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 |
|---|---|---|---|---|---|---|---|---|
| 6653-YNL265C_NumOfGenes_2 | YNL265C | IST1 | NA | Protein with positive role in the multivesicular body sorting pathway; functions and forms a complex with Did2p; recruitment to endosomes is mediated by the Vps2p-Vps24p subcomplex of ESCRT-III; also interacts with Vps4p | Accessory | Ancestral | NA | NA |
| 6654-YNL267W | YNL267W | PIK1 | 1-phosphatidylinositol 4-kinase|PIK120|PIK41 | Phosphatidylinositol 4-kinase; catalyzes first step in the biosynthesis of phosphatidylinositol-4,5-biphosphate; may control cytokinesis through the actin cytoskeleton; may control nonselective autophagy and mitophagy through trafficking of Atg9p | Accessory | Ancestral | NA | NA |
| 6655-YNL268W_NumOfGenes_2 | YNL268W | LYP1 | lysine permease | Lysine permease; one of three amino acid permeases (Alp1p, Can1p, Lyp1p) responsible for uptake of cationic amino acids | Accessory | Ancestral | NA | NA |
| 6656-YNL269W | YNL269W | BSC4 | NA | Protein of unknown function; protein-coding gene that evolved de novo via a series of point mutations in noncoding sequence; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression; readthrough is increased upon depletion of Sup35p; may be involved in DNA repair pathway during stationary phase and contribute to robustness of cells when shifted to a nutrient-poor environment | Accessory | Unknown | NA | NA |
| 6657-YNL270C_NumOfGenes_2 | YNL270C | ALP1 | arginine permease ALP1|APL1 | Arginine transporter; expression is normally very low and it is unclear what conditions would induce significant expression; ALP1 has a paralog, CAN1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6658-YNL271C | YNL271C | BNI1 | formin BNI1|SHE5|PPF3 | Formin; polarisome component; nucleates the formation of linear actin filaments, involved in cell processes such as budding and mitotic spindle orientation which require the formation of polarized actin cables; recruited to the division site in a Glc7p/Ref2p dependent manner following release of Bnr1p; functionally redundant with BNR1 | Core | NA | NA | NA |
| 6659-YNL272C | YNL272C | SEC2 | guanine nucleotide exchange factor SEC2 | Guanyl-nucleotide exchange factor for the small G-protein Sec4p; essential for post-Golgi vesicle transport and for autophagy; associates with the exocyst, via exocyst subunit Sec15p, on secretory vesicles | Core | NA | NA | NA |
| 6660-YNL273W | YNL273W | TOF1 | NA | Subunit of a replication-pausing checkpoint complex; Tof1p-Mrc1p-Csm3p acts at the stalled replication fork to promote sister chromatid cohesion after DNA damage, facilitating gap repair of damaged DNA; interacts with the MCM helicase; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6661-YNL274C | YNL274C | GOR1 | glyoxylate reductase | Glyoxylate reductase; null mutation results in increased biomass after diauxic shift; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6662-YNL275W | YNL275W | BOR1 | NA | Boron efflux transporter of the plasma membrane; binds HCO3-, I-, Br-, NO3- and Cl-; has similarity to the characterized boron efflux transporter A. thaliana BOR1 | Core | NA | NA | NA |
| 6663-YNL277W_NumOfGenes_2 | YNL277W | MET2 | homoserine O-acetyltransferase | L-homoserine-O-acetyltransferase; catalyzes the conversion of homoserine to O-acetyl homoserine which is the first step of the methionine biosynthetic pathway | Core | NA | NA | NA |
| 6664-YNL277W-A | YNL277W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6665-YNL278W | YNL278W | CAF120 | NA | Part of the CCR4-NOT transcriptional regulatory complex; involved in controlling mRNA initiation, elongation, and degradation; contains a PH-like domain; CAF120 has a paralog, SKG3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6666-YNL279W | YNL279W | PRM1 | pheromone-regulated protein PRM1 | Pheromone-regulated multispanning membrane protein; involved in membrane fusion during mating; predicted to have 5 transmembrane segments and a coiled coil domain; localizes to the shmoo tip; regulated by Ste12p | Core | NA | NA | NA |
| 6667-YNL280C | YNL280C | ERG24 | delta(14)-sterol reductase | C-14 sterol reductase; acts in ergosterol biosynthesis; mutants accumulate the abnormal sterol ignosterol (ergosta-8,14 dienol), and are viable under anaerobic growth conditions but inviable on rich medium under aerobic conditions | Core | NA | NA | NA |