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 |
|---|---|---|---|---|---|---|---|---|
| 4253-YHR007C-A | YHR007C-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry; SWAT-GFP fusion protein localizes to the nucleus | Core | NA | NA | NA |
| 4254-YHR008C | YHR008C | SOD2 | superoxide dismutase SOD2 | Mitochondrial manganese superoxide dismutase; protects cells against oxygen toxicity and oxidative stress; human mitochondrial SOD2 can complement a yeast null mutant and human cytoplasmic SOD1 can also complement when targeted to the mitochondrial matrix | Accessory | Ancestral | NA | NA |
| 4255-YHR009C | YHR009C | TDA3 | BTN3 | Putative oxidoreductase involved in late endosome to Golgi transport; physical and genetical interactions with Btn2p; null mutant is viable, has extended S phase, and sensitive to expression of top1-T722A allele; similar to human FOXRED1 | Core | NA | NA | NA |
| 4256-YHR010W | YHR010W | RPL27A | eL27|ribosomal 60S subunit protein L27A|L27e|L27A|RPL27 | Ribosomal 60S subunit protein L27A; homologous to mammalian ribosomal protein L27, no bacterial homolog; RPL27A has a paralog, RPL27B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4257-YHR011W | YHR011W | DIA4 | putative serine--tRNA ligase DIA4 | Probable mitochondrial seryl-tRNA synthetase; mutant displays increased invasive and pseudohyphal growth | Core | NA | NA | NA |
| 4258-YHR012W | YHR012W | VPS29 | retromer subunit VPS29|VPT6|PEP11 | Subunit of the membrane-associated retromer complex; endosomal protein; essential for endosome-to-Golgi retrograde transport; forms a subcomplex with Vps35p and Vps26p that selects cargo proteins for endosome-to-Golgi retrieval | Core | NA | NA | NA |
| 4259-YHR013C | YHR013C | ARD1 | peptide alpha-N-acetyltransferase complex A subunit ARD1|NAA10 | Subunit of protein N-terminal acetyltransferase NatA; NatA comprises Nat1p, Ard1p, Nat5p; acetylates many proteins to influence telomeric silencing, cell cycle, heat-shock resistance, mating, sporulation, early stages of mitophagy; protein abundance increases under DNA replication stress; mutations in human homolog X-linked NAA10 lead to Ogden syndrome (S37P) and intellectual disability (R116W); expression of human NAA10 and NAA15 can complement ard1 nat1 double mutant | Core | NA | NA | NA |
| 4260-YHR014W | YHR014W | SPO13 | NA | Meiotic regulator; involved in maintaining sister chromatid cohesion during meiosis I as well as promoting proper attachment of kinetochores to the spindle during meiosis I and meiosis II; anaphase-promoting complex (APC) substrate that is degraded during anaphase I; expressed only in meiotic cells | Core | NA | NA | NA |
| 4261-YHR015W | YHR015W | MIP6 | NA | Putative RNA-binding protein; interacts with Mex67p, which is a component of the nuclear pore involved in nuclear mRNA export; MIP6 has a paralog, PES4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4262-YHR016C | YHR016C | YSC84 | LSB4 | Actin-binding protein; involved in bundling of actin filaments and endocytosis of actin cortical patches; activity stimulated by Las17p; contains SH3 domain similar to Rvs167p; YSC84 has a paralog, LSB3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4263-YHR017W | YHR017W | YSC83 | NA | Non-essential mitochondrial protein of unknown function; mRNA induced during meiosis, peaking between mid to late prophase of meiosis I; similar to S. douglasii YSD83 | Core | NA | NA | NA |
| 4264-YHR018C | YHR018C | ARG4 | argininosuccinate lyase ARG4 | Argininosuccinate lyase; catalyzes the final step in the arginine biosynthesis pathway | Core | NA | NA | NA |
| 4265-YHR019C | YHR019C | DED81 | asparagine--tRNA ligase DED81 | Cytosolic asparaginyl-tRNA synthetase; required for protein synthesis, catalyzes the specific attachment of asparagine to its cognate tRNA | Core | NA | NA | NA |
| 4266-YHR020W | YHR020W | NA | proline--tRNA ligase | Prolyl-tRNA synthetase; N-terminal domain shows weak homology to prokaryotic posttransfer editing domain, but does not possess posttransfer editing activity; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |
| 4267-YHR021C | YHR021C | RPS27B | eS27|ribosomal 40S subunit protein S27B|S27e|rp61|YS20|S27B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S27, no bacterial homolog; RPS27B has a paralog, RPS27A, that arose from the whole genome duplication | Core | NA | NA | NA |