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 |
|---|---|---|---|---|---|---|---|---|
| 6788-YNR069C_NumOfGenes_2 | YNR069C | BSC5 | BUL3 | Protein of unknown function; shows homology with N-terminal end of Bul1p; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression; readthrough expression includes YNR068C and the locus for this readthrough is termed BUL3; Bul3p is involved in ubiquitin-mediated sorting of plasma membrane proteins; readthrough and shortened forms of Bul3p interact with Rsp5p differently in vitro | Accessory | Ancestral | NA | NA |
| 6789-YNR070W_NumOfGenes_2 | YNR070W | PDR18 | ATP-binding cassette multidrug transporter PDR18 | Putative transporter of the ATP-binding cassette (ABC) family; role in plasma membrane sterol incorporation; implicated in pleiotropic drug resistance; provides resistance to ethanol stress and contributes to a decreased intracellular accumulation of ethanol; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 6790-YNR071C | YNR071C | NA | aldose 1-epimerase superfamily protein | Putative aldose 1-epimerase | Accessory | Ancestral | NA | NA |
| 6791-YNR072W_NumOfGenes_4 | YNR072W | HXT17 | HLT4|hexose transporter HXT17 | Putative transmembrane polyol transporter; supports growth on and uptake of mannitol and sorbitol with moderate affinity when overexpressed in a strain deleted for hexose family members; minor hexose transport activity when overexpressed in a similar strain; induced by raffinose and galactose at pH 7.7 versus pH 4.7, repressed by high levels of glucose; HXT17 has a paralog, HXT13, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 6792-YNR073C_NumOfGenes_3 | YNR073C | MAN2 | putative mannitol dehydrogenase | Mannitol dehydrogenase; MAN2 has a paralog, DSF1, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 6793-YNR074C | YNR074C | AIF1 | CPD1 | Mitochondrial cell death effector; translocates to the nucleus in response to apoptotic stimuli, homolog of mammalian Apoptosis-Inducing Factor, putative reductase | Accessory | Ancestral | NA | NA |
| 6794-YNR075C-A_NumOfGenes_4 | YNR075C-A | NA | NA | Protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 6795-YNR075W | YNR075W | COS10 | NA | Endosomal protein involved in turnover of plasma membrane proteins; member of the DUP380 subfamily of conserved, often subtelomeric COS genes; required for the multivesicular vesicle body sorting pathway that internalizes plasma membrane proteins for degradation; Cos proteins provide ubiquitin in trans for nonubiquitinated cargo proteins | Accessory | Ancestral | NA | NA |
| 6796-YNR077C_NumOfGenes_2 | YNR077C | NA | NA | Protein of unknown function, abundance changes with carbon source | Accessory | Ancestral | NA | NA |
| 6797-YOL001W | YOL001W | PHO80 | phoR|VAC5|TUP7|AGS3 | Cyclin; interacts with cyclin-dependent kinase Pho85p; regulates the response to nutrient levels and environmental conditions, including the response to phosphate limitation and stress-dependent calcium signaling | Core | NA | NA | NA |
| 6798-YOL002C | YOL002C | IZH2 | PAQR-type receptor|PHO36 | Plasma membrane receptor for plant antifungal osmotin; involved in zinc ion homeostasis, apoptosis; negatively regulates ZRT1 and other functionally divergent genes through CCCTC promoter motif (IzRE); modulates FET3 activity in iron-independent manner; affects gene expression by influencing balance of competition between Msn2p/Msn4p and Nrg1p/Nrg2p for binding to IzRE; transcription regulated by Zap1p, zinc, fatty acid levels; homolog of mammalian adiponectin receptor | Core | NA | NA | NA |
| 6799-YOL003C | YOL003C | PFA4 | palmitoyltransferase PFA4 | Palmitoyltransferase with autoacylation activity; required for palmitoylation of amino acid permeases containing a C-terminal Phe-Trp-Cys site; required for modification of Chs3p; member of the DHHC family of putative palmitoyltransferases | Core | NA | NA | NA |
| 6800-YOL004W | YOL004W | SIN3 | transcriptional regulator SIN3|UME4|SDS16|SDI1|RPD1|GAM2|CPE1 | Component of both the Rpd3S and Rpd3L histone deacetylase complexes; involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity | Core | NA | NA | NA |
| 6801-YOL005C | YOL005C | RPB11 | DNA-directed RNA polymerase II core subunit RPB11|B12.5 | RNA polymerase II subunit B12.5; part of central core; similar to Rpc19p and bacterial alpha subunit | Core | NA | NA | NA |
| 6802-YOL006C | YOL006C | TOP1 | DNA topoisomerase 1|MAK17|MAK1 | Topoisomerase I; nuclear enzyme that relieves torsional strain in DNA by cleaving and re-sealing the phosphodiester backbone; relaxes both positively and negatively supercoiled DNA; functions in replication, transcription, and recombination; role in processing ribonucleoside monophosphates in genomic DNA into irreversible single-strand breaks; enzymatic activity and interaction with Nsr1p are negatively regulated by polyphosphorylation | Core | NA | NA | NA |