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
3593-YFR010W	YFR010W	UBP6	ubiquitin-specific protease UBP6	Ubiquitin-specific protease; situated in the base subcomplex of the 26S proteasome, releases free ubiquitin from branched polyubiquitin chains en bloc, rather than from the distal tip of the chain; negatively regulates degradation of ubiquitinated proteins by the proteasome; works in opposition to Hul5p polyubiquitin elongation activity; mutant has aneuploidy tolerance; human homolog UBP14 complements yeast null mutant	Core	NA	NA	NA
3594-YFR011C_NumOfGenes_2	YFR011C	MIC19	AIM13\|MCS19	Component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; Mic19p is peripheral to the inner membrane and may connect Mic60p with the Mic10p-Mic12p-Mic27p subcomplex; both yeast and human Mic19p become oxidized, and oxidation may regulate MICOS	Core	NA	NA	NA
3595-YFR012W	YFR012W	DCV1	NA	Protein of unknown function; deletion mutant shows strong genetic interaction with cdc28-as1 mutant in the presence of 1-NM-PP1; DCV1 has a paralog, YOL019W, that arose from the whole genome duplication	Core	NA	NA	NA
3596-YFR012W-A	YFR012W-A	NA	NA	Putative protein of unknown function; identified by homology	Core	NA	NA	NA
3597-YFR013W	YFR013W	IOC3	NA	Subunit of the Isw1a complex; Isw1a has nucleosome-stimulated ATPase activity and represses transcription initiation by specific positioning of a promoter proximal dinucleosome; promotes nucleosome shifts in the 5 prime direction; IOC3 has a paralog, ESC8, that arose from the whole genome duplication	Core	NA	NA	NA
3598-YFR014C	YFR014C	CMK1	calmodulin-dependent protein kinase CMK1	Calmodulin-dependent protein kinase; may play a role in stress response, many Ca++/calmodulin dependent phosphorylation substrates demonstrated in vitro, amino acid sequence similar to mammalian Cam Kinase II; CMK1 has a paralog, CMK2, that arose from the whole genome duplication	Core	NA	NA	NA
3599-YFR015C	YFR015C	GSY1	glycogen (starch) synthase GSY1	Glycogen synthase; expression induced by glucose limitation, nitrogen starvation, environmental stress, and entry into stationary phase; GSY1 has a paralog, GSY2, that arose from the whole genome duplication; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress	Accessory	Ancestral	NA	NA
3600-YFR016C	YFR016C	NA	NA	Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and bud; interacts with Spa2p; YFR016C is not an essential gene	Core	NA	NA	NA
3601-YFR017C	YFR017C	IGD1	NA	Cytoplasmic protein that inhibits Gdb1p glycogen debranching activity; required for normal intracellular accumulation of glycogen; phosphorylated in vivo; expression increases during wine fermentation; protein abundance increases in response to DNA replication stress; IGD1 has a paralog, YOL024W, that arose from the whole genome duplication	Core	NA	NA	NA
3602-YFR018C	YFR018C	NA	NA	Putative protein of unknown function; SWAT-GFP and seamless GFP fusion proteins localize to the endoplasmic reticulum and mCherry fusion protein localizes to the vacuole	Core	NA	NA	NA
3603-YFR019W	YFR019W	FAB1	1-phosphatidylinositol-3-phosphate 5-kinase\|SVL7	1-phosphatidylinositol-3-phosphate 5-kinase; vacuolar membrane kinase that generates phosphatidylinositol (3,5)P2, which is involved in vacuolar sorting and homeostasis	Core	NA	NA	NA
3604-YFR020W	YFR020W	CSS2	NA	Protein of unknown function, secreted when constitutively expressed; SWAT-GFP fusion protein localizes to the endoplasmic reticulum (ER) and extracellular region, while mCherry fusion protein localizes to the ER and vacuole; mRNA identified as translated by ribosome profiling data; CSS2 is a non-essential gene	Core	NA	NA	NA
3605-YFR021W	YFR021W	ATG18	phosphoinositide binding protein ATG18\|SVP1\|AUT10\|CVT18\|NMR1	Phosphoinositide binding protein; required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; binds both phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol 3-phosphate; WD-40 repeat protein; relocalizes from vacuole to cytoplasm upon DNA replication stress; has 4 mammalian homologs WIPI1, WIPI2, WIPI3 and WIPI4/WDR45; mutations in human WDR45 cause static encephalopathy of childhood with neurodegeneration in adulthood	Core	NA	NA	NA
3606-YFR022W	YFR022W	ROG3	ART7	Alpha-arrestin involved in ubiquitin-dependent endocytosis; contributes to desensitization of agonist-occupied alpha-factor receptor Ste2p by Rsp5p-independent internalization; PPXY motif-mediated binding of the ubiquitin ligase Rsp5p is not required for adaptation; mutation suppresses the temperature sensitivity of an mck1 rim11 double mutant; SWAT-GFP and mCherry fusion proteins localize to the cytosol; ROG3 has a paralog, ROD1, that arose from the whole genome duplication	Core	NA	NA	NA
3607-YFR023W	YFR023W	PES4	NA	Poly(A) binding protein, suppressor of DNA polymerase epsilon mutation; PES4 has a paralog, MIP6, that arose from the whole genome duplication	Core	NA	NA	NA