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 |
|---|---|---|---|---|---|---|---|---|
| 5498-YLR037C | YLR037C | PAU23 | seripauperin PAU23|DAN2 | Cell wall mannoprotein; has similarity to Tir1p, Tir2p, Tir3p, and Tir4p; member of the seripauperin multigene family encoded mainly in subtelomeric regions; expressed under anaerobic conditions, completely repressed during aerobic growth | Accessory | Unknown | NA | NA |
| 5499-YLR038C | YLR038C | COX12 | cytochrome c oxidase subunit VIb | Subunit VIb of cytochrome c oxidase; cytochrome c oxidase is also known as respiratory Complex IV and is the terminal member of the mitochondrial inner membrane electron transport chain; required for assembly of cytochrome c oxidase but not required for activity after assembly; phosphorylated; easily released from the intermembrane space, suggesting a loose association with Complex IV | Core | NA | NA | NA |
| 5500-YLR039C | YLR039C | RIC1 | NA | Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes | Core | NA | NA | NA |
| 5501-YLR040C | YLR040C | AFB1 | NA | MATalpha-specific a-factor blocker; contributes to mating efficiency under certain conditions; localizes to the cell wall; predicted to be a GPI-attached protein; upregulated by Mcm1p-Alpha1p transcription factor; partially overlaps the dubious ORF YLR041W | Core | NA | NA | NA |
| 5502-YLR041W | YLR041W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YLR040C | Accessory | Ancestral | NA | NA |
| 5503-YLR042C | YLR042C | NA | NA | Cell wall protein of unknown function; localizes to the cytoplasm; deletion improves xylose fermentation in industrially engineered strains; YLR042C is not an essential gene | Core | NA | NA | NA |
| 5504-YLR043C | YLR043C | TRX1 | thioredoxin TRX1|LMA1 | Cytoplasmic thioredoxin isoenzyme; part of thioredoxin system which protects cells against oxidative and reductive stress; forms LMA1 complex with Pbi2p; acts as a cofactor for Tsa1p; required for ER-Golgi transport and vacuole inheritance; with Trx2p, facilitates mitochondrial import of small Tims Tim9p, Tim10p, Tim13p by maintaining them in reduced form; abundance increases iunder DNA replication stress; TRX1 has a paralog, TRX2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5505-YLR044C | YLR044C | PDC1 | indolepyruvate decarboxylase 1 | Major of three pyruvate decarboxylase isozymes; key enzyme in alcoholic fermentation; decarboxylates pyruvate to acetaldehyde; involved in amino acid catabolism; subject to glucose-, ethanol-, and autoregulation; activated by phosphorylation in response to glucose levels; N-terminally propionylated in vivo | Core | NA | NA | NA |
| 5506-YLR045C | YLR045C | STU2 | NA | Microtubule-associated protein (MAP) of the XMAP215/Dis1 family; regulates microtubule dynamics during spindle orientation and metaphase chromosome alignment; interacts with spindle pole body component Spc72p | Core | NA | NA | NA |
| 5507-YLR046C | YLR046C | NA | RLA1 | Putative membrane protein; member of the fungal lipid-translocating exporter (LTE) family of proteins; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance; YLR046C has a paralog, RTA1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5508-YLR047C | YLR047C | FRE8 | putative ferric-chelate reductase | Protein with sequence similarity to iron/copper reductases; involved in iron homeostasis; deletion mutant has iron deficiency/accumulation growth defects; expression increased in the absence of copper-responsive transcription factor Mac1p | Core | NA | NA | NA |
| 5509-YLR048W | YLR048W | RPS0B | uS2|ribosomal 40S subunit protein S0B|S2|S0B|YST2|NAB1B | Protein component of the small (40S) ribosomal subunit; RPS0B has a paralog, RPS0A, that arose from the whole genome duplication; required for maturation of 18S rRNA along with Rps0Ap; deletion of either RPS0 gene reduces growth rate, deletion of both genes is lethal; homologous to human ribosomal protein SA and bacterial S2 | Core | NA | NA | NA |
| 5510-YLR049C | YLR049C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5511-YLR050C | YLR050C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YLR050C is not an essential gene | Core | NA | NA | NA |
| 5512-YLR051C | YLR051C | FCF2 | NA | Nucleolar protein involved in the early steps of 35S rRNA processing; interacts with Faf1p; member of a transcriptionally co-regulated set of genes called the RRB regulon; essential gene | Core | NA | NA | NA |