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 |
|---|---|---|---|---|---|---|---|---|
| 4433-YHR174W | YHR174W | ENO2 | phosphopyruvate hydratase ENO2 | Enolase II, a phosphopyruvate hydratase; catalyzes conversion of 2-phosphoglycerate to phosphoenolpyruvate during glycolysis and the reverse reaction during gluconeogenesis; expression induced in response to glucose; ENO2 has a paralog, ENO1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4434-YHR175W | YHR175W | CTR2 | low-affinity Cu transporter | Low-affinity copper transporter of the vacuolar membrane; mutation confers resistance to toxic copper concentrations, while overexpression confers resistance to copper starvation; regulated by nonsense-mediated mRNA decay pathway | Accessory | Ancestral | NA | NA |
| 4435-YHR175W-A | YHR175W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 4436-YHR176W | YHR176W | FMO1 | N,N-dimethylaniline monooxygenase | Flavin-containing monooxygenase; localized to the cytoplasmic face of the ER membrane; catalyzes oxidation of biological thiols to maintain the ER redox buffer ratio for correct folding of disulfide-bonded proteins | Accessory | Ancestral | NA | NA |
| 4437-YHR177W | YHR177W | NA | GON3 | Putative transcription factor containing a WOPR domain; binds DNA in vitro; similar to C. albicans Wor1p transcription factor that regulates white-opaque switching; overexpression causes a cell cycle delay or arrest | Core | NA | NA | NA |
| 4438-YHR178W | YHR178W | STB5 | NA | Transcription factor; involved in regulating multidrug resistance and oxidative stress response; forms a heterodimer with Pdr1p; contains a Zn(II)2Cys6 zinc finger domain that interacts with a pleiotropic drug resistance element in vitro | Core | NA | NA | NA |
| 4439-YHR179W | YHR179W | OYE2 | NADPH dehydrogenase | Conserved NADPH oxidoreductase containing flavin mononucleotide (FMN); responsible for geraniol reduction into citronellol during fermentation; homologous to Oye3p with different ligand binding and catalytic properties; may be involved in sterol metabolism, oxidative stress response, and programmed cell death; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 4440-YHR180W | YHR180W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains | Accessory | Introgression | S. paradoxus | NA |
| 4441-YHR180W-A_NumOfGenes_2 | YHR180W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps dubious ORF YHR180C-B and long terminal repeat YHRCsigma3 | Accessory | Unknown | S. paradoxus | NA |
| 4442-YHR181W | YHR181W | SVP26 | ERV26 | Integral membrane protein of the early Golgi apparatus and ER; involved in COP II vesicle transport; may also function to promote retention of proteins in the early Golgi compartment | Accessory | Introgression | S. paradoxus | NA |
| 4443-YHR182W | YHR182W | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and cytoplasm; relocalizes from bud neck to cytoplasm upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 4444-YHR183W_NumOfGenes_3 | YHR183W | GND1 | phosphogluconate dehydrogenase (decarboxylating) GND1 | 6-phosphogluconate dehydrogenase (decarboxylating); catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone and adaptation to oxidative stress; GND1 has a paralog, GND2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4445-YHR184W_NumOfGenes_2 | YHR184W | SSP1 | SPO3 | Protein involved in the control of meiotic nuclear division; involved in the coordination of meiosis with spore formation; subunit of the leading edge protein (LEP) complex (Ssp1-Ady3-Don1-Irc10) that forms a ring-like structure at the leading edge of the prospore membrane during meiosis II; required for assembly of the leading edge coat and both prospore membrane shaping and organization; transcription is induced midway through meiosis | Core | NA | NA | NA |
| 4446-YHR185C_NumOfGenes_2 | YHR185C | PFS1 | ADY1 | Sporulation protein required for prospore membrane formation; required for prospore membrane formation at selected spindle poles; ensures functionality of all four spindle pole bodies during meiosis II; not required for meiotic recombination or meiotic chromosome segregation | Core | NA | NA | NA |
| 4447-YHR186C | YHR186C | KOG1 | ubiquitin-binding TORC1 subunit KOG1|LAS24 | Subunit of TORC1; TORC1 is a rapamycin-sensitive complex involved in growth control that contains Tor1p or Tor2p, Lst8p and Tco89p; contains four HEAT repeats and seven WD-40 repeats; may act as a scaffold protein to couple TOR and its effectors | Core | NA | NA | NA |