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 |
|---|---|---|---|---|---|---|---|---|
| 5288-YKL219W_NumOfGenes_2 | YKL219W | COS9 | NA | Endosomal protein involved in turnover of plasma membrane proteins; member of the DUP380 subfamily of conserved, often subtelomeric COS genes; required for the multivesicular vesicle body sorting pathway that internalizes plasma membrane proteins for degradation; Cos proteins provide ubiquitin in trans for nonubiquitinated cargo proteins | Accessory | Ancestral | NA | NA |
| 5289-YKL220C | YKL220C | FRE2 | ferric/cupric-chelate reductase | Ferric reductase and cupric reductase; reduces siderophore-bound iron and oxidized copper prior to uptake by transporters; expression induced by low iron levels but not by low copper levels | Accessory | Ancestral | NA | NA |
| 5290-YKL221W_NumOfGenes_2 | YKL221W | MCH2 | NA | Protein with similarity to mammalian monocarboxylate permeases; monocarboxylate permeases are involved in transport of monocarboxylic acids across the plasma membrane but mutant is not deficient in monocarboxylate transport | Accessory | Ancestral | NA | NA |
| 5291-YKL222C | YKL222C | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; similar to transcriptional regulators from the zinc cluster (binuclear cluster) family; null mutant is sensitive to caffeine | Accessory | Ancestral | NA | NA |
| 5292-YKL223W_NumOfGenes_4 | YKL223W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5293-YKL225W | YKL225W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 5294-YKR001C | YKR001C | VPS1 | dynamin-like GTPase VPS1|VPT26|VPL1|SPO15|LAM1|GRD1 | Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, endocytosis, late Golgi-retention of some proteins, regulation of peroxisome biogenesis | Core | NA | NA | NA |
| 5295-YKR002W | YKR002W | PAP1 | polynucleotide adenylyltransferase PAP1 | Poly(A) polymerase; one of three factors required for mRNA 3'-end polyadenylation, forms multiprotein complex with polyadenylation factor I (PF I), also required for mRNA nuclear export; may also polyadenylate rRNAs; required for gene looping | Core | NA | NA | NA |
| 5296-YKR003W | YKR003W | OSH6 | oxysterol-binding protein OSH6 | Member of an oxysterol-binding protein family; family members have overlapping, redundant functions in sterol metabolism and collectively perform a function essential for viability; GFP-fusion protein localizes to the cell periphery; overexpression extends lifespan by promoting vacuolar fusion; OSH6 has a paralog, OSH7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5297-YKR004C | YKR004C | ECM9 | YKR004C-A | Non-essential protein of unknown function | Core | NA | NA | NA |
| 5298-YKR005C | YKR005C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5299-YKR006C | YKR006C | MRPL13 | mitochondrial 54S ribosomal protein YmL13|YmL13|YK105 | Mitochondrial ribosomal protein of the large subunit; not essential for mitochondrial translation | Core | NA | NA | NA |
| 5300-YKR007W | YKR007W | MEH1 | GSE2|EGO1 | Component of the EGO and GSE complexes; EGO is involved in the regulation of microautophagy and GSE is required for proper sorting of amino acid permease Gap1p; loss results in a defect in vacuolar acidification | Core | NA | NA | NA |
| 5301-YKR008W | YKR008W | RSC4 | NA | Component of the RSC chromatin remodeling complex; found in close proximity to nucleosomal DNA; displaced from the surface of nucleosomal DNA after chromatin remodeling; acetylated (K25) by Gcn5p, altering replication stress tolerance; contains tandem bromodomains that recognize histone H3 acetylated on K14 (H3K14ac) by Gcn5p | Core | NA | NA | NA |
| 5302-YKR009C | YKR009C | FOX2 | bifunctional hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase FOX2|POX2 | 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase; multifunctional enzyme of the peroxisomal fatty acid beta-oxidation pathway; mutation is functionally complemented by human HSD17B4 | Core | NA | NA | NA |