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 |
|---|---|---|---|---|---|---|---|---|
| 6383-YMR311C | YMR311C | GLC8 | NA | Regulatory subunit of protein phosphatase 1 (Glc7p); involved in glycogen metabolism and chromosome segregation; proposed to regulate Glc7p activity via conformational alteration; ortholog of the mammalian protein phosphatase inhibitor 2; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6384-YMR312W | YMR312W | ELP6 | Elongator subunit ELP6|KTI4|TOT6|HAP3 | Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex; which is required for modification of wobble nucleosides in tRNA; required for Elongator structural integrity | Core | NA | NA | NA |
| 6385-YMR313C | YMR313C | TGL3 | bifunctional triglyceride lipase/lysophosphatidylethanolamine acyltransferase | Bifunctional triacylglycerol lipase and LPE acyltransferase; major lipid particle-localized triacylglycerol (TAG) lipase; catalyzes acylation of lysophosphatidylethanolamine (LPE), a function which is essential for sporulation; protein level and stability of Tgl3p are markedly reduced in the absence of lipid droplets; required with Tgl4p for timely bud formation | Core | NA | NA | NA |
| 6386-YMR314W | YMR314W | PRE5 | proteasome core particle subunit alpha 6 | Alpha 6 subunit of the 20S proteasome; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6387-YMR315W | YMR315W | NA | NA | Protein with NADP(H) oxidoreductase activity; transcription is regulated by Stb5p in response to NADPH depletion induced by diamide; promoter contains a putative Stb5p binding site; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6388-YMR315W-A | YMR315W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6389-YMR316C-A | YMR316C-A | NA | NA | Protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; mRNA identified as translated by ribosome profiling data; overlaps the verified gene DIA1/YMR316W | Core | NA | NA | NA |
| 6390-YMR316W | YMR316W | DIA1 | NA | Protein of unknown function; involved in invasive and pseudohyphal growth; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 6391-YMR317W_NumOfGenes_3 | YMR317W | NA | NA | Putative protein of unknown function; has some similarity to sialidase from Trypanosoma; YMR317W is not an essential gene | Core | NA | NA | NA |
| 6392-YMR318C | YMR318C | ADH6 | NADP-dependent alcohol dehydrogenase|ADHVI | NADPH-dependent medium chain alcohol dehydrogenase; has broad substrate specificity; member of the cinnamyl family of alcohol dehydrogenases; may be involved in fusel alcohol synthesis or in aldehyde tolerance; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6393-YMR319C | YMR319C | FET4 | NA | Low-affinity Fe(II) transporter of the plasma membrane | Core | NA | NA | NA |
| 6394-YMR320W | YMR320W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR320W is not an essential gene | Accessory | Unknown | NA | NA |
| 6395-YMR324C | YMR324C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; transcription is AZF1 dependent in glycerol-lactate medium and SLT2 dependent in response to the lipid hydroperoxides | Accessory | Unknown | NA | NA |
| 6396-YMR326C_NumOfGenes_2 | YMR326C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the telomere on the right arm of chromosome 13 | Accessory | Ancestral | NA | NA |
| 6397-YNL001W | YNL001W | DOM34 | ribosome dissociation factor DOM34 | Protein that facilitates ribosomal subunit dissociation; Dom34-Hbs1 complex and Rli1p have roles in dissociating inactive ribosomes to facilitate translation restart, particularly ribosomes stalled in 3' UTRs; required for RNA cleavage in no-go decay, but reports conflict on endonuclease activity; Pelota ortholog; protein abundance increases in response to DNA replication stress; DOM34 has a paralog, YCL001W-B, that arose from the whole genome duplication | Core | NA | NA | NA |