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 |
|---|---|---|---|---|---|---|---|---|
| 7643-YPR017C | YPR017C | DSS4 | guanine nucleotide exchange factor DSS4 | Guanine nucleotide dissociation stimulator for Sec4p; functions in the post-Golgi secretory pathway; binds zinc, found both on membranes and in the cytosol | Core | NA | NA | NA |
| 7644-YPR018W | YPR018W | RLF2 | CAC1 | Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1); chromatin assembly by CAF-1 is important for multiple processes including silencing at telomeres, mating type loci, and rDNA; maintenance of kinetochore structure; deactivation of the DNA damage checkpoint after DNA repair; chromatin dynamics during transcription; and repression of divergent noncoding transcription | Core | NA | NA | NA |
| 7645-YPR019W | YPR019W | MCM4 | MCM DNA helicase complex subunit MCM4|CDC54|HCD21 | Essential helicase component of heterohexameric MCM2-7 complexes; MCM2-7 complexes bind pre-replication complexes on DNA and melt DNA prior to replication; forms an Mcm4p-6p-7p subcomplex; shows nuclear accumulation in G1; homolog of S. pombe Cdc21p | Core | NA | NA | NA |
| 7646-YPR020W | YPR020W | ATP20 | F1F0 ATP synthase subunit g | Subunit g of the mitochondrial F1F0 ATP synthase; reversibly phosphorylated on two residues; unphosphorylated form is required for dimerization of the ATP synthase complex, which in turn determines oligomerization of the complex and the shape of inner membrane cristae | Core | NA | NA | NA |
| 7647-YPR021C | YPR021C | AGC1 | amino acid transporter AGC1 | Mitochondrial amino acid transporter; acts both as a glutamate uniporter and as an aspartate-glutamate exchanger; involved in nitrogen metabolism and nitrogen compound biosynthesis; human homolog SLC25A13 complements yeast null mutant | Core | NA | NA | NA |
| 7648-YPR022C | YPR022C | SDD4 | NA | Putative transcription factor, as suggested by computational analysis; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS; overproduction of a truncation allele suppresses lethality due to expression of the dominant PET9 allele AAC2-A128P | Core | NA | NA | NA |
| 7649-YPR023C | YPR023C | EAF3 | NA | Component of the Rpd3S histone deacetylase complex; Esa1p-associated factor, nonessential component of the NuA4 acetyltransferase complex, homologous to Drosophila dosage compensation protein MSL3; plays a role in regulating Ty1 transposition | Core | NA | NA | NA |
| 7650-YPR024W | YPR024W | YME1 | i-AAA protease YME1|YTA11|OSD1 | Catalytic subunit of i-AAA protease complex; complex is located in mitochondrial inner membrane; responsible for degradation of unfolded or misfolded mitochondrial gene products; serves as nonconventional translocation motor to pull PNPase into intermembrane space; also has role in intermembrane space protein folding; mutation causes elevated rate of mitochondrial turnover; human homolog YME1L1 can complement yeast null mutant | Core | NA | NA | NA |
| 7651-YPR025C | YPR025C | CCL1 | TFIIH complex kinase subunit CCL1 | Cyclin associated with protein kinase Kin28p; Kin28p is the TFIIH-associated carboxy-terminal domain (CTD) kinase involved in transcription initiation at RNA polymerase II promoters; human homolog CCNH allows growth of yeast ccl1 temperature-sensitive mutant at restrictive temperature | Core | NA | NA | NA |
| 7652-YPR026W | YPR026W | ATH1 | alpha,alpha-trehalase ATH1 | Acid trehalase required for utilization of extracellular trehalose; involved in intracellular trehalose degradation during growth recovery after saline stress | Core | NA | NA | NA |
| 7653-YPR027C | YPR027C | NA | NA | Putative protein of unknown function; SWAT-GFP and seamless-GFP fusion proteins localize to the endoplasmic reticulum, while the mCherry fusion protein localizes to the vacuole | Core | NA | NA | NA |
| 7654-YPR028W | YPR028W | YOP1 | YIP2 | Reticulon-interacting protein; ER integral membrane protein involved in the generation of tubular ER morphology; promotes membrane curvature; forms tubules in vitro; regulates the ER asymmetry-induced inheritance block during ER stress; role in ER-derived peroxisomal biogenesis; interacts with Yip1p to mediate membrane traffic and with Sey1p to maintain ER morphology; facilitates lipid exchange between the ER and mitochondria; forms ER foci upon DNA replication stress | Core | NA | NA | NA |
| 7655-YPR029C | YPR029C | APL4 | NA | Gamma-adaptin; large subunit of the clathrin-associated protein (AP-1) complex; binds clathrin; involved in vesicle mediated transport | Core | NA | NA | NA |
| 7656-YPR030W | YPR030W | CSR2 | ART8|MRG19 | Nuclear ubiquitin protein ligase binding protein; may regulate utilization of nonfermentable carbon sources and endocytosis of plasma membrane proteins; overproduction suppresses chs5 spa2 lethality at high temp; ubiquitinated by Rsp5p, deubiquitinated by Ubp2p; CSR2 has a paralog, ECM21, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7657-YPR031W | YPR031W | NTO1 | NA | Subunit of the NuA3 histone acetyltransferase complex; this complex acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3 | Core | NA | NA | NA |