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 |
|---|---|---|---|---|---|---|---|---|
| 6728-YNR010W | YNR010W | CSE2 | MED9 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; component of the Middle domain of mediator; required for regulation of RNA polymerase II activity; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6729-YNR011C | YNR011C | PRP2 | DEAH-box RNA-dependent ATPase PRP2|RNA2 | RNA-dependent DExD/H-box ATPase; required for activation of spliceosome before first transesterification step in RNA splicing; implicated in rearranging and proofreading snRNA structure in catalytic activation of spliceosome; ortholog of human protein DHX16 | Core | NA | NA | NA |
| 6730-YNR012W | YNR012W | URK1 | uridine kinase URK1 | Uridine/cytidine kinase; component of the pyrimidine ribonucleotide salvage pathway that converts uridine into UMP and cytidine into CMP; involved in the pyrimidine deoxyribonucleotide salvage pathway, converting deoxycytidine into dCMP | Core | NA | NA | NA |
| 6731-YNR013C | YNR013C | PHO91 | NA | Low-affinity vacuolar phosphate transporter; exports phosphate from the vacuolar lumen to the cytosol; regulates phosphate and polyphosphate metabolism; acts upstream of Pho81p in regulation of the PHO pathway; localizes to sites of contact between the vacuole and mitochondria (vCLAMPs); deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth | Core | NA | NA | NA |
| 6732-YNR014W | YNR014W | NA | NA | Putative protein of unknown function; expression is cell-cycle regulated, Azf1p-dependent, and heat-inducible; YNR014W has a paralog, YMR206W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6733-YNR015W | YNR015W | SMM1 | DUS2 | Dihydrouridine synthase; member of a family of dihydrouridine synthases including Dus1p, Smm1p, Dus3p, and Dus4p; modifies uridine residues at position 20 of cytoplasmic tRNAs | Core | NA | NA | NA |
| 6734-YNR016C | YNR016C | ACC1 | acetyl-CoA carboxylase ACC1|MTR7|FAS3|ABP2 | Acetyl-CoA carboxylase, biotin containing enzyme; catalyzes carboxylation of cytosolic acetyl-CoA to form malonyl-CoA and regulates histone acetylation by regulating the availablity of acetyl-CoA; required for de novo biosynthesis of long-chain fatty acids; ACC1 has a paralog, HFA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6735-YNR017W | YNR017W | TIM23 | protein transporter TIM23|MAS6|MPI3|MIM23 | Essential component of the TIM23 complex; involved in protein import into mitochondrial matrix and inner membrane; with Tim17p, contributes to architecture and function of the import channel; TIM23 complex is short for the translocase of the inner mitochondrial membrane | Core | NA | NA | NA |
| 6736-YNR018W | YNR018W | RCF2 | AIM38 | Cytochrome c oxidase subunit; has a role in assembly of respiratory supercomplexes; similar to Rcf1p, and either Rcf1p or Rcf2p is required for late-stage assembly of the Cox12p and Cox13p subunits and for cytochrome c oxidase activity; associates with the cytochrome c oxidase - cytochrome bc1 supercomplex; null mutant accumulates reactive oxygen species; member of the conserved hypoxia induced gene family; C. elegans homolog is functional in yeast | Core | NA | NA | NA |
| 6737-YNR019W | YNR019W | ARE2 | sterol acyltransferase|SAT1 | Acyl-CoA:sterol acyltransferase; endoplasmic reticulum enzyme that contributes the major sterol esterification activity in the presence of oxygen; ARE2 has a paralog, ARE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6738-YNR020C | YNR020C | ATP23 | putative metalloprotease | Putative metalloprotease of the mitochondrial inner membrane; required for processing of Atp6p; has an additional role in assembly of the F0 sector of the F1F0 ATP synthase complex; substrate of the Mia40p-Erv1p disulfide relay system, and folding is assisted by Mia40p | Core | NA | NA | NA |
| 6739-YNR021W | YNR021W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YNR021W is not an essential gene | Core | NA | NA | NA |
| 6740-YNR022C | YNR022C | MRPL50 | mitochondrial 54S ribosomal protein MRPL50 | Mitochondrial ribosomal protein of the large subunit; not essential for mitochondrial translation | Core | NA | NA | NA |
| 6741-YNR023W | YNR023W | SNF12 | SWP73 | 73 kDa subunit of the SWI/SNF chromatin remodeling complex; involved in transcriptional regulation; relocates to the cytosol under hypoxic conditions; deletion mutants are temperature-sensitive; SNF12 has a paralog, RSC6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6742-YNR024W | YNR024W | MPP6 | NA | Nuclear exosome-associated RNA binding protein; involved in surveillance of pre-rRNAs and pre-mRNAs, and the degradation of cryptic non-coding RNAs (ncRNA); copurifies with ribosomes; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |