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 |
|---|---|---|---|---|---|---|---|---|
| 2798-YDR109C | YDR109C | NA | putative phosphotransferase | Putative kinase | Core | NA | NA | NA |
| 2799-YDR110W | YDR110W | FOB1 | replication fork barrier binding protein FOB1|HRM1 | Nucleolar protein that binds the rDNA replication fork barrier site; required for replication fork blocking, recombinational hotspot activity, condensin recruitment to replication fork barrier (RFB), and rDNA repeat segregation; related to retroviral integrases | Core | NA | NA | NA |
| 2800-YDR111C | YDR111C | ALT2 | alanine transaminase ALT2 | Catalytically inactive alanine transaminase; expression is repressed in the presence of alanine and repression is mediated by Nrg1p; ALT2 has a paralog, ALT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2801-YDR112W | YDR112W | IRC2 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ALT2/YDR111C; null mutant displays increased levels of spontaneous Rad52p foci | Accessory | Ancestral | NA | NA |
| 2802-YDR113C | YDR113C | PDS1 | securin | Securin; inhibits anaphase by binding separin Esp1p; blocks cyclin destruction and mitotic exit, essential for meiotic progression and mitotic cell cycle arrest; localization is cell-cycle dependent and regulated by Cdc28p phosphorylation | Core | NA | NA | NA |
| 2803-YDR114C | YDR114C | NA | NA | Putative protein of unknown function; deletion mutant exhibits poor growth at elevated pH and calcium | Core | NA | NA | NA |
| 2804-YDR115W | YDR115W | MRX14 | putative mitochondrial 54S ribosomal protein | Putative mitochondrial ribosomal protein of the large subunit; similar to E. coli L34 ribosomal protein; required for respiratory growth, as are most mitochondrial ribosomal proteins; protein increases in abundance and relocalizes to the plasma membrane upon DNA replication stress | Core | NA | NA | NA |
| 2805-YDR116C | YDR116C | MRPL1 | mitochondrial 54S ribosomal protein MRPL1 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 2806-YDR117C | YDR117C | TMA64 | RBF64 | Protein of unknown function that associates with ribosomes; has a putative RNA binding domain; in mammals the corresponding protein, eIF2D, has been shown to possess translation initiation factor activity | Core | NA | NA | NA |
| 2807-YDR118W | YDR118W | APC4 | anaphase promoting complex subunit 4 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; component of the platform domain of the APC/C, based on structural analysis; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2808-YDR118W-A | YDR118W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; identified using a combination of expression profiling and mass spectrometry | Accessory | Ancestral | NA | NA |
| 2809-YDR119W | YDR119W | VBA4 | NA | Protein of unknown function; proposed role as a basic amino acid permease based on phylogeny; GFP-fusion protein localizes to vacuolar membrane; physical interaction with Atg27p suggests a possible role in autophagy; non-essential gene | Core | NA | NA | NA |
| 2810-YDR119W-A | YDR119W-A | COX26 | NA | Stabilizes or regulates formation of respiratory chain supercomplexes composed of Complex III (ubiquinol-cytochrome c reductase) and Complex IV (cytochrome c oxidase) | Core | NA | NA | NA |
| 2811-YDR120C | YDR120C | TRM1 | tRNA (guanine26-N2)-dimethyltransferase | tRNA methyltransferase; two forms of protein are made by alternative translation starts; localizes to both nucleus and mitochondrion to produce modified base N2,N2-dimethylguanosine in tRNAs in both compartments; nuclear Trm1p is evenly distributed around inner nuclear membrane in WT, but mislocalizes as puncta near ER-nucleus junctions in spindle pole body (SPB) mutants; both Trm1p inner nuclear membrane targeting and maintenance depend upon SPB | Core | NA | NA | NA |
| 2812-YDR121W | YDR121W | DPB4 | DNA polymerase epsilon noncatalytic subunit | Subunit of DNA pol epsilon and of ISW2 chromatin accessibility complex; involved in both chromosomal DNA replication and inheritance of telomeric silencing; stabilizes the interaction of Pol epsilon with primer-template DNA, positively affecting the processivity of the polymerase and exonuclease activities of Pol epsilon; interacts with extranucleosomal DNA and acts as anchor point for ISW2 complex that retains its position on DNA during nucleosome mobilization | Core | NA | NA | NA |