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 |
|---|---|---|---|---|---|---|---|---|
| 1943-YBL071C-B | YBL071C-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 |
| 1944-YBL071W-A | YBL071W-A | KTI11 | DPH3 | Zn-ribbon protein that co-purifies with Dph1 and Dph2; in a complex required for synthesis of diphthamide on translation factor eEF2 and with Elongator subunits Iki3p, Elp2p, and Elp3p; involved in modification of wobble nucleosides in tRNAs; forms a stable heterodimer with Ats1p | Core | NA | NA | NA |
| 1945-YBL073W | YBL073W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the essential gene AAR2/YBL074C | Core | NA | NA | NA |
| 1946-YBL074C | YBL074C | AAR2 | U5 snRNP complex subunit AAR2 | Component of the U5 snRNP complex; required for splicing of U3 precursors; originally described as a splicing factor specifically required for splicing pre-mRNA of the MATa1 cistron | Core | NA | NA | NA |
| 1947-YBL075C | YBL075C | SSA3 | Hsp70 family ATPase SSA3|YG106 | ATPase involved in protein folding and the response to stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm; SSA3 has a paralog, SSA4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1948-YBL076C | YBL076C | ILS1 | isoleucine--tRNA ligase ILS1 | Cytoplasmic isoleucine-tRNA synthetase; target of the G1-specific inhibitor reveromycin A | Core | NA | NA | NA |
| 1949-YBL077W | YBL077W | 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 ILS1/YBL076C | Accessory | Ancestral | NA | NA |
| 1950-YBL078C | YBL078C | ATG8 | ubiquitin-like protein ATG8|AUT7|CVT5|APG8 | Component of autophagosomes and Cvt vesicles; regulator of Atg1p, targets it to autophagosomes; binds the Atg1p-Atg13p complex, triggering its vacuolar degradation; unique ubiquitin-like protein whose conjugation target is lipid phosphatidylethanolamine (PE); Atg8p-PE is anchored to membranes, is involved in phagophore expansion, and may mediate membrane fusion during autophagosome formation; deconjugation of Atg8p-PE is required for efficient autophagosome biogenesis | Core | NA | NA | NA |
| 1951-YBL079W | YBL079W | NUP170 | NLE3 | Subunit of inner ring of nuclear pore complex (NPC); contributes to NPC assembly and nucleocytoplasmic transport; interacts with genomic regions that contain ribosomal protein and subtelomeric genes, where it functions in nucleosome positioning and as a repressor of transcription; both Nup170p and NUP157p are similar to human Nup155p; NUP170 has a paralog, NUP157, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1952-YBL080C | YBL080C | PET112 | glutamyl-tRNA(Gln) amidotransferase subunit PET112 | Subunit of the trimeric GatFAB AmidoTransferase(AdT) complex; involved in the formation of Q-tRNAQ; mutation is functionally complemented by the bacterial GatB ortholog | Core | NA | NA | NA |
| 1953-YBL081W | YBL081W | NA | NA | Non-essential protein of unknown function; null mutation results in a decrease in plasma membrane electron transport | Core | NA | NA | NA |
| 1954-YBL082C_NumOfGenes_2 | YBL082C | ALG3 | dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase|RHK1 | Dolichol-P-Man dependent alpha(1-3) mannosyltransferase; involved in synthesis of dolichol-linked oligosaccharide donor for N-linked glycosylation of proteins; G353A missense mutation in human ortholog ALG3 implicated in carbohydrate deficient glycoprotein syndrome type IV, which is characterized by microcephaly, severe epilepsy, minimal psychomotor development, partial deficiency of sialic acids in serum glycoproteins; wild-type human ALG3 can complement yeast alg3 mutant | Core | NA | NA | NA |
| 1955-YBL084C | YBL084C | CDC27 | anaphase promoting complex subunit CDC27|SNB1|APC3 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition | Core | NA | NA | NA |
| 1956-YBL085W | YBL085W | BOI1 | BOB1|GIN7 | Protein implicated in polar growth; functionally redundant with Boi2p; interacts with bud-emergence protein Bem1p; contains an SH3 (src homology 3) domain and a PH (pleckstrin homology) domain; relocalizes from bud neck to cytoplasm upon DNA replication stress; BOI1 has a paralog, BOI2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1957-YBL086C | YBL086C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery | Core | NA | NA | NA |