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 |
|---|---|---|---|---|---|---|---|---|
| 7673-YPR047W | YPR047W | MSF1 | phenylalanine--tRNA ligase | Mitochondrial phenylalanyl-tRNA synthetase; active as a monomer, unlike the cytoplasmic subunit which is active as a dimer complexed to a beta subunit dimer; similar to the alpha subunit of E. coli phenylalanyl-tRNA synthetase | Core | NA | NA | NA |
| 7674-YPR048W | YPR048W | TAH18 | NAPDH-dependent diflavin reductase | Conserved NAPDH-dependent diflavin reductase; component of an early step in the cytosolic Fe-S protein assembly (CIA) machinery; transfers electrons from NADPH to the Fe-S cluster of Dre2p; plays a pro-death role under oxidative stress; Tah18p-dependent nitric oxide synthesis confers high-temperature stress tolerance; possible target for development of antifungal drugs | Core | NA | NA | NA |
| 7675-YPR049C | YPR049C | ATG11 | autophagy protein ATG11|CVT3|CVT9 | Adapter protein for pexophagy and the Cvt targeting pathway; directs receptor-bound cargo to the phagophore assembly site (PAS) for packaging into vesicles; required for recruiting other proteins to the PAS; recruits Dnm1p to facilitate fission of mitochondria that are destined for removal by mitophagy | Core | NA | NA | NA |
| 7676-YPR051W_NumOfGenes_2 | YPR051W | MAK3 | peptide alpha-N-acetyltransferase MAK3|NAA30 | Catalytic subunit of the NatC type N-terminal acetyltransferase (NAT); involved in subcellular targeting of select N-terminally acetylated substrates to the Golgi apparatus (Arl3p and Grh1p) and the inner nuclear membrane (Trm1p); required for replication of dsRNA virus; human NatC ortholog, Naa60, functionally complements the null, requiring either auxiliary subunit Mak10p or co-expression of human ortholog, Naa35; Naa60, the human NatF gene, also complements the null allele | Core | NA | NA | NA |
| 7677-YPR052C | YPR052C | NHP6A | high-mobility group nucleosome-binding protein | High-mobility group (HMG) protein; binds to and remodels nucleosomes; involved in recruiting FACT and other chromatin remodelling complexes to chromosomes; functionally redundant with Nhp6Bp; required for transcriptional initiation fidelity of some tRNA genes; homologous to mammalian HMGB1 and HMGB2; NHP6A has a paralog, NHP6B, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 7678-YPR053C | YPR053C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YPR053C is not an essential gene; partially overlaps verified ORF NHP6A/YPR052C | Core | NA | NA | NA |
| 7679-YPR054W | YPR054W | SMK1 | mitogen-activated protein kinase SMK1 | Middle sporulation-specific mitogen-activated protein kinase (MAPK); required for production of the outer spore wall layers; negatively regulates activity of the glucan synthase subunit Gsc2p | Core | NA | NA | NA |
| 7680-YPR055W | YPR055W | SEC8 | exocyst subunit SEC8 | Essential 121 kDa subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis at the plasma membrane prior to SNARE-mediated fusion; involved in ER and Golgi inheritance in small buds; relocalizes away from bud neck upon DNA replication stress | Core | NA | NA | NA |
| 7681-YPR056W | YPR056W | TFB4 | TFIIH/NER complex subunit TFB4 | Subunit of TFIIH complex; involved in transcription initiation, similar to 34 kDa subunit of human TFIIH; interacts with Ssl1p | Core | NA | NA | NA |
| 7682-YPR057W | YPR057W | BRR1 | NA | snRNP protein component of spliceosomal snRNPs; required for pre-mRNA splicing and snRNP biogenesis; in null mutant newly-synthesized snRNAs are destabilized and 3'-end processing is slowed | Core | NA | NA | NA |
| 7683-YPR058W_NumOfGenes_2 | YPR058W | YMC1 | organic acid transporter | Secondary mitochondrial inner membrane glycine transporter; required with HEM25 for the transport of glycine into mitochondria for the initiation of heme biosynthesis; proposed role in oleate metabolism and glutamate biosynthesis; member of the mitochondrial carrier (MCF) family; localizes to the vacuole in response to H2O2; YMC1 has a paralog, YMC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7684-YPR060C | YPR060C | ARO7 | chorismate mutase ARO7|TYR7|OSM2|HGS1 | Chorismate mutase; catalyzes the conversion of chorismate to prephenate to initiate the tyrosine/phenylalanine-specific branch of aromatic amino acid biosynthesis | Core | NA | NA | NA |
| 7685-YPR061C | YPR061C | JID1 | NA | Probable Hsp40p co-chaperone; has a DnaJ-like domain and appears to be involved in ER-associated degradation of misfolded proteins containing a tightly folded cytoplasmic domain; inhibits replication of Brome mosaic virus in S. cerevisiae | Core | NA | NA | NA |
| 7686-YPR062W | YPR062W | FCY1 | cytosine deaminase|yCD | Cytosine deaminase; zinc metalloenzyme that catalyzes the hydrolytic deamination of cytosine to uracil; of biomedical interest because it also catalyzes the deamination of 5-fluorocytosine (5FC) to form anticancer drug 5-fluorouracil (5FU) | Core | NA | NA | NA |
| 7687-YPR063C | YPR063C | NA | NA | ER-localized protein of unknown function | Core | NA | NA | NA |