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 |
|---|---|---|---|---|---|---|---|---|
| 4763-YJL068C | YJL068C | NA | S-formylglutathione hydrolase|SFGH | Esterase that can function as an S-formylglutathione hydrolase; non-essential intracellular esterase; may be involved in the detoxification of formaldehyde, which can be metabolized to S-formylglutathione; similar to human esterase D | Core | NA | NA | NA |
| 4764-YJL069C | YJL069C | UTP18 | NA | Small-subunit processome protein involved in pre-18S rRNA maturation; part of a subunit of the 90S preribosomal particle capable of interacting directly with the 5' ETS of the 35S pre-rRNA; contains WD40 repeats | Core | NA | NA | NA |
| 4765-YJL070C | YJL070C | NA | metallo-dependent hydrolase superfamily protein | Putative metallo-dependent hydrolase superfamily protein; similar to AMP deaminases but lacks key catalytic residues and does not rescue purine nucleotide metabolic defect of quadruple aah1 ade8 amd1 his1 mutant; may regulate purine nucleotide homeostasis as overexpression in an AMD1 strain grown in adenine results in greatly reduced GDP and GTP intracellular levels; not an essential gene; YJL070C has a paralog, YBR284W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4766-YJL071W | YJL071W | ARG2 | acetyl-CoA:L-glutamate N-acetyltransferase|HRB574 | Acetylglutamate synthase (glutamate N-acetyltransferase); mitochondrial enzyme that catalyzes the first step in the biosynthesis of the arginine precursor ornithine; forms a complex with Arg5,6p | Core | NA | NA | NA |
| 4767-YJL072C | YJL072C | PSF2 | DNA replication protein PSF2|CDC102 | Subunit of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p); complex is localized to DNA replication origins and implicated in assembly of the DNA replication machinery | Core | NA | NA | NA |
| 4768-YJL073W | YJL073W | JEM1 | KAR8 | DnaJ-like chaperone required for nuclear membrane fusion during mating; localizes to the ER membrane; exhibits genetic interactions with KAR2 | Core | NA | NA | NA |
| 4769-YJL074C | YJL074C | SMC3 | cohesin subunit SMC3 | Subunit of the multiprotein cohesin complex; required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member | Core | NA | NA | NA |
| 4770-YJL076W_NumOfGenes_2 | YJL076W | NET1 | SRM8|CFI1|ESC5 | Core subunit of the RENT complex; involved in nucleolar silencing and telophase exit; stimulates transcription by RNA polymerase I and regulates nucleolar structure; NET1 has a paralog, TOF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4771-YJL077W-A_NumOfGenes_2 | YJL077W-A | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data; completely overlaps the verified gene YJL077C/ICS3 | Core | NA | NA | NA |
| 4772-YJL077W-B | YJL077W-B | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Core | NA | NA | NA |
| 4773-YJL078C | YJL078C | PRY3 | NA | Cell wall-associated protein involved in export of acetylated sterols; member of the CAP protein superfamily (cysteine-rich secretory proteins (CRISP), antigen 5, and pathogenesis related 1 proteins); role in mating efficiency; expression of full-length transcript is daughter cell-specific; in response to alpha factor, a short transcript starting at +452 is expressed and the long form is repressed by Ste12p | Core | NA | NA | NA |
| 4774-YJL079C | YJL079C | PRY1 | sterol-binding protein | Sterol binding protein involved in the export of acetylated sterols; secreted glycoprotein and member of the CAP protein superfamily (cysteine-rich secretory proteins (CRISP), antigen 5, and pathogenesis related 1 proteins); sterol export function is redundant with that of PRY2; may be involved in detoxification of hydrophobic compounds; PRY1 has a paralog, PRY2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4775-YJL080C | YJL080C | SCP160 | NA | Essential RNA-binding G protein effector of mating response pathway; ligand-activated RNA-binding protein that delivers RNAs involved in polarization and perpetualizing mating signal to shmoo tip during pheromone signaling; Scp160p-mediated RNA trafficking essential for chemotropism and successful mating; mainly associated with nuclear envelope and ER, interacts in mRNA-dependent manner with translating ribosomes via multiple KH domains, similar to vertebrate vigilins | Core | NA | NA | NA |
| 4776-YJL081C | YJL081C | ARP4 | ACT3 | Nuclear actin-related protein involved in chromatin remodeling; component of chromatin-remodeling enzyme complexes | Core | NA | NA | NA |
| 4777-YJL082W | YJL082W | IML2 | NA | Protein required for clearance of inclusion bodies; localizes to the inclusion bodies formed under protein misfolding stress; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; protein abundance increases in response to DNA replication stress; IML2 has a paralog, YKR018C, that arose from the whole genome duplication | Core | NA | NA | NA |