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 |
|---|---|---|---|---|---|---|---|---|
| 5468-YLR007W_NumOfGenes_2 | YLR007W | NSE1 | Smc5-Smc6 complex subunit NSE1 | 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 |
| 5469-YLR008C_NumOfGenes_2 | YLR008C | PAM18 | TIM14 | Subunit of the import motor (PAM complex); the PAM complex is a component of the Translocase of the Inner Mitochondrial membrane (TIM23 complex); essential J-protein cochaperone that stimulates Ssc1p ATPase activity to drive import; inhibited by Pam16p | Core | NA | NA | NA |
| 5470-YLR009W_NumOfGenes_2 | YLR009W | RLP24 | ATPase-activating ribosome biosynthesis protein | Essential protein required for ribosomal large subunit biogenesis; associated with pre-60S ribosomal subunits; stimulates the ATPase activity of Afg2p, which is required for release of Rlp24p from the pre-60S particle; has similarity to Rpl24Ap and Rpl24Bp | Core | NA | NA | NA |
| 5471-YLR010C_NumOfGenes_2 | YLR010C | TEN1 | NA | Protein that regulates telomeric length; protects telomeric ends in a complex with Cdc13p and Stn1p; similar to human Ten1 which is critical for the telomeric function of the CST (Cdc13p-Stn1p-Ten1p) complex | Core | NA | NA | NA |
| 5472-YLR011W_NumOfGenes_2 | YLR011W | LOT6 | flavin-dependent quinone reductase | FMN-dependent NAD(P)H:quinone reductase; role in apoptosis-like cell death; may be involved in quinone detoxification; expression elevated at low temperature; sequesters the Cin5p transcription factor in the cytoplasm in complex with the proteasome under reducing conditions | Core | NA | NA | NA |
| 5473-YLR012C_NumOfGenes_2 | YLR012C | NA | NA | Putative protein of unknown function; YLR012C is not an essential gene | Core | NA | NA | NA |
| 5474-YLR013W_NumOfGenes_2 | YLR013W | GAT3 | NA | Protein containing GATA family zinc finger motifs; involved in spore wall assembly; sequence similarity to GAT4, and the double mutant gat3 gat4 exhibits reduced dityrosine fluorescence relative to the single mutants | Core | NA | NA | NA |
| 5475-YLR014C_NumOfGenes_2 | YLR014C | PPR1 | NA | Zinc finger transcription factor; contains a Zn(2)-Cys(6) binuclear cluster domain, positively regulates transcription of URA1, URA3, URA4, and URA10, which are involved in de novo pyrimidine biosynthesis, in response to pyrimidine starvation; activity may be modulated by interaction with Tup1p | Core | NA | NA | NA |
| 5476-YLR015W_NumOfGenes_2 | YLR015W | BRE2 | CPS60 | Subunit of COMPASS (Set1C) complex; COMPASS methylates Lys4 of histone H3 and functions in silencing at telomeres; has a C-terminal Sdc1 Dpy-30 Interaction (SDI) domain that mediates binding to Sdc1p; similar to trithorax-group protein ASH2L | Core | NA | NA | NA |
| 5477-YLR016C_NumOfGenes_2 | YLR016C | PML1 | NA | Subunit of the RES complex; RES complex is required for nuclear retention of unspliced pre-mRNAs; acts in the same pathway as Pml39p and Mlp1p | Core | NA | NA | NA |
| 5478-YLR017W_NumOfGenes_2 | YLR017W | MEU1 | S-methyl-5-thioadenosine phosphorylase | Methylthioadenosine phosphorylase (MTAP); catalyzes the initial step in the methionine salvage pathway; affects polyamine biosynthesis through regulation of ornithine decarboxylase (Spe1p) activity; regulates ADH2 gene expression | Core | NA | NA | NA |
| 5479-YLR018C_NumOfGenes_2 | YLR018C | POM34 | NA | Subunit of the transmembrane ring of the nuclear pore complex (NPC); contributes to nucleocytoplasmic transport, NPC biogenesis and spindle pole body duplication | Core | NA | NA | NA |
| 5480-YLR019W_NumOfGenes_2 | YLR019W | PSR2 | putative phosphatase | Plasma membrane phosphatase involved in the general stress response; required with Psr1p and Whi2p for full activation of STRE-mediated gene expression, possibly through dephosphorylation of Msn2p; PSR2 has a paralog, PSR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5481-YLR020C_NumOfGenes_2 | YLR020C | YEH2 | sterol esterase | Steryl ester hydrolase; catalyzes steryl ester hydrolysis at the plasma membrane; involved in sterol metabolism; YEH2 has a paralog, YEH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5482-YLR021W_NumOfGenes_2 | YLR021W | IRC25 | DMP2|PBA3|POC3 | Component of a heterodimeric Poc4p-Irc25p chaperone; involved in assembly of alpha subunits into the 20S proteasome; may regulate formation of proteasome isoforms with alternative subunits under different conditions; upregulates proteasome assembly in response to the unfolded protein response activated by mistargeting of proteins (UPRam) | Core | NA | NA | NA |