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 |
|---|---|---|---|---|---|---|---|---|
| 5453-YLL056C | YLL056C | NA | NA | Putative protein of unknown function; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p and genes involved in pleiotropic drug resistance (PDR); expression is induced in cells treated with the mycotoxin patulin; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Accessory | Ancestral | NA | NA |
| 5454-YLL057C | YLL057C | JLP1 | sulfonate dioxygenase | Fe(II)-dependent sulfonate/alpha-ketoglutarate dioxygenase; involved in sulfonate catabolism for use as a sulfur source; contains sequence that resembles a J domain (typified by the E. coli DnaJ protein); induced by sulphur starvation | Accessory | Ancestral | NA | NA |
| 5455-YLL058W | YLL058W | NA | cystathionine gamma-synthase | Putative protein of unknown function with similarity to Str2p; Str2p is a cystathionine gamma-synthase important in sulfur metabolism; YLL058W is not an essential gene | Core | NA | NA | NA |
| 5456-YLL059C | YLL059C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5457-YLL060C | YLL060C | GTT2 | glutathione transferase GTT2 | Glutathione S-transferase capable of homodimerization; functional overlap with Gtt2p, Grx1p, and Grx2p; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5458-YLL061W | YLL061W | MMP1 | S-methylmethionine permease MMP1 | High-affinity S-methylmethionine permease; required for utilization of S-methylmethionine as a sulfur source; has similarity to S-adenosylmethionine permease Sam3p | Accessory | Ancestral | NA | NA |
| 5459-YLL062C | YLL062C | MHT1 | S-adenosylmethionine-homocysteine S-methyltransferase MHT1 | S-methylmethionine-homocysteine methyltransferase; functions along with Sam4p in the conversion of S-adenosylmethionine (AdoMet) to methionine to control the methionine/AdoMet ratio | Accessory | Introgression | S. paradoxus | NA |
| 5460-YLL063C | YLL063C | AYT1 | acetyltransferase | Acetyltransferase; catalyzes trichothecene 3-O-acetylation, suggesting a possible role in trichothecene biosynthesis | Accessory | Introgression | S. paradoxus | NA |
| 5461-YLL066W-B | YLL066W-B | NA | NA | Putative protein of unknown function; overexpression causes a cell cycle delay or arrest | Accessory | Unknown | S. paradoxus | NA |
| 5462-YLR001C_NumOfGenes_2 | YLR001C | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; predicted to be palmitoylated | Core | NA | NA | NA |
| 5463-YLR002C_NumOfGenes_2 | YLR002C | NOC3 | NA | Subunit of a nuclear complex with Noc2p and pre-replicative complexes; the Noc2p-Noc3p complex binds to 66S ribosomal precursors to mediate their maturation and intranuclear transport; binds to chromatin at active replication origins, and is required for pre-RC formation and maintenance during DNA replication licensing | Core | NA | NA | NA |
| 5464-YLR003C_NumOfGenes_2 | YLR003C | CMS1 | NA | Putative subunit of the 90S preribosome processome complex; overexpression rescues supressor mutant of mcm10; null mutant is viable; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 5465-YLR004C_NumOfGenes_2 | YLR004C | THI73 | NA | Putative plasma membrane permease; proposed to be involved in carboxylic acid uptake and repressed by thiamine; substrate of Dbf2p/Mob1p kinase; transcription is altered if mitochondrial dysfunction occurs | Core | NA | NA | NA |
| 5466-YLR005W_NumOfGenes_2 | YLR005W | SSL1 | TFIIH/NER complex subunit SSL1 | Subunit of the core form of RNA polymerase transcription factor TFIIH; has both protein kinase and DNA-dependent ATPase/helicase activities; essential for transcription and nucleotide excision repair; interacts with Tfb4p | Core | NA | NA | NA |
| 5467-YLR006C_NumOfGenes_2 | YLR006C | SSK1 | mitogen-activated protein kinase kinase kinase SSK1 | Cytoplasmic phosphorelay intermediate osmosensor and regulator; part of a two-component signal transducer that mediates osmosensing via a phosphorelay mechanism; required for mitophagy; dephosphorylated form is degraded by the ubiquitin-proteasome system; potential Cdc28p substrate | Core | NA | NA | NA |