Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (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 |
|---|---|---|---|---|---|---|---|---|
| 2543-YDL095W_NumOfGenes_2 | YDL095W | PMT1 | dolichyl-phosphate-mannose-protein mannosyltransferase PMT1 | Protein O-mannosyltransferase of the ER membrane; transfers mannose from dolichyl phosphate-D-mannose to protein serine and threonine residues; 1 of 7 related proteins involved in O-glycosylation which is essential for cell wall rigidity; involved in ER quality control; amino terminus faces cytoplasm, carboxyl terminus faces ER lumen | Core | NA | NA | NA |
| 2544-YDL097C | YDL097C | RPN6 | proteasome regulatory particle lid subunit RPN6|NAS4 | Essential, non-ATPase regulatory subunit of the 26S proteasome lid; required for the assembly and activity of the 26S proteasome; the human homolog (S9 protein) partially rescues Rpn6p depletion; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2545-YDL098C | YDL098C | SNU23 | U4/U6-U5 snRNP complex subunit SNU23 | Component of the U4/U6.U5 snRNP complex; involved in mRNA splicing via spliceosome | Core | NA | NA | NA |
| 2546-YDL099W | YDL099W | BUG1 | NA | Cis-golgi localized protein involved in ER to Golgi transport; forms a complex with the mammalian GRASP65 homolog, Grh1p; mutants are compromised for the fusion of ER-derived vesicles with Golgi membranes | Core | NA | NA | NA |
| 2547-YDL100C | YDL100C | GET3 | guanine nucleotide exchange factor GET3|ARR4 | Guanine nucleotide exchange factor for Gpa1p; amplifies G protein signaling; functions as a chaperone under ATP-depleted oxidative stress conditions; subunit of GET complex, involved in ATP dependent Golgi to ER trafficking and insertion of tail-anchored (TA) proteins into ER membrane under non-stress conditions; binds as dimer to transmembrane domain (TMD) cargo, shielding TMDs from aqueous solvent; protein abundance increases under DNA replication stress | Core | NA | NA | NA |
| 2548-YDL101C | YDL101C | DUN1 | serine/threonine protein kinase DUN1 | Cell-cycle checkpoint S/T protein kinase; required for transient G2/M arrest after DNA damage, damage-induced transcription, and nuclear-to-cytoplasmic redistribution of Rnr2p-Rnr4p after genotoxic stress and iron deprivation; phosphorylates repair protein Rad55p, transcriptional repressor Sml1p, superoxide dismutase, and ribonucleotide reductase inhibitors Crt1p and Dif1p; functions in the Mec1p pathway to regulate dNTP pools and telomere length; postreplicative repair role | Core | NA | NA | NA |
| 2549-YDL102W | YDL102W | POL3 | DNA-directed DNA polymerase delta POL3|CDC2|TEX1|HPR6 | Catalytic subunit of DNA polymerase delta; required for chromosomal DNA replication during mitosis and meiosis, intragenic recombination, repair of double strand DNA breaks, and DNA replication during nucleotide excision repair (NER) | Core | NA | NA | NA |
| 2550-YDL103C | YDL103C | QRI1 | UDP-N-acetylglucosamine diphosphorylase|UAP1 | UDP-N-acetylglucosamine pyrophosphorylase; catalyzes the formation of UDP-N-acetylglucosamine (UDP-GlcNAc), which is important in cell wall biosynthesis, protein N-glycosylation, and GPI anchor biosynthesis; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2551-YDL104C | YDL104C | QRI7 | putative N(6)-L-threonylcarbamoyladenine synthase | Protein involved in threonylcarbamoyl adenosine biosynthesis; Sua5p and Qri7p are necessary and sufficient for RNA t6A modification in vitro; highly conserved mitochondrial protein; essential for t6A modification of mitochondrial tRNAs that decode ANN codons; similar to Kae1p and E. coli YgjD, both of which are also required for tRNA t6A modification; when directed to the cytoplasm, complements the essential function of Kae1p in the KEOPS complex | Core | NA | NA | NA |
| 2552-YDL105W | YDL105W | NSE4 | Smc5-Smc6 complex subunit NSE4|QRI2 | Component of the SMC5-SMC6 complex; this complex plays a key role in the removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair | Core | NA | NA | NA |
| 2553-YDL106C | YDL106C | PHO2 | phoB|GRF10|BAS2 | Homeobox transcription factor; regulatory targets include genes involved in phosphate metabolism; binds cooperatively with Pho4p to the PHO5 promoter; phosphorylation of Pho2p facilitates interaction with Pho4p; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2554-YDL107W | YDL107W | MSS2 | NA | Peripherally bound inner membrane protein of the mitochondrial matrix; involved in membrane insertion of C-terminus of Cox2p, interacts genetically and physically with Cox18p | Core | NA | NA | NA |
| 2555-YDL108W | YDL108W | KIN28 | TFIIH complex serine/threonine-protein kinase subunit KIN28 | Serine/threonine protein kinase, subunit of transcription factor TFIIH; involved in transcription initiation at RNA polymerase II promoters; phosphorylates Ser5 residue of the PolII C-terminal domain (CTD) at gene promoters; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2556-YDL109C | YDL109C | NA | putative lipase | Putative lipase; involved in lipid metabolism; not an essential gene; YDL109C has a paralog, ROG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2557-YDL110C | YDL110C | TMA17 | ADC17 | ATPase dedicated chaperone that adapts proteasome assembly to stress; Tma17p is induced upon stress; interacts with Rpt6p to assist its pairing to Rpt3p and early steps in proteasome biogenesis; associates with ribosomes; heterozygous deletion demonstrated increases in chromosome instability in a rad9 deletion background; protein abundance is decreased upon intracellular iron depletion | Core | NA | NA | NA |