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 |
|---|---|---|---|---|---|---|---|---|
| 4148-YGR248W | YGR248W | SOL4 | 6-phosphogluconolactonase SOL4 | 6-phosphogluconolactonase; protein abundance increases in response to DNA replication stress; SOL4 has a paralog, SOL3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4149-YGR249W | YGR249W | MGA1 | NA | Protein similar to heat shock transcription factor; multicopy suppressor of pseudohyphal growth defects of ammonium permease mutants | Core | NA | NA | NA |
| 4150-YGR250C | YGR250C | RIE1 | NA | Putative RNA binding protein; localizes to stress granules induced by glucose deprivation; interacts with Rbg1p in a two-hybrid assay; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4151-YGR251W | YGR251W | NOP19 | DHI1 | Ribosome biogenesis factor; nucleolar protein associated with pre-rRNA components of the 90S preribosome, required for cleavage of pre-rRNA at A0, A1 and A2 sites; interacts with RNA helicase Dhr2p and RNA helicase-like protein Utp25p; required for incorporation of Utp25p into preribosomes | Core | NA | NA | NA |
| 4152-YGR252W | YGR252W | GCN5 | histone acetyltransferase GCN5|AAS104|KAT2|SWI9|ADA4 | Catalytic subunit of ADA and SAGA histone acetyltransferase complexes; modifies N-terminal lysines on histones H2B and H3; acetylates Rsc4p, a subunit of the RSC chromatin-remodeling complex, altering replication stress tolerance; relocalizes to the cytosol in response to hypoxia; mutant displays reduced transcription elongation in the G-less-based run-on (GLRO) assay; greater involvement in repression of RNAPII-dependent transcription than in activation | Core | NA | NA | NA |
| 4153-YGR253C | YGR253C | PUP2 | proteasome core particle subunit alpha 5|DOA5 | Alpha 5 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit zeta | Core | NA | NA | NA |
| 4154-YGR254W | YGR254W | ENO1 | phosphopyruvate hydratase ENO1|HSP48 | Enolase I, a phosphopyruvate hydratase; catalyzes conversion of 2-phosphoglycerate to phosphoenolpyruvate during glycolysis and the reverse reaction during gluconeogenesis; expression repressed in response to glucose; protein abundance increases in response to DNA replication stress; N-terminally propionylated in vivo; ENO1 has a paralog, ENO2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4155-YGR255C | YGR255C | COQ6 | putative N,N-dimethylaniline monooxygenase COQ6 | Flavin-dependent monooxygenase involved in ubiquinone biosynthesis; responsible for hydroxylation at position C5 and deamination at C4 during ubiquinone (Coenzyme Q) biosynthesis; localizes to matrix face of mitochondrial inner membrane in a large complex with other ubiquinone biosynthetic enzymes; human homolog COQ6 can complement yeast null mutant and is implicated in steroid-resistant nephrotic syndrome (SRNS) | Core | NA | NA | NA |
| 4156-YGR256W | YGR256W | GND2 | phosphogluconate dehydrogenase (decarboxylating) GND2 | 6-phosphogluconate dehydrogenase (decarboxylating); catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone; GND2 has a paralog, GND1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4157-YGR257C | YGR257C | MTM1 | NA | Mitochondrial protein of the mitochondrial carrier family; high affinity pyridoxal 5'-phosphate (PLP) transporter, important for delivery of PLP cofactor to mitochondrial enzymes; involved in mitochondrial iron homeostasis and in activating mitochondrial Sod2p by facilitating insertion of an essential manganese cofactor | Core | NA | NA | NA |
| 4158-YGR258C | YGR258C | RAD2 | ssDNA endodeoxyribonuclease RAD2 | Single-stranded DNA endonuclease; cleaves single-stranded DNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPG protein | Core | NA | NA | NA |
| 4159-YGR260W_NumOfGenes_2 | YGR260W | TNA1 | NA | High affinity nicotinic acid plasma membrane permease; responsible for uptake of low levels of nicotinic acid; expression of the gene increases in the absence of extracellular nicotinic acid or para-aminobenzoate (PABA) | Core | NA | NA | NA |
| 4160-YGR261C | YGR261C | APL6 | YKS5 | Beta3-like subunit of the yeast AP-3 complex; functions in transport of alkaline phosphatase to the vacuole via the alternate pathway; exists in both cytosolic and peripherally associated membrane-bound pools | Core | NA | NA | NA |
| 4161-YGR262C | YGR262C | BUD32 | serine/threonine protein kinase BUD32|LDB14 | Protein kinase; component of the EKC/KEOPS complex with Kae1p, Cgi121p, Pcc1p, and Gon7p; Pyrococcus Bud32 ortholog functions as a P-loop ATPase rather than a protein kinase in the context of the complex; EKC/KEOPS complex is required for t6A tRNA modification and telomeric TG1-3 recombination; may have role in transcription; mutation is functionally complemented by human TP53RK | Core | NA | NA | NA |
| 4162-YGR263C | YGR263C | SAY1 | steryl deacetylase | Sterol deacetylase; component of the sterol acetylation/deacetylation cycle along with Atf2p; active both in the endoplasmic reticulum (ER) and in lipid droplets; integral membrane protein with active site in the ER lumen; green fluorescent protein (GFP)-fusion protein localizes to the ER | Core | NA | NA | NA |