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 |
|---|---|---|---|---|---|---|---|---|
| 2498-YDL049C | YDL049C | KNH1 | NA | Protein with similarity to Kre9p; Kre9p is involved in cell wall beta 1,6-glucan synthesis; overproduction suppresses growth defects of a kre9 null mutant; required for propionic acid resistance | Accessory | Ancestral | NA | NA |
| 2499-YDL051W_NumOfGenes_2 | YDL051W | LHP1 | YLA1|LAH1 | RNA binding protein required for maturation of tRNA and U6 snRNA; acts as a molecular chaperone for RNAs transcribed by polymerase III; homologous to human La (SS-B) autoantigen | Accessory | Ancestral | NA | NA |
| 2500-YDL052C | YDL052C | SLC1 | 1-acylglycerol-3-phosphate O-acyltransferase SLC1 | 1-acyl-sn-glycerol-3-phosphate acyltransferase; catalyzes the acylation of lysophosphatidic acid to form phosphatidic acid, a key intermediate in lipid metabolism; enzymatic activity detected in lipid particles and microsomes | Core | NA | NA | NA |
| 2501-YDL053C | YDL053C | PBP4 | NA | Pbp1p binding protein; interacts strongly with Pab1p-binding protein 1 (Pbp1p) in the yeast two-hybrid system; also interacts with Lsm12p in a copurification assay; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2502-YDL054C | YDL054C | MCH1 | NA | Protein with similarity to mammalian monocarboxylate permeases; monocarboxylate permeases are involved in transport of monocarboxylic acids across the plasma membrane but mutant is not deficient in monocarboxylate transport | Core | NA | NA | NA |
| 2503-YDL055C | YDL055C | PSA1 | mannose-1-phosphate guanylyltransferase|SRB1|VIG9|MPG1 | GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase); synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure | Core | NA | NA | NA |
| 2504-YDL056W | YDL056W | MBP1 | transcription factor MBP1 | Transcription factor; involved in regulation of cell cycle progression from G1 to S phase, forms a complex with Swi6p that binds to MluI cell cycle box regulatory element in promoters of DNA synthesis genes | Core | NA | NA | NA |
| 2505-YDL057W | YDL057W | NA | NA | Putative protein of unknown function; YDL057W is not an essential gene | Core | NA | NA | NA |
| 2506-YDL058W | YDL058W | USO1 | INT1 | Essential protein involved in vesicle-mediated ER to Golgi transport; binds membranes and functions during vesicle docking to the Golgi; required for assembly of the ER-to-Golgi SNARE complex | Core | NA | NA | NA |
| 2507-YDL059C | YDL059C | RAD59 | NA | Protein involved DNA double-strand break repair; repairs breaks in DNA during vegetative growth via recombination and single-strand annealing; anneals complementary single-stranded DNA; forms nuclear foci upon DNA replication stress; required for loading of Rad52p to DSBs; regulates replication fork progression in DNA ligase I-deficient cells; paralog of Rad52p | Core | NA | NA | NA |
| 2508-YDL060W | YDL060W | TSR1 | NA | Protein required for processing of 20S pre-rRNA in the cytoplasm; associates with pre-40S ribosomal particles; inhibits the premature association of 60S subunits with assembling 40S subunits in the cytoplasm; similar to Bms1p; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2509-YDL061C | YDL061C | RPS29B | uS14|ribosomal 40S subunit protein S29B|S14|YS29|S36B|S29B|YS29B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S29 and bacterial S14; RPS29B has a paralog, RPS29A, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2510-YDL062W | YDL062W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized ORF YDL063C; YDL062W is not essential | Accessory | Ancestral | NA | NA |
| 2511-YDL063C | YDL063C | SYO1 | NA | Transport adaptor or symportin; facilitates synchronized nuclear coimport of the two 5S-rRNA binding proteins Rpl5p and Rpl11p; binds to nascent Rpl5p during translation; required for biogenesis of the large ribosomal subunit; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus | Core | NA | NA | NA |
| 2512-YDL064W | YDL064W | UBC9 | E2 SUMO-conjugating protein UBC9 | SUMO-conjugating enzyme involved in the Smt3p conjugation pathway; nuclear protein required for S- and M-phase cyclin degradation and mitotic control; involved in proteolysis mediated by the anaphase-promoting complex cyclosome (APCC) | Core | NA | NA | NA |