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 |
|---|---|---|---|---|---|---|---|---|
| 6938-YOL140W | YOL140W | ARG8 | acetylornithine transaminase | Acetylornithine aminotransferase; catalyzes the fourth step in the biosynthesis of the arginine precursor ornithine | Accessory | Ancestral | NA | NA |
| 6939-YOL141W | YOL141W | PPM2 | tRNA methyltransferase PPM2|TYW4 | AdoMet-dependent tRNA methyltransferase; also involved in methoxycarbonylation; required for the synthesis of wybutosine (yW), a modified guanosine found at the 3'-position adjacent to the anticodon of phe-tRNA; similarity to Ppm1p | Core | NA | NA | NA |
| 6940-YOL142W | YOL142W | RRP40 | exosome non-catalytic core subunit RRP40|MTR14 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain both S1 and KH RNA binding domains; mutations in the human homolog, EXOSC3, cause pontocerebellar hypoplasia with motor neuron degeneration | Core | NA | NA | NA |
| 6941-YOL143C | YOL143C | RIB4 | lumazine synthase RIB4 | Lumazine synthase (DMRL synthase); catalyzes synthesis of immediate precursor to riboflavin; DMRL synthase stands for 6,7-dimethyl-8-ribityllumazine synthase | Core | NA | NA | NA |
| 6942-YOL144W | YOL144W | NOP8 | NA | Nucleolar protein required for 60S ribosomal subunit biogenesis | Core | NA | NA | NA |
| 6943-YOL145C | YOL145C | CTR9 | CDP1 | Component of the Paf1p complex involved in transcription elongation; binds to and modulates the activity of RNA polymerases I and II; required for expression of a subset of genes, including cyclin genes; involved in SER3 repression by helping to maintain SRG1 transcription-dependent nucleosome occupancy; contains TPR repeats | Core | NA | NA | NA |
| 6944-YOL146W | YOL146W | PSF3 | DNA replication protein PSF3 | Subunit of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p); complex is localized to DNA replication origins and implicated in assembly of the DNA replication machinery | Accessory | Ancestral | NA | NA |
| 6945-YOL147C | YOL147C | PEX11 | PMP27|PMP24 | Peroxisomal protein required for medium-chain fatty acid oxidation; also required for peroxisome proliferation, possibly by inducing membrane curvature; localization regulated by phosphorylation; transcription regulated by Adr1p and Pip2p-Oaf1p | Accessory | Ancestral | NA | NA |
| 6946-YOL148C | YOL148C | SPT20 | ADA5 | Subunit of the SAGA transcriptional regulatory complex; involved in maintaining the integrity of the complex; mutant displays reduced transcription elongation in the G-less-based run-on (GLRO) assay | Accessory | Ancestral | NA | NA |
| 6947-YOL149W | YOL149W | DCP1 | MRT2 | Subunit of the Dcp1p-Dcp2p decapping enzyme complex; decapping complex removes the 5' cap structure from mRNAs prior to their degradation; enhances the activity of catalytic subunit Dcp2p; regulated by DEAD box protein Dhh1p; forms cytoplasmic foci upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 6948-YOL151W_NumOfGenes_2 | YOL151W | GRE2 | methylglyoxal reductase (NADPH-dependent) GRE2 | 3-methylbutanal reductase and NADPH-dependent methylglyoxal reductase; stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway; restores resistance to glycolaldehyde by coupling reduction of glycolaldehyde to ethylene glycol and oxidation of NADPH to NADP+; protein abundance increases in response to DNA replication stress; methylglyoxal reductase (NADPH-dependent) is also known as D-lactaldehyde dehydrogenase | Accessory | Ancestral | NA | NA |
| 6949-YOL152W | YOL152W | FRE7 | putative ferric-chelate reductase | Putative ferric reductase with similarity to Fre2p; expression induced by low copper levels | Accessory | Ancestral | NA | NA |
| 6950-YOL153C | YOL153C | NA | NA | Blocked reading frame, contains two in-frame stops in translation; this ORF is conserved, without the stops, in Saccharomyces paradoxus, S. mikatae, and S. bayanus; RNA sequencing data indicate the presence of a transcription unit at this reading frame | Accessory | Ancestral | NA | NA |
| 6951-YOL154W | YOL154W | ZPS1 | NA | Putative GPI-anchored protein; transcription is induced under low-zinc conditions, as mediated by the Zap1p transcription factor, and at alkaline pH | Accessory | Ancestral | NA | NA |
| 6952-YOL155C_NumOfGenes_3 | YOL155C | HPF1 | mannoprotein | Haze-protective mannoprotein; reduces the particle size of aggregated proteins in white wines | Accessory | Ancestral | NA | NA |