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 |
|---|---|---|---|---|---|---|---|---|
| 3968-YGR068C_NumOfGenes_2 | YGR068C | ART5 | NA | Protein proposed to regulate endocytosis of plasma membrane proteins; regulates by recruiting the ubiquitin ligase Rsp5p to its target in the plasma membrane; SWAT-GFP and mCherry fusion proteins localize to the cytosol | Core | NA | NA | NA |
| 3969-YGR069W | YGR069W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 3970-YGR070W | YGR070W | ROM1 | Rho family guanine nucleotide exchange factor ROM1|SKC1 | Guanine nucleotide exchange factor (GEF) for Rho1p; mutations are synthetically lethal with mutations in rom2, which also encodes a GEP; ROM1 has a paralog, ROM2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3971-YGR071C | YGR071C | ENV11 | NA | Protein proposed to be involved in vacuolar functions; mutant shows defect in CPY processing and fragmented vacuoles; deletion mutant has increased glycogen accumulation and displays elongated buds; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; ENV11 has a paralog, VID22, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3972-YGR072W | YGR072W | UPF3 | SUP112|SUA6 | Component of the nonsense-mediated mRNA decay (NMD) pathway; along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance | Core | NA | NA | NA |
| 3973-YGR073C | YGR073C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; extensively overlaps essential SMD1 gene encoding a U6 snRNP protein | Accessory | Ancestral | NA | NA |
| 3974-YGR074W | YGR074W | SMD1 | mRNA splicing protein SMD1|SPP92 | Core Sm protein Sm D1; part of heteroheptameric complex (with Smb1p, Smd2p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; relocalizes to the cytosol in response to hypoxia; homolog of human Sm D1; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3975-YGR075C | YGR075C | PRP38 | U4/U6-U5 snRNP complex subunit PRP38 | Unique component of the U4/U6.U5 tri-snRNP particle; tri-snRNP is required for conformational changes which result in the catalytic activation of the spliceosome; dispensable for spliceosome assembly | Core | NA | NA | NA |
| 3976-YGR076C | YGR076C | MRPL25 | mitochondrial 54S ribosomal protein YmL25|AFO1|YmL25|YMR26 | Mitochondrial ribosomal protein of the large subunit; mutation confers increased replicative lifespan | Core | NA | NA | NA |
| 3977-YGR077C | YGR077C | PEX8 | PAS6 | Intraperoxisomal organizer of the peroxisomal import machinery; organizes the formation of the importomer complex, bridging the docking complex with the RING finger complex; tightly associated with the lumenal face of the peroxisomal membrane; essential for peroxisome biogenesis; binds PTS1-signal receptor Pex5p, and PTS2-signal receptor Pex7p | Core | NA | NA | NA |
| 3978-YGR078C | YGR078C | PAC10 | tubulin-binding prefolding complex subunit PAC10|RKS2|PFD3|GIM2 | Part of the heteromeric co-chaperone GimC/prefoldin complex; complex promotes efficient protein folding | Core | NA | NA | NA |
| 3979-YGR079W | YGR079W | NA | NA | Putative protein of unknown function; YGR079W is not an essential gene | Core | NA | NA | NA |
| 3980-YGR080W | YGR080W | TWF1 | NA | Twinfilin; highly conserved actin monomer-sequestering protein involved in regulation of the cortical actin cytoskeleton; coordinates actin filament severing and monomer sequestering at sites of rapid actin turnover; composed of two cofilin-like regions, stimulates actin depolymerization as does the mouse homolog, mTwf1 | Core | NA | NA | NA |
| 3981-YGR081C | YGR081C | SLX9 | NA | Protein required for pre-rRNA processing; associated with the 90S pre-ribosome and 43S small ribosomal subunit precursor; interacts with U3 snoRNA; deletion mutant has synthetic fitness defect with an sgs1 deletion mutant | Core | NA | NA | NA |
| 3982-YGR082W | YGR082W | TOM20 | MOM19|MAS20 | Component of the TOM (translocase of outer membrane) complex; responsible for recognition and initial import steps for all mitochondrially directed proteins; acts as a receptor for incoming precursor proteins | Core | NA | NA | NA |