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 |
|---|---|---|---|---|---|---|---|---|
| 2393-YCR042C | YCR042C | TAF2 | TafII150|TSM1|TAF150 | TFIID subunit (150 kDa); involved in RNA polymerase II transcription initiation | Core | NA | NA | NA |
| 2394-YCR043C | YCR043C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the Golgi apparatus; YCR043C is not an essential gene | Core | NA | NA | NA |
| 2395-YCR044C | YCR044C | PER1 | COS16 | Protein of the endoplasmic reticulum; required for GPI-phospholipase A2 activity that remodels the GPI anchor as a prerequisite for association of GPI-anchored proteins with lipid rafts; functionally complemented by human ortholog PERLD1 | Core | NA | NA | NA |
| 2396-YCR045W-A_NumOfGenes_2 | YCR045W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps with YCR045C; identified by gene-trapping, microarray expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 2397-YCR046C | YCR046C | IMG1 | mitochondrial 54S ribosomal protein IMG1 | Mitochondrial ribosomal protein of the large subunit; required for respiration and for maintenance of the mitochondrial genome | Core | NA | NA | NA |
| 2398-YCR047C_NumOfGenes_2 | YCR047C | BUD23 | 18S rRNA (guanine1575-N7)-methyltransferase | Methyltransferase that methylates residue G1575 of 18S rRNA; required for rRNA processing and nuclear export of 40S ribosomal subunits independently of methylation activity; diploid mutant displays random budding pattern; functional homolog of human WBSCR22 | Core | NA | NA | NA |
| 2399-YCR048W_NumOfGenes_3 | YCR048W | ARE1 | sterol acyltransferase|SAT2 | Acyl-CoA:sterol acyltransferase; endoplasmic reticulum enzyme that contributes the major sterol esterification activity in the absence of oxygen; ARE1 has a paralog, ARE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2400-YCR051W | YCR051W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; contains ankyrin (Ank) repeats; YCR051W is not an essential gene | Core | NA | NA | NA |
| 2401-YCR052W | YCR052W | RSC6 | NA | Component of the RSC chromatin remodeling complex; essential for mitotic growth; RSC6 has a paralog, SNF12, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2402-YCR053W | YCR053W | THR4 | threonine synthase THR4 | Threonine synthase; conserved protein that catalyzes formation of threonine from O-phosphohomoserine; expression is regulated by the GCN4-mediated general amino acid control pathway | Core | NA | NA | NA |
| 2403-YCR054C | YCR054C | CTR86 | NA | Essential protein of unknown function; with orthologs in Ashbya gossypii and Candida albicans; similar to human ATXN10, mutations in which cause spinocerebellar ataxia type 10; codon usage corresponds to that observed for yeast genes expressed at low levels; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2404-YCR057C | YCR057C | PWP2 | snoRNA-binding rRNA-processing protein PWP2|UTP1|YCR058C|YCR055C | Conserved 90S pre-ribosomal component; essential for proper endonucleolytic cleavage of the 35 S rRNA precursor at A0, A1, and A2 sites; contains eight WD-repeats; PWP2 deletion leads to defects in cell cycle and bud morphogenesis | Core | NA | NA | NA |
| 2405-YCR059C | YCR059C | YIH1 | NA | Negative regulator of eIF2 kinase Gcn2p; competes with Gcn2p for binding to Gcn1p; may contribute to regulation of translation in response to starvation via regulation of Gcn2p; binds to monomeric actin and to ribosomes and polyribosomes; ortholog of mammalian IMPACT | Core | NA | NA | NA |
| 2406-YCR060W_NumOfGenes_2 | YCR060W | TAH1 | NA | Component of conserved R2TP complex (Rvb1-Rvb2-Tah1-Pih1); R2TP complex interacts with Hsp90 (Hsp82p and Hsc82p) to mediate assembly of large protein complexes such as box C/D snoRNPs and RNA polymerase II; contains a single TPR domain with at least two TPR motifs; plays a role in determining prion variants | Accessory | Ancestral | NA | NA |
| 2407-YCR061W | YCR061W | NA | YCR062W | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; induced by treatment with 8-methoxypsoralen and UVA irradiation | Core | NA | NA | NA |