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 |
|---|---|---|---|---|---|---|---|---|
| 7703-YPR080W_NumOfGenes_2 | YPR080W | TEF1 | translation elongation factor EF-1 alpha|eEF1A|EF-1 alpha | Translational elongation factor EF-1 alpha; in the GTP-bound active form, binds to and delivers aminoacylated tRNA to the A-site of ribosomes for elongation of nascent polypeptides; associates with vacuolar Rho1p GTPase; may also have a role in tRNA re-export from the nucleus; TEF1 has a paralog, TEF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7704-YPR081C | YPR081C | GRS2 | putative glycine--tRNA ligase | Glycine-tRNA synthetase, not expressed under normal growth conditions; expression is induced under heat, oxidative, pH, or ethanol stress conditions; more stable than the major glycine-tRNA synthetase Grs1p at 37 deg C; GRS2 has a paralog, GRS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7705-YPR082C | YPR082C | DIB1 | U4/U6-U5 snRNP complex subunit DIB1|SNU16 | 17-kDa component of the U4/U6aU5 tri-snRNP; plays an essential role in pre-mRNA splicing; human ortholog TXNL4A (the human U5-specific 15-kDa protein) complements yeast dib1 null mutant | Core | NA | NA | NA |
| 7706-YPR083W | YPR083W | MDM36 | NA | Mitochondrial protein; required for normal mitochondrial morphology and inheritance; component of the mitochondria-ER-cortex-ancor (MECA); interacts with Num1p to link the ER and mitochondria at the cell cortex; proposed involvement in the formation of Dnm1p and Num1p-containing cortical anchor complexes that promote mitochondrial fission | Core | NA | NA | NA |
| 7707-YPR084W | YPR084W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 7708-YPR085C | YPR085C | ASA1 | NA | Subunit of the ASTRA complex, involved in chromatin remodeling; telomere length regulator involved in the stability or biogenesis of PIKKs such as TORC1 | Core | NA | NA | NA |
| 7709-YPR086W | YPR086W | SUA7 | transcription factor TFIIB|TFIIB|SOH4 | Transcription factor TFIIB; a general transcription factor required for transcription initiation and start site selection by RNA polymerase II | Core | NA | NA | NA |
| 7710-YPR088C_NumOfGenes_2 | YPR088C | SRP54 | RNA-binding signal recognition particle subunit SRP54|SRH1 | Signal recognition particle (SRP) subunit (homolog of mammalian SRP54); contains the signal sequence-binding activity of SRP, interacts with the SRP RNA, and mediates binding of SRP to signal receptor; contains GTPase domain | Core | NA | NA | NA |
| 7711-YPR089W | YPR089W | NA | YPR090W | Protein of unknown function; exhibits genetic interaction with ERG11 and protein-protein interaction with Hsp82p | Core | NA | NA | NA |
| 7712-YPR091C | YPR091C | NVJ2 | NA | Lipid-binding ER protein, enriched at nucleus-vacuolar junctions (NVJ); may be involved in sterol metabolism or signaling at the NVJ; contains a synaptotagmin-like-mitochondrial-lipid binding protein (SMP) domain; binds phosphatidylinositols and other lipids in a large-scale study; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |
| 7713-YPR092W | YPR092W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 7714-YPR093C | YPR093C | ASR1 | ubiquitin-protein ligase ASR1 | Ubiquitin ligase that modifies and regulates RNA Pol II; involved in a putative alcohol-responsive signaling pathway; accumulates in the nucleus under alcohol stress; has a role in organization of septins and the actin cytoskeleton; contains a Ring/PHD finger domain similar to the mammalian rA9 protein | Core | NA | NA | NA |
| 7715-YPR094W | YPR094W | RDS3 | U2 snRNP complex subunit RDS3 | Component of the SF3b subcomplex of the U2 snRNP; zinc cluster protein involved in pre-mRNA splicing and cycloheximide resistance | Core | NA | NA | NA |
| 7716-YPR095C | YPR095C | SYT1 | Arf family guanine nucleotide exchange factor SYT1 | Guanine nucleotide exchange factor (GEF) for Arf proteins; promotes activation of Arl1p, which recruits Imh1p to the Golgi; involved in vesicular transport; member of the Sec7-domain family; contains a PH domain | Core | NA | NA | NA |
| 7717-YPR096C | YPR096C | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |