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
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

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