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 |
|---|---|---|---|---|---|---|---|---|
| 3308-YEL074W | YEL074W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; large scale expression analysis showed an increase in mRNA accumulation in strains mutant for exosome components | Accessory | Unknown | S. paradoxus | NA |
| 3309-YEL075W-A_NumOfGenes_2 | YEL075W-A | NA | YEL076W-C | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Introgression | S. paradoxus | NA |
| 3310-YER001W | YER001W | MNN1 | alpha-1,3-mannosyltransferase MNN1 | Alpha-1,3-mannosyltransferase; integral membrane glycoprotein of the Golgi complex, required for addition of alpha1,3-mannose linkages to N-linked and O-linked oligosaccharides, one of five S. cerevisiae proteins of the MNN1 family | Core | NA | NA | NA |
| 3311-YER002W | YER002W | NOP16 | NA | Constituent of 66S pre-ribosomal particles; involved in 60S ribosomal subunit biogenesis | Core | NA | NA | NA |
| 3312-YER003C | YER003C | PMI40 | mannose-6-phosphate isomerase PMI40|PMI | Mannose-6-phosphate isomerase; catalyzes the interconversion of fructose-6-P and mannose-6-P; required for early steps in protein mannosylation | Core | NA | NA | NA |
| 3313-YER004W | YER004W | FMP52 | NA | Protein of unknown function; localized to the mitochondrial outer membrane; induced by treatment with 8-methoxypsoralen and UVA irradiation | Core | NA | NA | NA |
| 3314-YER005W | YER005W | YND1 | apyrase|YEJ5|APY1 | Apyrase with wide substrate specificity; helps prevent inhibition of glycosylation by hydrolyzing nucleoside tri- and diphosphates that inhibit glycotransferases; partially redundant with Gda1p; mediates adenovirus E4orf4-induced toxicity | Core | NA | NA | NA |
| 3315-YER006C-A | YER006C-A | 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 PAC2/YER007W | Accessory | Ancestral | NA | NA |
| 3316-YER006W | YER006W | NUG1 | RNA-binding GTPase NUG1 | GTPase that associates with nuclear 60S pre-ribosomes; required for export of 60S ribosomal subunits from the nucleus | Core | NA | NA | NA |
| 3317-YER007C-A | YER007C-A | TMA20 | RBF20 | Protein of unknown function that associates with ribosomes; has a putative RNA binding domain; interacts with Tma22p; null mutant exhibits translation defects; has homology to human oncogene MCT-1; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3318-YER007W | YER007W | PAC2 | NA | Microtubule effector required for tubulin heterodimer formation; binds alpha-tubulin, required for normal microtubule function, null mutant exhibits cold-sensitive microtubules and sensitivity to benomyl | Core | NA | NA | NA |
| 3319-YER008C | YER008C | SEC3 | GTP-Rho binding exocyst subunit SEC3|PSL1 | Subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to sites of exocytosis prior to SNARE-mediated fusion; PtdIns[4,5]P2-binding protein that localizes to exocytic sites in a Rho1p-dependent, actin-independent manner, targeting and anchoring the exocyst to the plasma membrane with Exo70p; direct GTP Rho1p effector; required for ER inheritance; relocalizes away from bud neck upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 3320-YER009W_NumOfGenes_2 | YER009W | NTF2 | Ran GTPase-binding protein NTF2 | Nuclear envelope protein; interacts with GDP-bound Gsp1p and with proteins of the nuclear pore to transport Gsp1p into the nucleus where it is an essential player in nucleocytoplasmic transport | Core | NA | NA | NA |
| 3321-YER010C_NumOfGenes_2 | YER010C | NA | bifunctional 4-hydroxy-4-methyl-2-oxoglutarate aldolase/oxaloacetate decarboxylase | Bifunctional HMG aldolase/oxaloacetate decarboxylase; requires divalent metal ions for activity; competitively inhibited by oxalate; forms a ring-shaped homotrimer; similar to members of the prokaryotic RraA family of class II (divalent metal ion dependent) pyruvate aldolases from the meta cleavage pathways of protocatechuate and gallate | Accessory | Ancestral | NA | NA |
| 3322-YER011W_NumOfGenes_2 | YER011W | TIR1 | GPI-anchored mannoprotein|SRP1 | Cell wall mannoprotein; expression is downregulated at acidic pH and induced by cold shock and anaerobiosis; abundance is increased in cells cultured without shaking; member of the Srp1p/Tip1p family of serine-alanine-rich proteins | Accessory | Ancestral | NA | NA |