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 |
|---|---|---|---|---|---|---|---|---|
| 7823-Q0085 | Q0085 | ATP6 | F1F0 ATP synthase subunit a|PHO1|OLI4|OLI2 | Subunit a of the F0 sector of mitochondrial F1F0 ATP synthase; mitochondrially encoded; translation is specifically activated by Atp22p; ATP6 and ATP8 mRNAs are not translated in the absence of the F1 sector of ATPase; mutations in human ortholog MT-ATP6 are associated with neurodegenerative disorders such as Neurogenic Ataxia and Retinitis Pigmentosa (NARP), Leigh syndrome (LS), Charcot-Marie-Tooth (CMT), and ataxia telangiectasia | Accessory | Mithocondrial ORF | NA | NA |
| 7824-Q0092 | Q0092 | NA | ORF5 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Mithocondrial ORF | NA | NA |
| 7825-Q0105_NumOfGenes_4 | Q0105 | COB | cytochrome b|CYTB|COB1 | Cytochrome b; mitochondrially encoded subunit of the ubiquinol-cytochrome c reductase complex which includes Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p | Accessory | Mithocondrial ORF | NA | NA |
| 7826-Q0130_NumOfGenes_2 | Q0130 | OLI1 | F0 ATP synthase subunit c|OLI3|ATP9 | F0-ATP synthase subunit c (ATPase-associated proteolipid); encoded on the mitochondrial genome; mutation confers oligomycin resistance; expression is specifically dependent on the nuclear genes AEP1 and AEP2 | Accessory | Mithocondrial ORF | NA | NA |
| 7827-Q0140 | Q0140 | VAR1 | mitochondrial 37S ribosomal protein VAR1|VARI | Mitochondrial ribosomal protein of the small subunit; mitochondrially-encoded; polymorphic in different strains due to variation in number of AAT (asparagine) codons; translated near the mitochondrial inner membrane; may have a role in loss of mitochondrial DNA under stress conditions | Accessory | Mithocondrial ORF | NA | NA |
| 7828-Q0142 | Q0142 | NA | ORF9 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps dubious open reading frame Q0143 | Accessory | Mithocondrial ORF | NA | NA |
| 7829-Q0143 | Q0143 | NA | ORF10 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Mithocondrial ORF | NA | NA |
| 7830-Q0144 | Q0144 | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Mithocondrial ORF | NA | NA |
| 7831-Q0160 | Q0160 | SCEI | intron-encoded endonuclease I-SceI|I-SceIV|OMEGA | I-SceI DNA endonuclease; encoded by the mitochondrial group I intron of the 21S_rRNA gene; mediates gene conversion that propagates the intron into intron-less copies of the 21S_rRNA gene | Accessory | Mithocondrial ORF | NA | NA |
| 7832-Q0182 | Q0182 | NA | ORF11 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Mithocondrial ORF | NA | NA |
| 7833-Q0250 | Q0250 | COX2 | cytochrome c oxidase subunit 2|OXII|OXI1 | Subunit II of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits | Accessory | Mithocondrial ORF | NA | NA |
| 7834-Q0255 | Q0255 | NA | maturase-like protein|RF1|ORF1 | Maturase-like protein | Accessory | Mithocondrial ORF | NA | NA |
| 7835-Q0275 | Q0275 | COX3 | cytochrome c oxidase subunit 3|OXI2 | Subunit III of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits | Accessory | Mithocondrial ORF | NA | NA |
| 7836-Q0297 | Q0297 | NA | ORF12 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene RPM1 | Accessory | Mithocondrial ORF | NA | NA |
| 7837-R0010W_NumOfGenes_2 | R0010W | FLP1 | NA | Site-specific recombinase encoded on the 2-micron plasmid; required for 2-micron plasmid propagation as part of a plasmid amplification system that compensates for any copy number decreases caused by missegregation events | Accessory | Plasmid | NA | NA |