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 |
|---|---|---|---|---|---|---|---|---|
| 5648-YLR189C | YLR189C | ATG26 | UGT51 | UDP-glucose:sterol glucosyltransferase; conserved enzyme involved in synthesis of sterol glucoside membrane lipids; in contrast to ATG26 from P. pastoris, S. cerevisiae ATG26 is not involved in autophagy | Accessory | Ancestral | NA | NA |
| 5649-YLR190W | YLR190W | MMR1 | NA | Phosphorylated protein of the mitochondrial outer membrane; localizes only to mitochondria of the bud; interacts with Myo2p to mediate mitochondrial distribution to buds; mRNA is targeted to the bud via the transport system involving She2p | Accessory | Ancestral | NA | NA |
| 5650-YLR191W | YLR191W | PEX13 | peroxin PEX13|PAS20 | Peroxisomal importomer complex component; integral peroxisomal membrane protein required for docking and translocation of peroxisomal matrix proteins; interacts with the PTS1 signal recognition factor Pex5p and the PTS2 signal recognition factor Pex7p; forms a complex with Pex14p and Pex17p; human homolog PEX13 complements yeast null mutant | Accessory | Ancestral | NA | NA |
| 5651-YLR192C | YLR192C | HCR1 | translation initiation factor eIF3 core subunit j | eIF3j component of translation initiation factor 3 (eIF3); dual function protein involved in translation initiation as a substoichiometric component (eIF3j) of eIF3; required for 20S pre-rRNA processing; required at post-transcriptional step for efficient retrotransposition; absence decreases Ty1 Gag:GFP protein levels; binds eIF3 subunits Rpg1p, Prt1p and 18S rRNA; eIF3 also involved in programmed stop codon read through; human homolog EIF3J can complement yeast hcr1 mutant | Accessory | Ancestral | NA | NA |
| 5652-YLR193C | YLR193C | UPS1 | NA | Phosphatidic acid transfer protein; plays a role in phospholipid metabolism by transporting phosphatidic acid from the outer to the inner mitochondrial membrane; localizes to the mitochondrial intermembrane space; null mutant has altered cardiolipin and phosphatidic acid levels; ortholog of human PRELI | Accessory | Ancestral | NA | NA |
| 5653-YLR194C | YLR194C | NCW2 | NA | Structural constituent of the cell wall; attached to the plasma membrane by a GPI-anchor; expression is upregulated in response to cell wall stress; null mutant is sensitive to the antifungal agent polyhexamethylene biguanide, resistant to zymolyase treatment and has increased chitin deposition | Accessory | Ancestral | NA | NA |
| 5654-YLR195C | YLR195C | NMT1 | glycylpeptide N-tetradecanoyltransferase NMT1|CDC72 | N-myristoyl transferase; catalyzes the cotranslational, covalent attachment of myristic acid to the N-terminal glycine residue of several proteins involved in cellular growth and signal transduction | Accessory | Ancestral | NA | NA |
| 5655-YLR196W | YLR196W | PWP1 | rRNA-processing protein PWP1 | Protein with WD-40 repeats involved in rRNA processing; associates with trans-acting ribosome biogenesis factors; similar to beta-transducin superfamily | Accessory | Ancestral | NA | NA |
| 5656-YLR197W_NumOfGenes_2 | YLR197W | NOP56 | snoRNP complex protein NOP56|SIK1 | Essential evolutionarily-conserved nucleolar protein; component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects | Core | NA | NA | NA |
| 5657-YLR199C | YLR199C | PBA1 | POC1 | Protein involved in 20S proteasome assembly; forms a heterodimer with Add66p that binds to proteasome precursors; interaction with Pba1p-Add66p may affect function of the mature proteasome and its role in maintaining respiratory metabolism; similar to human PAC1 constituent of the PAC1-PAC2 complex involved in proteasome assembly | Core | NA | NA | NA |
| 5658-YLR200W | YLR200W | YKE2 | tubulin-binding prefolding complex subunit YKE2|PFD6|GIM1 | Subunit of the heterohexameric Gim/prefoldin protein complex; involved in the folding of alpha-tubulin, beta-tubulin, and actin; prefoldin complex also localizes to chromatin of actively transcribed genes in the nucleus and facilitates transcriptional elongation | Core | NA | NA | NA |
| 5659-YLR201C | YLR201C | COQ9 | ubiquinone biosynthesis protein COQ9|FMP53 | Protein required for ubiquinone biosynthesis and respiratory growth; localizes to matrix face of mitochondrial inner membrane in a large complex with ubiquinone biosynthetic enzymes; ubiquinone is also known as coenzyme Q; human homolog COQ9 can complement yeast coq9 null mutant | Accessory | Ancestral | NA | NA |
| 5660-YLR202C | YLR202C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF YLR201C; ORF contains a putative intron | Accessory | Unknown | S. paradoxus | NA |
| 5661-YLR203C | YLR203C | MSS51 | NA | Specific translational activator for the mitochondrial COX1 mRNA; loosely associated with the matrix face of the mitochondrial inner membrane; localizes to vacuole membrane in response to H2O2; influences both COX1 mRNA translation and Cox1p assembly into cytochrome c oxidase; binds to heme B, which may be a mechanism for sensing oxygen levels in order to regulate cytochrome c oxidase biogenesis | Accessory | Ancestral | NA | NA |
| 5662-YLR204W | YLR204W | QRI5 | COX24 | Mitochondrial inner membrane protein; required for accumulation of spliced COX1 mRNA; may have an additional role in translation of COX1 mRNA | Core | NA | NA | NA |