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 |
|---|---|---|---|---|---|---|---|---|
| 4103-YGR202C | YGR202C | PCT1 | choline-phosphate cytidylyltransferase|CCT1|BSR2 | Cholinephosphate cytidylyltransferase; a rate-determining enzyme of the CDP-choline pathway for phosphatidylcholine synthesis, inhibited by Sec14p, activated upon lipid-binding; contains an element within the regulatory domain involved in both silencing and activation of enzymatic activity | Core | NA | NA | NA |
| 4104-YGR203W | YGR203W | YCH1 | phosphatase YCH1 | Phosphatase with sequence similarity to Cdc25p; Arr2p and Mih1p; member of the single-domain rhodanese homology superfamily; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus | Core | NA | NA | NA |
| 4105-YGR204C-A | YGR204C-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Core | NA | NA | NA |
| 4106-YGR204W | YGR204W | ADE3 | trifunctional formate-tetrahydrofolate ligase/methenyltetrahydrofolate cyclohydrolase/methylenetetrahydrofolate dehydrogenase ADE3 | Cytoplasmic trifunctional enzyme C1-tetrahydrofolate synthase; involved in single carbon metabolism and required for biosynthesis of purines, thymidylate, methionine, and histidine; null mutation causes auxotrophy for adenine and histidine | Core | NA | NA | NA |
| 4107-YGR205W | YGR205W | TDA10 | putative ATP-dependent kinase | ATP-binding protein of unknown function; crystal structure resembles that of E.coli pantothenate kinase and other small kinases; null mutant is sensitive to expression of the top1-T722A allele | Core | NA | NA | NA |
| 4108-YGR206W | YGR206W | MVB12 | ubiquitin-binding ESCRT-I subunit protein MVB12 | ESCRT-I subunit required to stabilize ESCRT-I core complex oligomers; the ESCRT-I core complex (Stp22p, Vps28p, Srn2p) is involved in ubiquitin-dependent sorting of proteins into the endosome; deletion mutant is sensitive to rapamycin and nystatin | Core | NA | NA | NA |
| 4109-YGR207C | YGR207C | CIR1 | NA | Mitochondrial protein that interacts with frataxin (Yfh1p); putative ortholog of mammalian electron transfer flavoprotein complex subunit ETF-beta; may have a role in oxidative stress response | Core | NA | NA | NA |
| 4110-YGR208W | YGR208W | SER2 | phosphoserine phosphatase | Phosphoserine phosphatase of the phosphoglycerate pathway; involved in serine and glycine biosynthesis, expression is regulated by the available nitrogen source | Core | NA | NA | NA |
| 4111-YGR209C | YGR209C | TRX2 | thioredoxin TRX2|LMA1 | Cytoplasmic thioredoxin isoenzyme; part of thioredoxin system which protects cells against oxidative and reductive stress; forms LMA1 complex with Pbi2p; acts as a cofactor for Tsa1p; required for ER-Golgi transport and vacuole inheritance; with Trx1p, facilitates mitochondrial import of small Tims Tim9p, Tim10p, Tim13p by maintaining them in reduced form; abundance increases under DNA replication stress; TRX2 has a paralog, TRX1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4112-YGR210C | YGR210C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 4113-YGR211W | YGR211W | ZPR1 | zinc finger-containing protein ZPR1 | Essential protein with two zinc fingers; present in nucleus of growing cells, relocates to cytoplasm in starved cells via a process mediated by Cpr1p; binds translation elongation factor eEF-1 (Tef1p); relative distribution to nucleus increases upon DNA replication stress; human ZPR1 gene can complement yeast by allowing growth during down-regulation of yeast zpr1 | Core | NA | NA | NA |
| 4114-YGR212W | YGR212W | SLI1 | N-acetyltransferase | N-acetyltransferase; confers resistance to the sphingolipid biosynthesis inhibitor myriocin (ISP-1) by converting it into N-acetyl-myriocin, co-operates with Ypk1p in mediating resistance to myriocin | Core | NA | NA | NA |
| 4115-YGR213C | YGR213C | RTA1 | NA | Protein involved in 7-aminocholesterol resistance; has seven potential membrane-spanning regions; expression is induced under both low-heme and low-oxygen conditions; member of the fungal lipid-translocating exporter (LTE) family of protein; RTA1 has a paralog, YLR046C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4116-YGR214W | YGR214W | RPS0A | uS2|ribosomal 40S subunit protein S0A|S2|S0A|YST1|NAB1A|NAB1 | Ribosomal 40S subunit protein S0A; required for maturation of 18S rRNA along with Rps0Bp; deletion of either RPS0 gene reduces growth rate, deletion of both genes is lethal; homologous to human ribosomal protein SA and bacterial S2; RPS0A has a paralog, RPS0B, that arose from the whole genome duplication; | Core | NA | NA | NA |
| 4117-YGR215W | YGR215W | RSM27 | mitochondrial 37S ribosomal protein RSM27 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |