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 |
|---|---|---|---|---|---|---|---|---|
| 7043-YOR075W | YOR075W | UFE1 | YOR29-26 | t-SNARE protein required for retrograde vesicular traffic; involved in Sey1p-independent homotypic ER fusion; required for efficient nuclear fusion during mating; forms a complex with the SNAREs Sec22p, Sec20p and Use1p to mediate fusion of Golgi-derived vesicles at the ER | Core | NA | NA | NA |
| 7044-YOR076C | YOR076C | SKI7 | YOR29-27 | GTP-binding protein that couples the Ski complex and exosome; putative pseudo-translational GTPase involved in 3'-to-5' mRNA decay pathway; interacts with both the cytoplasmic exosome and the Ski complex; eRF3-like domain targets nonstop mRNA for degradation; null mutants have a superkiller phenotype; SKI7 has a paralog, HBS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7045-YOR077W | YOR077W | RTS2 | YOR29-28 | Basic zinc-finger protein; similar to human and mouse Kin17 proteins which are chromatin-associated proteins involved in UV response and DNA replication | Core | NA | NA | NA |
| 7046-YOR078W | YOR078W | BUD21 | YOR29-29|UTP16 | Component of small ribosomal subunit (SSU) processosome; this complex contains U3 snoRNA; required at post-transcriptional step for efficient retrotransposition; absence results in decreased Ty1 Gag:GFP protein levels; originally isolated as bud-site selection mutant that displays a random budding pattern | Core | NA | NA | NA |
| 7047-YOR079C | YOR079C | ATX2 | Mn(2+) transporter ATX2|YOR29-30 | Golgi membrane protein involved in manganese homeostasis; overproduction suppresses the sod1 (copper, zinc superoxide dismutase) null mutation | Core | NA | NA | NA |
| 7048-YOR080W | YOR080W | DIA2 | DNA-binding SCF ubiquitin ligase subunit DIA2|YOR29-31 | Origin-binding F-box protein; forms SCF ubiquitin ligase complex with Skp1p and Cdc53p; functions in ubiquitination of silent chromatin structural protein Sir4p; required to target Cdc6p for destruction during G1 phase; required for deactivation of Rad53 checkpoint kinase, completion of DNA replication during recovery from DNA damage, assembly of RSC complex, RSC-mediated transcription regulation, and nucleosome positioning; involved in invasive and pseudohyphal growth | Core | NA | NA | NA |
| 7049-YOR081C | YOR081C | TGL5 | STC2 | Bifunctional triacylglycerol lipase and LPA acyltransferase; lipid particle-localized triacylglycerol (TAG) lipase involved in triacylglycerol mobilization; catalyzes acylation of lysophosphatidic acid (LPA); potential Cdc28p substrate; TGL5 has a paralog, TGL4, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 7050-YOR082C | YOR082C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YOR083W | Accessory | Unknown | S. paradoxus | NA |
| 7051-YOR083W | YOR083W | WHI5 | transcriptional repressor WHI5 | Repressor of G1 transcription; binds to SCB binding factor (SBF) at SCB target promoters in early G1; dilution of Whi5p concentration during cell growth determines cell size; phosphorylation of Whi5p by the CDK, Cln3p/Cdc28p relieves repression and promoter binding by Whi5, and contributes to both the determination of critical cell size at START and cell fate; periodically expressed in G1 | Accessory | Unknown | S. paradoxus | NA |
| 7052-YOR084W | YOR084W | LPX1 | triglyceride lipase | Peroxisomal matrix-localized lipase; required for normal peroxisome morphology; contains a peroxisomal targeting signal type 1 (PTS1) and a lipase motif; peroxisomal import requires the PTS1 receptor, Pex5p and self-interaction; transcriptionally activated by Yrm1p along with genes involved in multidrug resistance; oleic acid inducible | Accessory | Ancestral | NA | NA |
| 7053-YOR085W | YOR085W | OST3 | dolichyl-diphosphooligosaccharide--protein glycotransferase OST3 | Gamma subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes asparagine-linked glycosylation of newly synthesized proteins; Ost3p is important for N-glycosylation of a subset of proteins | Accessory | Ancestral | NA | NA |
| 7054-YOR086C | YOR086C | TCB1 | tricalbin | Lipid-binding ER protein involved in ER-plasma membrane tethering; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to plasma membrane and regulate PI4P levels by controlling access of Sac1p phosphatase to its substrate PI4P in PM; contains 3 calcium and lipid binding domains; non-tagged protein also localizes to mitochondria; C-termini of Tcb1p, Tcb2p and Tcb3p interact; TCB1 has a paralog, TCB2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 7055-YOR087W | YOR087W | YVC1 | TRPY1|YOR088W | Vacuolar cation channel; mediates release of Ca(2+) from the vacuole in response to hyperosmotic shock | Core | NA | NA | NA |
| 7056-YOR089C | YOR089C | VPS21 | Rab family GTPase VPS21|YPT51|YPT21|VPT12|VPS12 | Endosomal Rab family GTPase; required for endocytic transport and sorting of vacuolar hydrolases; required for endosomal localization of the CORVET complex; required with YPT52 for MVB biogenesis and sorting; involved in autophagy and ionic stress tolerance; geranylgeranylation required for membrane association; protein abundance increases in response to DNA replication stress; mammalian Rab5 homolog; VPS21 has a paralog, YPT53, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7057-YOR090C | YOR090C | PTC5 | type 2C protein phosphatase PTC5|PPP1 | Mitochondrial type 2C protein phosphatase (PP2C); involved in regulation of pyruvate dehydrogenase activity by dephosphorylating the serine 133 of the Pda1p subunit; localizes to the intermembrane space and is imported via the presequence pathway and processed by the inner membrane protease (Imp1p-Imp2p); acts in concert with kinases Pkp1p and Pkp2p and phosphatase Ptc6p | Core | NA | NA | NA |