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 |
|---|---|---|---|---|---|---|---|---|
| 2693-YDR003W | YDR003W | RCR2 | SSH5 | Vacuolar protein; presumably functions within the endosomal-vacuolar trafficking pathway, affecting events that determine whether plasma membrane proteins are degraded or routed to the plasma membrane; RCR2 has a paralog, RCR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2694-YDR003W-A | YDR003W-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 2695-YDR004W | YDR004W | RAD57 | putative DNA-dependent ATPase RAD57 | Protein that stimulates strand exchange; stimulates strand exchange by stabilizing the binding of Rad51p to single-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; forms heterodimer with Rad55p | Core | NA | NA | NA |
| 2696-YDR005C | YDR005C | MAF1 | RNA polymerase III-inhibiting protein MAF1 | Highly conserved negative regulator of RNA polymerase III; involved in tRNA processing and stability; inhibits tRNA degradation via rapid tRNA decay (RTD) pathway; binds N-terminal domain of Rpc160p subunit of Pol III to prevent closed-complex formation; regulated by phosphorylation mediated by TORC1, protein kinase A, Sch9p, casein kinase 2; localizes to cytoplasm during vegetative growth and translocates to nucleus and nucleolus under stress conditions | Accessory | Ancestral | NA | NA |
| 2697-YDR006C | YDR006C | SOK1 | NA | Protein of unknown function; overexpression suppresses the growth defect of mutants lacking protein kinase A activity; involved in cAMP-mediated signaling; localized to the nucleus; similar to the mouse testis-specific protein PBS13 | Accessory | Ancestral | NA | NA |
| 2698-YDR007W_NumOfGenes_2 | YDR007W | TRP1 | phosphoribosylanthranilate isomerase TRP1 | Phosphoribosylanthranilate isomerase; catalyzes the third step in tryptophan biosynthesis; in 2004, the sequence of TRP1 from strain S228C was updated by changing the previously annotated internal STOP (TAA) to serine (TCA); enhances vegetative growth at low and high temperatures when used as an auxotrophic marker in strains such as W303 | Accessory | Ancestral | NA | NA |
| 2699-YDR009W | YDR009W | GAL3 | transcriptional regulator GAL3 | Transcriptional regulator; involved in activation of the GAL genes in response to galactose; forms a complex with Gal80p to relieve Gal80p inhibition of Gal4p; binds galactose and ATP but does not have galactokinase activity; GAL3 has a paralog, GAL1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2700-YDR010C | YDR010C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 2701-YDR011W | YDR011W | SNQ2 | ATP-binding cassette transporter SNQ2 | Plasma membrane ATP-binding cassette (ABC) transporter; multidrug transporter involved in multidrug resistance and resistance to singlet oxygen species | Accessory | Ancestral | NA | NA |
| 2702-YDR012W_NumOfGenes_2 | YDR012W | RPL4B | uL4|ribosomal 60S subunit protein L4B|L4|rp2|YL2|L4B|L2B | Ribosomal 60S subunit protein L4B; homologous to mammalian ribosomal protein L4 and bacterial L4; RPL4B has a paralog, RPL4A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2703-YDR013W | YDR013W | PSF1 | DNA replication protein PSF1|CDC101 | Subunit of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p); complex is localized to DNA replication origins and implicated in assembly of the DNA replication machinery | Core | NA | NA | NA |
| 2704-YDR014W | YDR014W | RAD61 | WPL1 | Subunit of a complex that inhibits sister chromatid cohesion; also negatively regulates chromosome condensation; inhibited by Eco1p-acetylated cohesin subunits Smc3p and Mcd1p; binds Smc3p ATPase head of cohesin; related to the human Wapl protein that controls the association of cohesin with chromatin | Core | NA | NA | NA |
| 2705-YDR014W-A_NumOfGenes_3 | YDR014W-A | HED1 | NA | Meiosis-specific protein; down-regulates Rad51p-mediated mitotic recombination when the meiotic recombination machinery is impaired; promotes synapsis and required for the normal morphogenesis of synaptonemal complex; prevents the recruitment of Rad54p to site-specific DNA double-strand breaks in vivo; early meiotic gene, transcribed specifically during meiotic prophase | Core | NA | NA | NA |
| 2706-YDR016C_NumOfGenes_2 | YDR016C | DAD1 | 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 |
| 2707-YDR017C | YDR017C | KCS1 | inositol polyphosphate kinase KCS1 | Inositol hexakisphosphate and inositol heptakisphosphate kinase; generation of high energy inositol pyrophosphates by Kcs1p is required for many processes such as vacuolar biogenesis, stress response, RNA polymerase I-mediated rRNA transcription and telomere maintenance; inositol hexakisphosphate is also known as IP6; inositol heptakisphosphate is also known as IP7 | Core | NA | NA | NA |