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 |
|---|---|---|---|---|---|---|---|---|
| 3938-YGR038W | YGR038W | ORM1 | sphingolipid homeostasis protein ORM1 | Protein that mediates sphingolipid homeostasis; evolutionarily conserved, required for resistance to agents that induce unfolded protein response; Orm1p and Orm2p together control membrane biogenesis by coordinating lipid homeostasis with protein quality control; ORM1 has a paralog, ORM2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3939-YGR039W | YGR039W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YGR039W is not an essential gene | Core | NA | NA | NA |
| 3940-YGR040W | YGR040W | KSS1 | mitogen-activated serine/threonine-protein kinase KSS1 | Mitogen-activated protein kinase (MAPK); involved in signal transduction pathways that control filamentous growth and pheromone response; regulates septum assembly, and may directly phosphorylate Bni4p; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains | Core | NA | NA | NA |
| 3941-YGR041W | YGR041W | BUD9 | NA | Protein involved in bud-site selection; mutant has increased aneuploidy tolerance; diploid mutants display a unipolar budding pattern instead of the wild-type bipolar pattern, and bud at the distal pole; BUD9 has a paralog, BUD8, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3942-YGR042W | YGR042W | MTE1 | NA | Protein of unknown function; involved in maintenance of proper telomere length; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 3943-YGR043C | YGR043C | NQM1 | sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate transaldolase NQM1 | Transaldolase of unknown function; transcription is repressed by Mot1p and induced by alpha-factor and during diauxic shift; NQM1 has a paralog, TAL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3944-YGR044C | YGR044C | RME1 | CSP1 | Zinc finger protein involved in control of meiosis; prevents meiosis by repressing IME1 expression and promotes mitosis by activating CLN2 expression; directly repressed by a1-alpha2 regulator; mediates cell type control of sporulation; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3945-YGR045C | YGR045C | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains | Core | NA | NA | NA |
| 3946-YGR046W | YGR046W | TAM41 | putative phosphatidate cytidylyltransferase|MMP37 | Mitochondrial phosphatidate cytidylyltransferase (CDP-DAG synthase); required for cardiolipin biosynthesis; viability of null mutant is strain-dependent; mRNA is targeted to the bud; mutant displays defect in mitochondrial protein import, likely due to altered membrane lipid composition | Core | NA | NA | NA |
| 3947-YGR047C | YGR047C | TFC4 | transcription factor TFIIIC subunit TFC4|tau 131|PCF1 | Subunit of RNA polymerase III transcription initiation factor complex; one of six subunits of RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauA domain of TFIIIC that binds BoxA DNA promoter sites of tRNA and similar genes; has TPR motifs; human homolog is TFIIIC-102 | Core | NA | NA | NA |
| 3948-YGR048W | YGR048W | UFD1 | polyubiquitin-binding protein UFD1 | Substrate-recruiting cofactor of the Cdc48p-Npl4p-Ufd1p segregase; polyubiquitin binding protein that assists in the dislocation of misfolded, ERAD substrates that are subsequently delivered to the proteasome for degradation; involved in regulated destruction of ER membrane proteins such as HMG-CoA reductase (Hmg1/2p) and cytoplasmic proteins (Fbp1p); involved in mobilizing membrane bound transcription factors by regulated Ub/proteasome-dependent processing (RUP) | Accessory | Ancestral | NA | NA |
| 3949-YGR049W | YGR049W | SCM4 | NA | Mitochondrial outer membrane protein of unknown function; predicted to have 4 transmembrane segments; import is mediated by Tom70p and Mim1p; interacts genetically with a cdc4 mutation; SCM4 has a paralog, ATG33, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3950-YGR050C | YGR050C | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data | Core | NA | NA | NA |
| 3951-YGR051C | YGR051C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YGR051C is not an essential gene | Core | NA | NA | NA |
| 3952-YGR052W | YGR052W | FMP48 | protein kinase FMP48 | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; induced by treatment with 8-methoxypsoralen and UVA irradiation | Core | NA | NA | NA |