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 |
|---|---|---|---|---|---|---|---|---|
| 5273-YKL204W | YKL204W | EAP1 | NA | eIF4E-associated protein, competes with eIF4G for binding to eIF4E; accelerates mRNA degradation by promoting decapping, facilitated by interaction with eIF4E; essential for Puf5p mediated repression; associates with Puf5p and Dhh1p; inhibits cap-dependent translation; functions independently of eIF4E to maintain genetic stability; plays a role in cell growth, implicated in the TOR signaling cascade | Core | NA | NA | NA |
| 5274-YKL205W | YKL205W | LOS1 | Ran GTPase-binding protein LOS1 | Nuclear pore protein; involved in nuclear export of pre-tRNA and in re-export of mature tRNAs after their retrograde import from the cytoplasm; deletion mutation extends replicative lifespan, as does exclusion of Los1p from the nucleus in response to caloric restriction | Core | NA | NA | NA |
| 5275-YKL206C | YKL206C | ADD66 | POC2|PBA2 | Protein involved in 20S proteasome assembly; forms a heterodimer with Pba1p that binds to proteasome precursors; interaction with Pba1p-Add66p may affect function of the mature proteasome and its role in maintaining respiratory metabolism; similar to human PAC2 constituent of the PAC1-PAC2 complex involved in proteasome assembly | Core | NA | NA | NA |
| 5276-YKL207W | YKL207W | EMC3 | AIM27|LRC3 | Member of conserved ER transmembrane complex; required for efficient folding of proteins in the ER; required for respiratory growth; null mutant displays induction of the unfolded protein response; homologous to worm Y62E10A.10/EMC-3, fly CG6750, human TMEM111 | Core | NA | NA | NA |
| 5277-YKL208W | YKL208W | CBT1 | SOC1 | Protein involved in 5' RNA end processing; substrates include mitochondrial COB, 15S_rRNA, and RPM1 transcripts; may also have a role in 3' end processing of the COB pre-mRNA; displays genetic interaction with cell cycle-regulated kinase Dbf2p | Core | NA | NA | NA |
| 5278-YKL209C | YKL209C | STE6 | ATP-binding cassette a-factor transporter STE6 | Plasma membrane ATP-binding cassette (ABC) transporter; required for the export of a-factor, catalyzes ATP hydrolysis coupled to a-factor transport; contains 12 transmembrane domains and two ATP binding domains; expressed only in MATa cells; human homolog ABCB1 mediates multidrug resistance in many chemotherapy-resistant tumors by effluxing toxic compounds from the cell | Core | NA | NA | NA |
| 5279-YKL210W | YKL210W | UBA1 | E1 ubiquitin-activating protein UBA1 | Ubiquitin activating enzyme (E1); involved in ubiquitin-mediated protein degradation and essential for viability; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5280-YKL211C | YKL211C | TRP3 | bifunctional anthranilate synthase/indole-3-glycerol-phosphate synthase | Indole-3-glycerol-phosphate synthase; forms bifunctional hetero-oligomeric anthranilate synthase:indole-3-glycerol phosphate synthase enzyme complex with Trp2p | Core | NA | NA | NA |
| 5281-YKL212W | YKL212W | SAC1 | phosphatidylinositol-3-phosphatase SAC1|RSD1 | Phosphatidylinositol phosphate (PtdInsP) phosphatase; involved in hydrolysis of PtdIns[4]P in the early and medial Golgi; regulated by interaction with Vps74p; ER localized transmembrane protein which cycles through the Golgi; involved in protein trafficking and processing, secretion, and cell wall maintenance; regulates sphingolipid biosynthesis through the modulation of PtdIns(4)P metabolism | Core | NA | NA | NA |
| 5282-YKL213C | YKL213C | DOA1 | ZZZ4|UFD3 | WD repeat protein required for ubiquitin-mediated protein degradation; ubiquitin binding cofactor that complexes with Cdc48p; required for ribophagy; controls cellular ubiquitin concentration; promotes efficient NHEJ in postdiauxic/stationary phase; facilitates N-terminus-dependent proteolysis of centromeric histone H3 (Cse4p) for faithful chromosome segregation; protein increases in abundance and relocalizes from nucleus to nuclear periphery upon DNA replication stress | Core | NA | NA | NA |
| 5283-YKL214C | YKL214C | YRA2 | NA | Member of the REF (RNA and export factor binding proteins) family; when overexpressed, can substitute for the function of Yra1p in export of poly(A)+ mRNA from the nucleus | Core | NA | NA | NA |
| 5284-YKL215C | YKL215C | OXP1 | 5-oxoprolinase | 5-oxoprolinase; enzyme is ATP-dependent and functions as a dimer; similar to mouse Oplah gene; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5285-YKL216W | YKL216W | URA1 | dihydroorotate dehydrogenase | Dihydroorotate dehydrogenase; catalyzes the fourth enzymatic step in the de novo biosynthesis of pyrimidines, converting dihydroorotic acid into orotic acid | Core | NA | NA | NA |
| 5286-YKL217W | YKL217W | JEN1 | NA | Monocarboxylate/proton symporter of the plasma membrane; transport activity is dependent on the pH gradient across the membrane; mediates high-affinity uptake of carbon sources lactate, pyuvate, and acetate, and also of the micronutrient selenite, whose structure mimics that of monocarboxylates; expression and localization are tightly regulated, with transcription repression, mRNA degradation, and protein endocytosis and degradation all occurring in the presence of glucose | Core | NA | NA | NA |
| 5287-YKL218C | YKL218C | SRY1 | threo-3-hydroxy-L-aspartate ammonia-lyase SRY1 | 3-hydroxyaspartate dehydratase; deaminates L-threo-3-hydroxyaspartate to form oxaloacetate and ammonia; required in the presence of hydroxyaspartate; highly similar to mouse serine racemase (Srr) but has no serine racemase activity | Core | NA | NA | NA |