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 |
|---|---|---|---|---|---|---|---|---|
| 2888-YDR194W-A | YDR194W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 2889-YDR195W | YDR195W | REF2 | RNA-processing protein REF2 | RNA-binding protein; involved in the cleavage step of mRNA 3'-end formation prior to polyadenylation, and in snoRNA maturation; part of holo-CPF subcomplex APT, which associates with 3'-ends of snoRNA- and mRNA-encoding genes; putative regulatory subunit of type 1 protein phosphatase Glc7p, required for actomyosin ring formation, and for timely dephosphorylation and release of Bnr1p from the division site; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2890-YDR196C | YDR196C | CAB5 | putative dephospho-CoA kinase | Subunit of the CoA-Synthesizing Protein Complex (CoA-SPC); subunits of this complex are: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p; probable dephospho-CoA kinase (DPCK) that catalyzes the last step in coenzyme A biosynthesis; null mutant lethality is complemented by human homolog DCAKD and by E. coli coaE (encoding DPCK); detected in purified mitochondria in high-throughput studies; also localized to lipid droplets | Core | NA | NA | NA |
| 2891-YDR197W | YDR197W | CBS2 | CBP7 | Mitochondrial translational activator of the COB mRNA; interacts with translating ribosomes, acts on the COB mRNA 5'-untranslated leader | Core | NA | NA | NA |
| 2892-YDR198C | YDR198C | RKM2 | protein-lysine N-methyltransferase | Ribosomal protein lysine methyltransferase; responsible for trimethylation of the lysine residue at position 3 of Rpl12Ap and Rpl12Bp | Core | NA | NA | NA |
| 2893-YDR199W | YDR199W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene VPS64/YDR200C; computationally predicted to have thiol-disulfide oxidoreductase activity | Accessory | Ancestral | NA | NA |
| 2894-YDR200C | YDR200C | VPS64 | FAR9 | Protein required for cytoplasm to vacuole targeting of proteins; forms a complex with Far3p and Far7p to Far11p involved in recovery from pheromone-induced cell cycle arrest; mutant has increased aneuploidy tolerance; VPS64 has a paralog, FAR10, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2895-YDR201W | YDR201W | SPC19 | NA | Essential subunit of the Dam1 complex (aka DASH complex); complex couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; also localized to nuclear side of spindle pole body | Core | NA | NA | NA |
| 2896-YDR202C_NumOfGenes_2 | YDR202C | RAV2 | NA | Subunit of RAVE complex (Rav1p, Rav2p, Skp1p); the RAVE complex associates with the V1 domain of the vacuolar membrane (H+)-ATPase (V-ATPase) and promotes assembly and reassembly of the holoenzyme | Core | NA | NA | NA |
| 2897-YDR204W | YDR204W | COQ4 | ubiquinone biosynthesis protein COQ4 | Protein with a role in ubiquinone (Coenzyme Q) biosynthesis; possibly functioning in stabilization of Coq7p; located on matrix face of mitochondrial inner membrane; component of a mitochondrial ubiquinone-synthesizing complex; human homolog COQ4 can complement yeast coq4 null mutant | Core | NA | NA | NA |
| 2898-YDR205W | YDR205W | MSC2 | metal cation transporter MSC2 | Endoplasmic reticulum zinc transporter; part of a heterodimeric transporter with Zrg17p that transfers zinc from the cytosol to the ER lumen; member of the cation diffusion facilitator family of efflux pumps; localizes to ER and nucleus; mutations affect the cellular distribution of zinc and also confer defects in meiotic recombination between homologous chromatids | Core | NA | NA | NA |
| 2899-YDR206W | YDR206W | EBS1 | NA | Protein involved in translation inhibition and nonsense-mediated decay; interacts with cap binding protein Cdc33p and with Nam7p; localizes to P-bodies upon glucose starvation; mRNA abundance regulated by mRNA decay factors; EBS1 has a paralog, EST1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2900-YDR207C | YDR207C | UME6 | DNA-binding transcriptional regulator UME6|RIM16|NIM2|CAR80 | Rpd3L histone deacetylase complex subunit; key transcriptional regulator of early meiotic genes; involved in chromatin remodeling and transcriptional repression via DNA looping; binds URS1 upstream regulatory sequence, represses transcription by recruiting conserved histone deacetylase Rpd3p (through co-repressor Sin3p) and chromatin-remodeling factor Isw2p; couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms compl | Accessory | Ancestral | NA | NA |
| 2901-YDR208W | YDR208W | MSS4 | 1-phosphatidylinositol-4-phosphate 5-kinase | Phosphatidylinositol-4-phosphate 5-kinase; involved in actin cytoskeleton organization and cell morphogenesis; multicopy suppressor of stt4 mutation | Core | NA | NA | NA |
| 2902-YDR210W_NumOfGenes_2 | YDR210W | NA | NA | Predicted tail-anchored plasma membrane protein; contains a conserved CYSTM module; related proteins in other organisms may be involved in response to stress; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery | Core | NA | NA | NA |