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 |
|---|---|---|---|---|---|---|---|---|
| 1808-YAL036C | YAL036C | RBG1 | GTP-binding protein RBG1|FUN11 | Member of the DRG family of GTP-binding proteins; associates with translating ribosomes; interacts with Tma46p, Ygr250cp, Gir2p and Yap1p via two-hybrid | Accessory | Ancestral | NA | NA |
| 1809-YAL037C-A | YAL037C-A | NA | NA | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 1810-YAL037W | YAL037W | NA | NA | Putative protein of unknown function; YAL037W has a paralog, YOR342C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 1811-YAL038W_NumOfGenes_2 | YAL038W | CDC19 | pyruvate kinase CDC19|PYK1 | Pyruvate kinase; functions as a homotetramer in glycolysis to convert phosphoenolpyruvate to pyruvate, the input for aerobic (TCA cycle) or anaerobic (glucose fermentation) respiration; regulated via allosteric activation by fructose bisphosphate; CDC19 has a paralog, PYK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1812-YAL039C | YAL039C | CYC3 | holocytochrome c synthase CYC3|CCHL | Cytochrome c heme lyase (holocytochrome c synthase); attaches heme to apo-cytochrome c (Cyc1p or Cyc7p) in mitochondrial intermembrane space; human homolog HCCS implicated in microphthalmia with linear skin defects (MLS), and can complement yeast null mutant | Accessory | Ancestral | NA | NA |
| 1813-YAL040C | YAL040C | CLN3 | cyclin CLN3|WHI1|FUN10|DAF1 | G1 cyclin involved in cell cycle progression; activates Cdc28p kinase to promote G1 to S phase transition; plays a role in regulating transcription of other G1 cyclins, CLN1 and CLN2; regulated by phosphorylation and proteolysis; acetyl-CoA induces CLN3 transcription in response to nutrient repletion to promote cell-cycle entry; cell cycle arrest phenotype of the cln1 cln2 cln3 triple null mutant is complemented by any of human cyclins CCNA2, CCNB1, CCNC, CCND1, or CCNE1 | Core | NA | NA | NA |
| 1814-YAL041W | YAL041W | CDC24 | Rho family guanine nucleotide exchange factor CDC24|CLS4 | Guanine nucleotide exchange factor (GEF) for Cdc42p; required for polarity establishment and maintenance, and mutants have morphological defects in bud formation and shmooing; relocalizes from nucleus to cytoplasm upon DNA replication stress; thermosensitivity of the cdc24-4 mutant in the presence of sorbitol is functionally complemented by human CDC42 | Core | NA | NA | NA |
| 1815-YAL042W_NumOfGenes_2 | YAL042W | ERV46 | FUN9 | Protein localized to COPII-coated vesicles; forms a complex with Erv41p; involved in the membrane fusion stage of transport | Core | NA | NA | NA |
| 1816-YAL043C | YAL043C | PTA1 | RNA-processing protein PTA1|FUN39 | Subunit of holo-CPF; holo-CPF is a multiprotein complex and functional homolog of mammalian CPSF, required for the cleavage and polyadenylation of mRNA and snoRNA 3' ends; involved in pre-tRNA processing; binds to the phosphorylated CTD of RNAPII | Core | NA | NA | NA |
| 1817-YAL044C | YAL044C | GCV3 | glycine decarboxylase subunit H | H subunit of the mitochondrial glycine decarboxylase complex; glycine decarboxylase is required for the catabolism of glycine to 5,10-methylene-THF; also required for all protein lipoylation; expression is regulated by levels of 5,10-methylene-THF | Core | NA | NA | NA |
| 1818-YAL044W-A_NumOfGenes_2 | YAL044W-A | BOL1 | NA | Mitochondrial matrix protein involved in Fe-S cluster biogenesis; facilitates [4Fe-2S] cluster inception into mitochondrial proteins such as lipoate synthase and succinate dehydrogenase; interacts and may function with Grx5p at an early step in Fe-S cluster biosynthesis; forms dimeric complexes with Grx5p and Nfu1p that alter the stability of shared Fe/S clusters; sequence similarity to human BOLA family member, BOLA1 and S. pombe uvi31, a putative DNA repair protein | Core | NA | NA | NA |
| 1819-YAL046C | YAL046C | BOL3 | AIM1 | Protein involved in Fe-S cluster transfer to mitochondrial clients; protects [4Fe-4S] clusters from damage due to oxidative stress by acting along with Nfu1p at a late step in the transfer of [4Fe-4S] clusters from the ISA complex to mitochondrial client proteins like lipoate synthase and succinate dehydrogenase; sequence similarity to human BOLA family member, BOLA3, mutations of which are associated with Multiple Mitochondria Dysfunctions Syndrome (MMDS2) | Core | NA | NA | NA |
| 1820-YAL047C | YAL047C | SPC72 | gamma-tubulin complex subunit SPC72|LDB4 | Gamma-tubulin small complex (gamma-TuSC) receptor; recruits the gamma-TuSC complex to the cytoplasmic side of the SPB, connecting nuclear microtubules to the SPB; involved in astral microtubule formation, stabilization, and with Stu2p, anchoring astral MTs at the cytoplasmic face of the SPB, and regulating plus-end MT dynamics; regulated by Cdc5 kinase | Accessory | Ancestral | NA | NA |
| 1821-YAL047W-A | YAL047W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF GEM1/YAL048C | Accessory | Ancestral | NA | NA |
| 1822-YAL048C | YAL048C | GEM1 | ERMES complex Ca(2+)-binding regulatory GTPase GEM1|GON1 | Outer mitochondrial membrane GTPase, subunit of the ERMES complex; potential regulatory subunit of the ERMES complex that links the ER to mitochondria and may promote inter-organellar calcium and phospholipid exchange as well as coordinating mitochondrial DNA replication and growth; cells lacking Gem1p contain collapsed, globular, or grape-like mitochondria; ortholog of metazoan Miro GTPases | Accessory | Ancestral | NA | NA |