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 |
|---|---|---|---|---|---|---|---|---|
| 6443-YNL050C | YNL050C | NA | NA | Putative protein of unknown function; YNL050c is not an essential gene | Core | NA | NA | NA |
| 6444-YNL051W | YNL051W | COG5 | Golgi transport complex subunit COG5|COD4|API4 | Component of the conserved oligomeric Golgi complex; a cytosolic tethering complex (Cog1p through Cog8p) that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments | Core | NA | NA | NA |
| 6445-YNL052W | YNL052W | COX5A | cytochrome c oxidase subunit Va | Subunit Va of cytochrome c oxidase; cytochrome c oxidase is the terminal member of the mitochondrial inner membrane electron transport chain; Cox5Ap is predominantly expressed during aerobic growth while its isoform Vb (Cox5Bp) is expressed during anaerobic growth; COX5A has a paralog, COX5B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6446-YNL053W | YNL053W | MSG5 | tyrosine/serine/threonine protein phosphatase MSG5 | Dual-specificity protein phosphatase; exists in 2 isoforms; required for maintenance of a low level of signaling through the cell integrity pathway, adaptive response to pheromone; regulates and is regulated by Slt2p; dephosphorylates Fus3p; MSG5 has a paralog, SDP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6447-YNL054W | YNL054W | VAC7 | NA | Integral vacuolar membrane protein; involved in vacuole inheritance and morphology; activates Fab1p kinase activity under basal conditions and also after hyperosmotic shock | Core | NA | NA | NA |
| 6448-YNL055C | YNL055C | POR1 | porin POR1|VDAC|YVDAC1|OMP2 | Mitochondrial porin (voltage-dependent anion channel); outer membrane protein required for maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; couples the glutathione pools of the intermembrane space (IMS) and the cytosol; interacts with Om45 and Om14 in the outer membrane; phosphorylated; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6449-YNL056W | YNL056W | OCA2 | NA | Protein of unknown function; similar to predicted tyrosine phosphatases Oca1p and Siw14p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YNL056W is not an essential gene | Core | NA | NA | NA |
| 6450-YNL058C_NumOfGenes_2 | YNL058C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to vacuole; not an essential gene; YNL058C has a paralog, PRM5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6451-YNL059C | YNL059C | ARP5 | NA | Nuclear actin-related protein involved in chromatin remodeling; component of chromatin-remodeling enzyme complexes; promotes nucleosome shifts in the 3 prime direction | Core | NA | NA | NA |
| 6452-YNL061W | YNL061W | NOP2 | rRNA (cytosine-C5-)-methyltransferase NOP2|YNA1 | rRNA m5C methyltransferase; methylates cytosine at position 2870 of 25S rRNA; has an essential function independent of rRNA methylation; contains seven beta-strand methyltransferase motif; essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles; rRNA methylation defect and lethality are functionally complemented by human NOP2, a gene upregulated in cancer | Core | NA | NA | NA |
| 6453-YNL062C | YNL062C | GCD10 | tRNA 1-methyladenosine methyltransferase subunit GCD10|TRM6 | Subunit of tRNA (1-methyladenosine) methyltransferase with Gcd14p; required for the modification of the adenine at position 58 in tRNAs, especially tRNAi-Met; first identified as a negative regulator of GCN4 expression | Core | NA | NA | NA |
| 6454-YNL063W | YNL063W | MTQ1 | S-adenosylmethionine-dependent methyltransferase | S-adenosylmethionine-dependent methyltransferase; methylates translational release factor Mrf1p; similar to E.coli PrmC; is not an essential gene | Core | NA | NA | NA |
| 6455-YNL064C | YNL064C | YDJ1 | MAB3|type I HSP40 co-chaperone YDJ1|HSP40|MAS5 | Type I HSP40 co-chaperone; involved in regulation of HSP90 and HSP70 functions; acts as an adaptor that helps Rsp5p recognize cytosolic misfolded proteins for ubiquitination after heat shock; critical for determining cell size at Start as a function of growth rate; involved in protein translocation across membranes; member of the DnaJ family; chimeric protein in which human p58IPK J domain replaces yeast Ydj1p J domain can complement yeast ydj1 mutant | Core | NA | NA | NA |
| 6456-YNL065W | YNL065W | AQR1 | NA | Plasma membrane transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; confers resistance to short-chain monocarboxylic acids and quinidine; involved in the excretion of excess amino acids; AQR1 has a paralog, QDR1, that arose from the whole genome duplication; relocalizes from plasma membrane to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 6457-YNL066W | YNL066W | SUN4 | putative glucosidase SUN4|SCW3 | Cell wall protein related to glucanases; possibly involved in cell wall septation; member of the SUN family; SUN4 has a paralog, SIM1, that arose from the whole genome duplication | Core | NA | NA | NA |