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 |
|---|---|---|---|---|---|---|---|---|
| 3698-YGL051W_NumOfGenes_2 | YGL051W | MST27 | DUP240 family protein MST27 | Putative integral membrane protein, involved in vesicle formation; forms complex with Mst28p; member of DUP240 gene family; binds COPI and COPII vesicles; MST27 has a paralog, MST28, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 3699-YGL052W | YGL052W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF MST27 | Accessory | Ancestral | NA | NA |
| 3700-YGL053W | YGL053W | PRM8 | pheromone-regulated DUP240 family protein PRM8 | Pheromone-regulated protein; contains with 2 predicted transmembrane segments and an FF sequence, a motif involved in COPII binding; forms a complex with Prp9p in the ER; member of DUP240 gene family; PRM8 has a paralog, PRM9, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 3701-YGL054C | YGL054C | ERV14 | cornichon family protein | COPII-coated vesicle protein; involved in vesicle formation and incorporation of specific secretory cargo; required for the delivery of bud-site selection protein Axl2p and Nha1p antiporter to cell surface; related to Drosophila cornichon; ERV14 has a paralog, ERV15, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3702-YGL055W_NumOfGenes_2 | YGL055W | OLE1 | stearoyl-CoA 9-desaturase|MDM2 | Delta(9) fatty acid desaturase; required for monounsaturated fatty acid synthesis and for normal distribution of mitochondria | Core | NA | NA | NA |
| 3703-YGL056C | YGL056C | SDS23 | NA | Protein involved in cell separation during budding; one of two S. cerevisiae homologs (Sds23p and Sds24p) of the S. pombe Sds23 protein, which is implicated in APC/cyclosome regulation; SDS23 has a paralog, SDS24, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3704-YGL057C | YGL057C | GEP7 | NA | Protein of unknown function; null mutant exhibits a respiratory growth defect and synthetic interactions with prohibitin (phb1) and gem1; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 3705-YGL058W | YGL058W | RAD6 | E2 ubiquitin-conjugating protein RAD6|PSO8|UBC2 | Ubiquitin-conjugating enzyme (E2); involved in postreplication repair as a heterodimer with Rad18p, regulation of K63 polyubiquitination in response to oxidative stress, DSBR and checkpoint control as a heterodimer with Bre1p, ubiquitin-mediated N-end rule protein degradation as a heterodimer with Ubr1p, ERAD with Ubr1p in the absence of canonical ER membrane ligases, and Rpn4p turnover as part of proteasome homeostasis, in complex with Ubr2p and Mub1p | Core | NA | NA | NA |
| 3706-YGL059W | YGL059W | PKP2 | protein kinase PKP2 | Mitochondrial protein kinase; negatively regulates activity of the pyruvate dehydrogenase complex by phosphorylating the ser-133 residue of the Pda1p subunit; acts in concert with kinase Pkp1p and phosphatases Ptc5p and Ptc6p; relocalizes from mitochondrion to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3707-YGL060W | YGL060W | YBP2 | YBH1 | Central kinetochore associated protein; mediates mitotic progression; interacts with several central kinetochore proteins and centromeric histone Cse4p; role in resistance to oxidative stress; similar to Slk19p; YBP2 has a paralog, YBP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3708-YGL061C | YGL061C | DUO1 | NA | Essential subunit of the Dam1 complex (aka DASH complex); cooperates with Dam1p to connect the DASH complex with microtubules (MT); couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; is transferred to the kinetochore prior to mitosis | Core | NA | NA | NA |
| 3709-YGL062W_NumOfGenes_2 | YGL062W | PYC1 | pyruvate carboxylase 1 | Pyruvate carboxylase isoform; cytoplasmic enzyme that converts pyruvate to oxaloacetate; differentially regulated than isoform Pyc2p; mutations in the human homolog are associated with lactic acidosis; PYC1 has a paralog, PYC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3710-YGL063W_NumOfGenes_2 | YGL063W | PUS2 | pseudouridine synthase PUS2 | Mitochondrial tRNA:pseudouridine synthase; acts at positions 27 and 28, but not at position 72; efficiently and rapidly targeted to mitochondria, specifically dedicated to mitochondrial tRNA modification; mutation also affects pseudouridylation of some nuclear-encoded mRNAs; PUS2 has a paralog, PUS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3711-YGL064C | YGL064C | MRH4 | ATP-dependent RNA helicase | Mitochondrial ATP-dependent RNA helicase of the DEAD-box family; required for assembly of the large subunit of mitochondrial ribosomes; binds to the large subunit rRNA, 21S_rRNA; localizes to the matrix face of the mitochondrial inner membrane and associates with the large subunit precursor and with mature ribosomes | Core | NA | NA | NA |
| 3712-YGL065C | YGL065C | ALG2 | GDP-Man:Man(1)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase | Mannosyltransferase in the N-linked glycosylation pathway; catalyzes two consecutive steps in the N-linked glycosylation pathway; alg2 mutants exhibit temperature-sensitive growth and abnormal accumulation of the lipid-linked oligosaccharide Man2GlcNAc2-PP-Dol; human ALG2 complements the temperature sensitivity and dolichol-linked oligosaccharide biosynthesis defect of the alg2-1 mutant, but mutant form from a patient with CDG-Ii fails to complement | Core | NA | NA | NA |