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 |
|---|---|---|---|---|---|---|---|---|
| 6893-YOL095C | YOL095C | HMI1 | ATP-dependent 3'-5' DNA helicase | Mitochondrial inner membrane localized ATP-dependent DNA helicase; required for the maintenance of the mitochondrial genome; not required for mitochondrial transcription; has homology to E. coli helicase uvrD | Core | NA | NA | NA |
| 6894-YOL096C | YOL096C | COQ3 | hexaprenyldihydroxybenzoate methyltransferase | O-methyltransferase; catalyzes two different O-methylation steps in ubiquinone (Coenzyme Q) biosynthesis; component of a mitochondrial ubiquinone-synthesizing complex; phosphoprotein | Core | NA | NA | NA |
| 6895-YOL097C | YOL097C | WRS1 | tryptophan--tRNA ligase WRS1|HRE342 | Cytoplasmic tryptophanyl-tRNA synthetase; aminoacylates tryptophanyl-tRNA; human homolog WARS can complement yeast null mutant | Accessory | Ancestral | NA | NA |
| 6896-YOL097W-A | YOL097W-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Accessory | Unknown | NA | NA |
| 6897-YOL098C | YOL098C | SDD3 | NA | Putative metalloprotease; overproduction suppresses lethality due to expression of the dominant PET9 allele AAC2-A128P | Accessory | Ancestral | NA | NA |
| 6898-YOL100W_NumOfGenes_2 | YOL100W | PKH2 | serine/threonine protein kinase PKH2 | Serine/threonine protein kinase; involved in sphingolipid-mediated signaling pathway that controls endocytosis; activates Ypk1p and Ykr2p, components of signaling cascade required for maintenance of cell wall integrity; contains a PH-like domain; redundant with Pkh1p; PKH2 has a paralog, PKH1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6899-YOL101C | YOL101C | IZH4 | NA | Membrane protein involved in zinc ion homeostasis; member of the four-protein IZH family; expression induced by fatty acids and altered zinc levels; deletion reduces sensitivity to excess zinc; possible role in sterol metabolism; protein increases in abundance and relocalizes from nucleus to ER upon DNA replication stress; IZH4 has a paralog, IZH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6900-YOL102C | YOL102C | TPT1 | tRNA 2'-phosphotransferase | tRNA 2'-phosphotransferase that catalyzes final step in tRNA splicing: the transfer of the 2'-PO(4) from the splice junction to NAD(+) to form ADP-ribose 1''-2''cyclic phosphate and nicotinamide | Core | NA | NA | NA |
| 6901-YOL103W | YOL103W | ITR2 | myo-inositol transporter ITR2|HRB612 | Myo-inositol transporter; member of the sugar transporter superfamily; expressed constitutively; ITR2 has a paralog, ITR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6902-YOL104C | YOL104C | NDJ1 | TAM1 | Protein that regulates meiotic SPB cohesion and telomere clustering; localizes to both spindle pole bodies (SPBs) and telomeres; required for bouquet formation, effective homolog pairing, ordered cross-over distribution, sister chromatid cohesion at meiotic telomeres, chromosomal segregation and telomere-led rapid prophase movement | Core | NA | NA | NA |
| 6903-YOL105C | YOL105C | WSC3 | NA | Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway; involved in maintenance of cell wall integrity; involved in response to heat shock and other stressors; regulates 1,3-beta-glucan synthesis; WSC3 has a paralog, WSC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6904-YOL106W | YOL106W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6905-YOL107W | YOL107W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and colocalizes in a punctate pattern with the early golgi/COPI vesicles; YOL107W is not an essential protein | Core | NA | NA | NA |
| 6906-YOL108C | YOL108C | INO4 | NA | Transcription factor involved in phospholipid synthesis; required for derepression of inositol-choline-regulated genes involved in phospholipid synthesis; forms a complex, with Ino2p, that binds the inositol-choline-responsive element through a basic helix-loop-helix domain | Core | NA | NA | NA |
| 6907-YOL109W | YOL109W | ZEO1 | NA | Peripheral membrane protein of the plasma membrane; interacts with Mid2p; regulates the cell integrity pathway mediated by Pkc1p and Slt2p; the authentic protein is detected in a phosphorylated state in highly purified mitochondria | Core | NA | NA | NA |