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 |
|---|---|---|---|---|---|---|---|---|
| 6968-YOR004W | YOR004W | UTP23 | rRNA-binding ribosome biosynthesis protein UTP23 | Component of the small subunit processome; involved in 40S ribosomal subunit biogenesis; interacts with snR30 and is required for dissociation of snR30 from large pre-ribosomal particles; has homology to PINc domain protein Fcf1p, although the PINc domain of Utp23p is not required for function; essential protein | Core | NA | NA | NA |
| 6969-YOR005C | YOR005C | DNL4 | DNA ligase (ATP) DNL4|LIG4 | DNA ligase required for nonhomologous end-joining (NHEJ); forms stable heterodimer with required cofactor Lif1p, interacts with Nej1p; involved in meiosis, not essential for vegetative growth; mutations in human ortholog lead to ligase IV syndrome and Dubowitz syndrome | Core | NA | NA | NA |
| 6970-YOR006C | YOR006C | TSR3 | NA | Protein required for 20S pre-rRNA processing; involved in processing of the 20S pre-rRNA at site D to generate mature 18S rRNA; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 6971-YOR007C | YOR007C | SGT2 | NA | Glutamine-rich cytoplasmic cochaperone; serves as a scaffold bringing together Get4, Get5p, and other TRC complex members that are required to mediate posttranslational insertion of tail-anchored proteins into the ER membrane; interacts with the prion domain of Sup35p; amyloid sensor; plays a role in targeting chaperones to prion aggregates; similar to human cochaperone SGT; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 6972-YOR008C | YOR008C | SLG1 | WSC1|HCS77 | Sensor-transducer of the stress-activated PKC1-MPK1 kinase pathway; involved in maintenance of cell wall integrity; required for mitophagy; involved in organization of the actin cytoskeleton; secretory pathway Wsc1p is required for the arrest of secretion response | Core | NA | NA | NA |
| 6973-YOR008C-A | YOR008C-A | NA | NA | Putative protein of unknown function; includes a potential transmembrane domain; deletion results in slightly lengthened telomeres; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Accessory | Unknown | NA | NA |
| 6974-YOR008W-B | YOR008W-B | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6975-YOR009W_NumOfGenes_2 | YOR009W | TIR4 | NA | Cell wall mannoprotein; expressed under anaerobic conditions and required for anaerobic growth; transcription is also induced by cold shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins | Accessory | Ancestral | NA | NA |
| 6976-YOR010C | YOR010C | TIR2 | putative GPI-anchored mannoprotein|SRP2 | Putative cell wall mannoprotein; member of the Srp1p/Tip1p family of serine-alanine-rich proteins; transcription is induced by cold shock and anaerobiosis; TIR2 has a paralog, TIR3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6977-YOR011W | YOR011W | AUS1 | ATP-binding cassette sterol transporter AUS1 | Plasma membrane sterol transporter of the ATP-binding cassette family; required, along with Pdr11p, for uptake of exogenous sterols and their incorporation into the plasma membrane; activity is stimulated by phosphatidylserine; sterol uptake is required for anaerobic growth because sterol biosynthesis requires oxygen; AUS1 has a paralog, PDR11, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6978-YOR011W-A | YOR011W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6979-YOR012W | YOR012W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6980-YOR013W | YOR013W | IRC11 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized gene YOR012C; null mutant displays increased levels of spontaneous Rad52 foci | Accessory | Ancestral | NA | NA |
| 6981-YOR014W | YOR014W | RTS1 | protein phosphatase 2A regulatory subunit RTS1|SCS1 | B-type regulatory subunit of protein phosphatase 2A (PP2A); Rts1p and Cdc55p are alternative regulatory subunits for PP2A catalytic subunits, Pph21p and Pph22p; PP2A-Rts1p protects cohesin when recruited by Sgo1p to the pericentromere; highly enriched at centromeres in the absence of Cdc55p; required for maintenance of septin ring organization during cytokinesis, for ring disassembly in G1 and for dephosphorylation of septin, Shs1p; homolog of the mammalian B' subunit of PP2A | Core | NA | NA | NA |
| 6982-YOR015W | YOR015W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YOR015W is not an essential gene | Core | NA | NA | NA |