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 |
|---|---|---|---|---|---|---|---|---|
| 2423-YCR079W | YCR079W | PTC6 | type 2C protein phosphatase PTC6|PPP2|AUP1 | Mitochondrial type 2C protein phosphatase (PP2C); has similarity to mammalian PP1Ks; involved in mitophagy; null mutant is sensitive to rapamycin and has decreased phosphorylation of the Pda1 subunit of pyruvate dehydrogenase | Core | NA | NA | NA |
| 2424-YCR081W_NumOfGenes_2 | YCR081W | SRB8 | MED12|YCR080W|SSN5|NUT6|GIG1 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation; involved in glucose repression | Core | NA | NA | NA |
| 2425-YCR082W | YCR082W | AHC2 | NA | Component of the ADA histone acetyltransferase complex; Ahc2p and Ahc1p are unique to the ADA complex and not shared with the related SAGA and SLIK complexes; may tether Ahc1p to the complex | Core | NA | NA | NA |
| 2426-YCR083W | YCR083W | TRX3 | NA | Mitochondrial thioredoxin; highly conserved oxidoreductase required to maintain the redox homeostasis of the cell, forms the mitochondrial thioredoxin system with Trr2p, redox state is maintained by both Trr2p and Glr1p | Core | NA | NA | NA |
| 2427-YCR084C | YCR084C | TUP1 | chromatin-silencing transcriptional regulator TUP1|UMR7|SFL2|ROX4|FLK1|CYC9|CRT4|AMM1|AER2|AAR1 | General repressor of transcription; forms complex with Cyc8p, involved in the establishment of repressive chromatin structure through interactions with histones H3 and H4, appears to enhance expression of some genes | Core | NA | NA | NA |
| 2428-YCR085W | YCR085W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YCR085W is not an essential gene | Core | NA | NA | NA |
| 2429-YCR086W | YCR086W | CSM1 | NA | Nucleolar protein that mediates homolog segregation during meiosis I; forms a complex with Lrs4p and then Mam1p at kinetochores; required for condensin recruitment to the replication fork barrier site and rDNA repeat segregation | Core | NA | NA | NA |
| 2430-YCR087W_NumOfGenes_2 | YCR087W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized gene YCR087C-A; YCR087W is not an essential gene | Core | NA | NA | NA |
| 2431-YCR088W | YCR088W | ABP1 | NA | Actin-binding protein of the cortical actin cytoskeleton; important for activation of the Arp2/3 complex that plays a key role actin in cytoskeleton organization; inhibits barbed-end actin filament elongation; phosphorylation within its Proline-Rich Regio, mediated by Cdc28p and Pho85p, protects Abp1p from proteolysis mediated by its own PEST sequences; mammalian homolog of HIP-55 (hematopoietic progenitor kinase 1 [HPK1]-interacting protein of 55 kDa) | Core | NA | NA | NA |
| 2432-YCR089W | YCR089W | FIG2 | NA | Cell wall adhesin, expressed specifically during mating; may be involved in maintenance of cell wall integrity during mating; FIG2 has a paralog, AGA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2433-YCR090C | YCR090C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YCR090C is not an essential gene | Core | NA | NA | NA |
| 2434-YCR091W | YCR091W | KIN82 | putative serine/threonine protein kinase KIN82|FPK2 | Putative serine/threonine protein kinase; implicated in the regulation of phospholipid asymmetry through the activation of phospholipid translocases (flippases); involved in the phosphorylation of upstream inhibitory kinase Ypk1p along with Fpk1p; has a redundant role in the cellular response to mating pheromone; KIN82 has a paralog, FPK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2435-YCR092C | YCR092C | MSH3 | mismatch repair protein MSH3 | Mismatch repair protein; forms dimers with Msh2p that mediate repair of insertion or deletion mutations and removal of nonhomologous DNA ends, contains a PCNA (Pol30p) binding motif required for genome stability | Core | NA | NA | NA |
| 2436-YCR093W | YCR093W | CDC39 | CCR4-NOT core subunit CDC39|SMD6|ROS1|NOT1 | Subunit of the CCR4-NOT1 core complex; this complex has multiple roles in the regulation of mRNA levels including regulation of transcription and destabilization of mRNA by deadenylation; basal transcription factor that increases initiation and elongation; activates the ATPase activity of Dhh1p, resulting in processing body disassembly | Core | NA | NA | NA |
| 2437-YCR094W | YCR094W | CDC50 | aminophospholipid translocase regulatory protein CDC50 | Endosomal protein that interacts with phospholipid flippase Drs2p; interaction with Cdc50p is essential for Drs2p catalytic activity; mutations affect cell polarity and polarized growth; similar to Lem3p; CDC50 has a paralog, YNR048W, that arose from the whole genome duplication | Core | NA | NA | NA |