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 |
|---|---|---|---|---|---|---|---|---|
| 5153-YKL080W | YKL080W | VMA5 | H(+)-transporting V1 sector ATPase subunit C|VAT3|CSL5 | Subunit C of the V1 peripheral membrane domain of V-ATPase; part of the electrogenic proton pump found throughout the endomembrane system; required for the V1 domain to assemble onto the vacuolar membrane; the V1 peripheral membrane domain of vacuolar H+-ATPase (V-ATPase) has eight subunits | Core | NA | NA | NA |
| 5154-YKL081W | YKL081W | TEF4 | translation elongation factor EF1B gamma|EFC1 | Gamma subunit of translational elongation factor eEF1B; stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing eEF1A (Tef1p/Tef2p) from the ribosomal complex | Core | NA | NA | NA |
| 5155-YKL082C_NumOfGenes_2 | YKL082C | RRP14 | ribosome biosynthesis protein RRP14 | Essential protein, constituent of 66S pre-ribosomal particles; interacts with proteins involved in ribosomal biogenesis and cell polarity; member of the SURF-6 family | Core | NA | NA | NA |
| 5156-YKL084W | YKL084W | HOT13 | NA | Zinc-binding mitochondrial intermembrane space (IMS) protein; involved in a disulfide relay system for IMS import of cysteine-containing proteins; binds Mia40p and stimulates its Erv1p-dependent oxidation, probably by sequestering zinc | Core | NA | NA | NA |
| 5157-YKL085W | YKL085W | MDH1 | malate dehydrogenase MDH1 | Mitochondrial malate dehydrogenase; catalyzes interconversion of malate and oxaloacetate; involved in the tricarboxylic acid (TCA) cycle; phosphorylated | Core | NA | NA | NA |
| 5158-YKL086W | YKL086W | SRX1 | sulfiredoxin | Sulfiredoxin; contributes to oxidative stress resistance by reducing cysteine-sulfinic acid groups in the peroxiredoxin Tsa1p, which is formed upon exposure to oxidants; conserved in higher eukaryotes; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5159-YKL087C | YKL087C | CYT2 | cytochrome c1 heme lyase CYT2|CC1HL | Cytochrome c1 heme lyase; involved in maturation of cytochrome c1, which is a subunit of the mitochondrial ubiquinol-cytochrome-c reductase; links heme covalently to apocytochrome c1; human homolog HCCS can complement yeast cyt2 null mutant | Core | NA | NA | NA |
| 5160-YKL088W | YKL088W | CAB3 | phosphopantothenoylcysteine decarboxylase complex subunit CAB3 | Subunit of PPCDC and CoA-SPC complexes involved in CoA biosynthesis; subunits of the phosphopantothenoylcysteine decarboxylase (PPCDC) complex are: Cab3p, Sis2p, Vhs3p, while the subunits of the CoA-synthesizing protein complex (CoA-SPC) are: Cab2p, Cab3p, Cab4p, and Cab5p as well as Sis2p and Vhs3p; null mutant lethality is complemented by E. coli coaBC | Core | NA | NA | NA |
| 5161-YKL089W | YKL089W | MIF2 | NA | Protein required for structural integrity of elongating spindles; localizes to the kinetochore; interacts with histones H2A, H2B, and H4; phosphorylated by Ipl1p; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-C and fission yeast cnp3 | Core | NA | NA | NA |
| 5162-YKL090W | YKL090W | CUE2 | NA | Protein of unknown function; has two CUE domains that bind ubiquitin, which may facilitate intramolecular monoubiquitination | Core | NA | NA | NA |
| 5163-YKL091C | YKL091C | NA | phosphatidylinositol/phosphatidylcholine-binding protein|SFH1 | Putative phosphatidylinositol/phosphatidylcholine transfer protein; possibly involved in lipid metabolism; localizes to the nucleus; contains a CRAL/TRIO domain and binds several lipids in a large-scale study; YKL091C has a paralog, SEC14, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5164-YKL092C | YKL092C | BUD2 | ERC25|CLA2 | GTPase activating factor for Rsr1p/Bud1p; plays a role in spindle position checkpoint distinct from its role in bud site selection; required for both axial and bipolar budding patterns; mutants exhibit random budding in all cell types; contains two PH-like domains | Core | NA | NA | NA |
| 5165-YKL093W | YKL093W | MBR1 | NA | Protein involved in mitochondrial functions and stress response; overexpression suppresses growth defects of hap2, hap3, and hap4 mutants; MBR1 has a paralog, ISF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5166-YKL094W | YKL094W | YJU3 | acylglycerol lipase | Monoglyceride lipase (MGL); functional ortholog of mammalian MGL, localizes to lipid particles and membranes, also member of the eukaryotic serine hydrolase family | Accessory | Ancestral | NA | NA |
| 5167-YKL095W | YKL095W | YJU2 | mRNA splicing protein YJU2|CWC16 | Essential protein required for pre-mRNA splicing; associates transiently with the spliceosomal NTC ("nineteen complex") and acts after Prp2p to promote the first catalytic reaction of splicing | Accessory | Ancestral | NA | NA |