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
5003-YJR097W YJR097W JJJ3 DPH4 Protein of unknown function; contains a CSL Zn finger and a DnaJ-domain; involved in diphthamide biosynthesis; ortholog human Dph4 Core NA NA NA
5004-YJR098C YJR098C NA NA Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies Core NA NA NA
5005-YJR099W YJR099W YUH1 ubiquitin-specific protease YUH1 Ubiquitin C-terminal hydrolase; cleaves ubiquitin-protein fusions to generate monomeric ubiquitin; hydrolyzes the peptide bond at the C-terminus of ubiquitin; also the major processing enzyme for the ubiquitin-like protein Rub1p Core NA NA NA
5006-YJR100C YJR100C AIM25 SLM35 Mitochondria protein of unknown function; interacts genetically with TOR1 to regulate chronological lifespan, and the response to both heat shock and oxidative stress; involved in maintaining the integrity of the mitochondrial network; negative regulator of mitophagy flux; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant is viable and displays an elevated frequency of mitochondrial genome loss; similar to murine NOR1 Core NA NA NA
5007-YJR101W YJR101W RSM26 mitochondrial 37S ribosomal protein RSM26 Mitochondrial ribosomal protein of the small subunit Core NA NA NA
5008-YJR102C YJR102C VPS25 ESCRT-II subunit protein VPS25|VPL12|VPT25 Component of the ESCRT-II complex; ESCRT-II is involved in ubiquitin-dependent sorting of proteins into the endosome Core NA NA NA
5009-YJR103W YJR103W URA8 CTP synthase URA8 Minor CTP synthase isozyme (see also URA7); catalyzes the ATP-dependent transfer of the amide nitrogen from glutamine to UTP, forming CTP, the final step in de novo biosynthesis of pyrimidines; involved in phospholipid biosynthesis; capable of forming cytoplasmic filaments termed cytoophidium, especially during conditions of glucose depletion; URA8 has a paralog, URA7, that arose from the whole genome duplication Core NA NA NA
5010-YJR104C YJR104C SOD1 superoxide dismutase SOD1|CRS4 Cytosolic copper-zinc superoxide dismutase; detoxifies superoxide; stabilizes Yck1p and Yck2p kinases in glucose to repress respiration; phosphorylated by Dun1p, enters nucleus under oxidative stress to promote transcription of stress response genes; human ortholog SOD1 implicated in ALS complements a null allele; abundance increases under DNA replication stress and during exposure to boric acid; localization to mitochondrial intermembrane space is modulated by MICOS complex Core NA NA NA
5011-YJR105W YJR105W ADO1 adenosine kinase Adenosine kinase; required for the utilization of S-adenosylmethionine (AdoMet); may be involved in recycling adenosine produced through the methyl cycle Core NA NA NA
5012-YJR106W YJR106W ECM27 NA Protein involved in calcium homeostasis and exit from quiescence; required for proper trehalose levels during quiescence; may play a role in cell wall biosynthesis, mutants are hypersensitive to antifungal, Papulacandin B; null mutants have increased plasmid loss; interacts with Pdr5p Core NA NA NA
5013-YJR107W YJR107W LIH1 putative lipase Putative lipase Core NA NA NA
5014-YJR108W YJR108W ABM1 NA Protein of unknown function; required for normal microtubule organization Core NA NA NA
5015-YJR109C YJR109C CPA2 carbamoyl-phosphate synthase (glutamine-hydrolyzing) CPA2 Large subunit of carbamoyl phosphate synthetase; carbamoyl phosphate synthetase catalyzes a step in the synthesis of citrulline, an arginine precursor Core NA NA NA
5016-YJR110W YJR110W YMR1 phosphatidylinositol-3-phosphatase YMR1 Phosphatidylinositol 3-phosphate (PI3P) phosphatase; involved in various protein sorting pathways, including CVT targeting and endosome to vacuole transport; has similarity to the conserved myotubularin dual specificity phosphatase family Core NA NA NA
5017-YJR111C YJR111C PXP2 NA Peroxisomal matrix protein with naturally active promoter; well-conserved in fungi; localized to peroxisomes under physiological growth conditions; levels of some amino acids are altered upon both knockout and overexpression, suggesting potential involvement of Pxp2p in amino acid metabolism or related cellular metabolic processes (needs further study); GFP-fusion protein displays inherent dual localization with large proportion localizing to cytosol Core NA NA NA

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