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 |
|---|---|---|---|---|---|---|---|---|
| 2858-YDR168W | YDR168W | CDC37 | SMO1 | Essential Hsp90p co-chaperone; necessary for passage through the START phase of the cell cycle; stabilizes protein kinase nascent chains and participates along with Hsp90p in their folding | Core | NA | NA | NA |
| 2859-YDR169C | YDR169C | STB3 | NA | Ribosomal RNA processing element (RRPE)-binding protein; involved in the glucose-induced transition from quiescence to growth; restricted to nucleus in quiescent cells, released into cytoplasm after glucose repletion; binds Sin3p; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2860-YDR169C-A | YDR169C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 2861-YDR170C | YDR170C | SEC7 | Arf family guanine nucleotide exchange factor SEC7 | Guanine nucleotide exchange factor (GEF) for ADP ribosylation factors; involved in proliferation of the Golgi, intra-Golgi transport and ER-to-Golgi transport; found in the cytoplasm and on Golgi-associated coated vesicles | Core | NA | NA | NA |
| 2862-YDR171W | YDR171W | HSP42 | heat shock protein HSP42 | Small heat shock protein (sHSP) with chaperone activity; forms barrel-shaped oligomers that suppress unfolded protein aggregation; involved in cytoskeleton reorganization after heat shock; protein abundance increases and forms cytoplasmic foci in response to DNA replication stress | Core | NA | NA | NA |
| 2863-YDR172W | YDR172W | SUP35 | translation termination factor GTPase eRF3|eRF3|[PSI(+)]|[PSI]|SUP36|SUP2|SUF12|SAL3|PNM2|GST1 | Translation termination factor eRF3; has a role in mRNA deadenylation and decay; altered protein conformation creates the [PSI(+)] prion that modifies cellular fitness, alters translational fidelity by affecting reading frame selection, and results in a nonsense suppressor phenotype; many stress-response genes are repressed in the presence of [PSI(+)] | Core | NA | NA | NA |
| 2864-YDR173C | YDR173C | ARG82 | inositol polyphosphate multikinase|ARGRIII|IPK2|ARGR3 | Inositol polyphosphate multikinase (IPMK); sequentially phosphorylates Ins(1,4,5)P3 to form Ins(1,3,4,5,6)P5; also has diphosphoinositol polyphosphate synthase activity; regulates arginine-, phosphate-, and nitrogen-responsive genes | Core | NA | NA | NA |
| 2865-YDR174W | YDR174W | HMO1 | HSM2 | Chromatin associated high mobility group (HMG) family member; involved in compacting, bending, bridging and looping DNA; rDNA-binding component that regulates transcription from RNA polymerase I promoters; regulates start site selection of ribosomal protein genes via RNA polymerase II promoters; role in genome maintenance; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2866-YDR175C | YDR175C | RSM24 | mitochondrial 37S ribosomal protein RSM24 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 2867-YDR176W | YDR176W | NGG1 | histone acetyltransferase NGG1|SWI7|ADA3 | Subunit of chromatin modifying histone acetyltransferase complexes; member of the ADA complex, the SAGA complex, and the SLIK complex; transcriptional regulator involved in glucose repression of Gal4p-regulated genes | Core | NA | NA | NA |
| 2868-YDR177W | YDR177W | UBC1 | E2 ubiquitin-conjugating protein UBC1 | Ubiquitin-conjugating enzyme; key E2 partner with Ubc4p for the anaphase-promoting complex (APC); mediates selective degradation of short-lived and abnormal proteins; plays a role in vesicle biogenesis and ER-associated protein degradation (ERAD); component of the cellular stress response; protein abundance increases in response to DNA replication stress key E2 partner with Ubc4p for the anaphase-promoting complex (APC) | Core | NA | NA | NA |
| 2869-YDR178W | YDR178W | SDH4 | succinate dehydrogenase membrane anchor subunit SDH4|ACN18 | Membrane anchor subunit of succinate dehydrogenase (SDH); involved in coupling the oxidation of succinate to the transfer of electrons to ubiquinone as part of the TCA cycle and the mitochondrial respiratory chain; has similarity to human SDH subunit D (SDHD), which is implicated in paraganglioma | Core | NA | NA | NA |
| 2870-YDR179C | YDR179C | CSN9 | NA | Subunit of the Cop9 signalosome; Cop9 signalosome is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone signaling | Core | NA | NA | NA |
| 2871-YDR179W-A | YDR179W-A | NVJ3 | NA | Protein with a potential role in tethering ER and vacuoles; localizes to nucleus-vacuole junctions in an Mdm1p-dependent manner; contains a lipid-binding PXA domain | Core | NA | NA | NA |
| 2872-YDR180W | YDR180W | SCC2 | cohesin-loading factor complex subunit SCC2 | Subunit of cohesin loading factor (Scc2p-Scc4p); a complex required for loading of cohesin complexes onto chromosomes; involved in establishing sister chromatid cohesion during DSB repair via histone H2AX; promotes gene expression program that supports translational fidelity; evolutionarily-conserved adherin; relocalizes to cytosol in response to hypoxia; human disorder Cornelia de Lange syndrome is caused by mutations in NIPBL, the human ortholog of SCC2 | Core | NA | NA | NA |