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 |
|---|---|---|---|---|---|---|---|---|
| 2378-YCR026C | YCR026C | NPP1 | nucleotide diphosphatase/phosphodiesterase NPP1 | Nucleotide pyrophosphatase/phosphodiesterase; mediates extracellular nucleotide phosphate hydrolysis along with Npp2p and Pho5p; activity and expression enhanced during conditions of phosphate starvation; involved in spore wall assembly; NPP1 has a paralog, NPP2, that arose from the whole genome duplication, and an npp1 npp2 double mutant exhibits reduced dityrosine fluorescence relative to the single mutants | Core | NA | NA | NA |
| 2379-YCR027C | YCR027C | RHB1 | putative GTPase RHB1|RSG1 | Putative Rheb-related GTPase; involved in regulating canavanine resistance and arginine uptake; member of the Ras superfamily of G-proteins | Core | NA | NA | NA |
| 2380-YCR028C | YCR028C | FEN2 | NA | Plasma membrane H+-pantothenate symporter; confers sensitivity to the antifungal agent fenpropimorph; relocalizes from vacuole to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 2381-YCR028C-A | YCR028C-A | RIM1 | NA | ssDNA-binding protein essential for mitochondrial genome maintenance; involved in mitochondrial DNA replication; stimulates utilization by Mip1p DNA polymerase of RNA primers synthesized by Rpo41p | Core | NA | NA | NA |
| 2382-YCR030C | YCR030C | SYP1 | YCR029C-A | Negative regulator of WASP-Arp23 complex; involved in endocytic site formation; directly inhibits Las17p stimulation of Arp23 complex-mediated actin assembly in vitro; may regulate assembly and disassembly of the septin ring; colocalizes and interacts with septin subunits; potential role in actin cytoskeletal organization | Core | NA | NA | NA |
| 2383-YCR031C | YCR031C | RPS14A | uS11|ribosomal 40S subunit protein S14A|S11|rp59A|S14A|RPL59|CRY1 | Protein component of the small (40S) ribosomal subunit; required for ribosome assembly and 20S pre-rRNA processing; mutations confer cryptopleurine resistance; homologous to mammalian ribosomal protein S14 and bacterial S11; RPS14A has a paralog, RPS14B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2384-YCR032W | YCR032W | BPH1 | NA | Protein homologous to Chediak-Higashi syndrome and Beige proteins; both of which are implicated in disease syndromes in human and mouse, respectively, due to defective lysosomal trafficking; mutant phenotype and genetic interactions suggest a role in protein sorting | Core | NA | NA | NA |
| 2385-YCR033W | YCR033W | SNT1 | NA | Subunit of the Set3C deacetylase complex; interacts directly with the Set3C subunit, Sif2p; putative DNA-binding protein; mutant has increased aneuploidy tolerance; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2386-YCR034W | YCR034W | ELO2 | fatty acid elongase ELO2|FEN1|VBM2|GNS1 | Fatty acid elongase, involved in sphingolipid biosynthesis; acts on fatty acids of up to 24 carbons in length; mutations have regulatory effects on 1,3-beta-glucan synthase, vacuolar ATPase, and the secretory pathway; ELO2 has a paralog, ELO1, that arose from the whole genome duplication; lethality of the elo2 elo3 double null mutation is functionally complemented by human ELOVL1 and weakly complemented by human ELOVL3 or ELOV7 | Core | NA | NA | NA |
| 2387-YCR035C | YCR035C | RRP43 | exosome non-catalytic core subunit RRP43 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp43p (OIP2, EXOSC8); protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2388-YCR036W | YCR036W | RBK1 | putative ribokinase | Putative ribokinase | Core | NA | NA | NA |
| 2389-YCR037C | YCR037C | PHO87 | SPX domain-containing inorganic phosphate transporter | Low-affinity inorganic phosphate (Pi) transporter; acts upstream of Pho81p in regulation of the PHO pathway; expression is independent of Pi concentration and Pho4p activity; contains 12 membrane-spanning segments; PHO87 has a paralog, PHO90, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2390-YCR038C_NumOfGenes_3 | YCR038C | BUD5 | Ras family guanine nucleotide exchange factor BUD5 | GTP/GDP exchange factor for Rsr1p (Bud1p); required for both axial and bipolar budding patterns; mutants exhibit random budding in all cell types | Core | NA | NA | NA |
| 2391-YCR040W_NumOfGenes_2 | YCR040W | MATALPHA1 | transcriptional co-activator mating type protein alpha|ALPHA1 | Transcriptional co-activator that regulates mating-type-specific genes; targets the transcription factor Mcm1p to the promoters of alpha-specific genes; one of two genes encoded by the MATalpha mating type cassette | Accessory | Ancestral | NA | NA |
| 2392-YCR041W_NumOfGenes_2 | YCR041W | NA | NA | Protein of unknown function; overexpression suppresses the high-frequency loss of mini-chromosomes, probably by increasing the rate of proper chromosome segregation; translated gene product of YCR041W, but not its transcript, is responsible for suppression; suppression ability of YCR041W is completely dependent on silencing protein Sir4p | Accessory | Ancestral | NA | NA |