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 |
|---|---|---|---|---|---|---|---|---|
| 3503-YER174C | YER174C | GRX4 | monothiol glutaredoxin GRX4 | Glutathione-dependent oxidoreductase; hydroperoxide and superoxide-radical responsive; monothiol glutaredoxin subfamily member along with Grx3p and Grx5p; protects cells from oxidative damage; with Grx3p, binds to Aft1p in iron-replete conditions, promoting its dissociation from promoters; mutant has increased aneuploidy tolerance; transcription regulated by Yap5p; GRX4 has a paralog, GRX3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3504-YER175C | YER175C | TMT1 | TAM1 | Trans-aconitate methyltransferase; cytosolic enzyme that catalyzes the methyl esterification of 3-isopropylmalate, an intermediate of the leucine biosynthetic pathway, and trans-aconitate, which inhibits the citric acid cycle | Core | NA | NA | NA |
| 3505-YER175W-A | YER175W-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 |
| 3506-YER176W | YER176W | ECM32 | MTT1|HEL1 | DNA dependent ATPase/DNA helicase; helicase belonging to the Dna2p- and Nam7p-like family of helicases that is involved in modulating translation termination; interacts with the translation termination factors, localized to polysomes | Core | NA | NA | NA |
| 3507-YER177W | YER177W | BMH1 | 14-3-3 family protein BMH1|APR6 | 14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of exocytosis, vesicle transport, Ras/MAPK and rapamycin-sensitive signaling, aggresome formation, spindle position checkpoint; protein increases in abundance and relative distribution to the nucleus increases upon DNA replication stress; antiapoptotic gene similar to human 14-3-3; BMH1 has a paralog, BMH2, that arose from whole genome duplication | Core | NA | NA | NA |
| 3508-YER178W | YER178W | PDA1 | pyruvate dehydrogenase (acetyl-transferring) subunit E1 alpha | E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex; catalyzes the direct oxidative decarboxylation of pyruvate to acetyl-CoA; phosphorylated; regulated by glucose; PDH complex is concentrated in spots within the mitochondrial matrix, often near the ERMES complex and near peroxisomes | Core | NA | NA | NA |
| 3509-YER179W | YER179W | DMC1 | recombinase DMC1|ISC2 | Meiosis-specific recombinase required for double-strand break repair; also required for pairing between homologous chromosomes; required for the normal morphogenesis of synaptonemal complex; homolog of Rad51p and the bacterial RecA protein; binds ssDNA and dsDNA, forms helical filaments; stimulated by Rdh54p | Core | NA | NA | NA |
| 3510-YER180C | YER180C | ISC10 | NA | Protein required for sporulation; transcript is induced 7.5 hours after induction of meiosis, expected to play significant role in the formation of reproductive cells | Accessory | Ancestral | NA | NA |
| 3511-YER180C-A | YER180C-A | SLO1 | NA | Protein interacting with Arl3p; Arl3p is a GTPase of the Ras superfamily involved in vesicle-tethering at the Golgi; putative ortholog of human SCOCO | Accessory | Ancestral | NA | NA |
| 3512-YER181C | YER181C | NA | NA | Mitochondrial protein of unknown function; conserved among S. cerevisiae strains; extensively overlaps a Ty1 LTR; YER181C is not an essential gene | Accessory | Ancestral | NA | NA |
| 3513-YER182W | YER182W | FMP10 | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 3514-YER183C | YER183C | FAU1 | 5-formyltetrahydrofolate cyclo-ligase | 5,10-methenyltetrahydrofolate synthetase; involved in folic acid biosynthesis | Accessory | Ancestral | NA | NA |
| 3515-YER184C | YER184C | TOG1 | NA | Transcriptional activator of oleate genes; regulates genes involved in fatty acid utilization; zinc cluster protein; deletion confers sensitivity to Calcufluor white, and prevents growth on glycerol or lactate as sole carbon source | Accessory | Ancestral | NA | NA |
| 3516-YER185W | YER185W | PUG1 | NA | Plasma membrane protein involved in protoprophyrin and heme transport; roles in the uptake of protoprophyrin IX and the efflux of heme; expression is induced under both low-heme and low-oxygen conditions; member of the fungal lipid-translocating exporter (LTE) family of proteins | Accessory | Ancestral | NA | NA |
| 3517-YER186C_NumOfGenes_2 | YER186C | NA | NA | Putative protein of unknown function | Accessory | Introgression | S. paradoxus | NA |