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 |
|---|---|---|---|---|---|---|---|---|
| 4073-YGR173W | YGR173W | RBG2 | GIR1 | Protein with a role in translation; forms a complex with Gir2p; has similarity to mammalian developmentally regulated GTP-binding protein | Core | NA | NA | NA |
| 4074-YGR174C | YGR174C | CBP4 | NA | Mitochondrial protein required for assembly of cytochrome bc1 complex; interacts with the Cbp3p-Cbp6p complex and newly synthesized cytochrome b (Cobp) to promote assembly of Cobp into the cytochrome bc1 complex | Core | NA | NA | NA |
| 4075-YGR174W-A | YGR174W-A | NA | NA | Putative protein of unknown function; predicted to have a role in cell budding based on computational "guilt by association" analysis | Accessory | Unknown | NA | NA |
| 4076-YGR175C | YGR175C | ERG1 | squalene monooxygenase | Squalene epoxidase; catalyzes the epoxidation of squalene to 2,3-oxidosqualene; plays an essential role in the ergosterol-biosynthesis pathway and is the specific target of the antifungal drug terbinafine; human SQLE functionally complements the lethality of the erg1 null mutation | Core | NA | NA | NA |
| 4077-YGR176W | YGR176W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Introgression | S. paradoxus | NA |
| 4078-YGR177C | YGR177C | ATF2 | alcohol O-acetyltransferase | Alcohol acetyltransferase; may play a role in steroid detoxification; forms volatile esters during fermentation, which is important for brewing and winemaking | Core | NA | NA | NA |
| 4079-YGR178C | YGR178C | PBP1 | MRS16 | Component of glucose deprivation induced stress granules; involved in P-body-dependent granule assembly; similar to human ataxin-2; interacts with Pab1p to regulate mRNA polyadenylation; interacts with Mkt1p to regulate HO translation; protein increases in abundance and relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4080-YGR179C | YGR179C | OKP1 | NA | Outer kinetochore protein required for accurate chromosome segregation; component of COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) a kinetochore sub-complex which functions as a platform for kinetochore assembly; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-Q and fission yeast fta7 | Core | NA | NA | NA |
| 4081-YGR180C | YGR180C | RNR4 | ribonucleotide-diphosphate reductase subunit RNR4|PSO3|CRT3 | Ribonucleotide-diphosphate reductase (RNR) small subunit; the RNR complex catalyzes the rate-limiting step in dNTP synthesis and is regulated by DNA replication and DNA damage checkpoint pathways via localization of the small subunits; relocalizes from nucleus to cytoplasm upon DNA replication stress; RNR4 has a paralog, RNR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4082-YGR181W | YGR181W | TIM13 | protein translocase subunit TIM13 | Mitochondrial intermembrane space protein; forms a complex with Tim8p that delivers a subset of hydrophobic proteins to the TIM22 complex for insertion into the inner membrane | Core | NA | NA | NA |
| 4083-YGR182C | YGR182C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF TIM13/YGR181W | Accessory | Ancestral | NA | NA |
| 4084-YGR183C | YGR183C | QCR9 | ubiquinol--cytochrome-c reductase subunit 9|UCR9 | Subunit 9 of ubiquinol cytochrome-c reductase (Complex III); Complex III is a component of the mitochondrial inner membrane electron transport chain; required for electron transfer at the ubiquinol oxidase site of the complex | Core | NA | NA | NA |
| 4085-YGR184C | YGR184C | UBR1 | E3 ubiquitin-protein ligase UBR1|PTR1 | E3 ubiquitin ligase (N-recognin); heterodimerizes with Rad6p to recognize and ubiquitinate substrates of the N-end rule pathway; role in endoplasmic reticulum-associated protein degradation (ERAD) in the absence of canonical ER membrane ligases or after stress; major role in targeting misfolded cytosolic proteins for degradation; regulates peptide transport via Cup9p ubiquitination; mutation in human UBR1 causes Johansson-Blizzard Syndrome (JBS) | Core | NA | NA | NA |
| 4086-YGR185C | YGR185C | TYS1 | tyrosine--tRNA ligase TYS1|TyrRS|TTS1 | Cytoplasmic tyrosyl-tRNA synthetase; required for cytoplasmic protein synthesis; interacts with positions 34 and 35 of the tRNATyr anticodon; mutations in human ortholog YARS are associated with Charcot-Marie-Tooth (CMT) neuropathies; human ortholog YARS functionally complements the heat sensitivity of a ts allele; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4087-YGR186W | YGR186W | TFG1 | transcription factor IIF subunit TFG1|RAP74|SSU71 | TFIIF (Transcription Factor II) largest subunit; involved in both transcription initiation and elongation of RNA polymerase II; homologous to human RAP74 | Core | NA | NA | NA |