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 |
|---|---|---|---|---|---|---|---|---|
| 4328-YHR074W | YHR074W | QNS1 | glutamine-dependent NAD(+) synthetase | Glutamine-dependent NAD(+) synthetase; essential for the formation of NAD(+) from nicotinic acid adenine dinucleotide | Core | NA | NA | NA |
| 4329-YHR075C | YHR075C | PPE1 | carboxylesterase-mitochondrial 37S ribosomal protein YmS2|YmS2|MRPS2 | Protein with carboxyl methyl esterase activity; may have a role in demethylation of the phosphoprotein phosphatase catalytic subunit; also identified as a small subunit mitochondrial ribosomal protein | Core | NA | NA | NA |
| 4330-YHR076W | YHR076W | PTC7 | type 2C protein phosphatase PTC7 | Type 2C serine/threonine protein phosphatase (PP2C); alternatively spliced to create two mRNA isoforms; protein from spliced form localizes to the mitochondria while the one from the unspliced form is localized to the nuclear envelope; activates coenzyme Q6 biosynthesis by dephosphorylation of demethoxy-Q6 hydroxylase Coq7p | Core | NA | NA | NA |
| 4331-YHR077C | YHR077C | NMD2 | SUP111|UPF2|SUA1|IFS1 | Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance | Core | NA | NA | NA |
| 4332-YHR078W | YHR078W | NA | NA | High osmolarity-regulated gene of unknown function | Core | NA | NA | NA |
| 4333-YHR079C | YHR079C | IRE1 | bifunctional endoribonuclease/protein kinase IRE1|ERN1 | Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; role in homeostatic adaptation to ER stress; Kar2p binds inactive Ire1p and releases from it upon ER stress | Core | NA | NA | NA |
| 4334-YHR079C-A | YHR079C-A | SAE3 | YHR079BC|YHR079C-B | Meiosis-specific protein involved in meiotic recombination; involved in DMC1-dependent meiotic recombination; forms heterodimer with Mei5p; proposed to be an assembly factor for Dmc1p | Core | NA | NA | NA |
| 4335-YHR080C | YHR080C | LAM4 | LTC3 | Sterol-binding protein that localizes to puncta in the cortical ER; sterol binding occurs via two StART-like domains; one of six StART-like domain-containing proteins in yeast that may be involved in intracellular sterol transfer between membranes; conserved across eukaryotes; has both GRAM and StART-like (VASt) domains; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 4336-YHR081W | YHR081W | LRP1 | RRP47|YC1D | Nuclear exosome-associated nucleic acid binding protein; involved in RNA processing, surveillance, degradation, tethering, and export; forms a stable heterodimer with Rrp6p and regulates its exonucleolytic activity; rapidly degraded by the proteasome in the absence of Rrp6p; homolog of mammalian nuclear matrix protein C1D involved in regulation of DNA repair and recombination | Core | NA | NA | NA |
| 4337-YHR082C | YHR082C | KSP1 | putative serine/threonine protein kinase KSP1 | Serine/threonine protein kinase; associates with TORC1 and likely involved in TOR signaling cascades; negative regulator of autophagy; nuclear translocation required for haploid filamentous growth; regulates filamentous growth induced nuclear translocation of Bcy1p, Fus3p, and Sks1p; overproduction causes allele-specific suppression of prp20-10; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4338-YHR083W | YHR083W | SAM35 | SAM complex subunit SAM35|TOM38|TOB38|FMP20 | Component of the sorting and assembly machinery (SAM) complex; the SAM (or TOB) complex is located in the mitochondrial outer membrane; the complex binds precursors of beta-barrel proteins and facilitates their insertion into the outer membrane | Core | NA | NA | NA |
| 4339-YHR084W | YHR084W | STE12 | homeodomain family transcription factor STE12 | Transcription factor that is activated by a MAPK signaling cascade; activates genes involved in mating or pseudohyphal/invasive growth pathways; cooperates with Tec1p transcription factor to regulate genes specific for invasive growth | Core | NA | NA | NA |
| 4340-YHR085W | YHR085W | IPI1 | NA | Component of the Rix1 complex and possibly pre-replicative complexes; required for processing of ITS2 sequences from 35S pre-rRNA; component of the pre-60S ribosomal particle with the dynein-related AAA-type ATPase Mdn1p; required for pre-replicative complex (pre-RC) formation and maintenance during DNA replication licensing; relocalizes to the cytosol in response to hypoxia; essential gene | Core | NA | NA | NA |
| 4341-YHR086W | YHR086W | NAM8 | MUD15|MRE2 | RNA binding protein, component of the U1 snRNP protein; mutants are defective in meiotic recombination and in formation of viable spores, involved in the formation of DSBs through meiosis-specific splicing of REC107 pre-mRNA; Nam8p regulon embraces the meiotic pre-mRNAs of REC107, HFM1, AMA1 SPO22 and PCH2; the putative RNA binding domains RRM2 and RRM3 are required for Nam8p meiotic function | Core | NA | NA | NA |
| 4342-YHR086W-A | YHR086W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Core | NA | NA | NA |