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 |
|---|---|---|---|---|---|---|---|---|
| 5708-YLR251W | YLR251W | SYM1 | ethanol metabolism protein | Protein required for ethanol metabolism; induced by heat shock and localized to the inner mitochondrial membrane; homologous to mammalian peroxisomal membrane protein Mpv17; human homolog MPV17 is implicated in hepatocerebral mtDNA depletion syndromes (MDDS), and complements yeast null mutant | Core | NA | NA | NA |
| 5709-YLR252W | YLR252W | 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 SYM1, a mitochondrial protein involved in ethanol metabolism | Core | NA | NA | NA |
| 5710-YLR253W | YLR253W | MCP2 | MRX13 | Mitochondrial protein of unknown function involved in lipid homeostasis; associates with mitochondrial ribosome; integral membrane protein that localizes to the mitochondrial inner membrane; involved in mitochondrial morphology; non-essential gene which interacts genetically with MDM10, and other members of the ERMES complex; transcription is periodic during the metabolic cycle; homologous to human aarF domain containing kinase, ADCK1 | Core | NA | NA | NA |
| 5711-YLR254C | YLR254C | NDL1 | NA | Homolog of nuclear distribution factor NudE; NUDEL; interacts with Pac1p and regulates dynein targeting to microtubule plus ends | Core | NA | NA | NA |
| 5712-YLR255C | YLR255C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5713-YLR256W | YLR256W | HAP1 | CYP1 | Zinc finger transcription factor; involved in the complex regulation of gene expression in response to levels of heme and oxygen; localizes to the mitochondrion as well as to the nucleus; the S288C sequence differs from other strain backgrounds due to a Ty1 insertion in the carboxy terminus | Core | NA | NA | NA |
| 5714-YLR257W | YLR257W | NA | NA | Protein of unknown function; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5715-YLR258W | YLR258W | GSY2 | glycogen (starch) synthase GSY2 | Glycogen synthase; expression induced by glucose limitation, nitrogen starvation, heat shock, and stationary phase; activity regulated by cAMP-dependent, Snf1p and Pho85p kinases as well as by the Gac1p-Glc7p phosphatase; GSY2 has a paralog, GSY1, that arose from the whole genome duplication; relocalizes from cytoplasm to plasma membrane upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5716-YLR259C | YLR259C | HSP60 | chaperone ATPase HSP60|MNA2|MIF4|CPN60 | Tetradecameric mitochondrial chaperonin; required for ATP-dependent folding of precursor polypeptides and complex assembly; prevents aggregation and mediates protein refolding after heat shock; role in mtDNA transmission; phosphorylated | Core | NA | NA | NA |
| 5717-YLR260W | YLR260W | LCB5 | sphinganine kinase LCB5 | Minor sphingoid long-chain base kinase; possibly involved in synthesis of long-chain base phosphates, which function as signaling molecules; LCB5 has a paralog, LCB4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5718-YLR261C_NumOfGenes_2 | YLR261C | VPS63 | NA | Putative protein of unknown function; not conserved in closely related Saccharomyces species; 98% of ORF overlaps the verified gene YPT6; deletion causes a vacuolar protein sorting defect; decreased levels of protein in enolase deficient mutant | Core | NA | NA | NA |
| 5719-YLR262C-A | YLR262C-A | TMA7 | RBF7 | Protein of unknown that associates with ribosomes; null mutant exhibits translation defects, altered polyribosome profiles, and resistance to the translation inhibitor anisomcyin; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5720-YLR263W | YLR263W | RED1 | NA | Protein component of the synaptonemal complex axial elements; involved in chromosome segregation during the first meiotic division; critical for coupling checkpoint signaling to SC formation; promotes interhomolog recombination by phosphorylating Hop1p; also interacts with Mec3p and Ddc1p | Core | NA | NA | NA |
| 5721-YLR264C-A | YLR264C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5722-YLR264W | YLR264W | RPS28B | eS28|ribosomal 40S subunit protein S28B|S28e|YS27|S33B|S28B|RPS33B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S28, no bacterial homolog; has an extraribosomal function in autoregulation, in which Rps28Bp binds to a decapping complex via Edc3p, which then binds to RPS28B mRNA leading to its decapping and degradation; RPS28B has a paralog, RPS28A, that arose from the whole genome duplication | Core | NA | NA | NA |