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 |
|---|---|---|---|---|---|---|---|---|
| 3248-YEL015W | YEL015W | EDC3 | LSM16|DCP3 | Non-essential conserved protein with a role in mRNA decapping; specifically affects the function of the decapping enzyme Dcp1p; mediates decay of the RPS28B mRNA via binding to both Rps28Bp (or Rps28Ap) and the RPS28B mRNA; mediates decay of the YRA1 mRNA by a different, translation-independent mechanism; localizes to cytoplasmic mRNA processing bodies; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 3249-YEL016C | YEL016C | NPP2 | nucleotide diphosphatase/phosphodiesterase NPP2 | Nucleotide pyrophosphatase/phosphodiesterase; mediates extracellular nucleotide phosphate hydrolysis along with Npp1p and Pho5p; activity and expression enhanced during conditions of phosphate starvation; involved in spore wall assembly; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; NPP2 has a paralog, NPP1, that arose from the whole genome duplication; npp1 npp2 double mutant exhibits reduced dityrosine fluorescence relative to single mutants | Core | NA | NA | NA |
| 3250-YEL017C-A | YEL017C-A | PMP2 | proteolipid ATPase | Proteolipid associated with plasma membrane H(+)-ATPase (Pma1p); regulates plasma membrane H(+)-ATPase activity; protein abundance increases in response to DNA replication stress; PMP2 has a paralog, PMP1, that arose from the whole genome duplication | Accessory | Introgression | S. paradoxus | NA |
| 3251-YEL017W | YEL017W | GTT3 | NA | Protein of unknown function may be involved in glutathione metabolism; function suggested by computational analysis of large-scale protein-protein interaction data; N- and C-terminal fusion proteins localize to the cell periphery | Core | NA | NA | NA |
| 3252-YEL018W_NumOfGenes_2 | YEL018W | EAF5 | NA | Non-essential subunit of the NuA4 acetyltransferase complex; Esa1p-associated factor; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3253-YEL019C | YEL019C | MMS21 | SUMO ligase MMS21|PSO10|NSE2 | Highly conserved SUMO E3 ligase subunit of SMC5-SMC6 complex; required for anchoring dsDNA breaks to the nuclear periphery; SMC5-SMC6 plays a key role in removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair; required for efficient sister chromatid cohesion; mutants are sensitive to MMS, show increased spontaneous mutation and mitotic recombination; SUMOylates and inhibits Snf1p function; supports nucleolar function | Core | NA | NA | NA |
| 3254-YEL020C | YEL020C | PXP1 | putative indolepyruvate decarboxylase family protein | Peroxisomal matrix protein; well-conserved in fungi; contains tripartite homology domain of thiamine pyrophosphate (TPP) enzymes; targeted to peroxisomes by Pex5p; contains low sequence identity with Pdc1p; mRNA identified as translated by ribosome profiling data | Core | NA | NA | NA |
| 3255-YEL020W-A_NumOfGenes_2 | YEL020W-A | TIM9 | protein transporter TIM9 | Essential protein of the mitochondrial intermembrane space; forms a complex with Tim10p (TIM10 complex) that delivers hydrophobic proteins to the TIM22 complex for insertion into the inner membrane | Core | NA | NA | NA |
| 3256-YEL021W | YEL021W | URA3 | orotidine-5'-phosphate decarboxylase | Orotidine-5'-phosphate (OMP) decarboxylase; catalyzes the sixth enzymatic step in the de novo biosynthesis of pyrimidines, converting OMP into uridine monophosphate (UMP); converts 5-FOA into 5-fluorouracil, a toxic compound | Accessory | Ancestral | NA | NA |
| 3257-YEL022W | YEL022W | GEA2 | Arf family guanine nucleotide exchange factor GEA2 | Guanine nucleotide exchange factor for ADP ribosylation factors (ARFs); involved in vesicular transport between the Golgi and ER, Golgi organization, and actin cytoskeleton organization; GEA2 has a paralog, GEA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3258-YEL023C | YEL023C | NA | NA | Putative protein of unknown function; expression is increased greatly during sporulation; YEL023C is not an essential gene | Core | NA | NA | NA |
| 3259-YEL024W | YEL024W | RIP1 | ubiquinol--cytochrome-c reductase catalytic subunit RIP1 | Ubiquinol-cytochrome-c reductase; a Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex; transfers electrons from ubiquinol to cytochrome c1 during respiration; during import, Rip1p is first imported into the mitochondrial matrix where it is processed, acquires its Fe-S cluster, and is folded, then is translocated into the inner membrane by the action of a homo-oligomer of Bcs1p, and finally is delivered by Bcs1p to Complex III for assembly | Core | NA | NA | NA |
| 3260-YEL025C | YEL025C | NA | SRI1 | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus | Core | NA | NA | NA |
| 3261-YEL026W | YEL026W | SNU13 | RNA binding protein SNU13 | RNA binding protein; part of U3 snoRNP involved in rRNA processing, part of U4/U6-U5 tri-snRNP involved in mRNA splicing, similar to human 15.5K protein | Core | NA | NA | NA |
| 3262-YEL027W | YEL027W | VMA3 | H(+)-transporting V0 sector ATPase subunit c|CUP5|GEF2|CLS7 | Proteolipid subunit c of the V0 domain of vacuolar H(+)-ATPase; dicyclohexylcarbodiimide binding subunit; required for vacuolar acidification and important for copper and iron metal ion homeostasis | Core | NA | NA | NA |