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 |
|---|---|---|---|---|---|---|---|---|
| 4598-YIL117C | YIL117C | PRM5 | pheromone-regulated protein PRM5 | Pheromone-regulated protein, predicted to have 1 transmembrane segment; induced during cell integrity signaling; PRM5 has a paralog, YNL058C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4599-YIL118W | YIL118W | RHO3 | Rho family GTPase RHO3 | Non-essential small GTPase of the Rho/Rac family of Ras-like proteins; involved in the establishment of cell polarity; GTPase activity positively regulated by the GTPase activating protein (GAP) Rgd1p | Core | NA | NA | NA |
| 4600-YIL119C_NumOfGenes_2 | YIL119C | RPI1 | NA | Transcription factor, allelic differences between S288C and Sigma1278b; mediates fermentation stress tolerance by modulating cell wall integrity; overexpression suppresses heat shock sensitivity of wild-type RAS2 overexpression and also suppresses cell lysis defect of mpk1 mutation; allele from S288c can confer fMAPK pathway independent transcription of FLO11; S288C and Sigma1278b alleles differ in number of tandem repeats within ORF | Accessory | Ancestral | NA | NA |
| 4601-YIL120W | YIL120W | QDR1 | multidrug transporter | Multidrug transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; involved in spore wall assembly; sequence similarity to DTR1 and QDR3, and the triple mutant dtr1 qdr1 qdr3 exhibits reduced dityrosine fluorescence relative to the single mutants; required for resistance to quinidine, ketoconazole, fluconazole, and barban; QDR1 has a paralog, AQR1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4602-YIL121W | YIL121W | QDR2 | cation transporter | Plasma membrane transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; exports copper; has broad substrate specificity and can transport many mono- and divalent cations; transports a variety of drugs and is required for resistance to quinidine, barban, cisplatin, and bleomycin; contributes to potassium homeostasis; expression is regulated by copper | Core | NA | NA | NA |
| 4603-YIL122W | YIL122W | POG1 | NA | Nuclear chromatin-associated protein of unknown function; may have a role in cell cycle regulation; overexpression promotes recovery from pheromone induced arrest and suppresses the stress sensitivity caused by a mutation in the E3 ubiquitin ligase Rsp5p; binds upstream of BAR1 and cell cycle-related genes; phsosphoylated form may be ubiquitinated by Dma2p; potential Cdc28p substrate; SBF regulated | Accessory | Ancestral | NA | NA |
| 4604-YIL123W | YIL123W | SIM1 | putative glucosidase SIM1 | Protein of the SUN family (Sim1p, Uth1p, Nca3p, Sun4p); may participate in DNA replication; promoter contains SCB regulation box at -300 bp indicating that expression may be cell cycle-regulated; SIM1 has a paralog, SUN4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4605-YIL124W | YIL124W | AYR1 | GBG1|acylglycerone-phosphate reductase | Bifunctional triacylglycerol lipase and 1-acyl DHAP reductase; NADPH-dependent 1-acyl dihydroxyacetone phosphate reductase involved in phosphatidic acid biosynthesis; lipid droplet triacylglycerol lipase involved in the mobilization of non-polar lipids; found in lipid particles, the endoplasmic reticulum and the mitochondrial outer membrane; required for spore germination; role in cell wall biosynthesis; capable of metabolizing steroid hormones; oleic acid inducible | Core | NA | NA | NA |
| 4606-YIL125W | YIL125W | KGD1 | alpha-ketoglutarate dehydrogenase KGD1|OGD1 | Subunit of the mitochondrial alpha-ketoglutarate dehydrogenase complex; catalyzes a key step in the tricarboxylic acid (TCA) cycle, the oxidative decarboxylation of alpha-ketoglutarate to form succinyl-CoA | Core | NA | NA | NA |
| 4607-YIL126W | YIL126W | STH1 | RSC chromatin remodeling complex ATPase subunit STH1|NPS1 | ATPase component of the RSC chromatin remodeling complex; required for expression of early meiotic genes; promotes base excision repair in chromatin; essential helicase-related protein homologous to Snf2p | Core | NA | NA | NA |
| 4608-YIL127C | YIL127C | RRT14 | NA | Putative protein of unknown function; identified in a screen for mutants with decreased levels of rDNA transcription; green fluorescent protein (GFP)-fusion protein localizes to the nucleolus; predicted to be involved in ribosome biogenesis | Core | NA | NA | NA |
| 4609-YIL128W | YIL128W | MET18 | MMS19 | Component of cytosolic iron-sulfur protein assembly (CIA) machinery; acts at a late step of Fe-S cluster assembly; forms the CIA targeting complex with Cia1p and Cia2p that directs Fe-S cluster incorporation into a subset of proteins involved in methionine biosynthesis, DNA replication and repair, transcription, and telomere maintenance; ortholog of human MMS19 | Core | NA | NA | NA |
| 4610-YIL129C | YIL129C | TAO3 | PAG1 | Component of the RAM signaling network; is involved in regulation of Ace2p activity and cellular morphogenesis, interacts with protein kinase Cbk1p and also with Kic1p | Core | NA | NA | NA |
| 4611-YIL130W | YIL130W | ASG1 | NA | Zinc cluster protein proposed to be a transcriptional regulator; regulator involved in the stress response; null mutants have a respiratory deficiency, calcofluor white sensitivity and slightly increased cycloheximide resistance | Core | NA | NA | NA |
| 4612-YIL131C | YIL131C | FKH1 | forkhead family transcription factor FKH1 | Forkhead family transcription factor; rate-limiting replication origin activator; evolutionarily conserved lifespan regulator; binds multiple chromosomal elements with distinct specificities, cell cycle dynamics; regulates transcription elongation, chromatin silencing at mating loci, expression of G2/M phase genes; facilitates clustering, activation of early-firing replication origins; binds HML recombination enhancer, regulates donor preference during mating-type switching | Core | NA | NA | NA |