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 |
|---|---|---|---|---|---|---|---|---|
| 4658-YIR004W | YIR004W | DJP1 | PAS22|ICS1 | Cytosolic J-domain-containing protein; required for peroxisomal protein import and involved in peroxisome assembly; facilitates import of Mim1p and Mim2p into the mitochondrial outer membrane; homologous to E. coli DnaJ | Core | NA | NA | NA |
| 4659-YIR005W | YIR005W | IST3 | U2 snRNP complex subunit IST3|SNU17 | Component of the U2 snRNP; required for the first catalytic step of splicing and for spliceosomal assembly; interacts with Rds3p and is required for Mer1p-activated splicing; diploid mutants have a specific defect in MATa1 pre-mRNA splicing which leads to haploid gene expression in diploids | Core | NA | NA | NA |
| 4660-YIR006C | YIR006C | PAN1 | DIM2|MIP3|MDP3 | Part of actin cytoskeleton-regulatory complex Pan1p-Sla1p-End3p; associates with actin patches on cell cortex; promotes protein-protein interactions essential for endocytosis; binds to and activates Arp2/3 complex in vitro; phosphorylation of Thr-1225 is regulated by MAPK Hog1p in response to osmotic stress; previously thought to be a subunit of poly(A) ribonuclease | Core | NA | NA | NA |
| 4661-YIR007W | YIR007W | EGH1 | hydrolase | Steryl-beta-glucosidase with broad specificity for aglycones; has a role in ergosteryl-beta-glucoside catabolism; required for normal vacuolar morphology; has similarity to the C. neoformans ergosteryl-beta-glucosidase EGCrP2; localizes to the cytosol | Core | NA | NA | NA |
| 4662-YIR008C | YIR008C | PRI1 | DNA primase subunit PRI1 | Subunit of DNA primase; DNA primase is required for DNA synthesis and double-strand break repair | Core | NA | NA | NA |
| 4663-YIR009W | YIR009W | MSL1 | U2 snRNP complex subunit MSL1|YIB9|YIB9w | U2B component of U2 snRNP; involved in splicing, binds the U2 snRNA stem-loop IV in vitro but requires association of Lea1p for in vivo binding; does not contain the conserved C-terminal RNA binding domain found in other family members | Core | NA | NA | NA |
| 4664-YIR010W | YIR010W | DSN1 | MIND complex subunit DSN1 | Essential component of the MIND kinetochore complex; joins kinetochore subunits contacting DNA to those contacting microtubules; Dsn1p phosphorylation promotes interaction between outer and inner kinetochore proteins; kinetochore receptor for monopolin, via interaction with subunit Csm1p; essential for meiotic but not mitotic chromosome segregation; MIND complex consists of Mtw1p, Nnf1p, Nsl1p and Dsn1p; modified by sumoylation; phosphorylated by monopolin subunit Hrr25p | Core | NA | NA | NA |
| 4665-YIR011C | YIR011C | STS1 | SSM5|DBF8 | Protein required for localizing proteasomes to the nucleus; involved in cotranslational protein degradation; mediates interaction between nuclear import factor Srp1p and the proteasome; Sts1p and Srp1p couple proteasomes to nascent polypeptides emerging from the ribosome for cotranslational degradation; involved in ubiquitin-mediated protein degradation | Accessory | Ancestral | NA | NA |
| 4666-YIR012W | YIR012W | SQT1 | NA | Specific chaperone for ribosomal protein Rpl10p; binds nascent Rpl10p during translation; contains multiple WD repeats; interacts with Qsr1p in a two-hybrid assay; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 4667-YIR013C | YIR013C | GAT4 | NA | Protein containing GATA family zinc finger motifs; involved in spore wall assembly; sequence similarity to GAT3, and the double mutant gat3 gat4 exhibits reduced dityrosine fluorescence relative to the single mutants | Accessory | Ancestral | NA | NA |
| 4668-YIR014W | YIR014W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR014W is a non-essential gene | Accessory | Ancestral | NA | NA |
| 4669-YIR015W | YIR015W | RPR2 | ribonuclease P protein subunit RPR2 | Subunit of nuclear RNase P; nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; not shared between RNase MRP and RNase P, in contrast to all other RNase P protein subunits; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 4670-YIR016W | YIR016W | NA | NA | Putative protein of unknown function; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; overexpression causes a cell cycle delay or arrest; non-essential gene; YIR016W has a paralog, YOL036W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4671-YIR017C_NumOfGenes_2 | YIR017C | MET28 | NA | bZIP transcriptional activator in the Cbf1p-Met4p-Met28p complex; participates in the regulation of sulfur metabolism | Accessory | Ancestral | NA | NA |
| 4672-YIR018C-A | YIR018C-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Accessory | Unknown | NA | NA |