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 |
|---|---|---|---|---|---|---|---|---|
| 6338-YMR269W | YMR269W | TMA23 | YMR268W-A | Nucleolar protein implicated in ribosome biogenesis; deletion extends chronological lifespan | Core | NA | NA | NA |
| 6339-YMR270C | YMR270C | RRN9 | NA | Protein involved in promoting high level transcription of rDNA; subunit of UAF (upstream activation factor) for RNA polymerase I | Core | NA | NA | NA |
| 6340-YMR271C | YMR271C | URA10 | orotate phosphoribosyltransferase URA10 | Minor orotate phosphoribosyltransferase (OPRTase) isozyme; catalyzes the fifth enzymatic step in the de novo biosynthesis of pyrimidines, converting orotate into orotidine-5'-phosphate; URA10 has a paralog, URA5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6341-YMR272C_NumOfGenes_2 | YMR272C | SCS7 | fatty acid alpha-hydroxylase|FAH1 | Sphingolipid alpha-hydroxylase; functions in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids, has both cytochrome b5-like and hydroxylase/desaturase domains, not essential for growth | Core | NA | NA | NA |
| 6342-YMR272W-B | YMR272W-B | NA | NA | Protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to just the vacuole | Core | NA | NA | NA |
| 6343-YMR273C | YMR273C | ZDS1 | OSS1|NRC1|CKM1|CES1 | Protein with a role in regulating Swe1p-dependent polarized growth; involved in maintaining Cdc55p in the cytoplasm where it promotes mitotic entry; involved in mitotic exit through Cdc14p regulation; interacts with silencing proteins at telomeres; has a role in Bcy1p localization; implicated in mRNA nuclear export; ZDS1 has a paralog, ZDS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6344-YMR274C | YMR274C | RCE1 | CAAX prenyl protease | Type II CAAX prenyl protease; involved in the proteolysis and maturation of Ras and the a-factor mating pheromone | Core | NA | NA | NA |
| 6345-YMR275C | YMR275C | BUL1 | ubiquitin-ubiquitin ligase BUL1|SMM2|RDS1|DAG1 | Ubiquitin-binding component of the Rsp5p E3-ubiquitin ligase complex; disruption causes temperature-sensitive growth, overexpression causes missorting of amino acid permeases; BUL1 has a paralog, BUL2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6346-YMR276W | YMR276W | DSK2 | NA | Nuclear-enriched ubiquitin-like polyubiquitin-binding protein; required for spindle pole body (SPB) duplication and for transit through the G2/M phase of the cell cycle; involved in proteolysis; interacts with the proteasome; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6347-YMR277W | YMR277W | FCP1 | protein serine/threonine phosphatase | Carboxy-terminal domain (CTD) phosphatase; essential for dephosphorylation of the repeated C-terminal domain of the RNA polymerase II large subunit (Rpo21p); relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6348-YMR278W | YMR278W | PRM15 | PGM3|phosphoribomutase PRM15 | Phosphoribomutase; catalyzes interconversion of ribose-1-phosphate and ribose-5-phosphate; has some phosphoglucomutase activity but primary activity in vivo is phosphoribomutase; contributes to ribose recycling in the pentose phosphate pathway; transcription induced in response to stress; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; non-essential | Core | NA | NA | NA |
| 6349-YMR279C | YMR279C | NA | NA | Putative boron transporter involved in boron efflux and resistance; overexpression mutant but not null mutant displays boron tolerance phenotype; identified as a heat-induced gene in a high-throughout screen; YMR279C is not an essential gene; YMR279C has a paralog, ATR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6350-YMR280C | YMR280C | CAT8 | DNA-binding transcription factor CAT8|MSP8|DIL1 | Zinc cluster transcriptional activator; necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 6351-YMR281W | YMR281W | GPI12 | N-acetylglucosaminylphosphatidylinositol deacetylase | ER membrane protein involved in the second step of GPI anchor assembly; the second step is the de-N-acetylation of the N-acetylglucosaminylphosphatidylinositol intermediate; functional homolog of human PIG-Lp; GPI stands for glycosylphosphatidylinositol | Core | NA | NA | NA |
| 6352-YMR282C | YMR282C | AEP2 | ATP13 | Mitochondrial protein; likely involved in translation of the mitochondrial OLI1 mRNA; exhibits genetic interaction with the OLI1 mRNA 5'-untranslated leader | Core | NA | NA | NA |