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
5588-YLR128W	YLR128W	DCN1	NEDD8 ligase DCN1	Scaffold-type E3 ligase; required for cullin neddylation and ubiquitin ligase activation; contains a ubiquitin-binding domain (UBA) for ubiquitin and Nedd8 (Rub1p) interaction and a PONY domain involved in cullin binding and neddylation	Core	NA	NA	NA
5589-YLR129W	YLR129W	DIP2	snoRNA-binding rRNA-processing protein DIP2\|UTP12	Nucleolar protein; specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	Core	NA	NA	NA
5590-YLR130C	YLR130C	ZRT2	low-affinity Zn(2+) transporter ZRT2	Low-affinity zinc transporter of the plasma membrane; transcription is induced under low-zinc conditions by the Zap1p transcription factor	Accessory	Ancestral	NA	NA
5591-YLR131C	YLR131C	ACE2	DNA-binding transcription factor ACE2	Transcription factor required for septum destruction after cytokinesis; phosphorylation by Cbk1p blocks nuclear exit during M/G1 transition, causing localization to daughter cell nuclei, and also increases Ace2p activity; phosphorylation by Cdc28p and Pho85p prevents nuclear import during cell cycle phases other than cytokinesis; part of RAM network that regulates cellular polarity and morphogenesis; ACE2 has a paralog, SWI5, that arose from the whole genome duplication	Core	NA	NA	NA
5592-YLR132C	YLR132C	USB1	phosphoric diester hydrolase	Putative poly(U)-specific 3'-to-5' RNA exonuclease; involved in 3'-end processing of U6 snRNA removing uridines and generating a terminal 2′,3′ cyclic phosphate; essential protein that localizes to the nucleus and mitochondria; overexpression suppresses the respiratory defects of oxa1 and mtf2 mutants; homolog of S.pombe gene, mpn1 and human gene, hUSB1; mutations in hUSB1 are associated with a rare genodermatosis, poikiloderma with neutropenia (OMIM 604173)	Accessory	Ancestral	NA	NA
5593-YLR133W	YLR133W	CKI1	bifunctional choline kinase/ethanolamine kinase CKI1	Choline kinase; catalyzes the first step in phosphatidylcholine synthesis via the CDP-choline (Kennedy pathway); exhibits some ethanolamine kinase activity contributing to phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway; CKI1 has a paralog, EKI1, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5594-YLR134W	YLR134W	PDC5	indolepyruvate decarboxylase 5	Minor isoform of pyruvate decarboxylase; key enzyme in alcoholic fermentation, decarboxylates pyruvate to acetaldehyde, regulation is glucose- and ethanol-dependent, repressed by thiamine, involved in amino acid catabolism	Accessory	Ancestral	NA	NA
5595-YLR135W	YLR135W	SLX4	NA	Endonuclease involved in processing DNA; acts during recombination, repair; promotes template switching during break-induced replication (BIR), causing non-reciprocal translocations (NRTs); cleaves branched structures in complex with Slx1p; involved in interstrand cross-link repair, Rad1p/Rad10p-dependent removal of 3'-nonhomologous tails during DSBR via single-strand annealing; relative distribution to nuclear foci increases upon DNA replication stress; FANCP-related factor	Accessory	Ancestral	NA	NA
5596-YLR136C	YLR136C	TIS11	CTH2	mRNA-binding protein expressed during iron starvation; binds to a sequence element in the 3'-untranslated regions of specific mRNAs to mediate their degradation; involved in iron homeostasis; protein increases in abundance and relative distribution to the nucleus increases upon DNA replication stress; TIS11 has a paralog, CTH1, that arose from the whole genome duplication	Accessory	Ancestral	NA	NA
5597-YLR137W	YLR137W	RKM5	S-adenosylmethionine-dependent methyltransferase	Protein lysine methyltransferase; monomethylates Lys-46 of the ribosomal large subunit Rpl1a/Rpl1b; member of the seven beta-strand methyltransferase superfamily; orthologs only found among fungal species	Accessory	Ancestral	NA	NA
5598-YLR138W	YLR138W	NHA1	NA	Na+/H+ antiporter; involved in sodium and potassium efflux through the plasma membrane; required for alkali cation tolerance at acidic pH	Accessory	Ancestral	NA	NA
5599-YLR139C	YLR139C	SLS1	NA	Mitochondrial membrane protein; coordinates expression of mitochondrially-encoded genes; may facilitate delivery of mRNA to membrane-bound translation machinery	Accessory	Ancestral	NA	NA
5600-YLR140W	YLR140W	NA	NA	Dubious open reading frame unlikely to encode a functional protein; overlaps essential RRN5 gene which encodes a member of the UAF transcription factor involved in transcription of rDNA by RNA polymerase I	Accessory	Ancestral	NA	NA
5601-YLR141W	YLR141W	RRN5	NA	Protein involved in transcription of rDNA by RNA polymerase I; transcription factor, member of UAF (upstream activation factor) family along with Rrn9p and Rrn10p	Accessory	Ancestral	NA	NA
5602-YLR142W	YLR142W	PUT1	proline dehydrogenase	Proline oxidase; nuclear-encoded mitochondrial protein involved in utilization of proline as sole nitrogen source; PUT1 transcription is induced by Put3p in the presence of proline and the absence of a preferred nitrogen source	Accessory	Ancestral	NA	NA