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 |
|---|---|---|---|---|---|---|---|---|
| 5738-YLR281C_NumOfGenes_2 | YLR281C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YLR281C is not an essential gene | Core | NA | NA | NA |
| 5739-YLR282C | YLR282C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; deletion mutation confers an increase in Ty1 transposition | Accessory | Ancestral | NA | NA |
| 5740-YLR283W | YLR283W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YLR283W is not an essential gene | Core | NA | NA | NA |
| 5741-YLR284C | YLR284C | ECI1 | dodecenoyl-CoA isomerase | Peroxisomal delta3,delta2-enoyl-CoA isomerase; hexameric protein that converts 3-hexenoyl-CoA to trans-2-hexenoyl-CoA, essential for the beta-oxidation of unsaturated fatty acids, oleate-induced; ECI1 has a paralog, DCI1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5742-YLR285C-A | YLR285C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 5743-YLR285W | YLR285W | NNT1 | EFM7|S-adenosylmethionine-dependent methyltransferase | S-adenosylmethionine-dependent methyltransferase; novel N-terminal protein methyltransferase that trimethylates the N-terminal glycine residue (G2) and also dimethylates lysine (K3) on elongation factor eEF1A (Tef1p/Tef2p); has a role in rDNA silencing and in lifespan determination | Core | NA | NA | NA |
| 5744-YLR286C_NumOfGenes_2 | YLR286C | CTS1 | SCW2 | Endochitinase; required for cell separation after mitosis; transcriptional activation during the G1 phase of the cell cycle is mediated by transcription factor Ace2p | Core | NA | NA | NA |
| 5745-YLR287C | YLR287C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YLR287C is not an essential gene | Core | NA | NA | NA |
| 5746-YLR287C-A | YLR287C-A | RPS30A | eS30|ribosomal 40S subunit protein S30A|S30e|S30A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S30, no bacterial homolog; RPS30A has a paralog, RPS30B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5747-YLR288C | YLR288C | MEC3 | PSO9|PIP3 | DNA damage and meiotic pachytene checkpoint protein; subunit of a heterotrimeric complex (Rad17p-Mec3p-Ddc1p) that forms a sliding clamp, loaded onto partial duplex DNA by a clamp loader complex; homolog of human and S. pombe Hus1 | Core | NA | NA | NA |
| 5748-YLR289W | YLR289W | GUF1 | GTPase GUF1 | Mitochondrial matrix GTPase; associates with mitochondrial ribosomes; important for translation under temperature and nutrient stress; may have a role in translational fidelity; similar to bacterial LepA elongation factor | Core | NA | NA | NA |
| 5749-YLR290C | YLR290C | COQ11 | ubiquinone biosynthesis protein COQ11|MRX2 | Putative oxidoreductase, subunit of Coenzyme Q biosynthetic complexes; required for synthesis of wild-type levels of Coenzyme Q (ubiquinone); member of the short-chain dehydrogenase/reductase (SDR) superfamily; orthologous gene in some other fungi is fused to the COQ10 ortholog | Core | NA | NA | NA |
| 5750-YLR291C | YLR291C | GCD7 | translation initiation factor eIF2B subunit beta | Beta subunit of the translation initiation factor eIF2B; the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a negative regulator of GCN4 expression; human homolog EIF2B2 can complement yeast mutant, allows growth down-regulation of yeast gene | Core | NA | NA | NA |
| 5751-YLR292C | YLR292C | SEC72 | Sec63 complex subunit SEC72|SIM2|SEC67 | Non-essential subunit of Sec63 complex; with Sec61 complex, Kar2p/BiP and Lhs1p forms a channel competent for SRP-dependent and post-translational SRP-independent protein targeting and import into the ER; other members are Sec63p, Sec62p, and Sec66p | Core | NA | NA | NA |
| 5752-YLR293C | YLR293C | GSP1 | Ran GTPase GSP1|CST17|CNR1 | Ran GTPase; GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Srm1p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; GSP1 has a paralog, GSP2, that arose from the whole genome duplication | Core | NA | NA | NA |