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 |
|---|---|---|---|---|---|---|---|---|
| 3578-YFL055W_NumOfGenes_2 | YFL055W | AGP3 | NA | Low-affinity amino acid permease; may act to supply the cell with amino acids as nitrogen source in nitrogen-poor conditions; transcription is induced under conditions of sulfur limitation; plays a role in regulating Ty1 transposition | Accessory | Ancestral | NA | NA |
| 3579-YFL056C | YFL056C | AAD6 | YFL057C | Putative aryl-alcohol dehydrogenase; involved in oxidative stress response; similar to P. chrysosporium aryl-alcohol dehydrogenase; ORFs AAD6/YFL056C and AAD16/YFL057C are displaced from one another by -1 frameshift; members of the AAD gene family comprise three pairs (AAD3 + AAD15, AAD6/AAD16 + AAD4, AAD10 + AAD14) whose two genes are more related to one another than to other members of the family; expression induced in cells treated with the mycotoxin patulin | Accessory | Ancestral | NA | NA |
| 3580-YFL058W_NumOfGenes_4 | YFL058W | THI5 | 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase | Protein involved in synthesis of the thiamine precursor HMP; member of a subtelomeric gene family including THI5, THI11, THI12, and THI13; hydroxymethylpyrimidine is also known as HMP | Core | NA | NA | NA |
| 3581-YFL059W_NumOfGenes_3 | YFL059W | SNZ3 | pyridoxine biosynthesis protein SNZ3 | Member of a stationary phase-induced gene family; expressed in the presence of galactose; transcription of SNZ3 is induced prior to diauxic shift, and also in the absence of thiamin in a Thi2p-dependent manner; forms a coregulated gene pair with SNO3 | Accessory | Ancestral | NA | NA |
| 3582-YFL061W_NumOfGenes_3 | YFL061W | DDI2 | cyanamide hydratase | Cyanamide hydratase that detoxifies cyanamide; member of the HD domain metalloprotein superfamily; expression is induced over 100-fold by cyanamide and by SN2-type DNA alkylating agents such as MMS and DMA; induction decreased in rad6 and rad18 mutants; gene and protein are identical to DDI3 and Ddi3p | Accessory | Ancestral | NA | NA |
| 3583-YFL067W | YFL067W | NA | NA | Protein of unknown function; down-regulated at low calcium levels; mCherry fusion protein localizes to the vacuole | Accessory | Unknown | S. paradoxus | NA |
| 3584-YFR001W | YFR001W | LOC1 | NA | Nuclear protein involved in asymmetric localization of ASH1 mRNA; binds double-stranded RNA in vitro; constituent of 66S pre-ribosomal particles; required at post-transcriptional step for efficient retrotransposition; absence results in decreased Ty1 Gag:GFP protein levels; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3585-YFR002W | YFR002W | NIC96 | linker nucleoporin NIC96 | Linker nucleoporin component of the nuclear pore complex (NPC); also part of the NPC nuclear basket; contributes to nucleocytoplasmic transport and NPC biogenesis; forms stable associations with three FG-nucleoporins (Nsp1p, Nup57p, and Nup49p) | Core | NA | NA | NA |
| 3586-YFR003C | YFR003C | YPI1 | type 1 protein phosphatase-activating protein YPI1 | Regulatory subunit of the type I protein phosphatase (PP1) Glc7p; Glc7p participates in the regulation of a variety of metabolic processes including mitosis and glycogen metabolism; in vitro evidence suggests Ypi1p is an inhibitor of Glc7p while in vivo evidence suggests it is an activator; overproduction causes decreased cellular content of glycogen; partial depletion causes lithium sensitivity, while overproduction confers lithium-tolerance | Core | NA | NA | NA |
| 3587-YFR004W | YFR004W | RPN11 | proteasome regulatory particle lid subunit RPN11|MPR1 | Metalloprotease subunit of 19S regulatory particle; part of 26S proteasome lid; couples the deubiquitination and degradation of proteasome substrates; involved, independent of catalytic activity, in fission of mitochondria and peroxisomes; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3588-YFR005C | YFR005C | SAD1 | mRNA splicing protein SAD1 | Conserved zinc-finger domain protein involved in pre-mRNA splicing; critical for splicing of nearly all intron-containing genes; required for assembly of U4 snRNA into the U4/U6 particle | Core | NA | NA | NA |
| 3589-YFR006W | YFR006W | NA | putative Xaa-Pro dipeptidase | Putative X-Pro aminopeptidase; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YFR006W is not an essential gene | Core | NA | NA | NA |
| 3590-YFR007W | YFR007W | YFH7 | AIM12 | Putative kinase with similarity to the PRK/URK/PANK kinase subfamily; the PRK/URK/PANK subfamily of P-loop kinases is also known as phosphoribulokinase/uridine kinase/bacterial pantothenate kinase | Core | NA | NA | NA |
| 3591-YFR008W | YFR008W | FAR7 | NA | Protein involved in recovery from pheromone-induced cell cycle arrest; acts in a Far1p-independent pathway; interacts with Far3p, Far8p, Far9p, Far10p, and Far11p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3592-YFR009W_NumOfGenes_2 | YFR009W | GCN20 | putative AAA family ATPase GCN20 | Positive regulator of the Gcn2p kinase activity; forms a complex with Gcn1p; proposed to stimulate Gcn2p activation by an uncharged tRNA | Accessory | Ancestral | NA | NA |