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 |
|---|---|---|---|---|---|---|---|---|
| 3788-YGL145W | YGL145W | TIP20 | TIP1 | Peripheral membrane protein required for COPI vesicle fusion to the ER; mediates Sey1p-independent homotypic ER fusion; prohibits back-fusion of COPII vesicles with the ER; forms a tethering complex with Sec39p and Dsl1p that interacts with ER SNAREs Sec20p and Use1p | Core | NA | NA | NA |
| 3789-YGL146C | YGL146C | RRT6 | NA | Putative protein of unknown function; non-essential gene identified in a screen for mutants with increased levels of rDNA transcription; contains two putative transmembrane spans, but no significant homology to other known proteins | Core | NA | NA | NA |
| 3790-YGL147C | YGL147C | RPL9A | uL6|ribosomal 60S subunit protein L9A|L6|rp24|YL11|L9A|L8A | Ribosomal 60S subunit protein L9A; homologous to mammalian ribosomal protein L9 and bacterial L6; RPL9A has a paralog, RPL9B, that arose from a single-locus duplication | Accessory | Ancestral | NA | NA |
| 3791-YGL148W | YGL148W | ARO2 | bifunctional chorismate synthase/riboflavin reductase [NAD(P)H] ARO2 | Bifunctional chorismate synthase and flavin reductase; catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to form chorismate, which is a precursor to aromatic amino acids; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3792-YGL149W | YGL149W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YGL149W is not an essential gene | Core | NA | NA | NA |
| 3793-YGL150C | YGL150C | INO80 | chromatin-remodeling ATPase INO80 | ATPase and nucleosome spacing factor; subunit of complex containing actin and actin-related proteins that has chromatin remodeling activity and 3' to 5' DNA helicase activity in vitro; promotes nucleosome shifts in the 3 prime direction; has a role in modulating stress gene transcription | Core | NA | NA | NA |
| 3794-YGL151W | YGL151W | NUT1 | SSX4|MED5 | Component of the RNA polymerase II mediator complex; mediator is required for transcriptional activation and also has a role in basal transcription | Core | NA | NA | NA |
| 3795-YGL153W_NumOfGenes_2 | YGL153W | PEX14 | NA | Central component of the peroxisomal importomer complex; peroxisomal protein import machinery docking complex component; interacts with both PTS1 (Pex5p) and PTS2 (Pex7p) peroxisomal matrix protein signal recognition factors and membrane receptor Pex13p | Core | NA | NA | NA |
| 3796-YGL154C | YGL154C | LYS5 | holo-[acyl-carrier-protein] synthase | Phosphopantetheinyl transferase involved in lysine biosynthesis; converts inactive apo-form of Lys2p (alpha-aminoadipate reductase) into catalytically active holo-form by posttranslational addition of phosphopantetheine | Core | NA | NA | NA |
| 3797-YGL155W | YGL155W | CDC43 | protein geranylgeranyltransferase type I subunit CDC43|CAL1 | Beta subunit of geranylgeranyltransferase type I; subunit of the Ram2p-Cdc43p heterodimer that catalyzes the geranylgeranylation of the cysteine residue in proteins containing a C-terminal CaaX sequence ending in Leu or Phe; has substrates important for morphogenesis | Core | NA | NA | NA |
| 3798-YGL156W | YGL156W | AMS1 | alpha-mannosidase | Vacuolar alpha mannosidase; involved in free oligosaccharide (fOS) degradation; delivered to the vacuole in a novel pathway separate from the secretory pathway | Core | NA | NA | NA |
| 3799-YGL157W | YGL157W | ARI1 | carbonyl reductase (NADPH-dependent) ARI1 | NADPH-dependent aldehyde reductase; utilizes aromatic and alophatic aldehyde substrates; member of the short-chain dehydrogenase/reductase superfamily | Core | NA | NA | NA |
| 3800-YGL158W | YGL158W | RCK1 | putative serine/threonine protein kinase RCK1 | Protein kinase involved in oxidative stress response; promotes pseudohyphal growth via activation of Ubp3p phosphorylation; identified as suppressor of S. pombe cell cycle checkpoint mutations; RCK1 has a paralog, RCK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3801-YGL159W | YGL159W | NA | NA | Putative protein of unknown function; deletion mutant has no detectable phenotype | Core | NA | NA | NA |
| 3802-YGL160W | YGL160W | AIM14 | putative metalloreductase|YNO1 | NADPH oxidase localized to the perinuclear ER; produces superoxide from NADPH; overexpression causes MCA1 dependent apoptosis; likely involved in superoxide-mediated regulation of the actin cytoskeleton; member of a conserved superfamily of NADPH oxidases (NOX enzymes); has similarity to iron/copper reductases (FRE1-8), particularly Fre8p | Core | NA | NA | NA |