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 |
|---|---|---|---|---|---|---|---|---|
| 5783-YLR324W | YLR324W | PEX30 | peroxisome biogenesis protein | ER-resident protein involved in peroxisomal biogenesis; ER-localized protein that associates with peroxisomes; interacts with Pex29p and reticulons Rtn1p and Yop1p to regulate peroxisome biogenesis from the ER; role in peroxisomal-destined vesicular flow from the ER; partially redundant with Pex31p; may function at a step downstream of steps mediated by Pex28p and Pex29p; PEX30 has a paralog, PEX31, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5784-YLR325C | YLR325C | RPL38 | eL38|ribosomal 60S subunit protein L38|L38e|L38 | Ribosomal 60S subunit protein L38; homologous to mammalian ribosomal protein L38, no bacterial homolog | Core | NA | NA | NA |
| 5785-YLR326W | YLR326W | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the cell periphery; predicted to be palmitoylated | Core | NA | NA | NA |
| 5786-YLR327C | YLR327C | TMA10 | RBF9|SFL2 | Protein of unknown function that associates with ribosomes; protein abundance increases in response to DNA replication stress; TMA10 has a paralog, STF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5787-YLR328W | YLR328W | NMA1 | nicotinamide-nucleotide adenylyltransferase NMA1 | Nicotinic acid mononucleotide adenylyltransferase; catalyzes the transfer of the adenylyl moiety of ATP to nicotinamide mononucleotide to form NAD; involved in pathways of NAD biosynthesis, including the de novo, NAD(+) salvage, and nicotinamide riboside salvage pathways; homolog of human NMNAT; NMA1 has a paralog, NMA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5788-YLR329W | YLR329W | REC102 | NA | Protein involved in early stages of meiotic recombination; required for chromosome synapsis; forms a complex with Rec104p and Spo11p necessary during the initiation of recombination | Core | NA | NA | NA |
| 5789-YLR330W | YLR330W | CHS5 | CAL3 | Component of the exomer complex; the exomer which also contains Csh6p, Bch1p, Bch2p, and Bud7, is involved in the export of select proteins, such as chitin synthase Chs3p, from the Golgi to the plasma membrane; interacts selectively with the activated, GTP-bound form of Arf1p; Chs5p is the only protein with a BRCT domain that is not localized to the nucleus | Core | NA | NA | NA |
| 5790-YLR332W_NumOfGenes_2 | YLR332W | MID2 | KAI1 | O-glycosylated plasma membrane protein; acts as a sensor for cell wall integrity signaling and activates the pathway; interacts with Rom2p, a guanine nucleotide exchange factor for Rho1p, and with cell integrity pathway protein Zeo1p; MID2 has a paralog, MTL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5791-YLR333C | YLR333C | RPS25B | eS25|ribosomal 40S subunit protein S25B|S25e|rp45|YS23|S31B|S25B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S25, no bacterial homolog; RPS25B has a paralog, RPS25A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5792-YLR334C | YLR334C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps a stand-alone long terminal repeat sequence whose presence indicates a retrotransposition event occurred here | Core | NA | NA | NA |
| 5793-YLR335W | YLR335W | NUP2 | nucleoporin NUP2 | Nucleoporin involved in nucleocytoplasmic transport; binds to either the nucleoplasmic or cytoplasmic faces of the nuclear pore complex depending on Ran-GTP levels; also has a role in chromatin organization | Core | NA | NA | NA |
| 5794-YLR336C | YLR336C | SGD1 | NA | Essential nuclear protein; required for biogenesis of the small ribosomal subunit; has a possible role in the osmoregulatory glycerol response; putative homolog of human NOM1 which is implicated in acute myeloid leukemia | Core | NA | NA | NA |
| 5795-YLR337C_NumOfGenes_2 | YLR337C | VRP1 | YLR337W|MDP2|END5 | Verprolin, proline-rich actin-associated protein; involved in cytoskeletal organization and cytokinesis; promotes actin nucleation and endocytosis; related to mammalian Wiskott-Aldrich syndrome protein (WASP)-interacting protein (WIP) | Core | NA | NA | NA |
| 5796-YLR340W_NumOfGenes_2 | YLR340W | RPP0 | uL10|ribosomal protein P0|P0|L10E|A0|RPL10E | Conserved ribosomal protein P0 of the ribosomal stalk; involved in interaction between translational elongation factors and the ribosome; phosphorylated on serine 302; homologous to mammalian ribosomal protein LP0 and bacterial L10 | Core | NA | NA | NA |
| 5797-YLR341W | YLR341W | SPO77 | NA | Meiosis-specific protein of unknown function; required for spore wall formation during sporulation and for timely prospore membrane closure along with SPS1; required with Sps1p for phosphorylation and turnover of Ssp1p; dispensable for both nuclear divisions during meiosis | Core | NA | NA | NA |