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
3188-YDR500C	YDR500C	RPL37B	eL37\|ribosomal 60S subunit protein L37B\|L37e\|YL35\|L43\|L37B	Ribosomal 60S subunit protein L37B; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; protein abundance increases in response to DNA replication stress; homologous to mammalian ribosomal protein L37, no bacterial homolog; RPL37B has a paralog, RPL37A, that arose from the whole genome duplication	Core	NA	NA	NA
3189-YDR501W	YDR501W	PLM2	NA	Putative transcription factor, contains Forkhead Associated domain; found associated with chromatin; target of SBF transcription factor; induced in response to DNA damaging agents and deletion of telomerase; PLM2 has a paralog, TOS4, that arose from the whole genome duplication	Core	NA	NA	NA
3190-YDR502C	YDR502C	SAM2	methionine adenosyltransferase SAM2\|ETH2	S-adenosylmethionine synthetase; catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; comparative analysis suggests that a mitochondrially targeted form may result from translation starting at a non-canonical codon upstream of the annotated start codon	Core	NA	NA	NA
3191-YDR503C	YDR503C	LPP1	phosphatidate phosphatase LPP1	Lipid phosphate phosphatase; catalyzes Mg(2+)-independent dephosphorylation of phosphatidic acid (PA), lysophosphatidic acid, and diacylglycerol pyrophosphate; involved in control of the cellular levels of phosphatidylinositol and PA	Core	NA	NA	NA
3192-YDR504C	YDR504C	SPG3	NA	Protein required for high temperature survival during stationary phase; not required for growth on nonfermentable carbon sources; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum	Accessory	Ancestral	NA	NA
3193-YDR505C	YDR505C	PSP1	GIN5	Asn and gln rich protein of unknown function; high-copy suppressor of POL1 (DNA polymerase alpha) and partial suppressor of CDC2 (polymerase delta) and CDC6 (pre-RC loading factor) mutations; overexpression results in growth inhibition; PSP1 has a paralog, YLR177W, that arose from the whole genome duplication	Core	NA	NA	NA
3194-YDR506C	YDR506C	GMC1	putative oxidoreductase	Protein involved in meiotic progression; mutants are delayed in meiotic nuclear division and are defective in synaptonemal complex assembly; possible membrane-localized protein; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively	Core	NA	NA	NA
3195-YDR507C_NumOfGenes_2	YDR507C	GIN4	protein kinase GIN4\|ERC47	Protein kinase involved in bud growth and assembly of the septin ring; proposed to have kinase-dependent and kinase-independent activities; undergoes autophosphorylation; similar to Hsl1p; GIN4 has a paralog, KCC4, that arose from the whole genome duplication	Core	NA	NA	NA
3196-YDR508C_NumOfGenes_2	YDR508C	GNP1	glutamine permease GNP1	High-affinity glutamine permease; also transports Leu, Ser, Thr, Cys, Met and Asn; expression is fully dependent on Grr1p and modulated by the Ssy1p-Ptr3p-Ssy5p (SPS) sensor of extracellular amino acids; GNP1 has a paralog, AGP1, that arose from the whole genome duplication	Core	NA	NA	NA
3197-YDR509W	YDR509W	NA	NA	Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data	Accessory	Ancestral	NA	NA
3198-YDR510C-A	YDR510C-A	NA	NA	Dubious open reading frame unlikely to encode a functional protein; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching	Accessory	Unknown	NA	NA
3199-YDR510W_NumOfGenes_2	YDR510W	SMT3	SUMO family protein SMT3	Ubiquitin-like protein of the SUMO family; conjugated to lysine residues of target proteins; associates with transcriptionally active genes; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics; human homolog SUMO1 can complement yeast null mutant	Accessory	Ancestral	NA	NA
3200-YDR511W_NumOfGenes_3	YDR511W	SDH7	ACN9	Mitochondrial protein involved in assembly of succinate dehydrogenase; has a role in maturation of the Sdh2p subunit; localized to the mitochondrial intermembrane space; required for acetate utilization and gluconeogenesis; mutation in Drosophila ortholog SDHAF3 causes reduced succinate dehydrogenase activity and neuronal and muscular dysfunction; member of the LYR protein family	Accessory	Ancestral	NA	NA
3201-YDR512C_NumOfGenes_2	YDR512C	EMI1	NA	Non-essential protein of unknown function; required for transcriptional induction of the early meiotic-specific transcription factor IME1, also required for sporulation; contains twin cysteine-x9-cysteine motifs; deletion affects mitochondrial morphology	Accessory	Ancestral	NA	NA
3202-YDR513W_NumOfGenes_2	YDR513W	GRX2	dithiol glutaredoxin GRX2\|TTR1	Cytoplasmic glutaredoxin; thioltransferase, glutathione-dependent disulfide oxidoreductase involved in maintaining redox state of target proteins, also exhibits glutathione peroxidase activity, expression induced in response to stress; GRX2 has two in-frame start codons resulting in a shorter isoform that is retained in the cytosol and a longer form translocated to the mitochondrial matrix; GRX2 has a paralog, GRX1, that arose from the whole genome duplication	Core	NA	NA	NA