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 |
|---|---|---|---|---|---|---|---|---|
| 4748-YJL052W | YJL052W | TDH1 | glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) TDH1|GAPDH|GLD3 | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isozyme 1; involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell wall; protein abundance increases in response to DNA replication stress; GAPDH-derived antimicrobial peptides secreted by S. cerevisiae are active against a wide variety of wine-related yeasts and bateria | Core | NA | NA | NA |
| 4749-YJL053W | YJL053W | PEP8 | retromer subunit PEP8|VPT4|VPS26|GRD6 | Vacuolar protein component of the retromer; forms part of the multimeric membrane-associated retromer complex involved in vacuolar protein sorting along with Vps35p, Vps29p, Vps17p, and Vps5p; essential for endosome-to-Golgi retrograde protein transport; interacts with Ypt7p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4750-YJL054W | YJL054W | TIM54 | NA | Component of the mitochondrial TIM22 complex; involved in insertion of polytopic proteins into the inner membrane | Core | NA | NA | NA |
| 4751-YJL055W | YJL055W | NA | NA | Putative protein of unknown function; functions together with HAM1 to mediate resistance to 5-FU; specifically reduces the incorporation of 5-FU into RNA, without affecting uptake or incorporation of uracil into RNA; proposed to be involved in the metabolism of purine and pyrimidine base analogues; deletion mutants are sensitive to HAP and AHA | Core | NA | NA | NA |
| 4752-YJL056C | YJL056C | ZAP1 | ZRG10 | Zinc-regulated transcription factor; binds to zinc-responsive promoters to induce transcription of certain genes in presence of zinc, represses other genes in low zinc; regulates its own transcription; contains seven zinc-finger domains | Core | NA | NA | NA |
| 4753-YJL057C | YJL057C | IKS1 | protein kinase IKS1 | Protein kinase of unknown cellular role; putative serine/threonine kinase; expression is induced during mild heat stress; deletion mutants are hypersensitive to copper sulphate and resistant to sorbate; interacts with an N-terminal fragment of Sst2p | Core | NA | NA | NA |
| 4754-YJL058C | YJL058C | BIT61 | NA | Subunit of TORC2 membrane-associated complex; involved in regulation of cell cycle-dependent actin cytoskeletal dynamics during polarized growth and cell wall integrity; BIT61 has a paralog, BIT2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4755-YJL059W | YJL059W | YHC3 | amino acid transporter YHC3|BTN1 | Protein required for the ATP-dependent transport of arginine; vacuolar membrane protein; involved in the ATP-dependent transport of arginine into the vacuole and possibly in balancing ion homeostasis; human homolog CLN3 involved in Batten disease (juvenile onset neuronal ceroid lipofuscinosis) can complement yeast null mutant | Core | NA | NA | NA |
| 4756-YJL060W | YJL060W | BNA3 | kynurenine--oxoglutarate transaminase | Kynurenine aminotransferase; catalyzes formation of kynurenic acid from kynurenine; potential Cdc28p substrate | Core | NA | NA | NA |
| 4757-YJL061W | YJL061W | NUP82 | linker nucleoporin NUP82|HRB187 | Linker nucleoporin component of the nuclear pore complex (NPC); also part of the NPC cytoplasmic filaments; contributes to nucleocytoplasmic transport and NPC biogenesis; forms stable associations with three FG-nucleoporins (Nsp1p, Nup159p, and Nup116p); relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4758-YJL062W | YJL062W | LAS21 | mannose-ethanolamine phosphotransferase LAS21|GPI7 | Integral plasma membrane protein; involved in the synthesis of the glycosylphosphatidylinositol (GPI) core structure; mutations affect cell wall integrity | Core | NA | NA | NA |
| 4759-YJL062W-A | YJL062W-A | COA3 | COX25|RRG10 | Mitochondrial protein required for cytochrome c oxidase assembly; also involved in translational regulation of Cox1p and prevention of Cox1p aggregation before assembly; located in the mitochondrial inner membrane | Accessory | Ancestral | NA | NA |
| 4760-YJL063C | YJL063C | MRPL8 | mitochondrial 54S ribosomal protein YmL8|YmL8|HRD238 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 4761-YJL065C_NumOfGenes_2 | YJL065C | DLS1 | NA | Subunit of ISW2/yCHRAC chromatin accessibility complex; ISW2/yCHRAC also includes Itc1p, Isw2p, and Dpb4p; involved in inheritance of telomeric silencing; DLS1 has a paralog, DPB3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4762-YJL066C_NumOfGenes_2 | YJL066C | MPM1 | NA | Mitochondrial intermembrane space protein of unknown function | Core | NA | NA | NA |