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 |
|---|---|---|---|---|---|---|---|---|
| 3068-YDR376W | YDR376W | ARH1 | NADPH-adrenodoxin reductase | Oxidoreductase of the mitochondrial inner membrane; involved in cytoplasmic and mitochondrial iron homeostasis and required for activity of Fe-S cluster-containing enzymes; one of the few mitochondrial proteins essential for viability | Core | NA | NA | NA |
| 3069-YDR377W | YDR377W | ATP17 | F1F0 ATP synthase subunit f | Subunit f of the F0 sector of mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis | Core | NA | NA | NA |
| 3070-YDR378C | YDR378C | LSM6 | U4/U6-U5 snRNP complex subunit LSM6 | Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA | Core | NA | NA | NA |
| 3071-YDR379C-A | YDR379C-A | SDH6 | NA | Mitochondrial protein involved in assembly of succinate dehydrogenase; has a role in maturation of the Sdh2p subunit; member of the LYR protein family; mutations in human ortholog SDHAF1 are associated with infantile leukoencephalopathy | Core | NA | NA | NA |
| 3072-YDR379W | YDR379W | RGA2 | NA | GTPase-activating protein for polarity-establishment protein Cdc42p; implicated in control of septin organization, pheromone response, and haploid invasive growth; regulated by Pho85p and Cdc28p; RGA2 has a paralog, RGA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3073-YDR380W | YDR380W | ARO10 | phenylpyruvate decarboxylase ARO10 | Phenylpyruvate decarboxylase; catalyzes decarboxylation of phenylpyruvate to phenylacetaldehyde, which is the first specific step in the Ehrlich pathway; involved in protein N-terminal Met and Ala catabolism | Core | NA | NA | NA |
| 3074-YDR381C-A | YDR381C-A | NA | NA | Protein of unknown function; localized to the mitochondrial outer membrane | Core | NA | NA | NA |
| 3075-YDR381W | YDR381W | YRA1 | RNA-binding protein YRA1|SHE11 | Nuclear polyadenylated RNA-binding protein; required for export of poly(A)+ mRNA from the nucleus; proposed to couple mRNA export with 3' end processing via its interactions with Mex67p and Pcf11p; interacts with DBP2; inhibits the helicase activity of Dbp2; functionally redundant with Yra2p, another REF family member | Core | NA | NA | NA |
| 3076-YDR382W | YDR382W | RPP2B | ribosomal protein P2B|YP2beta|P2B|L45|YPA1|RPL45 | Ribosomal protein P2 beta; a component of the ribosomal stalk, which is involved in the interaction between translational elongation factors and the ribosome; free (non-ribosomal) P2 stimulates the phosphorylation of the eIF2 alpha subunit (Sui2p) by Gcn2p; regulates the accumulation of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm | Core | NA | NA | NA |
| 3077-YDR383C | YDR383C | NKP1 | NA | Central kinetochore protein and subunit of the Ctf19 complex; mutants have elevated rates of chromosome loss; orthologous to fission yeast kinetochore protein fta4 | Core | NA | NA | NA |
| 3078-YDR384C | YDR384C | ATO3 | putative ammonium permease ATO3 | Plasma membrane protein, putative ammonium transporter; regulation pattern suggests a possible role in export of ammonia from the cell; phosphorylated in mitochondria; member of the TC 9.B.33 YaaH family of putative transporters | Core | NA | NA | NA |
| 3079-YDR385W_NumOfGenes_2 | YDR385W | EFT2 | elongation factor 2 | Elongation factor 2 (EF-2), also encoded by EFT1; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin; EFT2 has a paralog, EFT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3080-YDR386W | YDR386W | MUS81 | SLX3 | Subunit of structure-specific Mms4p-Mus81p endonuclease; cleaves branched DNA; involved in DNA repair, replication fork stability, and joint molecule formation/resolution during meiotic recombination; promotes template switching during break-induced replication (BIR), causing non-reciprocal translocations (NRTs); helix-hairpin-helix protein; phosphorylation of non-catalytic subunit Mms4p by Cdc28p and Cdcp during mitotic cell cycle activates function of Mms4p-Mus81p | Core | NA | NA | NA |
| 3081-YDR387C | YDR387C | CIN10 | NA | Putative transporter; member of the sugar porter family; non-essential gene; overexpression results in elevated colony sectoring, an indicator of chromosomal instability | Core | NA | NA | NA |
| 3082-YDR388W | YDR388W | RVS167 | amphiphysin | Calmodulin-binding actin-associated protein; roles in endocytic membrane tabulation and constriction, and exocytosis; N-BAR domain protein that interacts with Rvs161p to regulate actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; recruited to bud tips by Gyl1p and Gyp5p during polarized growth; homolog of mammalian amphiphysin | Core | NA | NA | NA |