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 |
|---|---|---|---|---|---|---|---|---|
| 6488-YNL096C | YNL096C | RPS7B | eS7|ribosomal 40S subunit protein S7B|S7e|rp30|S7B | Protein component of the small (40S) ribosomal subunit; interacts with Kti11p; deletion causes hypersensitivity to zymocin; homologous to mammalian ribosomal protein S7, no bacterial homolog; RPS7B has a paralog, RPS7A, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6489-YNL097C_NumOfGenes_2 | YNL097C | PHO23 | NA | Component of the Rpd3L histone deacetylase complex; involved in transcriptional regulation of PHO5; affects termination of snoRNAs and cryptic unstable transcripts (CUTs); C-terminus shares significant sequence identity with the human candidate tumor suppressor p33-ING1 and its isoform ING3 | Core | NA | NA | NA |
| 6490-YNL097C-B | YNL097C-B | NA | YNL097C-A | Putative protein of unknown function | Core | NA | NA | NA |
| 6491-YNL098C | YNL098C | RAS2 | Ras family GTPase RAS2|TSL7|GLC5|CYR3|CTN5 | GTP-binding protein; regulates nitrogen starvation response, sporulation, and filamentous growth; farnesylation and palmitoylation required for activity and localization to plasma membrane; homolog of mammalian Ras proto-oncogenes; RAS2 has a paralog, RAS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6492-YNL099C | YNL099C | OCA1 | putative tyrosine protein phosphatase OCA1 | Putative protein tyrosine phosphatase; required for cell cycle arrest in response to oxidative damage of DNA | Core | NA | NA | NA |
| 6493-YNL100W | YNL100W | MIC27 | AIM37|MCS27 | Component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; forms a subcomplex with Mic10p and Mic12p whose assembly and stability requires cardiolipin | Core | NA | NA | NA |
| 6494-YNL101W | YNL101W | AVT4 | NA | Vacuolar transporter; exports large neutral amino acids from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters; localizes to sites of contact between the vacuole and mitochondria (vCLAMPs) | Core | NA | NA | NA |
| 6495-YNL102W | YNL102W | POL1 | DNA-directed DNA polymerase alpha catalytic subunit POL1|HPR3|CRT5|CDC17 | Catalytic subunit of the DNA polymerase I alpha-primase complex; required for the initiation of DNA replication during mitotic DNA synthesis and premeiotic DNA synthesis | Core | NA | NA | NA |
| 6496-YNL103W | YNL103W | MET4 | NA | Leucine-zipper transcriptional activator; responsible for regulation of sulfur amino acid pathway; requires different combinations of auxiliary factors Cbf1p, Met28p, Met31p and Met32p; feedforward loop exists in the regulation of genes controlled by Met4p and Met32p; can be ubiquitinated by ubiquitin ligase SCF-Met30p, is either degraded or maintained in an inactive state; regulates degradation of its own DNA-binding cofactors by targeting them to SCF-Met30p | Core | NA | NA | NA |
| 6497-YNL103W-A | YNL103W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene MET4/YNL104C | Accessory | Ancestral | NA | NA |
| 6498-YNL104C | YNL104C | LEU4 | 2-isopropylmalate synthase LEU4 | Alpha-isopropylmalate synthase (2-isopropylmalate synthase); the main isozyme responsible for the first step in the leucine biosynthesis pathway; LEU4 has a paralog, LEU9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6499-YNL106C_NumOfGenes_2 | YNL106C | INP52 | phosphatidylinositol-3-/phosphoinositide 5-phosphatase INP52|SJL2 | Polyphosphatidylinositol phosphatase; dephosphorylates a number of phosphatidylinositol phosphates (PtdInsPs, PIPs) to PI; involved in endocytosis; hyperosmotic stress causes translocation to actin patches; synaptojanin-like protein with a Sac1 domain; INP52 has a paralog, INP53, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6500-YNL107W | YNL107W | YAF9 | NA | Subunit of NuA4 histone H4 acetyltransferase and SWR1 complexes; may function to antagonize silencing near telomeres; interacts directly with Swc4p; has homology to human leukemogenic protein AF9; contains a YEATS domain | Core | NA | NA | NA |
| 6501-YNL108C_NumOfGenes_2 | YNL108C | NA | HUF | Protein phosphatase; similar to prokaryotic phosphotransfer enzymes; null mutant shows alterations in glucose metabolism; GFP-fusion protein localizes to the cytoplasm and nucleus; YNL108C has a paralog, TFC7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6502-YNL110C | YNL110C | NOP15 | rRNA-binding ribosome biosynthesis protein NOP15 | Constituent of 66S pre-ribosomal particles; involved in 60S ribosomal subunit biogenesis; localizes to both nucleolus and cytoplasm | Core | NA | NA | NA |