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 |
|---|---|---|---|---|---|---|---|---|
| 3743-YGL098W | YGL098W | USE1 | SNAP receptor USE1|SLT1 | Essential SNARE protein localized to the ER; involved in retrograde traffic from the Golgi to the ER and Sey1p-independent homotypic ER fusion; required for efficient nuclear fusion during mating; forms a complex with the SNAREs Sec22p, Sec20p and Ufe1p | Core | NA | NA | NA |
| 3744-YGL099W | YGL099W | LSG1 | putative GTPase LSG1|KRE35 | Putative GTPase involved in 60S ribosomal subunit biogenesis; required for the release of Nmd3p from 60S subunits in the cytoplasm | Core | NA | NA | NA |
| 3745-YGL100W | YGL100W | SEH1 | NA | Subunit of the Nup84 nuclear pore and SEACAT subcomplexes; involved in nucleocytoplasmic transport and NPC biogenesis in the nuclear pore subcomplex; subunit of SEACAT, a subcomplex of the SEA complex that inhibits the TORC1 inhibitory role of SEACIT (Iml1p-Npr2p-Npr3p), a GAP for Gtr1p in response to amino acid limitation, thereby resulting in activation of TORC1 signaling; SEA is a coatomer-related complex that associates dynamically with the vacuole; human SEH1 homolog | Core | NA | NA | NA |
| 3746-YGL101W | YGL101W | NA | NA | Protein of unknown function; non-essential gene; interacts with the DNA helicase Hpr5p; YGL101W has a paralog, YBR242W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3747-YGL103W_NumOfGenes_2 | YGL103W | RPL28 | uL15|ribosomal 60S subunit protein L28|L15|rp44|YL24|L29|L28|CYH2 | Ribosomal 60S subunit protein L28; homologous to mammalian ribosomal protein L27A and bacterial L15; may have peptidyl transferase activity; can mutate to cycloheximide resistance | Core | NA | NA | NA |
| 3748-YGL104C | YGL104C | VPS73 | putative sugar transporter | Mitochondrial protein; mutation affects vacuolar protein sorting; putative transporter; member of the sugar porter family; VPS73 has a paralog, YBR241C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3749-YGL105W | YGL105W | ARC1 | NA | Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases; involved in tRNA delivery, stimulating catalysis, and ensuring localization; also binds quadruplex nucleic acids; protein abundance increases in response to DNA replication stress; methionyl-tRNA synthetase is Mes1p; glutamyl-tRNA synthetase is Gus1p | Core | NA | NA | NA |
| 3750-YGL106W | YGL106W | MLC1 | NA | Essential light chain for Myo1p; light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition | Core | NA | NA | NA |
| 3751-YGL107C | YGL107C | RMD9 | NA | Mitochondrial protein required for respiratory growth; mutant phenotype and genetic interactions suggest a role in delivering mt mRNAs to ribosomes; located on matrix face of the inner membrane and loosely associated with mitoribosomes; RMD9 has a paralog, YBR238C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3752-YGL108C | YGL108C | NA | NA | Protein of unknown function, predicted to be palmitoylated; SWAT-GFP, seamless-GFP and mCherry C-terminal fusion proteins localize to the cytosol, while N-terminal GFP fusion protein localizes to the cell periphery; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3753-YGL109W | YGL109W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the uncharacterized gene YGL108C | Accessory | Ancestral | NA | NA |
| 3754-YGL110C | YGL110C | CUE3 | NA | Protein of unknown function; has a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitination | Core | NA | NA | NA |
| 3755-YGL111W | YGL111W | NSA1 | ribosome biosynthesis protein NSA1 | Constituent of 66S pre-ribosomal particles; involved in 60S ribosomal subunit biogenesis | Core | NA | NA | NA |
| 3756-YGL112C | YGL112C | TAF6 | TafII60|TAF60 | Subunit (60 kDa) of TFIID and SAGA complexes; involved in transcription initiation of RNA polymerase II and in chromatin modification, similar to histone H4; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3757-YGL113W | YGL113W | SLD3 | NA | Protein involved in the initiation of DNA replication; required for proper assembly of replication proteins at the origins of replication; interacts with Cdc45p; localizes to nuclear foci that become diffuse upon DNA replication stress; homologous to the human Treslin/Ticrr protein | Core | NA | NA | NA |