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 |
|---|---|---|---|---|---|---|---|---|
| 6068-YMR011W | YMR011W | HXT2 | hexose transporter HXT2 | High-affinity glucose transporter of the major facilitator superfamily; expression is induced by low levels of glucose and repressed by high levels of glucose | Core | NA | NA | NA |
| 6069-YMR012W | YMR012W | CLU1 | translation initiation factor 3 subunit CLU1|TIF31 | Subunit of the eukaryotic translation initiation factor 3 (eIF3); component of unknown function; deletion causes defects in mitochondrial organization but not in growth or translation initiation; can rescue cytokinesis and mitochondrial organization defects of the Dictyostelium cluA- mutant; eIF3 is also involved in programmed stop codon readthrough | Core | NA | NA | NA |
| 6070-YMR013C_NumOfGenes_2 | YMR013C | SEC59 | dolichol kinase | Dolichol kinase; catalyzes the terminal step in dolichyl monophosphate (Dol-P) biosynthesis; required for viability and for normal rates of lipid intermediate synthesis and protein N-glycosylation | Core | NA | NA | NA |
| 6071-YMR013W-A | YMR013W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps the characterized snoRNA gene snR73 | Core | NA | NA | NA |
| 6072-YMR014W | YMR014W | BUD22 | NA | Protein required for rRNA maturation and ribosomal subunit biogenesis; required for 18S rRNA maturation; also required for small ribosomal subunit biogenesis; cosediments with pre-ribosomal particles; mutation decreases efficiency of +1 Ty1 frameshifting and transposition, and affects budding pattern | Core | NA | NA | NA |
| 6073-YMR015C | YMR015C | ERG5 | C-22 sterol desaturase|CYP61 | C-22 sterol desaturase; a cytochrome P450 enzyme that catalyzes the formation of the C-22(23) double bond in the sterol side chain in ergosterol biosynthesis; may be a target of azole antifungal drugs | Core | NA | NA | NA |
| 6074-YMR016C | YMR016C | SOK2 | NA | Nuclear protein that negatively regulates pseudohyphal differentiation; plays a regulatory role in the cyclic AMP (cAMP)-dependent protein kinase (PKA) signal transduction pathway; relocalizes to the cytosol in response to hypoxia; SOK2 has a paralog, PHD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6075-YMR017W | YMR017W | SPO20 | DBI9 | Meiosis-specific subunit of the t-SNARE complex; required for prospore membrane formation during sporulation; similar to but not functionally redundant with Sec9p; binds to phosphatidic acid; SNAP-25 homolog | Core | NA | NA | NA |
| 6076-YMR018W | YMR018W | PEX9 | NA | Putative protein of unknown function with similarity to human PEX5Rp; transcription increases during colony development similar to genes involved in peroxisome biogenesis; YMR018W is not an essential gene; PEX5Rp is also known as peroxin protein 5 related protein | Core | NA | NA | NA |
| 6077-YMR019W | YMR019W | STB4 | NA | Putative transcription factor; contains a Zn(II)2Cys6 zinc finger domain characteristic of DNA-binding proteins; computational analysis suggests a role in regulation of expression of genes encoding transporters; binds Sin3p in a two-hybrid assay; | Core | NA | NA | NA |
| 6078-YMR020W | YMR020W | FMS1 | polyamine oxidase | Polyamine oxidase; converts spermine to spermidine, which is required for the essential hypusination modification of translation factor eIF-5A; also involved in pantothenic acid biosynthesis | Core | NA | NA | NA |
| 6079-YMR021C | YMR021C | MAC1 | CUA1 | Copper-sensing transcription factor; involved in regulation of genes required for high affinity copper transport; required for regulation of yeast copper genes in response to DNA-damaging agents; undergoes changes in redox state in response to changing levels of copper or MMS | Core | NA | NA | NA |
| 6080-YMR022W | YMR022W | UBC7 | E2 ubiquitin-conjugating protein UBC7|DER2|QRI8 | Ubiquitin conjugating enzyme; involved in the ER-associated protein degradation (ERAD) pathway and in the inner nuclear membrane-associated degradation (INMAD) pathway; requires Cue1p for recruitment to the ER membrane; proposed to be involved in chromatin assembly | Core | NA | NA | NA |
| 6081-YMR023C | YMR023C | MSS1 | PET53 | Mitochondrial protein; forms a heterodimer complex with Mto1p that performs the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs; similar to human GTPBP3 | Core | NA | NA | NA |
| 6082-YMR024W | YMR024W | MRPL3 | mitochondrial 54S ribosomal protein YmL3|YmL3 | Mitochondrial ribosomal protein of the large subunit; located in close proximity to the polypeptide exit channel of the ribosome; mutations in human homolog MRPL44 cause childhood cardiomyopathy; human MRPL44 deficiency results in inefficient assembly of the mitochondrial ribosome, and in tissue-specific respiratory chain deficiency, manifesting as either Complex I+Complex IV or Complex IV deficiency, depending on a cell type | Core | NA | NA | NA |