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 |
|---|---|---|---|---|---|---|---|---|
| 7418-YPL069C | YPL069C | BTS1 | farnesyltranstransferase | Geranylgeranyl diphosphate synthase (GGPS); increases the intracellular pool of geranylgeranyl diphosphate, suppressor of bet2 mutation that causes defective geranylgeranylation of small GTP-binding proteins that mediate vesicular traffic | Core | NA | NA | NA |
| 7419-YPL070W | YPL070W | MUK1 | guanine nucleotide exchange factor MUK1 | Guanine nucleotide exchange factor (GEF); involved in vesicle-mediated vacuolar transport, including Golgi-endosome trafficking and sorting through the multivesicular body (MVB); specifically stimulates the intrinsic guanine nucleotide exchange activity of Rab family members (Vps21p/Ypt52p/Ypt53p); partially redundant with GEF VPS9; required for localization of the CORVET complex to endosomes; contains a VPS9 domain | Core | NA | NA | NA |
| 7420-YPL071C | YPL071C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus | Core | NA | NA | NA |
| 7421-YPL072W_NumOfGenes_2 | YPL072W | UBP16 | putative ubiquitin-specific protease UBP16 | Deubiquitinating enzyme anchored to the outer mitochondrial membrane; probably not important for general mitochondrial functioning, but may perform a more specialized function at mitochondria | Core | NA | NA | NA |
| 7422-YPL074W | YPL074W | YTA6 | putative AAA family ATPase YTA6 | Putative ATPase of the CDC48/PAS1/SEC18 (AAA) family; localized to the cortex of mother cells but not to daughter cells; relocalizes from cytoplasm to plasma membrane foci upon DNA replication stress | Core | NA | NA | NA |
| 7423-YPL075W | YPL075W | GCR1 | transcription regulator GCR1|SIT3|LPF10 | Transcriptional activator of genes involved in glycolysis; DNA-binding protein that interacts and functions with the transcriptional activator Gcr2p | Core | NA | NA | NA |
| 7424-YPL076W | YPL076W | GPI2 | phosphatidylinositol N-acetylglucosaminyltransferase|GCR4 | Protein involved in the synthesis of GlcNAc-PI; GlcNAc-PI is the first intermediate in the synthesis of glycosylphosphatidylinositol (GPI) anchors; homologous to the human PIG-C protein; GlcNAc-PI stands for N-acetylglucosaminyl phosphatidylinositol | Core | NA | NA | NA |
| 7425-YPL077C | YPL077C | NA | NA | Putative protein of unknown function; regulates PIS1 expression; mutant displays spore wall assembly defect in ether sensitivity screen; YPL077C is not an essential gene; YPL077C has a paralog, YBR197C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7426-YPL078C | YPL078C | ATP4 | F1F0 ATP synthase subunit 4|LPF7 | Subunit b of the stator stalk of mitochondrial F1F0 ATP synthase; ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; contributes to the oligomerization of the complex, which in turn determines the shape of inner membrane cristae; phosphorylated | Core | NA | NA | NA |
| 7427-YPL079W | YPL079W | RPL21B | eL21|ribosomal 60S subunit protein L21B|L21e|L21B | Ribosomal 60S subunit protein L21B; homologous to mammalian ribosomal protein L21, no bacterial homolog; RPL21B has a paralog, RPL21A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7428-YPL080C | YPL080C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 7429-YPL081W | YPL081W | RPS9A | uS4|ribosomal 40S subunit protein S9A|rp21|YS11|S9A|S4|S13 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S9 and bacterial S4; RPS9A has a paralog, RPS9B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7430-YPL082C | YPL082C | MOT1 | DNA-binding ATPase|END10|BTAF1|LPF4|BUR3 | Essential protein involved in regulation of transcription; removes Spt15p (TBP) from DNA via its C-terminal ATPase activity; may have a role in ensuring that soluble TBP is available to bind TATA-less promoters; forms a complex with TBP that binds TATA DNA with high affinity but with altered specificity; the Mot1p-Spt15p-DNA ternary complex contains unbent DNA; coregulates transcription with Spt16p through assembly of preinitiation complex and organization of nucleosomes | Core | NA | NA | NA |
| 7431-YPL083C | YPL083C | SEN54 | tRNA splicing endonuclease subunit SEN54 | Subunit of the tRNA splicing endonuclease; tRNA splicing endonuclease (Sen complex) is composed of Sen2p, Sen15p, Sen34p, and Sen54p; Sen complex also cleaves the CBP1 mRNA at the mitochondrial surface | Core | NA | NA | NA |
| 7432-YPL084W | YPL084W | BRO1 | NPI3|ASI6|VPS31|LPF2 | Cytoplasmic class E vacuolar protein sorting (VPS) factor; coordinates deubiquitination in the multivesicular body (MVB) pathway by recruiting Doa4p to endosomes | Core | NA | NA | NA |