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 |
|---|---|---|---|---|---|---|---|---|
| 2453-YDL002C | YDL002C | NHP10 | HMO2 | Non-essential INO80 chromatin remodeling complex subunit; preferentially binds DNA ends, protecting them from exonucleatic cleavage; deletion affects telomere maintenance via recombination; related to mammalian high mobility group proteins | Core | NA | NA | NA |
| 2454-YDL003W | YDL003W | MCD1 | kleisin alpha|SCC1|RHC21|PDS3 | Essential alpha-kleisin subunit of the cohesin complex; required for sister chromatid cohesion in mitosis and meiosis; apoptosis induces cleavage and translocation of a C-terminal fragment to mitochondria; expression peaks in S phase | Core | NA | NA | NA |
| 2455-YDL004W | YDL004W | ATP16 | F1F0 ATP synthase subunit delta | Delta subunit of the central stalk of mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; F1 translationally regulates ATP6 and ATP8 expression to achieve a balanced output of ATP synthase genes encoded in nucleus and mitochondria; phosphorylated | Core | NA | NA | NA |
| 2456-YDL005C | YDL005C | MED2 | NA | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2457-YDL006W | YDL006W | PTC1 | type 2C protein phosphatase PTC1|TPD1|KCS2|CWH47 | Type 2C protein phosphatase (PP2C); dephosphorylates Hog1p, inactivating osmosensing MAPK cascade; involved in Fus3p activation during pheromone response; deletion affects precursor tRNA splicing, mitochondrial inheritance, and sporulation | Core | NA | NA | NA |
| 2458-YDL007C-A | YDL007C-A | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 2459-YDL007W | YDL007W | RPT2 | proteasome regulatory particle base subunit RPT2|YTA5|YHS4 | ATPase of the 19S regulatory particle of the 26S proteasome; one of six ATPases of the regulatory particle; involved in the degradation of ubiquitinated substrates; required for normal peptide hydrolysis by the core 20S particle; N-myristoylation of Rpt2p at Gly2 is involved in regulating the proper intracellular distribution of proteasome activity by controlling the nuclear localization of the 26S proteasome | Accessory | Ancestral | NA | NA |
| 2460-YDL008W | YDL008W | APC11 | anaphase promoting complex subunit 11 | Catalytic core subunit, Anaphase-Promoting Complex/Cyclosome (APC/C); which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; contains a RING-H2 domain that is required for activity | Accessory | Ancestral | NA | NA |
| 2461-YDL009C | YDL009C | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data; SWAT-GFP and mCherry fusion proteins localize to the cytosol; partially overlaps the verified ORF YDL010W; YDL009C is not an essential gene | Accessory | Ancestral | NA | NA |
| 2462-YDL010W_NumOfGenes_2 | YDL010W | GRX6 | glutathione-disulfide reductase GRX6 | Cis-golgi localized monothiol glutaredoxin, binds Fe-S cluster; more similar in activity to dithiol than other monothiol glutaredoxins; involved in the oxidative stress response; GRX6 has a paralog, GRX7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2463-YDL012C | YDL012C | NA | NA | Tail-anchored plasma membrane protein with a conserved CYSTM module; possibly involved in response to stress; may contribute to non-homologous end-joining (NHEJ) based on ydl012c htz1 double null phenotype; YDL012C has a paralog, YBR016W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2464-YDL013W | YDL013W | SLX5 | SUMO-targeted ubiquitin ligase complex subunit SLX5|ULS2|HEX3 | Subunit of the Slx5-Slx8 SUMO-targeted Ub ligase (STUbL) complex; role in Ub-mediated degradation of histone variant Cse4p preventing mislocalization to euchromatin; role in proteolysis of spindle positioning protein Kar9p, and DNA repair proteins Rad52p and Rad57p; forms SUMO-dependent nuclear foci, including DNA repair centers; contains a RING domain and two SIM motifs; associates with the centromere; required for maintenance of genome integrity like human ortholog RNF4 | Accessory | Ancestral | NA | NA |
| 2465-YDL014W | YDL014W | NOP1 | rRNA methyltransferase NOP1|LOT3 | Histone glutamine methyltransferase, modifies H2A at Q105 in nucleolus; component of the small subunit processome complex, which is required for processing of pre-18S rRNA; ortholog of mammalian fibrillarin; inviability of the null mutant is functionally complemented by human FBL | Core | NA | NA | NA |
| 2466-YDL015C | YDL015C | TSC13 | trans-2-enoyl-CoA reductase (NADPH) TSC13 | Enoyl reductase; catalyzes last step in each cycle of very long chain fatty acid elongation; localizes to ER, highly enriched in a structure marking nuclear-vacuolar junctions; coimmunoprecipitates with elongases Elo2p and Elo3p; protein increases in abundance and relative distribution to ER foci increases upon DNA replication stress; human homolog TECR implicated in nonsyndromic mental retardation, can complement yeast mutant | Core | NA | NA | NA |
| 2467-YDL016C | YDL016C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF CDC7/YDL153C, the catalytic subunit of a complex that regulates DNA replication | Core | NA | NA | NA |