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 |
|---|---|---|---|---|---|---|---|---|
| 5348-YKR056W | YKR056W | TRM2 | RNC1|NUD1|NUC2 | tRNA methyltransferase; 5-methylates the uridine residue at position 54 of tRNAs and may also have a role in tRNA stabilization or maturation; endo-exonuclease with a role in DNA repair | Core | NA | NA | NA |
| 5349-YKR057W | YKR057W | RPS21A | eS21|ribosomal 40S subunit protein S21A|S21e|YS25|S26A|S21A|RPS25 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S21, no bacterial homolog; RPS21A has a paralog, RPS21B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5350-YKR058W | YKR058W | GLG1 | glycogenin glucosyltransferase GLG1 | Glycogenin glucosyltransferase; self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; SWAT-GFP and mCherry fusion proteins localize to the cell periphery and vacuole respectively; similar to mammalian glycogenin; GLG1 has a paralog, GLG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5351-YKR059W_NumOfGenes_2 | YKR059W | TIF1 | translation initiation factor eIF4A|eIF4A | Translation initiation factor eIF4A; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G; protein abundance increases in response to DNA replication stress; TIF1 has a paralog, TIF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5352-YKR060W_NumOfGenes_2 | YKR060W | UTP30 | NA | Putative subunit of U3-containing 90S preribosome complex; complex is involved in production of 18S rRNA and assembly of small ribosomal subunit | Core | NA | NA | NA |
| 5353-YKR061W_NumOfGenes_2 | YKR061W | KTR2 | mannosyltransferase KTR2 | Mannosyltransferase involved in N-linked protein glycosylation; member of the KRE2/MNT1 mannosyltransferase family; KTR2 has a paralog, YUR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5354-YKR062W_NumOfGenes_2 | YKR062W | TFA2 | transcription factor TFIIE subunit TFA2 | TFIIE small subunit; involved in RNA polymerase II transcription initiation | Core | NA | NA | NA |
| 5355-YKR063C_NumOfGenes_2 | YKR063C | LAS1 | rRNA-processing protein LAS1 | Endonuclease involved in pre-rRNA processing at both ends of ITS2; functions with Grc3p in a conserved mechanism to modulate rRNA processing and ribosome biogenesis; may coordinate the action of the Rat1p-Rai1p exoRNAse; required for the G1/S cell cycle transition; human ortholog is Las1L; mutants require the SSD1-v allele for viability | Core | NA | NA | NA |
| 5356-YKR064W | YKR064W | OAF3 | NA | Putative transcriptional repressor with Zn(2)-Cys(6) finger; negatively regulates transcription in response to oleate levels, based on mutant phenotype and localization to oleate-responsive promoters; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; forms nuclear foci upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5357-YKR065C | YKR065C | PAM17 | FMP18 | Constituent of the TIM23 complex; proposed alternatively to be a component of the import motor (PAM complex) or to interact with and modulate the core TIM23 (Translocase of the Inner mitochondrial Membrane) complex; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5358-YKR066C | YKR066C | CCP1 | cytochrome-c peroxidase | Mitochondrial cytochrome-c peroxidase; degrades reactive oxygen species in mitochondria, involved in the response to oxidative stress | Accessory | Ancestral | NA | NA |
| 5359-YKR067W | YKR067W | GPT2 | bifunctional glycerol-3-phosphate/glycerone-phosphate O-acyltransferase GPT2|GAT1 | Glycerol-3-phosphate/dihydroxyacetone phosphate sn-1 acyltransferase; located in lipid particles and the ER; involved in the stepwise acylation of glycerol-3-phosphate and dihydroxyacetone in lipid biosynthesis; the most conserved motifs and functionally relevant residues are oriented towards the ER lumen | Accessory | Ancestral | NA | NA |
| 5360-YKR068C | YKR068C | BET3 | TRAPP complex core subunit BET3 | Core component of transport protein particle (TRAPP) complexes I-III; TRAPP complexes are related multimeric guanine nucleotide-exchange factors for the GTPase Ypt1, regulating ER-Golgi traffic (TRAPPI), intra-Golgi traffic (TRAPPII), endosome-Golgi traffic (TRAPPII and III) and autophagy (TRAPPIII); hydrophilic homodimeric protein that acts in conjunction with SNARE proteins in targeting and fusion of ER to Golgi transport vesicles | Accessory | Ancestral | NA | NA |
| 5361-YKR069W | YKR069W | MET1 | uroporphyrinogen-III C-methyltransferase|MET20 | S-adenosyl-L-methionine uroporphyrinogen III transmethylase; involved in the biosynthesis of siroheme, a prosthetic group used by sulfite reductase; required for sulfate assimilation and methionine biosynthesis | Accessory | Ancestral | NA | NA |
| 5362-YKR070W | YKR070W | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |