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 |
|---|---|---|---|---|---|---|---|---|
| 4628-YIL145C | YIL145C | PAN6 | pantoate--beta-alanine ligase PAN6 | Pantothenate synthase; also known as pantoate-beta-alanine ligase, required for pantothenic acid biosynthesis, deletion causes pantothenic acid auxotrophy, homologous to E. coli panC | Core | NA | NA | NA |
| 4629-YIL146C | YIL146C | ATG32 | mitophagy protein ATG32|ECM37 | Mitochondrial outer membrane protein required to initiate mitophagy; recruits the autophagy adaptor protein Atg11p and the ubiquitin-like protein Atg8p to the mitochondrial surface to initiate mitophagy, the selective vacuolar degradation of mitochondria in response to starvation; can promote pexophagy when placed ectopically in the peroxisomal membrane; regulates mitophagy and ethanol production during alcoholic fermentation | Core | NA | NA | NA |
| 4630-YIL147C | YIL147C | SLN1 | YPD2 | Transmembrane histidine phosphotransfer kinase and osmosensor; regulates MAP kinase cascade; transmembrane protein with an intracellular kinase domain that signals to Ypd1p and Ssk1p, thereby forming a phosphorelay system similar to bacterial two-component regulators | Core | NA | NA | NA |
| 4631-YIL148W | YIL148W | RPL40A | eL40|ubiquitin-ribosomal 60S subunit protein L40A fusion protein|L40e|L40A|UB11|UBI1|CEP52A | Ubiquitin-ribosomal 60S subunit protein L40A fusion protein; cleaved to yield ubiquitin and ribosomal protein L40A; ubiquitin may facilitate assembly of the ribosomal protein into ribosomes; homologous to mammalian ribosomal protein L40, no bacterial homolog; RPL40A has a paralog, RPL40B, that arose from the whole genome duplication; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4632-YIL149C | YIL149C | MLP2 | NA | Myosin-like protein associated with the nuclear envelope; nuclear basket protein that connects the nuclear pore complex with the nuclear interior; involved in the Tel1p pathway that controls telomere length; MLP2 has a paralog, MLP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4633-YIL150C | YIL150C | MCM10 | DNA43 | Essential chromatin-associated protein; involved in initiation of DNA replication; required for association of MCM2-7 complex with replication origins; required to stabilize catalytic subunit of DNA polymerase-alpha; self-associates through its N-terminal domain | Core | NA | NA | NA |
| 4634-YIL151C | YIL151C | ESL1 | NA | hEST1A/B (SMG5/6)-like protein; contributes to environment-sensing adaptive gene expression responses; Esl1p and Esl2p contain a 14-3-3-like domain and a putative PilT N-terminus ribonuclease domain; ESL1 has a paralog, ESL2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4635-YIL153W_NumOfGenes_3 | YIL153W | RRD1 | peptidylprolyl isomerase RRD1|YPA1 | Peptidyl-prolyl cis/trans-isomerase; activator of the phosphotyrosyl phosphatase activity of PP2A; involved in G1 phase progression, microtubule dynamics, bud morphogenesis and DNA repair; required for rapid reduction of Sgs1p levels in response to rapamycin; subunit of the Tap42p-Sit4p-Rrd1p complex; protein increases in abundance and relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4636-YIL154C_NumOfGenes_2 | YIL154C | IMP2' | IMP2 | Transcriptional activator involved in maintenance of ion homeostasis; also involved in protection against DNA damage caused by bleomycin and other oxidants; contains a C-terminal leucine-rich repeat | Core | NA | NA | NA |
| 4637-YIL155C_NumOfGenes_2 | YIL155C | GUT2 | glycerol-3-phosphate dehydrogenase | Mitochondrial glycerol-3-phosphate dehydrogenase; expression is repressed by both glucose and cAMP and derepressed by non-fermentable carbon sources in a Snf1p, Rsf1p, Hap2/3/4/5 complex dependent manner | Accessory | Ancestral | NA | NA |
| 4638-YIL156W_NumOfGenes_2 | YIL156W | UBP7 | ubiquitin-specific protease UBP7 | Ubiquitin-specific protease that cleaves ubiquitin-protein fusions; UBP7 has a paralog, UBP11, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4639-YIL156W-A | YIL156W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF COA1/YIL157C | Accessory | Ancestral | NA | NA |
| 4640-YIL156W-B_NumOfGenes_2 | YIL156W-B | NA | NA | Putative protein of unknown function; originally identified based on homology to <i>Ashbya gossypii</i> and other related yeasts; SWAT-GFP and mCherry fusion proteins localize to the vacuole, while SWAT-GFP fusion also localizes to the endoplasmic reticulum | Accessory | Ancestral | NA | NA |
| 4641-YIL157C_NumOfGenes_2 | YIL157C | COA1 | FMP35 | Mitochondrial inner membrane protein; required for assembly of the cytochrome c oxidase complex (complex IV); interacts with complex IV assembly factor Shy1p during the early stages of assembly | Core | NA | NA | NA |
| 4642-YIL158W_NumOfGenes_2 | YIL158W | AIM20 | NA | Protein of unknown function; overexpression causes cell cycle delay or arrest; green fluorescent protein (GFP)-fusion protein localizes to vacuole; null mutant displays elevated frequency of mitochondrial genome loss; relocalizes from nucleus to cytoplasm upon DNA replication stress; AIM20 has a paralog, SKG1, that arose from the whole genome duplication | Core | NA | NA | NA |