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 |
---|---|---|---|---|---|---|---|---|
5618-YLR154W-F | YLR154W-F | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; encoded within the 35S rRNA gene on the opposite strand | Core | NA | NA | NA |
5619-YLR157C_NumOfGenes_4 | YLR157C | ASP3-2 | asparaginase ASP3-2|ASP3 | Cell-wall L-asparaginase II involved in asparagine catabolism; expression induced during nitrogen starvation; ORF contains a short non-coding RNA that enhances expression of full-length gene; likely arose in via horizontal gene transfer from the wine yeast Wickerhamomyces anomalus or a close relative; reference strain S288C has four copies of ASP3; ASP3-2 has a paralog, ASP3-4, that arose from a segmental duplication | Accessory | HGT | Wickerhamomyces | Zygosaccharomyces parabailii chr16 |
5620-YLR161W_NumOfGenes_5 | YLR161W | NA | NA | Putative protein of unknown function; YLR156W, YLR159W, and YLR161W are three identical open reading frames in S288C encoded near the ribosomal DNA region of chromosome 12; YLR161W has a paralog, YLR157W-D, that arose from a segmental duplication | Accessory | Unknown | NA | NA |
5621-YLR162W | YLR162W | NA | NA | Protein of unknown function; overexpression confers resistance to the antimicrobial peptide MiAMP1 and causes growth arrest, apoptosis, and increased sensitivity to cobalt chloride | Accessory | Unknown | S. paradoxus | NA |
5622-YLR162W-A | YLR162W-A | RRT15 | NA | Putative protein of unknown function; identified by fungal homology comparisons and RT-PCR; identified in a screen for mutants with decreased levels of rDNA transcription | Accessory | Unknown | NA | NA |
5623-YLR163C_NumOfGenes_2 | YLR163C | MAS1 | MIF1 | Beta subunit of the mitochondrial processing protease (MPP); essential processing enzyme that cleaves the N-terminal targeting sequences from mitochondrially imported proteins | Accessory | Ancestral | NA | NA |
5624-YLR164W | YLR164W | SHH4 | protein SHH4 | Putative alternate subunit of succinate dehydrogenase (SDH); mitochondrial inner membrane protein; genetic interaction with SDH4 suggests that Shh4p can function as a functional SDH subunit; a fraction copurifies with SDH subunit Sdh3p; expression induced by nitrogen limitation in a GLN3, GAT1-dependent manner; Shh4p has greater similarity to human SDHD (subunit D of SDH, implicated in paraganglioma) than does its paralog Sdh4p | Accessory | Ancestral | NA | NA |
5625-YLR165C | YLR165C | PUS5 | pseudouridine synthase PUS5 | Pseudouridine synthase; catalyzes only the formation of pseudouridine (Psi)-2819 in mitochondrial 21S rRNA; not essential for viability | Accessory | Ancestral | NA | NA |
5626-YLR166C | YLR166C | SEC10 | exocyst subunit SEC10 | Essential 100kDa subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis at the plasma membrane prior to SNARE-mediated fusion | Accessory | Ancestral | NA | NA |
5627-YLR167W | YLR167W | RPS31 | eS31|ubiquitin-ribosomal 40S subunit protein S31 fusion protein|S31e|UB13|YS24|S37|S31|UBI3|RPS37 | Fusion protein cleaved to yield ribosomal protein S31 and ubiquitin; ubiquitin may facilitate assembly of the ribosomal protein into ribosomes; interacts genetically with translation factor eIF2B; homologous to mammalian ribosomal protein S27A, no bacterial homolog | Accessory | Ancestral | NA | NA |
5628-YLR168C | YLR168C | UPS2 | GEP1|AIM30|MSF1|MSF1' | Mitochondrial intermembrane space protein; involved in phospholipid metabolism; forms complex with Mdm35p that transfers phosphatidylserine from outer membrane to inner membrane for phosphatidylethanolamine synthesis; null mutant has defects in mitochondrial morphology; similar to Ups1p, Ups3p and to human PRELI; UPS2 has a paralog, UPS3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
5629-YLR169W | YLR169W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
5630-YLR170C_NumOfGenes_2 | YLR170C | APS1 | YAP19 | Small subunit of the clathrin-associated adaptor complex AP-1; AP-1 is involved in protein sorting at the trans-Golgi network; homolog of the sigma subunit of the mammalian clathrin AP-1 complex | Accessory | Ancestral | NA | NA |
5631-YLR172C | YLR172C | DPH5 | diphthine synthase | Methyltransferase required for synthesis of diphthamide; diphthamide is a modified histidine residue of translation elongation factor 2 (Eft1p or Eft2p); not essential for viability; GFP-Dph5p fusion protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
5632-YLR173W | YLR173W | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |