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 |
|---|---|---|---|---|---|---|---|---|
| 2783-YDR093W_NumOfGenes_2 | YDR093W | DNF2 | aminophospholipid-translocating P4-type ATPase DNF2 | Aminophospholipid translocase (flippase); type 4 P-type ATPase; involved in phospholipid translocation, contributing to endocytosis, protein transport, and cellular polarization; localizes primarily to the plasma membrane; localizes to the shmoo tip where it has a redundant role in the cellular response to mating pheromone; DNF2 has a paralog, DNF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2784-YDR095C | YDR095C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 2785-YDR096W | YDR096W | GIS1 | histone demethylase GIS1 | Histone demethylase and transcription factor; regulates genes during nutrient limitation; activity modulated by proteasome-mediated proteolysis; has JmjC and JmjN domain in N-terminus that interact, promoting stability and proper transcriptional activity; contains two transactivating domains downstream of Jmj domains and a C-terminal DNA binding domain; relocalizes to the cytosol in response to hypoxia; GIS1 has a paralog, RPH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2786-YDR097C | YDR097C | MSH6 | PMS6|mismatch repair ATPase MSH6|PMS3 | Protein required for mismatch repair in mitosis and meiosis; forms a complex with Msh2p to repair both single-base & insertion-deletion mispairs; also involved in interstrand cross-link repair; potentially phosphorylated by Cdc28p | Core | NA | NA | NA |
| 2787-YDR098C | YDR098C | GRX3 | monothiol glutaredoxin GRX3 | Glutathione-dependent oxidoreductase; hydroperoxide and superoxide-radical responsive; monothiol glutaredoxin subfamily member along with Grx4p and Grx5p; protects cells from oxidative damage; with Grx4p, binds to Aft1p in iron-replete conditions, promoting its dissociation from promoters; evidence exists indicating that the translation start site is not Met1 as currently annotated, but rather Met36; GRX3 has a paralog, GRX4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2788-YDR099W_NumOfGenes_2 | YDR099W | BMH2 | 14-3-3 family protein BMH2|SCD3 | 14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling; protein increases in abundance and relative distribution to the nucleus increases upon DNA replication stress; abundance relative to Bmh1p increases during sporulation | Core | NA | NA | NA |
| 2789-YDR100W | YDR100W | TVP15 | NA | Integral membrane protein; localized to late Golgi vesicles along with the v-SNARE Tlg2p | Accessory | Ancestral | NA | NA |
| 2790-YDR101C | YDR101C | ARX1 | putative hydrolase | Nuclear export factor for the ribosomal pre-60S subunit; shuttling factor which directly binds FG rich nucleoporins and facilities translocation through the nuclear pore complex; interacts directly with Alb1p; responsible for Tif6p recycling defects in the absence of Rei1; associated with the ribosomal export complex | Accessory | Ancestral | NA | NA |
| 2791-YDR102C | YDR102C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YDR102C is not an essential gene; homozygous diploid deletion strain exhibits high budding index | Accessory | Unknown | NA | NA |
| 2792-YDR103W | YDR103W | STE5 | NUL3|HMD3 | Pheromone-responsive MAPK scaffold protein; couples activation of the G-protein-coupled pheromone receptor to MAPK activation; intramolecular interaction of PH and VWA domains blocks activation of assembled signaling cascade components (Ste11p, Ste7p and Fus3p) under basal conditions; Gbeta-gamma (Ste4p-Ste18p)-dependent docking at the plasma membrane and binding of PI(4,5)P2 by the PH domain relieves autoinhibition, resulting in pheromone-dependent pathway activation | Accessory | Ancestral | NA | NA |
| 2793-YDR104C | YDR104C | SPO71 | NA | Meiosis-specific protein required for prospore membrane morphogenesis; localizes to the prospore membrane (PSM) during sporulation; required for PSM elongation and closure; genetically antagonistic to SPO1; recruits Vps13p to the PSM during sporulation; interacts and functions cooperatively with Spo73p; mutants have defects in the PSM, aberrant spore wall formation and reduced PtdIns-phosphate pools in the PSM; contains three PH-like domains | Accessory | Ancestral | NA | NA |
| 2794-YDR105C_NumOfGenes_2 | YDR105C | TMS1 | NA | Vacuolar membrane protein of unknown function; is conserved in mammals; predicted to contain eleven transmembrane helices; interacts with Pdr5p, a protein involved in multidrug resistance | Core | NA | NA | NA |
| 2795-YDR106W_NumOfGenes_2 | YDR106W | ARP10 | NA | Component of the dynactin complex; localized to the pointed end of the Arp1p filament; may regulate membrane association of the complex | Core | NA | NA | NA |
| 2796-YDR107C | YDR107C | TMN2 | NA | Protein with a role in cellular adhesion and filamentous growth; similar to Tmn3p; member of the evolutionarily conserved Transmembrane Nine family of proteins with nine membrane-spanning segments; TMN2 has a paralog, EMP70, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2797-YDR108W | YDR108W | TRS85 | GSG1|MUM1 | Component of transport protein particle (TRAPP) complex III; TRAPPIII is a multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating endosome-Golgi traffic and required for membrane expansion during autophagy and the CVT pathway; directs Ypt1p to the PAS; late post-replication meiotic role | Core | NA | NA | NA |