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 |
|---|---|---|---|---|---|---|---|---|
| 4823-YJL129C | YJL129C | TRK1 | NA | Component of the Trk1p-Trk2p potassium transport system; 180 kDa high affinity potassium transporter; phosphorylated in vivo and interacts physically with the phosphatase Ppz1p, suggesting Trk1p acitivy is regulated by phosphorylation; TRK1 has a paralog, TRK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4824-YJL130C | YJL130C | URA2 | bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase | Bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase; catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP | Core | NA | NA | NA |
| 4825-YJL131C | YJL131C | AIM23 | NA | Mitochondrial translation initiation factor 3 (IF3, mIF3); evolutionarily conserved; binds to E. coli ribosomes in vitro; null mutant displays severe respiratory growth defect and elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 4826-YJL132W | YJL132W | NA | NA | Putative protein of unknown function; localizes to the membrane fraction; possible Zap1p-regulated target gene induced by zinc deficiency; YJL132W is a non-essential gene | Core | NA | NA | NA |
| 4827-YJL133C-A | YJL133C-A | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 4828-YJL133W | YJL133W | MRS3 | Fe(2+) transporter | Iron transporter, mediates Fe2+ transport across inner mito membrane; mitochondrial carrier family member; active under low-iron conditions; may transport other cations; MRS3 has a paralog, MRS4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4829-YJL134W | YJL134W | LCB3 | sphinganine kinase LCB3|YSR2|LBP1 | Long-chain base-1-phosphate phosphatase; specific for dihydrosphingosine-1-phosphate, regulates ceramide and long-chain base phosphates levels, involved in incorporation of exogenous long chain bases in sphingolipids; LCB3 has a paralog, YSR3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4830-YJL135W | YJL135W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified genes YJL134W/LCB3 | Core | NA | NA | NA |
| 4831-YJL136C | YJL136C | RPS21B | eS21|ribosomal 40S subunit protein S21B|S21e|YS25|S26B|S21B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S21, no bacterial homolog; RPS21B has a paralog, RPS21A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4832-YJL136W-A | YJL136W-A | NA | NA | Putative protein of unknown function; identified by SAGE | Core | NA | NA | NA |
| 4833-YJL137C | YJL137C | GLG2 | glycogenin glucosyltransferase GLG2 | Glycogenin glucosyltransferase; self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian glycogenin; GLG2 has a paralog, GLG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4834-YJL139C | YJL139C | YUR1 | mannosyltransferase YUR1 | Mannosyltransferase involved in protein N-glycosylation; member of the KTR1 family; located in the Golgi apparatus; YUR1 has a paralog, KTR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4835-YJL140W | YJL140W | RPB4 | DNA-directed RNA polymerase II subunit RPB4|B32|CTF15 | RNA polymerase II subunit B32; forms dissociable heterodimer with Rpb7p; Rpb4/7 dissociates from RNAPII as Ser2 CTD phosphorylation increases; Rpb4/7 regulates cellular lifespan via mRNA decay process; involved in recruitment of 3'-end processing factors to transcribing RNAPII complex, export of mRNA to cytoplasm under stress conditions; also involved in translation initiation | Core | NA | NA | NA |
| 4836-YJL141C | YJL141C | YAK1 | serine/threonine protein kinase YAK1 | Serine-threonine protein kinase; component of a glucose-sensing system that inhibits growth in response to glucose availability; upon nutrient deprivation Yak1p phosphorylates Pop2p to regulate mRNA deadenylation, the co-repressor Crf1p to inhibit transcription of ribosomal genes, and the stress-responsive transcription factors Hsf1p and Msn2p; nuclear localization negatively regulated by the Ras/PKA signaling pathway in the presence of glucose | Core | NA | NA | NA |
| 4837-YJL142C | YJL142C | IRC9 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene YJL141C; null mutant displays increased levels of spontaneous Rad52p foci | Accessory | Ancestral | NA | NA |