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
6638-YNL249C	YNL249C	MPA43	NA	Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies	Core	NA	NA	NA
6639-YNL250W	YNL250W	RAD50	MRX complex DNA-binding subunit	Subunit of MRX complex with Mre11p and Xrs2p; complex is involved in processing double-strand DNA breaks in vegetative cells, initiation of meiotic DSBs, telomere maintenance, and nonhomologous end joining; forms nuclear foci upon DNA replication stress	Core	NA	NA	NA
6640-YNL251C_NumOfGenes_2	YNL251C	NRD1	Nrd1 complex RNA-binding subunit	RNA-binding subunit of Nrd1 complex; complex interacts with exosome to mediate 3'-end formation of some mRNAs, snRNAs, snoRNAs, and CUTs; interacts with CTD of RNA pol II large subunit Rpo21p at phosphorylated Ser5 to direct transcription termination of non-polyadenylated transcripts; H3K4 trimethylation of transcribed regions by Set1p enhances recruitment of Nrd1p to those sites; role in regulation of mitochondrial abundance and cell size	Core	NA	NA	NA
6641-YNL252C_NumOfGenes_2	YNL252C	MRPL17	mitochondrial 54S ribosomal protein YmL17/YmL30\|YmL17\|YmL30\|MRPL30	Mitochondrial ribosomal protein of the large subunit	Core	NA	NA	NA
6642-YNL253W_NumOfGenes_2	YNL253W	TEX1	NA	Protein involved in mRNA export; component of the transcription export (TREX) complex	Core	NA	NA	NA
6643-YNL254C	YNL254C	RTC4	NA	Protein of unknown function; null mutation suppresses cdc13-1 temperature sensitivity; (GFP)-fusion protein localizes to both the cytoplasm and the nucleus	Accessory	Ancestral	NA	NA
6644-YNL255C_NumOfGenes_2	YNL255C	GIS2	mRNA-binding translational activator GIS2	Translational activator for mRNAs with internal ribosome entry sites; associates with polysomes and binds to a specific subset of mRNAs; localizes to RNA processing bodies (P bodies) and to stress granules; may have a role in translation regulation under stress conditions; ortholog of human ZNF9/CNBP, a gene involved in myotonic dystrophy type 2	Core	NA	NA	NA
6645-YNL256W_NumOfGenes_2	YNL256W	FOL1	trifunctional dihydropteroate synthetase/dihydrohydroxymethylpterin pyrophosphokinase/dihydroneopterin aldolase FOL1	Multifunctional enzyme of the folic acid biosynthesis pathway; has dihydropteroate synthetase, dihydro-6-hydroxymethylpterin pyrophosphokinase, and dihydroneopterin aldolase activities	Accessory	Ancestral	NA	NA
6646-YNL257C	YNL257C	SIP3	LAM3	Putative sterol transfer protein; has a probable role in retrograde transport of sterols from the plasma membrane to the ER; co-localizes to puncta in the cortical ER with Ysp2p; contains GRAM, StART-like (VASt) and two PH-like domains; one of 6 StART-like domain-containing proteins in yeast that may be involved in sterol transfer between intracellular membranes; conserved across eukaryotes; previously identified as a transcription cofactor that interacts with DNA-bound Snf1p	Accessory	Ancestral	NA	NA
6647-YNL258C_NumOfGenes_2	YNL258C	DSL1	RNS1	Peripheral membrane protein needed for Golgi-to-ER retrograde traffic; mediates Sey1p-independent homotypic ER fusion; forms Dsl1 tethering complex with Sec39p and Tip20p that forms a stable complex with ER SNAREs Sec20p, Ufe1p and Use1p and is functionally conserved from yeast to mammalian cells; component of the ER target site that interacts with coatomer; interacts with different subunits of COPI vesicle coat; interacts with Cin5p; homolog of fly and human ZW10 gene	Core	NA	NA	NA
6648-YNL259C_NumOfGenes_3	YNL259C	ATX1	copper metallochaperone ATX1	Cytosolic copper metallochaperone; transports copper to the secretory vesicle copper transporter Ccc2p for eventual insertion into Fet3p, which is a multicopper oxidase required for high-affinity iron uptake; human homolog ATOX1 can complement yeast atx1 mutant; overexpression of human ATOX1 suppresses lysine auxotrophy of the yeast sod1 null mutant, as does overexpression of yeast ATX1	Core	NA	NA	NA
6649-YNL261W_NumOfGenes_2	YNL261W	ORC5	origin recognition complex subunit 5	Subunit of the origin recognition complex (ORC); ORC directs DNA replication by binding to replication origins and is also involved in transcriptional silencing	Core	NA	NA	NA
6650-YNL262W_NumOfGenes_2	YNL262W	POL2	DNA polymerase epsilon catalytic subunit\|DUN2	Catalytic subunit of DNA polymerase (II) epsilon; a chromosomal DNA replication polymerase that exhibits processivity and proofreading exonuclease activity; participates in leading-strand synthesis during DNA replication; also involved in DNA synthesis during DNA repair; interacts extensively with Mrc1p	Core	NA	NA	NA
6651-YNL263C	YNL263C	YIF1	NA	Integral membrane protein; required for the fusion of ER-derived COPII transport vesicles with the Golgi; interacts with Yip1p and Yos1p; localizes to the Golgi, the ER, and COPII vesicles; homolog of human YIPF3	Accessory	Ancestral	NA	NA
6652-YNL264C	YNL264C	PDR17	phosphatidylinositol transporter\|SFH4\|ISS1	Phosphatidylinositol transfer protein (PITP); downregulates Plb1p-mediated turnover of phosphatidylcholine; forms a complex with Psd2p which appears essential for maintenance of vacuolar PE levels; found in the cytosol and microsomes; homologous to Pdr16p; deletion affects phospholipid composition	Accessory	Ancestral	NA	NA