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 |
|---|---|---|---|---|---|---|---|---|
| 5048-YJR141W | YJR141W | IPA1 | putative polyadenylation protein | Essential protein of unknown function | Core | NA | NA | NA |
| 5049-YJR142W | YJR142W | NA | NA | 8-oxo-dGTP diphosphatase of the Nudix hydrolase family; converts diphosphates of damaged forms of thiamin to monophosphates; GST fusion protein is a Dbf2p-Mob1p phosphorylation target in a proteome chip analysis; synthetic lethal with PH085 deletion; plays a role in restricting Ty1 transposition | Core | NA | NA | NA |
| 5050-YJR143C | YJR143C | PMT4 | dolichyl-phosphate-mannose-protein mannosyltransferase | Protein O-mannosyltransferase; transfers mannose residues from dolichyl phosphate-D-mannose to protein serine/threonine residues; appears to form homodimers in vivo and does not complex with other Pmt proteins; target for new antifungals | Accessory | Ancestral | NA | NA |
| 5051-YJR144W | YJR144W | MGM101 | MGM9 | Protein with a role in mitochondrial DNA recombinational repair; also involved in interstrand cross-link repair; binds to and catalyzes the annealing of single-stranded mtDNA; oligomerizes to form rings and filaments; related to Rad52-type recombination proteins, with limited overall similarity but sharing conserved functionally important residues; component of the mitochondrial nucleoid, required for the repair of oxidative mtDNA damage and mitochondrial genome maintenance | Accessory | Ancestral | NA | NA |
| 5052-YJR145C_NumOfGenes_2 | YJR145C | RPS4A | eS4|ribosomal 40S subunit protein S4A|S4e|rp5|YS6|S7A|S4A | Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; homologous to mammalian ribosomal protein S4, no bacterial homolog; RPS4A has a paralog, RPS4B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5053-YJR146W | YJR146W | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels; partially overlaps HMS2 | Core | NA | NA | NA |
| 5054-YJR147W | YJR147W | HMS2 | NA | Protein with similarity to heat shock transcription factors; overexpression suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null mutant; HMS2 has a paralog, SKN7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5055-YJR148W | YJR148W | BAT2 | branched-chain-amino-acid transaminase BAT2|ECA40|TWT2 | Cytosolic branched-chain amino acid (BCAA) aminotransferase; preferentially involved in BCAA catabolism; homolog of murine ECA39; highly expressed during stationary phase and repressed during logarithmic phase; BAT2 has a paralog, BAT1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5056-YJR149W | YJR149W | NA | putative nitronate monooxygenase | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
| 5057-YJR150C | YJR150C | DAN1 | CCW13 | Cell wall mannoprotein; has similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth | Accessory | Ancestral | NA | NA |
| 5058-YJR151C_NumOfGenes_2 | YJR151C | DAN4 | NA | Cell wall mannoprotein; has similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth | Accessory | Ancestral | NA | NA |
| 5059-YJR151W-A | YJR151W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR; predicted to have a role in transcription based on computational "guilt by association" analysis | Accessory | Unknown | NA | NA |
| 5060-YJR152W | YJR152W | DAL5 | allantoate permease|UREP1 | Allantoate permease; ureidosuccinate permease; also transports dipeptides, though with lower affinity than for allantoate and ureidosuccinate; expression is constitutive but sensitive to nitrogen catabolite repression | Accessory | Ancestral | NA | NA |
| 5061-YJR153W_NumOfGenes_2 | YJR153W | PGU1 | PSM1|PGL1 | Endo-polygalacturonase; pectolytic enzyme that hydrolyzes the alpha-1,4-glycosidic bonds in the rhamnogalacturonan chains in pectins | Accessory | Ancestral | NA | NA |
| 5062-YJR154W_NumOfGenes_2 | YJR154W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |