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 |
|---|---|---|---|---|---|---|---|---|
| 4238-YHL044W | YHL044W | NA | DUP240 family protein | Putative integral membrane protein; member of DUP240 gene family; green fluorescent protein (GFP)-fusion protein localizes to the plasma membrane in a punctate pattern | Accessory | Unknown | NA | NA |
| 4239-YHL045W | YHL045W | NA | NA | Putative protein of unknown function; not an essential gene | Accessory | Unknown | NA | NA |
| 4240-YHL046W-A | YHL046W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF ARN2/YHL047C | Accessory | Ancestral | NA | NA |
| 4241-YHL047C_NumOfGenes_2 | YHL047C | ARN2 | siderophore transporter|TAF1 | Transporter; member of the ARN family of transporters that specifically recognize siderophore-iron chelates; responsible for uptake of iron bound to the siderophore triacetylfusarinine C | Accessory | Ancestral | NA | NA |
| 4242-YHL048C-A | YHL048C-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 4243-YHL048W | YHL048W | COS8 | NA | Endosomal protein involved in turnover of plasma membrane proteins; member of the DUP380 subfamily of conserved, often subtelomeric COS genes; required for the multivesicular vesicle body sorting pathway that internalizes plasma membrane proteins for degradation; Cos proteins provide ubiquitin in trans for nonubiquitinated cargo proteins | Accessory | Ancestral | NA | NA |
| 4244-YHR001W | YHR001W | OSH7 | oxysterol-binding protein related protein OSH7 | Oxysterol-binding protein; part of family with seven members in S. cerevisiae; family members have overlapping, redundant functions in sterol metabolism and collectively perform a function essential for viability; OSH7 has a paralog, OSH6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4245-YHR001W-A | YHR001W-A | QCR10 | ubiquinol--cytochrome-c reductase subunit 10 | Subunit of the ubiqunol-cytochrome c oxidoreductase complex; this complex comprises part of the mitochondrial respiratory chain; members include Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p and comprises part of the mitochondrial respiratory chain | Core | NA | NA | NA |
| 4246-YHR002W | YHR002W | LEU5 | coenzyme A transporter | Mitochondrial carrier protein; involved in the accumulation of CoA in the mitochondrial matrix; homolog of human Graves disease protein SLC25A16, which complements yeast null mutant; does not encode an isozyme of Leu4p, as first hypothesized | Accessory | Ancestral | NA | NA |
| 4247-YHR003C | YHR003C | TCD1 | tRNA threonylcarbamoyladenosine dehydratase | tRNA threonylcarbamoyladenosine dehydratase; required for the ct6A tRNA base modification, where an adenosine at position 37 is modified to form a cyclized active ester with an oxazolone ring; localized to the mitochondrial outer membrane; TCD1 has a paralog, TCD2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4248-YHR004C | YHR004C | NEM1 | Nem1-Spo7 phosphatase catalytic subunit NEM1 | Probable catalytic subunit of Nem1p-Spo7p phosphatase holoenzyme; regulates nuclear growth by controlling phospholipid biosynthesis, required for normal nuclear envelope morphology and sporulation; homolog of the human protein Dullard | Core | NA | NA | NA |
| 4249-YHR005C | YHR005C | GPA1 | guanine nucleotide-binding protein subunit alpha|SCG1|DAC1|CDC70 | Subunit of the G protein involved in pheromone response; GTP-binding alpha subunit of the heterotrimeric G protein; negatively regulates the mating pathway by sequestering G(beta)gamma and by triggering an adaptive response; activates Vps34p at the endosome; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4250-YHR005C-A_NumOfGenes_2 | YHR005C-A | TIM10 | protein transporter TIM10|MRS11 | Essential protein of the mitochondrial intermembrane space; forms a complex with Tim9p (TIM10 complex) that delivers hydrophobic proteins to the TIM22 complex for insertion into the inner membrane | Core | NA | NA | NA |
| 4251-YHR006W | YHR006W | STP2 | NA | Transcription factor; activated by proteolytic processing in response to signals from the SPS sensor system for external amino acids; activates transcription of amino acid permease genes; STP2 has a paralog, STP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4252-YHR007C | YHR007C | ERG11 | sterol 14-demethylase|CYP51 | Lanosterol 14-alpha-demethylase; catalyzes C-14 demethylation of lanosterol to form 4,4''-dimethyl cholesta-8,14,24-triene-3-beta-ol in ergosterol biosynthesis pathway; transcriptionally down-regulated when ergosterol is in excess; member of cytochrome P450 family; associated and coordinately regulated with the P450 reductase Ncp1p; human CYP51A1 functionally complements the lethality of the erg11 null mutation | Core | NA | NA | NA |