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 |
|---|---|---|---|---|---|---|---|---|
| 5363-YKR071C | YKR071C | DRE2 | electron carrier DRE2 | Component of the cytosolic Fe-S protein assembly (CIA) machinery; contains an Fe-S cluster that receives electrons from NADPH via the action of Tah18p in an early step in the CIA pathway; ortholog of human Ciapin1; protein abundance increases in response to DNA replication stress; inviability of the null mutant is functionally complemented by human CIAPIN1 | Accessory | Ancestral | NA | NA |
| 5364-YKR072C | YKR072C | SIS2 | phosphopantothenoylcysteine decarboxylase complex subunit SIS2|HAL3 | Negative regulatory subunit of protein phosphatase 1 (Ppz1p); involved in coenzyme A biosynthesis; subunit of phosphopantothenoylcysteine decarboxylase (PPCDC: Cab3p, Sis2p, Vhs3p) complex and the CoA-Synthesizing Protein Complex (CoA-SPC: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p); SIS2 has a paralog, VHS3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5365-YKR073C | YKR073C | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains | Accessory | Ancestral | NA | NA |
| 5366-YKR074W | YKR074W | AIM29 | NA | Protein of unknown function; epitope-tagged protein localizes to the cytoplasm; YKR074W is not an essential gene; null mutant displays elevated frequency of mitochondrial genome loss | Accessory | Ancestral | NA | NA |
| 5367-YKR075C_NumOfGenes_2 | YKR075C | NA | NA | Protein of unknown function; similar to Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; YKR075C has a paralog, YOR062C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5368-YKR076W | YKR076W | ECM4 | S-glutathionyl-(chloro)hydroquinone reductase|GTO2 | S-glutathionyl-(chloro)hydroquinone reductase (GS-HQR); glutathione transferase involved in cell-surface biosynthesis and architecture; catalyzes glutathione (GSH)-dependent reduction of GS-trichloro-p-hydroquinone to trichloro-p-hydroquinone; expression upregulated upon exposure to genotoxic agents, such as methyl methanesulfonate, cisplatin and bleomycin; not an essential gene; similar to YGR154C; green fluorescent protein (GFP)-fusion protein localizes to cytoplasm | Accessory | Ancestral | NA | NA |
| 5369-YKR077W | YKR077W | MSA2 | NA | Putative transcriptional activator; interacts with G1-specific transcription factor MBF and G1-specific promoters; MSA2 has a paralog, MSA1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5370-YKR078W | YKR078W | NA | NA | Cytoplasmic protein of unknown function; potential Cdc28p substrate; contains a Phox homology (PX) domain and specifically binds phosphatidylinositol 3-phosphate (PtdIns-3-P); YKR078W has a paralog, VPS5, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5371-YKR079C | YKR079C | TRZ1 | tRNase Z | tRNA 3'-end processing endonuclease tRNase Z; also localized to mitochondria and interacts genetically with Rex2 exonuclease; homolog of the human candidate prostate cancer susceptibility gene ELAC2 | Core | NA | NA | NA |
| 5372-YKR080W | YKR080W | MTD1 | methylenetetrahydrofolate dehydrogenase (NAD(+)) | NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase; plays a catalytic role in oxidation of cytoplasmic one-carbon units; expression is regulated by Bas1p and Bas2p, repressed by adenine, and may be induced by inositol and choline | Core | NA | NA | NA |
| 5373-YKR081C | YKR081C | RPF2 | rRNA-binding ribosome biosynthesis protein RPF2 | Essential protein involved in rRNA maturation and ribosomal assembly; involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles | Core | NA | NA | NA |
| 5374-YKR082W | YKR082W | NUP133 | RAT3 | Subunit of Nup84p subcomplex of nuclear pore complex (NPC); contributes to nucleocytoplasmic transport, NPC biogenesis; is involved in establishment of a normal nucleocytoplasmic concentration gradient of GTPase Gsp1p; also plays roles in several processes that may require localization of genes or chromosomes at nuclear periphery, including double-strand break repair, transcription and chromatin silencing; relocalizes to cytosol in response to hypoxia; homolog of human NUP133 | Core | NA | NA | NA |
| 5375-YKR083C | YKR083C | DAD2 | HSK1 | Essential subunit of the Dam1 complex (aka DASH complex); complex couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; is transferred to the kinetochore prior to mitosis | Core | NA | NA | NA |
| 5376-YKR084C | YKR084C | HBS1 | ribosome dissociation factor GTPase HBS1 | GTPase with similarity to translation release factors; together with binding partner Dom34p, facilitates ribosomal subunit dissociation and peptidyl-tRNA release when translation is stalled, particularly in 3' UTRs; genetically implicated in mRNA no-go decay; HBS1 has a paralog, SKI7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5377-YKR085C | YKR085C | MRPL20 | mitochondrial 54S ribosomal protein YmL20|YmL20 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |