic switch from fermentative to oxidative metabolism by phosphorylating the activation loop of Kin4p, Hsl1p and Snf4p respectively; cooperates with Hsl7p in recruiting Hsl1p to the septin ring, a prerequisite for subsequent recruitment, phosphorylation, and degradation of Swe1p; forms part of the bud neck ring; regulates cytokinesis | Core | NA | NA | NA |
| 5119-YKL049C | YKL049C | CSE4 | centromeric DNA-binding histone H3-like protein CSE4|CSL2 | Histone H3-like centromere protein; associated with promoters, accessible chromatin, RNAPII-bound regions; phosphorylated Cse4p associates with centromeres; required for proper kinetochore function; levels regulated by E3 ubiquitin ligase Psh1p; phosphorylation may destabilize defective kinetochores to promote bi-orientation; ubiquitination of N-terminus regulates proteolysis for faithful chromosome segregation; yeast CSE4 can complement mutations in human homolog CENPA | Core | NA | NA | NA |
| 5120-YKL050C | YKL050C | NA | NA | Protein of unknown function; the YKL050W protein is a target of the SCFCdc4 ubiquitin ligase complex and YKL050W transcription is regulated by Azf1p; YKL050C has a paralog, EIS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5121-YKL051W | YKL051W | SFK1 | NA | Plasma membrane protein that may act to generate normal levels of PI4P; may act together with or upstream of Stt4p; at least partially mediates proper localization of Stt4p to the plasma membrane | Core | NA | NA | NA |
| 5122-YKL052C | YKL052C | ASK1 | NA | Essential subunit of the Dam1 complex (aka DASH complex); couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; phosphorylated during the cell cycle by cyclin-dependent kinases; sumoylated in an Mms21p-dependent manner; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |