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 |
|---|---|---|---|---|---|---|---|---|
| 3413-YER087W_NumOfGenes_2 | YER087W | AIM10 | putative proline--tRNA ligase AIM10 | Protein with similarity to tRNA synthetases; non-tagged protein is detected in purified mitochondria; null mutant is viable and displays elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 3414-YER088C | YER088C | DOT6 | PBF2 | Protein involved in rRNA and ribosome biogenesis; activated in stochastic pulses of nuclear localization; binds polymerase A and C motif; subunit of the RPD3L histone deacetylase complex; has chromatin specific SANT domain; involved in telomeric gene silencing and filamentation; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 3415-YER088C-A | YER088C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORFs PTC2/YER089C and YER088W-B | Core | NA | NA | NA |
| 3416-YER089C_NumOfGenes_2 | YER089C | PTC2 | type 2C protein phosphatase PTC2 | Type 2C protein phosphatase (PP2C); dephosphorylates Hog1p to limit maximal osmostress induced kinase activity; dephosphorylates Ire1p to downregulate the unfolded protein response; dephosphorylates Cdc28p; inactivates the DNA damage checkpoint; PTC2 has a paralog, PTC3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3417-YER090W_NumOfGenes_2 | YER090W | TRP2 | anthranilate synthase TRP2 | Anthranilate synthase; catalyzes the initial step of tryptophan biosynthesis, forms multifunctional hetero-oligomeric anthranilate synthase:indole-3-glycerol phosphate synthase enzyme complex with Trp3p | Core | NA | NA | NA |
| 3418-YER091C | YER091C | MET6 | 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase | Cobalamin-independent methionine synthase; involved in methionine biosynthesis and regeneration; requires a minimum of two glutamates on the methyltetrahydrofolate substrate, similar to bacterial metE homologs | Core | NA | NA | NA |
| 3419-YER091C-A | YER091C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 3420-YER092W | YER092W | IES5 | NA | Non-essential INO80 chromatin remodeling complex subunit; deletion affects telomere maintenance via recombination | Core | NA | NA | NA |
| 3421-YER093C | YER093C | TSC11 | TORC2 complex subunit TSC11|AVO3 | Subunit of TORC2 (Tor2p-Lst8p-Avo1-Avo2-Tsc11p-Bit61p); TORC2 is a membrane-associated complex that regulates actin cytoskeletal dynamics during polarized growth and cell wall integrity; involved in sphingolipid metabolism; contains a RasGEFN domain | Core | NA | NA | NA |
| 3422-YER093C-A | YER093C-A | AIM11 | GEP8 | Protein of unknown function; null mutant is viable but shows increased loss of mitochondrial genome and synthetic interaction with prohibitin (phb1); contains an intron; SWAT-GFP and mCherry fusion proteins localize to the mitochondria; YER093C-A has a paralog, YBL059W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3423-YER094C | YER094C | PUP3 | proteasome core particle subunit beta 3|SCS32 | Beta 3 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit C10 | Core | NA | NA | NA |
| 3424-YER095W | YER095W | RAD51 | recombinase RAD51|MUT5 | Strand exchange protein; forms a helical filament with DNA that searches for homology; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; homolog of Dmc1p and bacterial RecA protein | Core | NA | NA | NA |
| 3425-YER096W | YER096W | SHC1 | NA | Sporulation-specific activator of Chs3p (chitin synthase III); required for the synthesis of the chitosan layer of ascospores; transcriptionally induced at alkaline pH; SHC1 has a paralog, SKT5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3426-YER097W | YER097W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 3427-YER098W_NumOfGenes_2 | YER098W | UBP9 | putative ubiquitin-specific protease UBP9 | Ubiquitin-specific protease that cleaves ubiquitin-protein fusions; UBP9 has a paralog, UBP13, that arose from the whole genome duplication | Core | NA | NA | NA |