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 |
|---|---|---|---|---|---|---|---|---|
| 6248-YMR183C_NumOfGenes_2 | YMR183C | SSO2 | syntaxin | Plasma membrane t-SNARE; involved in fusion of secretory vesicles at the plasma membrane; syntaxin homolog that is functionally redundant with Sso1p; SSO2 has a paralog, SSO1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6249-YMR184W_NumOfGenes_2 | YMR184W | ADD37 | NA | Protein of unknown function; involved in ER-associated protein degradation; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS; YMR184W is not an essential gene; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6250-YMR185W_NumOfGenes_2 | YMR185W | RTP1 | NA | Protein required for the nuclear import and biogenesis of RNA pol II; conflicting evidence on whether null mutant is viable with elongated buds, or inviable; interacts with Rpb2, Rpb3, Nup116p, Nup100p and components of the R2TP complex (Rvb1p, Rvb2p, Pih1p); similar to human TMCO7 gene | Core | NA | NA | NA |
| 6251-YMR186W_NumOfGenes_2 | YMR186W | HSC82 | Hsp90 family chaperone HSC82|HSP90 | Cytoplasmic chaperone of the Hsp90 family; plays a role in determining prion variants; redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock; contains two acid-rich unstructured regions that promote the solubility of chaperone-substrate complexes; HSC82 has a paralog, HSP82, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6252-YMR187C | YMR187C | NA | NA | Putative protein of unknown function; YMR187C is not an essential gene | Core | NA | NA | NA |
| 6253-YMR188C | YMR188C | MRPS17 | mitochondrial 37S ribosomal protein MRPS17 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 6254-YMR189W | YMR189W | GCV2 | glycine decarboxylase subunit P|GSD2 | P subunit of the mitochondrial glycine decarboxylase complex; glycine decarboxylase is required for the catabolism of glycine to 5,10-methylene-THF; expression is regulated by levels of 5,10-methylene-THF in the cytoplasm | Core | NA | NA | NA |
| 6255-YMR190C | YMR190C | SGS1 | ATP-dependent DNA helicase SGS1 | RecQ family nucleolar DNA helicase; role in genome integrity maintenance, chromosome synapsis, meiotic joint molecule/crossover formation; stimulates activity of Top3p; rapidly lost in response to rapamycin in Rrd1p-dependent manner; forms nuclear foci upon DNA replication stress; yeast SGS1 complements mutations in human homolog BLM implicated in Bloom syndrome; also similar to human WRN implicated in Werner syndrome; human BLM and WRN can each complement yeast null mutant | Core | NA | NA | NA |
| 6256-YMR191W | YMR191W | SPG5 | NA | Protein required for proteasome assembly during quiescence; binds to base of the proteasome regulartory particle; required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources | Core | NA | NA | NA |
| 6257-YMR192W | YMR192W | GYL1 | APP2 | Putative GTPase activating protein (GAP) with a role in exocytosis; stimulates Gyp5p GAP activity on Ypt1p, colocalizes with Gyp5p at sites of polarized growth; interacts with Gyp5p, Rvs161p, and Rvs167p; involved in recruiting Rvs167p to the bud tip during polarized growth; increases in abundance and relocalizes from bud neck to cytoplasm upon DNA replication stress; GYL1 has a paralog, GYP5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6258-YMR193W | YMR193W | MRPL24 | mitochondrial 54S ribosomal protein YmL24/YmL14|YmL14|YmL24|MRPL14 | Mitochondrial ribosomal protein of the large subunit; two mitochondrial ribosomal proteins, YmL14 and YmL24, have been assigned to the same gene | Core | NA | NA | NA |
| 6259-YMR194C-A | YMR194C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6260-YMR194C-B | YMR194C-B | CMC4 | NA | Protein that localizes to the mitochondrial intermembrane space; localizes via the Mia40p-Erv1p system; contains twin cysteine-x(9)-cysteine motifs | Core | NA | NA | NA |
| 6261-YMR194W_NumOfGenes_2 | YMR194W | RPL36A | eL36|ribosomal 60S subunit protein L36A|L36e|YL39|L39|L36A|RPL39B | Ribosomal 60S subunit protein L36A; N-terminally acetylated; binds to 5.8 S rRNA; homologous to mammalian ribosomal protein L36, no bacterial homolog; RPL36A has a paralog, RPL36B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6262-YMR195W | YMR195W | ICY1 | NA | Protein of unknown function; required for viability in rich media of cells lacking mitochondrial DNA; mutants have an invasive growth defect with elongated morphology; induced by amino acid starvation; ICY1 has a paralog, ICY2, that arose from the whole genome duplication | Core | NA | NA | NA |