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 |
|---|---|---|---|---|---|---|---|---|
| 3023-YDR330W | YDR330W | UBX5 | NA | UBX domain-containing protein that interacts with Cdc48p; ubiquitin regulatory X is also known as UBX | Core | NA | NA | NA |
| 3024-YDR331W | YDR331W | GPI8 | GPI-anchor transamidase | ER membrane glycoprotein subunit of the GPI transamidase complex; adds glycosylphosphatidylinositol (GPI) anchors to newly synthesized proteins; human PIG-K protein is a functional homolog | Core | NA | NA | NA |
| 3025-YDR332W | YDR332W | IRC3 | double-stranded DNA-dependent ATPase | Double-stranded DNA-dependent helicase of the DExH/D-box family; required for maintenance of the mitochondrial (mt) genome; null mutant accumulates double-stranded breaks in mt DNA; localizes to the mt matrix | Core | NA | NA | NA |
| 3026-YDR333C | YDR333C | RQC1 | NA | Component of the ribosome quality control complex (RQC); RQC (Rqc1p-Rkr1p-Tae2p-Cdc48p-Npl4p-Ufd1p) is a ribosome-bound complex required for the degradation of polypeptides arising from stalled translation; required along with Rkr1p for recruitment of the Cdc48p-Npl4p-Ufd1p AAA ATPase complex to the RQC | Core | NA | NA | NA |
| 3027-YDR334W | YDR334W | SWR1 | chromatin-remodeling protein SWR1 | Swi2/Snf2-related ATPase; structural component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; relocalizes to the cytosol in response to hypoxia; chronological aging factor that mediates lifespan extension by dietary restriction | Accessory | Ancestral | NA | NA |
| 3028-YDR335W | YDR335W | MSN5 | karyopherin MSN5|STE21|KAP142 | Karyopherin; involved in nuclear import and export of proteins, including import of replication protein A and export of Far1p and transcription factors Swi5p, Swi6p, Msn2p, and Pho4p; required for re-export of mature tRNAs after their retrograde import from the cytoplasm; exportin-5 homolog | Accessory | Ancestral | NA | NA |
| 3029-YDR336W | YDR336W | MRX8 | NA | Protein that associates with mitochondrial ribosome; sumoylated under stress conditions in a genome wide study; YDR336W is not an essential gene | Accessory | Ancestral | NA | NA |
| 3030-YDR337W | YDR337W | MRPS28 | mitochondrial 37S ribosomal protein MRPS28 | Mitochondrial ribosomal protein of the small subunit | Accessory | Ancestral | NA | NA |
| 3031-YDR338C | YDR338C | NA | NA | Putative protein of unknown function; member of the multi-drug and toxin extrusion (MATE) family of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily | Accessory | Ancestral | NA | NA |
| 3032-YDR339C | YDR339C | FCF1 | rRNA-processing protein FCF1|UTP24 | Putative PINc domain nuclease; required for early cleavages of 35S pre-rRNA and maturation of 18S rRNA; component of the SSU (small subunit) processome involved in 40S ribosomal subunit biogenesis; copurifies with Faf1p | Accessory | Ancestral | NA | NA |
| 3033-YDR340W | YDR340W | NA | NA | Putative protein of unknown function | Accessory | Unknown | S. paradoxus | NA |
| 3034-YDR341C | YDR341C | NA | arginine--tRNA ligase|ArgRS|RRS1 | Arginyl-tRNA synthetase; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDR341C has a paralog, MSR1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3035-YDR342C_NumOfGenes_2 | YDR342C | HXT7 | hexose transporter HXT7 | High-affinity glucose transporter; member of the major facilitator superfamily, nearly identical to Hxt6p, expressed at high basal levels relative to other HXTs, expression repressed by high glucose levels; HXT7 has a paralog, HXT4, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3036-YDR344C | YDR344C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains | Accessory | Unknown | NA | NA |
| 3037-YDR345C_NumOfGenes_2 | YDR345C | HXT3 | hexose transporter HXT3 | Low affinity glucose transporter of the major facilitator superfamily; expression is induced in low or high glucose conditions; HXT3 has a paralog, HXT5, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |