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 |
|---|---|---|---|---|---|---|---|---|
| 2228-YBR237W | YBR237W | PRP5 | DEAD-box RNA helicase PRP5|RNA5 | RNA helicase in the DEAD-box family; necessary for prespliceosome formation, bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA | Core | NA | NA | NA |
| 2229-YBR238C | YBR238C | NA | NA | Mitochondrial membrane protein; not required for respiratory growth but causes a synthetic respiratory defect in combination with rmd9 mutations; transcriptionally up-regulated by TOR; deletion increases life span; YBR238C has a paralog, RMD9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2230-YBR239C | YBR239C | ERT1 | NA | Transcriptional regulator; involved in regulation of gluconeogenesis and fermentable carbon utilization; GFP-fusion protein localizes to cytoplasm, nucleus; null mutation affects periodicity of transcriptional and metabolic oscillation; plays role in restricting Ty1 transposition; member of the zinc cluster family of proteins, similar to Rds2p | Core | NA | NA | NA |
| 2231-YBR240C | YBR240C | THI2 | phoF|PHO6 | Transcriptional activator of thiamine biosynthetic genes; interacts with regulatory factor Thi3p to control expression of thiamine biosynthetic genes with respect to thiamine availability; acts together with Pdc2p to respond to thiaminediphosphate demand, possibly as related to carbon source availability; zinc finger protein of the Zn(II)2Cys6 type | Core | NA | NA | NA |
| 2232-YBR241C | YBR241C | NA | NA | Putative transporter, member of the sugar porter family; green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane; YBR241C is not an essential gene; YBR241C has a paralog, VPS73, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2233-YBR242W | YBR242W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YBR242W is not an essential gene; YBR242W has a paralog, YGL101W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2234-YBR243C | YBR243C | ALG7 | UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase|TUR1 | UDP-N-acetyl-glucosamine-1-P transferase; transfers Glc-Nac-P from UDP-GlcNac to Dol-P in the ER in the first step of the dolichol pathway of protein asparagine-linked glycosylation; inhibited by tunicamycin; human homolog DPAGT1 can complement yeast ALG7 mutant | Core | NA | NA | NA |
| 2235-YBR244W | YBR244W | GPX2 | glutathione peroxidase GPX2|AMI1 | Phospholipid hydroperoxide glutathione peroxidase; protects cells from phospholipid hydroperoxides and nonphospholipid peroxides during oxidative stress; induced by glucose starvation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2236-YBR245C | YBR245C | ISW1 | chromatin-remodeling ATPase ISW1|SGN2 | ATPase subunit of imitation-switch (ISWI) class chromatin remodelers; with Ioc3p forms Isw1a complex involved in repression of transcription initiation; with Ioc2p and Ioc4p forms Isw1b complex involved in regulation of transcription elongation; Isw1b recruited to ORFs by H3K36 methylation and acts with Chd1p to prevent trans-histone exchange over coding regions; Isw1p import into nucleus depends on C-terminal bipartite nuclear targeting signal KRIR X19 KKAK | Core | NA | NA | NA |
| 2237-YBR246W | YBR246W | RRT2 | DPH7|diphthamide synthase|ERE1 | Methylesterase performing penultimate step of diphthamide biosynthesis; hydrolyzes methylated diphthine to produce diphthine and allows Dph6-catalyzed amidation reaction to occur; deletion leads to resistance to sordarin and accumulation of methylatediphthine; WD40 domain-containing protein; involved in endosomal recycling; forms complex with Rtt10p that functions in retromer-mediated pathway for recycling internalized cell-surface proteins | Core | NA | NA | NA |
| 2238-YBR247C | YBR247C | ENP1 | snoRNA-binding rRNA-processing protein ENP1|MEG1 | Protein associated with U3 and U14 snoRNAs; required for pre-rRNA processing and 40S ribosomal subunit synthesis; localized in the nucleus and concentrated in the nucleolus; human BYSL functionally complements the heat sensitivity of an enp1 ts mutant | Core | NA | NA | NA |
| 2239-YBR248C | YBR248C | HIS7 | imidazoleglycerol-phosphate synthase | Imidazole glycerol phosphate synthase; glutamine amidotransferase:cyclase that catalyzes the fifth step of histidine biosynthesis and also produces 5-aminoimidazole-4-carboxamide ribotide (AICAR), a purine precursor | Core | NA | NA | NA |
| 2240-YBR249C | YBR249C | ARO4 | 3-deoxy-7-phosphoheptulonate synthase ARO4 | 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase; catalyzes the first step in aromatic amino acid biosynthesis and is feedback-inhibited by tyrosine or high concentrations of phenylalanine or tryptophan; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2241-YBR250W | YBR250W | SPO23 | NA | Protein of unknown function; associates with meiosis-specific protein Spo1p | Core | NA | NA | NA |
| 2242-YBR251W | YBR251W | MRPS5 | mitochondrial 37S ribosomal protein MRPS5 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |