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 |
|---|---|---|---|---|---|---|---|---|
| 2168-YBR183W | YBR183W | YPC1 | phytoceramidase | Alkaline ceramidase; also has reverse (CoA-independent) ceramide synthase activity; catalyzes both breakdown and synthesis of phytoceramide; overexpression confers fumonisin B1 resistance; YPC1 has a paralog, YDC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2169-YBR184W | YBR184W | NA | NA | Putative protein of unknown function; YBR184W is not an essential gene | Core | NA | NA | NA |
| 2170-YBR185C | YBR185C | MBA1 | NA | Membrane-associated mitochondrial ribosome receptor; forms a complex with Mdm38p that may facilitate recruitment of mRNA-specific translational activators to ribosomes; possible role in protein export from the matrix to inner membrane | Core | NA | NA | NA |
| 2171-YBR186W | YBR186W | PCH2 | NA | Hexameric ring ATPase that remodels chromosome axis protein Hop1p; nucleolar component of the pachytene checkpoint, which prevents chromosome segregation when recombination and chromosome synapsis are defective; also represses meiotic interhomolog recombination in rDNA; required for meiotic double-stranded break formation | Accessory | Ancestral | NA | NA |
| 2172-YBR187W | YBR187W | GDT1 | putative ribosome biosynthesis protein GDT1 | Calcium transporter localized to the cis- and medial-Golgi apparatus; required for protein glycosylation; GFP-fusion protein localizes to the vacuole; TMEM165, a human gene which causes Congenital Disorders of Glycosylation is orthologous and functionally complements the null allele; expression pattern and physical interactions suggest a possible role in ribosome biogenesis; expression reduced in a gcr1 null mutant | Accessory | Ancestral | NA | NA |
| 2173-YBR188C | YBR188C | NTC20 | NA | Member of the NineTeen Complex (NTC); this complex contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs | Accessory | Unknown | NA | NA |
| 2174-YBR189W_NumOfGenes_2 | YBR189W | RPS9B | ribosomal 40S subunit protein S9B|rp21|YS11|S9B|S4|S13|SUP46|RPS13A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S9 and bacterial S4; RPS9B has a paralog, RPS9A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2175-YBR190W_NumOfGenes_2 | YBR190W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ribosomal protein gene RPL21A/YBR191W | Accessory | Ancestral | NA | NA |
| 2176-YBR191W | YBR191W | RPL21A | eL21|ribosomal 60S subunit protein L21A|L21e|L21A|URP1 | Ribosomal 60S subunit protein L21A; homologous to mammalian ribosomal protein L21, no bacterial homolog; RPL21A has a paralog, RPL21B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2177-YBR192W | YBR192W | RIM2 | PYT1 | Mitochondrial pyrimidine nucleotide transporter; imports pyrimidine nucleoside triphosphates and exports pyrimidine nucleoside monophosphates; member of the mitochondrial carrier family | Core | NA | NA | NA |
| 2178-YBR193C | YBR193C | MED8 | NA | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation | Core | NA | NA | NA |
| 2179-YBR194W | YBR194W | AIM4 | SOY1 | Protein proposed to be associated with the nuclear pore complex; null mutant is viable, displays elevated frequency of mitochondrial genome loss and is sensitive to freeze-thaw stress | Core | NA | NA | NA |
| 2180-YBR195C | YBR195C | MSI1 | CAC3 | Subunit of chromatin assembly factor I (CAF-1); chromatin assembly by CAF-1 affects multiple processes including silencing at telomeres, mating type loci, and rDNA; maintenance of kinetochore structure; deactivation of DNA damage checkpoint after DNA repair; chromatin dynamics during transcription; and repression of divergent noncoding transcription; Msi1p localizes to nucleus and cytoplasm and independently regulates the RAS/cAMP pathway via sequestration of Npr1p kinase | Core | NA | NA | NA |
| 2181-YBR196C | YBR196C | PGI1 | glucose-6-phosphate isomerase|CDC30 | Glycolytic enzyme phosphoglucose isomerase; catalyzes the interconversion of glucose-6-phosphate and fructose-6-phosphate; required for cell cycle progression and completion of the gluconeogenic events of sporulation | Core | NA | NA | NA |
| 2182-YBR196C-A | YBR196C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |