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 |
|---|---|---|---|---|---|---|---|---|
| 4778-YJL083W | YJL083W | TAX4 | NA | EH domain-containing protein; involved in regulating phosphatidylinositol 4,5-bisphosphate levels and autophagy; Irs4p and Tax4p bind and activate the PtdIns phosphatase Inp51p; Irs4p and Tax4p are involved in localizing Atg17p to the PAS; TAX4 has a paralog, IRS4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4779-YJL084C | YJL084C | ALY2 | ART3 | Alpha arrestin; controls nutrient-mediated intracellular sorting of permease Gap1p; interacts with AP-1 subunit Apl4p; phosphorylated by Npr1p and also by cyclin-CDK complex Pcl7p-Pho85p; promotes endocytosis of plasma membrane proteins; ALY2 has a paralog, ALY1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4780-YJL085W | YJL085W | EXO70 | GTP-Rho binding exocyst subunit EXO70 | Subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis prior to SNARE-mediated fusion; PtdIns[4,5]P2-binding protein that localizes to exocytic sites in an actin-independent manner, targeting and anchoring the exocyst with Sec3p; involved in exocyst assembly; direct downstream effector of Rho3p and Cdc42p; relocalizes from bud neck to cytoplasm upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 4781-YJL086C | YJL086C | 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 YJL085W/EXO70 and YJL087C/TRL1 | Accessory | Unknown | NA | NA |
| 4782-YJL087C | YJL087C | TRL1 | tRNA ligase|RLG1|LIG1 | tRNA ligase; required for tRNA splicing and for both splicing and translation of HAC1 mRNA in the UPR; has phosphodiesterase, polynucleotide kinase, and ligase activities; localized at the inner nuclear envelope and partially to polysomes | Accessory | Ancestral | NA | NA |
| 4783-YJL088W | YJL088W | ARG3 | ornithine carbamoyltransferase|argF | Ornithine carbamoyltransferase; also known as carbamoylphosphate:L-ornithine carbamoyltransferase; catalyzes the biosynthesis of the arginine precursor citrulline | Accessory | Ancestral | NA | NA |
| 4784-YJL089W | YJL089W | SIP4 | NA | C6 zinc cluster transcriptional activator; binds to the carbon source-responsive element (CSRE) of gluconeogenic genes; involved in the positive regulation of gluconeogenesis; regulated by Snf1p protein kinase; localized to the nucleus | Accessory | Ancestral | NA | NA |
| 4785-YJL090C | YJL090C | DPB11 | protein kinase activating protein DPB11 | DNA replication initiation protein; loads DNA pol epsilon onto pre-replication complexes at origins; checkpoint sensor recruited to stalled replication forks by the checkpoint clamp complex where it activates Mec1p; along with Rfa1p, binds to ultrafine anaphase bridges in mitotic cells and prevents accumulation of chromatin bridges by stimulating the Mec1p kinase and suppressing homologous recombination; ortholog of human TopBP1; forms nuclear foci upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 4786-YJL091C | YJL091C | GWT1 | glucosaminyl-phosphotidylinositol O-acyltransferase | Protein involved in the inositol acylation of GlcN-PI; the inositol acylation of glucosaminyl phosphatidylinositol (GlcN-PI) forms glucosaminyl(acyl)phosphatidylinositol (GlcN(acyl)PI), an intermediate in the biosynthesis of glycosylphosphatidylinositol (GPI) anchors | Core | NA | NA | NA |
| 4787-YJL092W | YJL092W | SRS2 | DNA helicase SRS2|HPR5|RADH1|RADH | DNA helicase and DNA-dependent ATPase; involved in DNA repair and checkpoint recovery, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; blocks trinucleotide repeat expansion; affects genome stability; disassembles Rad51p nucleoprotein filaments during meiotic recombination; stimulates activity of the Mus81p-Mms4p endonuclease, independently of Srs2p catalytic activity; functional homolog of human RTEL1 | Core | NA | NA | NA |
| 4788-YJL093C | YJL093C | TOK1 | YPK1|YORK|YKC1|DUK1 | Outward-rectifier potassium channel of the plasma membrane; has two pore domains in tandem, each of which forms a functional channel permeable to potassium; carboxy tail functions to prevent inner gate closures; target of K1 toxin | Core | NA | NA | NA |
| 4789-YJL094C | YJL094C | KHA1 | NA | Putative K+/H+ antiporter; has a probable role in intracellular cation homeostasis; localized to Golgi vesicles and detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 4790-YJL095W | YJL095W | BCK1 | mitogen-activated protein kinase kinase kinase BCK1|SSP31|SLK1|SAP3|LAS3 | MAPKKK acting in the protein kinase C signaling pathway; the kinase C signaling pathway controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p; MAPKKK is an acronym for mitogen-activated protein (MAP) kinase kinase kinase | Core | NA | NA | NA |
| 4791-YJL096W | YJL096W | MRPL49 | mitochondrial 54S ribosomal protein YmL49|YmL49 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 4792-YJL097W | YJL097W | PHS1 | enoyl-CoA hydratase PHS1 | Essential 3-hydroxyacyl-CoA dehydratase of the ER membrane; involved in elongation of very long-chain fatty acids; evolutionarily conserved, similar to mammalian PTPLA and PTPLB; involved in sphingolipid biosynthesis and protein trafficking | Core | NA | NA | NA |