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
5633-YLR174W	YLR174W	IDP2	isocitrate dehydrogenase (NADP(+)) IDP2	Cytosolic NADP-specific isocitrate dehydrogenase; catalyzes oxidation of isocitrate to alpha-ketoglutarate; levels are elevated during growth on non-fermentable carbon sources and reduced during growth on glucose; IDP2 has a paralog, IDP3, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5634-YLR175W	YLR175W	CBF5	pseudouridine synthase CBF5	Pseudouridine synthase catalytic subunit of box H/ACA snoRNPs; acts on large and small rRNAs, on snRNA U2, and on some mRNAs; mutations in human ortholog dyskerin cause the disorder dyskeratosis congenita; small nucleolar ribonucleoprotein particles are also known as snoRNPs	Accessory	Ancestral	NA	NA
5635-YLR176C	YLR176C	RFX1	CRT1	Major transcriptional repressor of DNA-damage-regulated genes; recruits repressors Tup1p and Cyc8p to their promoters; involved in DNA damage and replication checkpoint pathway; similar to a family of mammalian DNA binding RFX1-4 proteins	Accessory	Ancestral	NA	NA
5636-YLR177W	YLR177W	NA	NA	Putative protein of unknown function; phosphorylated by Dbf2p-Mob1p in vitro; some strains contain microsatellite polymophisms at this locus; not an essential gene; YLR177W has a paralog, PSP1, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5637-YLR178C	YLR178C	TFS1	DKA1	Inhibitor of carboxypeptidase Y (Prc1p), and Ras GAP (Ira2p); phosphatidylethanolamine-binding protein (PEBP) family member and ortholog of hPEBP1/RKIP, a natural metastasis suppressor; targets to vacuolar membranes during stationary phase; acetylated by NatB N-terminal acetyltransferase; protein abundance increases in response to DNA replication stress	Accessory	Ancestral	NA	NA
5638-YLR179C	YLR179C	NA	NA	Protein of unknown function with similarity to Tfs1p; transcription is activated by paralogous proteins Yrm1p and Yrr1p along with proteins involved in multidrug resistance; GFP-tagged protein localizes to the cytoplasm and nucleus	Accessory	Ancestral	NA	NA
5639-YLR180W	YLR180W	SAM1	methionine adenosyltransferase SAM1\|ETH10	S-adenosylmethionine synthetase; catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; SAM1 has a paralog, SAM2, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5640-YLR181C	YLR181C	VTA1	NA	Multivesicular body (MVB) protein; involved in endosomal protein sorting; regulates Vps4p activity by promoting its oligomerization; has an N-terminal Vps60- and Did2- binding domain, a linker region, and a C-terminal Vps4p binding domain	Accessory	Ancestral	NA	NA
5641-YLR182W	YLR182W	SWI6	transcriptional regulator SWI6\|SDS11\|PSL8	Transcription cofactor; forms complexes with Swi4p and Mbp1p to regulate transcription at the G1/S transition; involved in meiotic gene expression; also binds Stb1p to regulate transcription at START; cell wall stress induces phosphorylation by Mpk1p, which regulates Swi6p localization; required for the unfolded protein response, independently of its known transcriptional coactivators	Accessory	Ancestral	NA	NA
5642-YLR183C	YLR183C	TOS4	NA	Putative transcription factor, contains Forkhead Associated domain; binds chromatin; involved in expression homeostasis, buffering of mRNA synthesis rate against gene dosage changes during S phase; target of SBF transcription factor; expression is periodic and peaks in G1; involved in DNA replication checkpoint response; interacts with Rpd3 and Set3 histone deacetylase complexes; APCC(Cdh1) substrate; relative distribution to nucleus increases upon DNA replication stress	Accessory	Ancestral	NA	NA
5643-YLR184W	YLR184W	NA	NA	Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data	Accessory	Unknown	NA	NA
5644-YLR185W	YLR185W	RPL37A	eL37\|ribosomal 60S subunit protein L37A\|L37e\|YL35\|L43\|L37A	Ribosomal 60S subunit protein L37A; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; homologous to mammalian ribosomal protein L37, no bacterial homolog; RPL37A has a paralog, RPL37B, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5645-YLR186W	YLR186W	EMG1	18S rRNA pseudouridine methyltransferase\|NEP1	Methyltransferase for rRNA; methylates pseudouridine 18S rRNA residue 1191; member of the SPOUT methyltransferase family; required for maturation of 18S rRNA and for 40S ribosomal subunit production independent of methyltransferase activity; forms homodimers; human ortholog is mutated in Bowen-Conradi syndrome, and equivalent yeast mutation affects Emg1p dimerization and localization but not methyltransferase activity; human EMG1 complements lethality of null and ts mutant	Accessory	Ancestral	NA	NA
5646-YLR187W	YLR187W	SKG3	NA	Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; potential Cdc28p substrate; similar to Skg4p; relocalizes from bud neck to cytoplasm upon DNA replication stress; SKG3 has a paralog, CAF120, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5647-YLR188W	YLR188W	MDL1	ATP-binding cassette permease MDL1	Mitochondrial inner membrane half-type ABC transporter; mediates export of peptides generated upon proteolysis of mitochondrial proteins; plays a role in the regulation of cellular resistance to oxidative stress	Accessory	Ancestral	NA	NA