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 |
|---|---|---|---|---|---|---|---|---|
| 5678-YLR221C | YLR221C | RSA3 | NA | Protein with a likely role in ribosomal maturation; required for accumulation of wild-type levels of large (60S) ribosomal subunits; binds to the helicase Dbp6p in pre-60S ribosomal particles in the nucleolus | Core | NA | NA | NA |
| 5679-YLR222C | YLR222C | UTP13 | NA | Nucleolar protein; component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA | Core | NA | NA | NA |
| 5680-YLR222C-A | YLR222C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene IFH1 | Core | NA | NA | NA |
| 5681-YLR223C | YLR223C | IFH1 | NA | Coactivator, regulates transcription of ribosomal protein (RP) genes; recruited to RP gene promoters during optimal growth conditions via Fhl1p; subunit of CURI, a complex that coordinates RP production and pre-rRNA processing; regulated by acetylation and phosphorylation at different growth states via TORC1 signaling; IFH1 has a paralog, CRF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5682-YLR224W | YLR224W | UCC1 | NA | F-box protein and component of SCF ubiquitin ligase complexes; involved in ubiquitin-dependent protein catabolism; readily monoubiquitinated in vitro by SCF-Ubc4 complexes; SCF-Ucc1 regulates level of Cit2 citrate synthase protein to maintain citrate homeostasis, acts as metabolic switch for glyoxylate cycle; UCC1 transcription is downregulated in cells grown on C2-compounds | Core | NA | NA | NA |
| 5683-YLR225C | YLR225C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; not an essential gene; YLR225C has a paralog, YDR222W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5684-YLR226W | YLR226W | BUR2 | CST4 | Cyclin for the Sgv1p (Bur1p) protein kinase; Sgv1p and Bur2p comprise the CDK-cyclin BUR kinase complex which is involved in transcriptional regulation through its phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (Rpo21p); BUR kinase is also involved in the recruitment of Spt6p to the CTD at the onset of transcription | Core | NA | NA | NA |
| 5685-YLR227C | YLR227C | ADY4 | NA | Structural component of the meiotic outer plaque; outer plaque is a membrane-organizing center that assembles on the cytoplasmic face of the spindle pole body during meiosis II and triggers the formation of the prospore membrane | Core | NA | NA | NA |
| 5686-YLR228C | YLR228C | ECM22 | NA | Sterol regulatory element binding protein; regulates transcription of sterol biosynthetic genes upon sterol depletion, after relocating from intracellular membranes to perinuclear foci; redundant activator of filamentation with UPC2, up-regulating the expression of genes involved in filamentous growth; contains Zn[2]-Cys[6] binuclear cluster; ECM22 has a paralog, UPC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5687-YLR229C | YLR229C | CDC42 | Rho family GTPase CDC42 | Small rho-like GTPase; essential for establishment and maintenance of cell polarity; plays a role late in cell fusion via activation of key cell fusion regulator Fus2p; mutants have defects in the organization of actin and septins; human homolog CDC42 can complement yeast cdc42 mutant | Core | NA | NA | NA |
| 5688-YLR230W | YLR230W | NA | NA | Dubious open reading frame unlikely to encode a functional protein; overlaps 5' end of essential CDC42/YLR229C gene which encodes a small Rho-like GTPase essential for establishment and maintenance of cell polarity | Accessory | Ancestral | NA | NA |
| 5689-YLR231C_NumOfGenes_2 | YLR231C | BNA5 | kynureninase | Kynureninase; required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p | Core | NA | NA | NA |
| 5690-YLR233C | YLR233C | EST1 | NA | TLC1 RNA-associated factor involved in telomere length regulation; recruitment subunit of telomerase; has G-quadruplex promoting activity required for telomere elongation; role in activating telomere-bound Est2p-TLC1-RNA; EST1 has a paralog, EBS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5691-YLR234W | YLR234W | TOP3 | DNA topoisomerase 3|EDR1 | DNA Topoisomerase III; conserved protein that functions in a complex with Sgs1p and Rmi1p to relax single-stranded negatively-supercoiled DNA preferentially; DNA catenation/decatenation activity is stimulated by RPA and Sgs1p-Top3p-Rmi1p; involved in telomere stability and regulation of mitotic recombination | Core | NA | NA | NA |
| 5692-YLR235C | YLR235C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORFs TOP3/YLR234W and YLR236C | Accessory | Ancestral | NA | NA |