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 |
|---|---|---|---|---|---|---|---|---|
| 5558-YLR099C | YLR099C | ICT1 | lysophosphatidic acid acyltransferase ICT1 | Lysophosphatidic acid acyltransferase; responsible for enhanced phospholipid synthesis during organic solvent stress; null displays increased sensitivity to Calcofluor white; highly expressed during organic solvent stress; ICT1 has a paralog, ECM18, that arose from the whole genome duplication; human ABHD5 can complement ict1 null mutant | Core | NA | NA | NA |
| 5559-YLR099W-A | YLR099W-A | MIM2 | NA | Mitochondrial protein required for outer membrane protein import; involved in import of the subset of proteins with multiple alpha-helical transmembrane segments, including Ugo1p, Tom20p, and Fzo1p; component of a large protein complex in the outer membrane that includes Mim1p; not essential in W303 strain background | Core | NA | NA | NA |
| 5560-YLR100W | YLR100W | ERG27 | 3-keto-steroid reductase | 3-keto sterol reductase; catalyzes the last of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; mutants are sterol auxotrophs; mutation is functionally complemented by human HSD17B7 | Core | NA | NA | NA |
| 5561-YLR101C | YLR101C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified, essential ORF ERG27/YLR100W | Accessory | Ancestral | NA | NA |
| 5562-YLR102C | YLR102C | APC9 | anaphase promoting complex subunit 9 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition | Core | NA | NA | NA |
| 5563-YLR103C | YLR103C | CDC45 | DNA replication initiation factor CDC45|SLD4 | DNA replication initiation factor; recruited to MCM pre-RC complexes at replication origins; promotes release of MCM from Mcm10p, recruits elongation machinery; binds tightly to ssDNA, which disrupts interaction with the MCM helicase and stalls it during replication stress; mutants in human homolog may cause velocardiofacial and DiGeorge syndromes | Core | NA | NA | NA |
| 5564-YLR104W | YLR104W | LCL2 | NA | Putative protein of unknown function; mutant is deficient in cell wall mannosylphosphate and has long chronological lifespan; genetic interactions suggest a role in ER-associated protein degradation (ERAD); SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to just the vacuole | Core | NA | NA | NA |
| 5565-YLR105C | YLR105C | SEN2 | tRNA splicing endonuclease subunit SEN2 | Subunit of the tRNA splicing endonuclease; tRNA splicing endonuclease (Sen complex) is composed of Sen2p, Sen15p, Sen34p, and Sen54p; Sen complex also cleaves the CBP1 mRNA at the mitochondrial surface; Sen2p contains the active site for tRNA 5' splice site cleavage and has similarity to Sen34p and to Archaeal tRNA splicing endonuclease; | Core | NA | NA | NA |
| 5566-YLR106C | YLR106C | MDN1 | AAA family ATPase midasin|REA1 | Huge dynein-related AAA-type ATPase (midasin); forms extended pre-60S particle with the Rix1 complex (Rix1p-Ipi1p-Ipi3p); acts in removal of ribosomal biogenesis factors at successive steps of pre-60S assembly and export from nucleus | Core | NA | NA | NA |
| 5567-YLR107W | YLR107W | REX3 | RNA exonuclease | RNA exonuclease; required for maturation of the RNA component of RNase MRP; functions redundantly with Rnh70p and Rex2p in processing of U5 snRNA and RNase P RNA; member of RNase D family of exonucleases | Core | NA | NA | NA |
| 5568-YLR108C | YLR108C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YLR108C is not an esssential gene; protein abundance increases in response to DNA replication stress; YLR108C has a paralog, YDR132C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5569-YLR109W | YLR109W | AHP1 | thioredoxin peroxidase AHP1|cTPxIII | Thiol-specific peroxiredoxin; reduces hydroperoxides to protect against oxidative damage; function in vivo requires covalent conjugation to Urm1p | Core | NA | NA | NA |
| 5570-YLR110C | YLR110C | CCW12 | NA | Cell wall mannoprotein; plays a role in maintenance of newly synthesized areas of cell wall; localizes to periphery of small buds, septum region of larger buds, and shmoo tip; CCW12 has a paralog, YDR134C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5571-YLR111W | YLR111W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5572-YLR112W | YLR112W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |