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 |
|---|---|---|---|---|---|---|---|---|
| 6608-YNL218W | YNL218W | MGS1 | ssDNA-dependent ATPase MGS1 | Protein with DNA-dependent ATPase and ssDNA annealing activities; involved in maintenance of genome; interacts functionally with DNA polymerase delta; homolog of human Werner helicase interacting protein (WHIP); forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 6609-YNL219C | YNL219C | ALG9 | dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase | Mannosyltransferase, involved in N-linked glycosylation; catalyzes the transfer of both the seventh mannose residue on B-arm and ninth mannose residue on the C-arm from Dol-P-Man to lipid-linked oligosaccharides; human homolog ALG9 can complement yeast null mutant; mutation of human homolog causes type 1 congenital disorders of glycosylation | Core | NA | NA | NA |
| 6610-YNL220W | YNL220W | ADE12 | adenylosuccinate synthase|BRA9 | Adenylosuccinate synthase; catalyzes the first step in synthesis of adenosine monophosphate from inosine 5'monophosphate during purine nucleotide biosynthesis; exhibits binding to single-stranded autonomously replicating (ARS) core sequence | Accessory | Ancestral | NA | NA |
| 6611-YNL221C | YNL221C | POP1 | ribonuclease P/MRP protein subunit POP1 | Subunit of RNase MRP, nuclear RNase P and telomerase complexes; RNase MRP cleaves pre-rRNA, nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs, while telomerase replenishes telomeric DNA; binds to the RPR1 RNA subunit in RNase P | Core | NA | NA | NA |
| 6612-YNL222W | YNL222W | SSU72 | RNA polymerase II subunit A C-terminal domain phosphatase | Phosphatase and transcription/RNA-processing factor; associates with TFIIB and cleavage/polyadenylation factor Pta1p; exhibits phosphatase activity on serine-5 and serine-7 of the RNA polymerase II C-terminal domain; affects start site selection and transcriptional read through in vivo | Core | NA | NA | NA |
| 6613-YNL223W | YNL223W | ATG4 | cysteine protease ATG4|AUT2|APG4 | Conserved cysteine protease required for autophagy; cleaves Atg8p to a form required for autophagosome and Cvt vesicle generation | Core | NA | NA | NA |
| 6614-YNL224C | YNL224C | SQS1 | PFA1 | Protein that stimulates the ATPase and helicase activities of Prp43p; acts with Prp43p to stimulate 18s rRNA maturation by Nob1p; overexpression antagonizes the suppression of splicing defects by spp382 mutants; component of pre-ribosomal particles; relocalizes from nucleus to nucleolus upon DNA replication stress | Core | NA | NA | NA |
| 6615-YNL225C | YNL225C | CNM67 | NA | Component of the spindle pole body outer plaque; required for spindle orientation and mitotic nuclear migration; CNM67 has a paralog, ADY3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6616-YNL226W | YNL226W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene JJJ1/YNL227C | Accessory | Ancestral | NA | NA |
| 6617-YNL227C_NumOfGenes_2 | YNL227C | JJJ1 | NA | Co-chaperone that stimulates the ATPase activity of Ssa1p; required for a late step of ribosome biogenesis; associated with the cytosolic large ribosomal subunit; contains a J-domain; mutation causes defects in fluid-phase endocytosis | Core | NA | NA | NA |
| 6618-YNL229C | YNL229C | URE2 | [URE3] | Nitrogen catabolite repression transcriptional regulator; inhibits GLN3 transcription in good nitrogen source; role in sequestering Gln3p and Gat1p to the cytoplasm; has glutathione peroxidase activity and can mutate to acquire GST activity; self-assembly under limited nitrogen conditions creates [URE3] prion and releases catabolite repression | Core | NA | NA | NA |
| 6619-YNL230C | YNL230C | ELA1 | elongin A | Elongin A; F-box protein that forms a heterodimer with Elc1p and is required for ubiquitin-dependent degradation of the RNA Polymerase II subunit Rpo21p; subunit of the Elongin-Cullin-Socs (ECS) ligase complex | Core | NA | NA | NA |
| 6620-YNL231C | YNL231C | PDR16 | phosphatidylinositol transporter|SFH3 | Phosphatidylinositol transfer protein (PITP); controlled by the multiple drug resistance regulator Pdr1p; localizes to lipid particles and microsomes; controls levels of various lipids, may regulate lipid synthesis; homologous to Pdr17p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6621-YNL232W | YNL232W | CSL4 | exosome non-catalytic core subunit CSL4|SKI4 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain an S1 RNA binding domain; human homolog EXOSC1 partially complements yeast csl4 null mutant, and can complement inviability of strain in which expression of CSL4 is repressed | Core | NA | NA | NA |
| 6622-YNL233W | YNL233W | BNI4 | NA | Targeting subunit for Glc7p protein phosphatase; localized to the bud neck, required for localization of chitin synthase III to the bud neck via interaction with the chitin synthase III regulatory subunit Skt5p; phosphorylation by Slt2p and Kss1p involved in regulating Bni4p in septum assembly | Core | NA | NA | NA |