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 |
|---|---|---|---|---|---|---|---|---|
| 7838-R0020C | R0020C | REP1 | NA | Master regulator that regulates transcript levels of the FLP1 gene; acts in concert with Rep2p to regulate transcript levels of the FLP1 gene that promotes plasmid copy amplification and 2-micron plasmid-inheritance; also autoregulates levels of its own transcript; both Rep1p and Rep2p are sumoylated which is important for function | Accessory | Plasmid | NA | NA |
| 7839-R0030W_NumOfGenes_2 | R0030W | RAF1 | NA | Anti-repressor that increases 2 micron plasmid copy number; increases 2 micron plasmid copy number by relieving repression of the FLP1 site-specific recombinase caused by the Rep1-Rep2p trascription regulator; also itself repressed by the Rep1p-Rep2p complex | Accessory | Plasmid | NA | NA |
| 7840-R0040C_NumOfGenes_2 | R0040C | REP2 | NA | Master regulator that regulates transcript levels of the FLP1 gene; acts in concert with Rep1p to regulate transcript levels of the FLP1 gene that promotes plasmid copy amplification and 2-micron plasmid-inheritance; also autoregulates levels of its own transcript; required for Rep1p stability; both Rep1p and Rep2p are sumoylated which is important for function | Accessory | Plasmid | NA | NA |
| 7841-RDN25-1_NumOfGenes_5 | RDN25-1 | RDN25-1 | 26S rRNA|RDN25 | 25S ribosomal RNA (25S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript; formed by endonucleolytic cleavage at the C2 site of internal transcribed spacer 2 (ITS2) | Core | NA | NA | NA |
| 7842-RDN18-1 | RDN18-1 | RDN18-1 | RDN18 | 18S ribosomal RNA (18S rRNA); component of the small (40S) ribosomal subunit; involved in codon recognition by tRNAs or the release factor eRF1 (Sup45p); encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript | Core | NA | NA | NA |
| 7843-RDN58-1_NumOfGenes_2 | RDN58-1 | RDN58-1 | RDN58 | 5.8S ribosomal RNA (5.8S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript; 3' end formation involves processing by the exosome complex while 5' end is generated by Kem1p and Rat1p | Core | NA | NA | NA |
| 7844-YMRCTy1-4_NumOfGenes_31_NumOfGenes_68 | NA | NA | NA | NA | Accessory | Unknown | S. paradoxus | NA |
| 7845-YDRWTy2-3_NumOfGenes_13_NumOfGenes_28 | NA | NA | NA | NA | Accessory | Unknown | NA | NA |
| 7846-YGRWTy3-1_NumOfGenes_6 | YGRWTy3-1 | NA | Ty3 | Ty3 element, LTR retrotransposon of the Gypsy (Metaviridae) group; contains co-transcribed genes TYA Gag and TYB Pol, encoding proteins involved in structure and function of virus-like particles, flanked by two direct repeats; transposition is induced upon exposure to mating pheromone | Accessory | Unknown | S. paradoxus | NA |
| 7847-YHLWTy4-1_NumOfGenes_3_NumOfGenes_6 | NA | NA | NA | NA | Accessory | Unknown | S. paradoxus | NA |
| 7848-YCLWTy5-1_NumOfGenes_4 | YCLWTy5-1 | NA | Ty5 | Ty5 element, LTR retrotransposon of the Copia (Pseudoviridae) group; this is the only near-full length Ty5 retrotransposon in S288C and it is non-functional | Accessory | Unknown | S. paradoxus | NA |