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 |
|---|---|---|---|---|---|---|---|---|
| 3203-YDR514C_NumOfGenes_2 | YDR514C | NA | NA | Protein of unknown function that localizes to mitochondria; overexpression affects endocytic protein trafficking; YDR514C has a paralog, GFD2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3204-YDR515W_NumOfGenes_2 | YDR515W | SLF1 | SRO99 | RNA binding protein that associates with polysomes; may be involved in regulating mRNA translation; involved in the copper-dependent mineralization of copper sulfide complexes on cell surface in cells cultured in copper salts; SLF1 has a paralog, SRO9, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3205-YDR516C_NumOfGenes_2 | YDR516C | EMI2 | putative glucokinase | Non-essential protein of unknown function; required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulation; expression regulated by glucose-repression transcription factors Mig1/2p; EMI2 has a paralog, GLK1, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3206-YDR517W | YDR517W | GRH1 | NA | Acetylated cis-Golgi protein, involved in ER to Golgi transport; homolog of human GRASP65; forms a complex with the coiled-coil protein Bug1p; mutants are compromised for the fusion of ER-derived vesicles with Golgi membranes; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3207-YDR518W | YDR518W | EUG1 | protein disulfide isomerase EUG1 | Protein disulfide isomerase of the endoplasmic reticulum lumen; EUG1 has a paralog, PDI1, that arose from the whole genome duplication; function overlaps with that of Pdi1p; may interact with nascent polypeptides in the ER | Accessory | Ancestral | NA | NA |
| 3208-YDR519W | YDR519W | FPR2 | peptidylprolyl isomerase family protein FPR2|FKB2 | Membrane-bound peptidyl-prolyl cis-trans isomerase (PPIase); binds to the drugs FK506 and rapamycin; expression pattern suggests possible involvement in ER protein trafficking; relocalizes from nucleus to vacuole upon DNA replication stress; mutation is functionally complemented by human FKBP2 | Accessory | Ancestral | NA | NA |
| 3209-YDR520C_NumOfGenes_2 | YDR520C | URC2 | RRT4 | Putative Zn(II)2Cys6 motif containing transcription factor; non-essential gene identified in a screen for mutants with increased levels of rDNA transcription; similar to S. kluyveri Urc2p involved in uracil catabolism | Accessory | Ancestral | NA | NA |
| 3210-YDR522C | YDR522C | SPS2 | NA | Protein expressed during sporulation; SPS2 has a paralog, SPS22, that arose from the whole genome duplication; redundant with Sps22p for organization of the beta-glucan layer of the spore wall; S. pombe ortholog is a spore wall component | Accessory | Ancestral | NA | NA |
| 3211-YDR523C | YDR523C | SPS1 | putative serine/threonine protein kinase SPS1 | Putative protein serine/threonine kinase; localizes to the nucleus and cytoplasm; required for efficient spore packaging, prospore membrane development and closure and localization of enzymes involved in spore wall synthesis; interacts with and required for Ssp1p phosphorylation and turnover; member of the GCKIII subfamily of STE20 kinases; multiply phosphorylated on S/T residues; interacts with 14-3-3 proteins, Bmh1p and Bmh2p; expressed at the end of meiosis | Accessory | Ancestral | NA | NA |
| 3212-YDR524C | YDR524C | AGE1 | SAT1 | ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector; involved in the secretory and endocytic pathways; contains C2C2H2 cysteine/histidine motif | Accessory | Ancestral | NA | NA |
| 3213-YDR524C-A | YDR524C-A | NA | YDR524C-C | Dubious open reading frame unlikely to encode a functional protein; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 3214-YDR524C-B | YDR524C-B | NA | NA | Putative protein of unknown function; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; YDR524C-B has a paralog, YCL048W-A, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3215-YDR524W-C | YDR524W-C | NA | YDR524W-A | Putative protein of unknown function; small ORF identified by SAGE; deletion strains are moderately sensitive to the radiomimetic drug bleomycin | Accessory | Introgression | S. paradoxus | NA |
| 3216-YDR525W | YDR525W | API2 | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; not conserved in closely related Saccharomyces species; 26% of ORF overlaps the dubious ORF YDR524C-A; insertion mutation in a cdc34-2 mutant background causes altered bud morphology | Core | NA | NA | NA |
| 3217-YDR525W-A | YDR525W-A | SNA2 | NA | Protein of unknown function; has similarity to Pmp3p, which is involved in cation transport; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |