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 |
|---|---|---|---|---|---|---|---|---|
| 7298-YOR339C | YOR339C | UBC11 | putative E2 ubiquitin-protein ligase UBC11 | Ubiquitin-conjugating enzyme; most similar in sequence to Xenopus ubiquitin-conjugating enzyme E2-C, but not a true functional homolog of this E2; unlike E2-C, not required for the degradation of mitotic cyclin Clb2 | Core | NA | NA | NA |
| 7299-YOR340C | YOR340C | RPA43 | DNA-directed RNA polymerase I subunit RPA43|A43 | RNA polymerase I subunit A43 | Core | NA | NA | NA |
| 7300-YOR341W | YOR341W | RPA190 | DNA-directed RNA polymerase I core subunit RPA190|A190|RRN1 | RNA polymerase I largest subunit A190 | Accessory | Ancestral | NA | NA |
| 7301-YOR342C | YOR342C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus; relocalizes from nucleus to cytoplasm upon DNA replication stress; YOR342C has a paralog, YAL037W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 7302-YOR343C | YOR343C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 7303-YOR344C | YOR344C | TYE7 | SGC1 | Serine-rich protein that contains a bHLH DNA binding motif; binds E-boxes of glycolytic genes and contributes to their activation; may function as a transcriptional activator in Ty1-mediated gene expression; bHLH stands for basic-helix-loop-helix | Accessory | Ancestral | NA | NA |
| 7304-YOR346W_NumOfGenes_2 | YOR346W | REV1 | deoxycytidyl transferase | Deoxycytidyl transferase; involved in repair of abasic sites and adducted guanines in damaged DNA by translesion synthesis (TLS); forms a complex with the subunits of DNA polymerase zeta, Rev3p and Rev7p; relocalizes from nucleus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 7305-YOR347C | YOR347C | PYK2 | pyruvate kinase PYK2 | Pyruvate kinase; appears to be modulated by phosphorylation; transcription repressed by glucose, and Pyk2p may be active under low glycolytic flux; PYK2 has a paralog, CDC19, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7306-YOR348C | YOR348C | PUT4 | proline permease PUT4 | Proline permease; required for high-affinity transport of proline; also transports the toxic proline analog azetidine-2-carboxylate (AzC); PUT4 transcription is repressed in ammonia-grown cells | Core | NA | NA | NA |
| 7307-YOR349W | YOR349W | CIN1 | NA | Tubulin folding factor D involved in beta-tubulin (Tub2p) folding; isolated as mutant with increased chromosome loss and sensitivity to benomyl | Core | NA | NA | NA |
| 7308-YOR350C | YOR350C | MNE1 | NA | Protein involved in splicing Group I aI5-beta intron from COX1 mRNA; mitochondrial matrix protein | Core | NA | NA | NA |
| 7309-YOR351C | YOR351C | MEK1 | serine/threonine protein kinase MEK1|MRE4 | Meiosis-specific serine/threonine protein kinase; functions in meiotic checkpoint, promotes recombination between homologous chromosomes by suppressing double strand break repair between sister chromatids; stabilizes Hop1-Thr318 phosphorylation to promote interhomolog recombination and checkpoint responses during meiosis | Core | NA | NA | NA |
| 7310-YOR352W | YOR352W | TFB6 | TFIIH complex subunit TFB6 | Subunit of TFIIH complex; facilities dissociation of the Ssl2p helices from TFIIH; expression levels regulated by Arg5,6p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus | Core | NA | NA | NA |
| 7311-YOR353C | YOR353C | SOG2 | NA | Key component of the RAM signaling network; required for proper cell morphogenesis and cell separation after mitosis | Core | NA | NA | NA |
| 7312-YOR354C | YOR354C | MSC6 | NA | Multicopy suppressor of HER2 involved in mitochondrial translation; mutant is defective in directing meiotic recombination events to homologous chromatids | Core | NA | NA | NA |