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 |
|---|---|---|---|---|---|---|---|---|
| 5198-YKL125W | YKL125W | RRN3 | rDNA-binding RNA polymerase I transcriptional factor | Protein required for transcription of rDNA by RNA polymerase I; transcription factor independent of DNA template; involved in recruitment of RNA polymerase I to rDNA; structure reveals unique HEAT repeat fold and a surface serine patch; phosphorylation of serine patch impairs cell growth and reduces RNA polymerase I binding in vitro and RNA polymerase I recruitment to the rDNA gene in vivo | Core | NA | NA | NA |
| 5199-YKL126W | YKL126W | YPK1 | serine/threonine protein kinase YPK1|SLI2 | S/T protein kinase; phosphorylates, downregulates flippase activator Fpk1p; inactivates Orm1p and Orm2p by phosphorylation in response to compromised sphingolipid synthesis; involved in the TORC-dependent phosphorylation of ribosomal proteins Rps6a/b (S6); mutations affect receptor-mediated endocytosis and sphingolipid-mediated and cell integrity signaling pathways; human homolog SGK1 can complement a null mutant; human homolog SGK2 can complement a ypk1 ypk2 double mutant | Core | NA | NA | NA |
| 5200-YKL127W | YKL127W | PGM1 | phosphoglucomutase PGM1 | Phosphoglucomutase, minor isoform; catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism; PGM1 has a paralog, PGM2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5201-YKL128C | YKL128C | PMU1 | putative phosphomutase | Putative phosphomutase; contains a region homologous to the active site of phosphomutases; overexpression suppresses the histidine auxotrophy of an ade3 ade16 ade17 triple mutant and the temperature sensitivity of a tps2 mutant | Accessory | Ancestral | NA | NA |
| 5202-YKL129C | YKL129C | MYO3 | myosin 3 | One of two type I myosins; localizes to actin cortical patches; deletion of MYO3 has little effect on growth, but myo3 myo5 double deletion causes severe defects in growth and actin cytoskeleton organization; MYO3 has a paralog, MYO5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5203-YKL130C | YKL130C | SHE2 | NA | RNA-binding protein that binds specific mRNAs and interacts with She3p; part of the mRNA localization machinery that restricts accumulation of certain proteins to the bud; binds to ER-derived membranes and targets mRNAs to cortical ER | Core | NA | NA | NA |
| 5204-YKL131W | YKL131W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 5205-YKL132C | YKL132C | RMA1 | putative tetrahydrofolate synthase | Putative dihydrofolate synthetase; similar to E. coli folylpolyglutamate synthetase/dihydrofolate synthetase; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; RMA1 has a paralog, FOL3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5206-YKL133C | YKL133C | NA | NA | Putative protein of unknown function; not required for growth of cells lacking the mitochondrial genome; SWAT-GFP and mCherry fusion proteins localize to the mitochondria; YKL133C has a paralog, MGR3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5207-YKL134C | YKL134C | OCT1 | metalloendopeptidase | Mitochondrial intermediate peptidase; cleaves destabilizing N-terminal residues of a subset of proteins upon import, after their cleavage by mitochondrial processing peptidase (Mas1p-Mas2p); may contribute to mitochondrial iron homeostasis | Core | NA | NA | NA |
| 5208-YKL135C_NumOfGenes_2 | YKL135C | APL2 | NA | Beta-adaptin subunit of the clathrin-associated protein (AP-1) complex; binds clathrin; involved in clathrin-dependent Golgi protein sorting; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5209-YKL137W | YKL137W | CMC1 | NA | Copper-binding protein of the mitochondrial intermembrane space; evolutionarily conserved; may be involved in delivering copper from the matrix to the cytochrome c oxidase complex; contains a twin CX9C motif | Core | NA | NA | NA |
| 5210-YKL138C | YKL138C | MRPL31 | mitochondrial 54S ribosomal protein YmL31|YmL31 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 5211-YKL138C-A | YKL138C-A | HSK3 | NA | Essential subunit of the Dam1 complex (aka DASH complex); complex 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 |
| 5212-YKL139W | YKL139W | CTK1 | cyclin-dependent serine/threonine protein kinase CTK1 | Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I); phosphorylates both RNA pol II subunit Rpo21p to affect transcription and pre-mRNA 3' end processing, and ribosomal protein Rps2p to increase translational fidelity; required for H3K36 trimethylation but not dimethylation by Set2p; suggested stimulatory role in 80S formation during translation initiation; similar to the Drosophila dCDK12 and human CDK12 and probably CDK13 | Core | NA | NA | NA |