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 |
|---|---|---|---|---|---|---|---|---|
| 6743-YNR025C | YNR025C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; deletion reduces expression of PIS1 gene encoding phosphatidylinositol synthase | Accessory | Ancestral | NA | NA |
| 6744-YNR026C | YNR026C | SEC12 | Sar family guanine nucleotide exchange factor SEC12|SED2 | Guanine nucleotide exchange factor (GEF); activates Sar1p by catalyzing the exchange of GDP for GTP; required for the initiation of COPII vesicle formation in ER to Golgi transport; glycosylated integral membrane protein of the ER; SEC12 has a paralog, SED4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6745-YNR027W | YNR027W | BUD17 | putative pyridoxal kinase BUD17 | Putative pyridoxal kinase; a key enzyme in vitamin B6 metabolism; involved in bud-site selection; diploid mutants display a random rather than a bipolar budding pattern; similarity to yeast BUD16 and human pyridoxal kinase (PDXK) | Core | NA | NA | NA |
| 6746-YNR028W | YNR028W | CPR8 | peptidylprolyl isomerase family protein CPR8 | Peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; potential role in the secretory pathway; CPR8 has a paralog, CPR4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6747-YNR029C | YNR029C | NA | NA | Putative protein of unknown function; deletion confers reduced fitness in saline | Core | NA | NA | NA |
| 6748-YNR030W | YNR030W | ALG12 | dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase|ECM39 | Alpha-1,6-mannosyltransferase localized to the ER; responsible for addition of alpha-1,6 mannose to dolichol-linked Man7GlcNAc2; acts in the dolichol pathway for N-glycosylation; human homolog ALG12 complements yeast null mutant | Core | NA | NA | NA |
| 6749-YNR031C | YNR031C | SSK2 | mitogen-activated protein kinase kinase kinase SSK2 | MAP kinase kinase kinase of HOG1 mitogen-activated signaling pathway; interacts with Ssk1p, leading to autophosphorylation and activation of Ssk2p which phosphorylates Pbs2p; also mediates actin cytoskeleton recovery from osmotic stress; a HOG-independent function of Ssk2p mediates the calcium-sensitive phenotype of the ptp2 msg5 double disruptant; SSK2 has a paralog, SSK22, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6750-YNR032C-A | YNR032C-A | HUB1 | ubiquitin-like protein HUB1 | Ubiquitin-like protein modifier; promotes alternative splicing of SRC1 pre-mRNA; binds non-covalently to the HIND domain of Snu66, may function in modification of Sph1p and Hbt1p, functionally complemented by the human or S. pombe ortholog; mechanism of Hub1p adduct formation not yet clear | Core | NA | NA | NA |
| 6751-YNR032W | YNR032W | PPG1 | putative serine/threonine-protein kinase PPG1 | Putative serine/threonine protein phosphatase; putative phosphatase of the type 2A-like phosphatase family, required for glycogen accumulation; interacts with Tap42p, which binds to and regulates other protein phosphatases | Core | NA | NA | NA |
| 6752-YNR033W | YNR033W | ABZ1 | 4-amino-4-deoxychorismate synthase | Para-aminobenzoate (PABA) synthase; has similarity to Escherichia coli PABA synthase components PabA and PabB; required for the synthesis of para-aminobenzoic acid, an important intermediate for folate and ubiquinone Q biosynthesis; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6753-YNR034W | YNR034W | SOL1 | NA | Protein with a possible role in tRNA export; shows similarity to 6-phosphogluconolactonase non-catalytic domains but does not exhibit this enzymatic activity; homologous to Sol3p and Sol4p; SOL1 has a paralog, SOL2, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6754-YNR034W-A | YNR034W-A | EGO4 | NA | Protein of unknown function; expression is regulated by Msn2p/Msn4p; YNR034W-A has a paralog, YCR075W-A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6755-YNR035C | YNR035C | ARC35 | END9 | Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches; required for cortical localization of calmodulin | Core | NA | NA | NA |
| 6756-YNR036C | YNR036C | MRPS12 | putative mitochondrial 37S ribosomal protein MRPS12 | Mitochondrial protein; may interact with ribosomes based on co-purification experiments; similar to E. coli and human mitochondrial S12 ribosomal proteins | Core | NA | NA | NA |
| 6757-YNR037C | YNR037C | RSM19 | mitochondrial 37S ribosomal protein RSM19 | Mitochondrial ribosomal protein of the small subunit; has similarity to E. coli S19 ribosomal protein | Core | NA | NA | NA |