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 |
|---|---|---|---|---|---|---|---|---|
| 2198-YBR209W | YBR209W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YBR209W is not an essential gene | Core | NA | NA | NA |
| 2199-YBR210W | YBR210W | ERV15 | NA | Protein involved in export of proteins from the endoplasmic reticulum; ERV15 has a paralog, ERV14, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2200-YBR211C | YBR211C | AME1 | ARP100 | Essential kinetochore protein associated with microtubules and SPBs; component of the kinetochore sub-complex COMA (Ctf19p, Okp1p, Mcm21p, Ame1p); involved in spindle checkpoint maintenance; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-U and fission yeast Mis17; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2201-YBR212W | YBR212W | NGR1 | RBP1 | RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochondrial porin (POR1) mRNA and enhances its degradation; overexpression impairs mitochondrial function; interacts with Dhh1p to mediate POR1 mRNA decay; expressed in stationary phase | Core | NA | NA | NA |
| 2202-YBR213W | YBR213W | MET8 | bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase MET8 | Bifunctional dehydrogenase and ferrochelatase; involved in the biosynthesis of siroheme, a prosthetic group used by sulfite reductase; required for sulfate assimilation and methionine biosynthesis | Core | NA | NA | NA |
| 2203-YBR214W | YBR214W | SDS24 | NA | Protein involved in cell separation during budding; one of two S. cerevisiae homologs (Sds23p and Sds24p) of the S. pombe Sds23 protein, which is implicated in APC/cyclosome regulation; may play an indirect role in fluid-phase endocytosis; protein abundance increases in response to DNA replication stress; SDS24 has a paralog, SDS23, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2204-YBR215W | YBR215W | HPC2 | NA | Subunit of the HIR complex; HIR is a nucleosome assembly complex involved in regulation of histone gene transcription; mutants display synthetic defects with subunits of FACT, a complex that allows passage of RNA Pol II through nucleosomes | Core | NA | NA | NA |
| 2205-YBR216C | YBR216C | YBP1 | NA | Protein involved in cellular response to oxidative stress; required for oxidation of specific cysteine residues of transcription factor Yap1p, resulting in nuclear localization of Yap1p in response to stress; YBP1 has a paralog, YBP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2206-YBR217W | YBR217W | ATG12 | APG12 | Ubiquitin-like modifier involved in autophagy and the Cvt pathway; conserved; conjugated to Atg5p to form a complex involved in Atg8p lipidation; Atg5p-Atg12p conjugate enhances E2 activity of Atg3p by rearranging its catalytic site, also forms a complex with Atg16p; the Atg5-Atg12/Atg16 complex binds to membranes and is essential for autophagosome formation | Core | NA | NA | NA |
| 2207-YBR218C | YBR218C | PYC2 | pyruvate carboxylase 2 | Pyruvate carboxylase isoform; cytoplasmic enzyme that converts pyruvate to oxaloacetate; differentially regulated than isoform Pyc1p; mutations in the human homolog are associated with lactic acidosis; PYC2 has a paralog, PYC1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2208-YBR219C | YBR219C | NA | NA | Putative protein of unknown function; YBR219C is not an essential gene | Core | NA | NA | NA |
| 2209-YBR220C | YBR220C | NA | NA | Putative protein of unknown function; YBR220C is not an essential gene | Core | NA | NA | NA |
| 2210-YBR221C | YBR221C | PDB1 | pyruvate dehydrogenase (acetyl-transferring) subunit E1 beta | E1 beta subunit of the pyruvate dehydrogenase (PDH) complex; PDH is an evolutionarily conserved multi-protein complex found in mitochondria | Core | NA | NA | NA |
| 2211-YBR221W-A | YBR221W-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 2212-YBR222C | YBR222C | PCS60 | FAT2 | Oxalyl-CoA synthetase; capable of catalyzing conversion of oxalate to oxalyl-CoA; catalyzes first step in pathway of oxalate degradation that functions to protect yeast from inhibitory effects of oxalate; peroxisomal protein that binds mRNA; localizes to both peroxisomal peripheral membrane and matrix, expression is highly inducible by oleic acid; similar to E. coli long chain acyl-CoA synthetase | Core | NA | NA | NA |