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 |
|---|---|---|---|---|---|---|---|---|
| 6323-YMR254C | YMR254C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6324-YMR255W | YMR255W | GFD1 | NA | Coiled-coiled protein of unknown function; identified as a high-copy suppressor of a dbp5 mutation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6325-YMR256C | YMR256C | COX7 | cytochrome c oxidase subunit VII | Subunit VII of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain | Core | NA | NA | NA |
| 6326-YMR257C | YMR257C | PET111 | NA | Mitochondrial translational activator specific for the COX2 mRNA; located in the mitochondrial inner membrane | Core | NA | NA | NA |
| 6327-YMR258C | YMR258C | ROY1 | NA | GTPase inhibitor with similarity to F-box proteins; inhibits Ypt52p GTPase activity by preventing Ypt52p from binding GTP; involved in regulating intracellular trafficking; physically interacts with Skp1p | Core | NA | NA | NA |
| 6328-YMR259C | YMR259C | TRM732 | tRNA methylation protein TRM732 | Protein involved in 2'-O-methylation of C32 of substrate tRNAs; interacts with 2'-O-ribose methyltransferase Trm7p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; non-essential gene; yeast null mutant can be functionally complemented by human THADA, mutations in which have been implicated in epithelial thyroid adenomas, type 2 diabetes, and polycystic ovary syndrome (PCOS) | Core | NA | NA | NA |
| 6329-YMR260C | YMR260C | TIF11 | NA | Translation initiation factor eIF1A; essential protein that forms a complex with Sui1p (eIF1) and the 40S ribosomal subunit and scans for the start codon; C-terminus associates with Fun12p (eIF5B); N terminus interacts with eIF2 and eIF3 | Core | NA | NA | NA |
| 6330-YMR261C | YMR261C | TPS3 | trehalose 6-phosphate synthase/phosphatase complex subunit | Regulatory subunit of trehalose-6-phosphate synthase/phosphatase; involved in synthesis of storage carbohydrate trehalose; expression is induced by stress conditions and repressed by the Ras-cAMP pathway; TPS3 has a paralog, TSL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6331-YMR262W | YMR262W | NA | putative endodeoxyribonuclease | Protein of unknown function; interacts weakly with Knr4p; YMR262W is not an essential gene | Core | NA | NA | NA |
| 6332-YMR263W | YMR263W | SAP30 | NA | Component of Rpd3L histone deacetylase complex; involved in silencing at telomeres, rDNA, and silent mating-type loci; involved in telomere maintenance | Core | NA | NA | NA |
| 6333-YMR264W | YMR264W | CUE1 | KIS4 | Ubiquitin-binding protein; ER membrane protein that recruits and integrates the ubiquitin-conjugating enzyme Ubc7p into ER membrane-bound ubiquitin ligase complexes that function in the ER-associated degradation (ERAD) pathway for misfolded proteins; contains a CUE domain that binds ubiquitin to facilitate intramolecular monoubiquitination and to promote diubiquitin elongation, facilitating polyubiquitin chain formation | Core | NA | NA | NA |
| 6334-YMR265C | YMR265C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6335-YMR266W | YMR266W | RSN1 | NA | Membrane protein of unknown function; overexpression suppresses NaCl sensitivity of sro7 mutant cells by restoring sodium pump (Ena1p) localization to the plasma membrane | Accessory | Ancestral | NA | NA |
| 6336-YMR267W | YMR267W | PPA2 | inorganic diphosphatase PPA2|IPP2 | Mitochondrial inorganic pyrophosphatase; required for mitochondrial function and possibly involved in energy generation from inorganic pyrophosphate; human ortholog, PPA2, functionally complements the null mutant; mutations in human PPA2 cause a mitochondrial disease resulting in sudden unexpected cardiac arrest in infants | Core | NA | NA | NA |
| 6337-YMR268C | YMR268C | PRP24 | U6 snRNP complex subunit PRP24 | Splicing factor that reanneals snRNPs during spliceosome recycling; reanneals U4 and U6 snRNPs | Core | NA | NA | NA |