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 |
|---|---|---|---|---|---|---|---|---|
| 5813-YLR356W | YLR356W | ATG33 | NA | Mitochondrial mitophagy-specific protein; required primarily for mitophagy induced at post-log phase; not required for other types of selective autophagy or macroautophagy; conserved within fungi, but not in higher eukaryotes; ATG33 has a paralog, SCM4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5814-YLR358C_NumOfGenes_2 | YLR358C | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels; partially overlaps ORF RSC2/YLR357W | Core | NA | NA | NA |
| 5815-YLR359W | YLR359W | ADE13 | adenylosuccinase ADE13|BRA8|BRA1 | Adenylosuccinate lyase; catalyzes two steps in the 'de novo' purine nucleotide biosynthetic pathway; expression is repressed by adenine and activated by Bas1p and Pho2p; mutations in human ortholog ADSL cause adenylosuccinase deficiency; human ADSL can complement yeast ADE13 null mutant | Core | NA | NA | NA |
| 5816-YLR360W | YLR360W | VPS38 | VPL17 | Part of a Vps34p phosphatidylinositol 3-kinase complex; functions in carboxypeptidase Y (CPY) sorting; binds Vps30p and Vps34p to promote production of phosphatidylinositol 3-phosphate (PtdIns3P) which stimulates kinase activity; required for overflow degradation of misfolded proteins when ERAD is saturated | Core | NA | NA | NA |
| 5817-YLR361C | YLR361C | DCR2 | phosphoprotein phosphatase | Protein phosphatase; involved in downregulation of the unfolded protein response (UPR), at least in part through dephosphorylation of Ire1p; dosage-dependent positive regulator of the G1/S phase transition through control of the timing of START; physically interacts with, dephosphorylates and destabilizes Sic1p; SWAT-GFP and mCherry fusion proteins localize to the vacuole | Core | NA | NA | NA |
| 5818-YLR361C-A | YLR361C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5819-YLR362W | YLR362W | STE11 | mitogen-activated protein kinase kinase kinase STE11 | Signal transducing MEK kinase; involved in pheromone response and pseudohyphal/invasive growth pathways where it phosphorylates Ste7p, and the high osmolarity response pathway, via phosphorylation of Pbs2p; regulated by Ste20p and Ste50p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5820-YLR363C | YLR363C | NMD4 | NA | Protein that may be involved in nonsense-mediated mRNA decay; interacts with Nam7p, relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 5821-YLR363W-A | YLR363W-A | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; relocalizes from nucleus to nucleolus upon DNA replication stress | Core | NA | NA | NA |
| 5822-YLR364W | YLR364W | GRX8 | glutathione-disulfide reductase GRX8 | Glutaredoxin that employs a dithiol mechanism of catalysis; monomeric; activity is low and null mutation does not affect sensitivity to oxidative stress; GFP-fusion protein localizes to the cytoplasm; expression strongly induced by arsenic | Core | NA | NA | NA |
| 5823-YLR365W | YLR365W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YLR365W is not an essential gene | Core | NA | NA | NA |
| 5824-YLR366W_NumOfGenes_2 | YLR366W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR364C-A | Core | NA | NA | NA |
| 5825-YLR367W | YLR367W | RPS22B | uS8|ribosomal 40S subunit protein S22B|S8|rp50|YS22|S24B|S22B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S15A and bacterial S8; RPS22B has a paralog, RPS22A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5826-YLR368W_NumOfGenes_3 | YLR368W | MDM30 | SCF ubiquitin ligase complex subunit MDM30|DSG1 | F-box component of an SCF ubiquitin protein ligase complex; associates with and is required for Fzo1p ubiquitination and for mitochondria fusion; stimulates nuclear export of specific mRNAs; promotes ubiquitin-mediated degradation of Gal4p in some strains | Core | NA | NA | NA |
| 5827-YLR370C_NumOfGenes_2 | YLR370C | ARC18 | NA | Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches | Core | NA | NA | NA |