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 |
|---|---|---|---|---|---|---|---|---|
| 5513-YLR052W | YLR052W | IES3 | NA | Subunit of the INO80 chromatin remodeling complex | Core | NA | NA | NA |
| 5514-YLR053C | YLR053C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5515-YLR054C | YLR054C | OSW2 | NA | Protein of unknown function reputedly involved in spore wall assembly | Core | NA | NA | NA |
| 5516-YLR055C | YLR055C | SPT8 | SAGA complex subunit SPT8 | Subunit of the SAGA transcriptional regulatory complex; not present in SAGA-like complex SLIK/SALSA; required for SAGA-mediated inhibition at some promoters | Core | NA | NA | NA |
| 5517-YLR056W | YLR056W | ERG3 | C-5 sterol desaturase|PSO6|SYR1 | C-5 sterol desaturase; glycoprotein that catalyzes the introduction of a C-5(6) double bond into episterol, a precursor in ergosterol biosynthesis; transcriptionally down-regulated when ergosterol is in excess; mutants are viable, but cannot grow on non-fermentable carbon sources; substrate of HRD ubiquitin ligase; mutation is functionally complemented by human SC5D | Core | NA | NA | NA |
| 5518-YLR057W | YLR057W | MNL2 | putative mannosidase MNL2 | Putative mannosidase involved in ER-associated protein degradation; localizes to the endoplasmic reticulum; sequence similarity with seven-hairpin glycosidase (GH47) family members, such as Mns1p and Mnl1p, that hydrolyze 1,2-linked alpha-D-mannose residues; non-essential gene | Core | NA | NA | NA |
| 5519-YLR058C | YLR058C | SHM2 | glycine hydroxymethyltransferase SHM2|SHMT2 | Cytosolic serine hydroxymethyltransferase; converts serine to glycine plus 5,10 methylenetetrahydrofolate; major isoform involved in generating precursors for purine, pyrimidine, amino acid, and lipid biosynthesis | Core | NA | NA | NA |
| 5520-YLR059C | YLR059C | REX2 | YNT20 | 3'-5' RNA exonuclease; involved in 3'-end processing of U4 and U5 snRNAs, 5S and 5.8S rRNAs, and RNase P and RNase MRP RNA; localized to mitochondria and null suppresses escape of mtDNA to nucleus in yme1 yme2 mutants; RNase D exonuclease | Core | NA | NA | NA |
| 5521-YLR060W | YLR060W | FRS1 | phenylalanine--tRNA ligase subunit beta | Beta subunit of cytoplasmic phenylalanyl-tRNA synthetase; forms a tetramer with Frs2p to generate active enzyme; able to hydrolyze mis-aminoacylated tRNA-Phe, which could contribute to translational quality control | Core | NA | NA | NA |
| 5522-YLR061W_NumOfGenes_2 | YLR061W | RPL22A | eL22|ribosomal 60S subunit protein L22A|L22e|rp4|l1c|YL31|L22A | Ribosomal 60S subunit protein L22A; required for translation of long 5' UTR of IME1 mRNA and meiotic entry; required for the oxidative stress response, pseudohyphal and invasive growth; homologous to mammalian ribosomal protein L22, no bacterial homolog; RPL22A has a paralog, RPL22B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5523-YLR063W | YLR063W | BMT6 | 25S rRNA (uracil2843-N3)-methyltransferase | Methyltransferase required for m3U2843 methylation of the 25S rRNA; S-adenosylmethionine-dependent; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YLR063W is not an essential gene | Core | NA | NA | NA |
| 5524-YLR064W | YLR064W | PER33 | NA | Protein that localizes to the endoplasmic reticulum; also associates with the nuclear pore complex; deletion extends chronological lifespan; highly conserved across species, orthologous to human TMEM33 and paralogous to Pom33p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5525-YLR065C | YLR065C | ENV10 | SND2 | Protein involved in SRP-independent targeting of substrates to the ER; component of an alternative ER targeting pathway that has partial functional redundancy with the GET pathway; preference for substrates with downstream transmembrane domains; interacts with Snd1p, Pho88p/Snd3p, and Sec61p-translocon subunits; can compensate for loss of SRP; role in the late endosome-vacuole interface; putative role in secretory protein quality control | Core | NA | NA | NA |
| 5526-YLR066W | YLR066W | SPC3 | signal peptidase complex subunit SPC3 | Subunit of signal peptidase complex; complex catalyzes cleavage of N-terminal signal sequences of proteins targeted to the secretory pathway; homologous to mammalian SPC22/23; other members of the complex are Spc1p, Spc2p, and Sec11p | Core | NA | NA | NA |
| 5527-YLR067C | YLR067C | PET309 | NA | Specific translational activator for the COX1 mRNA; binds to the COX1 mRNA; also influences stability of intron-containing COX1 primary transcripts; localizes to the mitochondrial inner membrane; contains 12 pentatricopeptide repeats (PPRs) | Core | NA | NA | NA |