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 |
|---|---|---|---|---|---|---|---|---|
| 2408-YCR063W | YCR063W | BUD31 | U2 snRNP complex subunit BUD31|CWC14 | Component of the SF3b subcomplex of the U2 snRNP; increases efficiency of first and second step pre-mRNA splicing; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern; facilitates passage through G1/S Start, but is not required for G2/M transition or exit from mitosis | Core | NA | NA | NA |
| 2409-YCR064C | YCR064C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene BUD31 | Core | NA | NA | NA |
| 2410-YCR065W | YCR065W | HCM1 | NA | Forkhead transcription factor; drives S-phase activation of genes involved in chromosome segregation, spindle dynamics, budding; also activates genes involved in respiration, use of alternative energy sources (like proline), NAD synthesis, oxidative stress resistance; key factor in early adaptation to nutrient deficiency and diauxic shift; suppressor of calmodulin mutants with specific SPB assembly defects; ortholog of C. elegans lifespan regulator PHA-4 | Core | NA | NA | NA |
| 2411-YCR066W | YCR066W | RAD18 | E3 ubiquitin-protein ligase RAD18 | E3 ubiquitin ligase; forms heterodimer with Rad6p to monoubiquitinate PCNA-K164; heterodimer binds single-stranded DNA and has single-stranded DNA dependent ATPase activity; required for postreplication repair; SUMO-targeted ubiquitin ligase (STUbl) that contains a SUMO-interacting motif (SIM) which stimulates its ubiquitin ligase activity towards the sumoylated form of PCNA | Core | NA | NA | NA |
| 2412-YCR067C | YCR067C | SED4 | NA | Integral ER membrane protein that stimulates Sar1p GTPase activity; involved in COPII vesicle budding through disassociation of coat proteins from membranes onto liposomes; binds Sec16p; SED4 has a paralog, SEC12, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2413-YCR068W | YCR068W | ATG15 | triglyceride lipase ATG15|CVT17|AUT5 | Phospholipase; preferentially hydrolyses phosphatidylserine, with minor activity against cardiolipin and phosphatidylethanolamine; required for lysis of autophagic and CVT bodies; targeted to intravacuolar vesicles during autophagy via the multivesicular body (MVB) pathway; required for the maintenance of lipid droplet quantity after the diauxic shift; regulates lipolysis; expression regulated by Yap1p during autophagy | Core | NA | NA | NA |
| 2414-YCR069W | YCR069W | CPR4 | peptidylprolyl isomerase family protein CPR4|SCC3|YCR070W|CYP4 | Peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; has a potential role in the secretory pathway; CPR4 has a paralog, CPR8, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2415-YCR071C | YCR071C | IMG2 | mitochondrial 54S ribosomal protein IMG2 | Mitochondrial ribosomal protein of the large subunit; conserved in metazoa, with similarity to human mitochondrial ribosomal protein MRPL49 | Core | NA | NA | NA |
| 2416-YCR072C | YCR072C | RSA4 | NA | WD-repeat protein involved in ribosome biogenesis; may interact with ribosomes; required for maturation and efficient intra-nuclear transport or pre-60S ribosomal subunits, localizes to the nucleolus | Accessory | Ancestral | NA | NA |
| 2417-YCR073C | YCR073C | SSK22 | mitogen-activated protein kinase kinase kinase SSK22 | MAP kinase kinase kinase of HOG1 mitogen-activated signaling pathway; functionally redundant with Ssk2p; interacts with and is activated by Ssk1p; phosphorylates Pbs2p; SSK22 has a paralog, SSK2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2418-YCR073W-A | YCR073W-A | SOL2 | YCRX13W | Protein with a possible role in tRNA export; shows similarity to 6-phosphogluconolactonase non-catalytic domains but does not exhibit this enzymatic activity; homologous to Sol3p and Sol4p; SOL2 has a paralog, SOL1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2419-YCR075C | YCR075C | ERS1 | cystinosin-like protein ERS1 | Protein involved in cystine transport; localizes to the vacuole, plasma membrane and endosome; similarity to human cystinosin, a H(+)-driven transporter involved in L-cystine export from lysosomes and implicated in the disease cystinosis; contains seven transmembrane domains; mutation is functionally complemented by human CTNS | Core | NA | NA | NA |
| 2420-YCR075W-A | YCR075W-A | EGO2 | NA | Component of the EGO and GSE complexes; identified by homology to Ashbya gossypii; YCR075W-A has a paralog, YNR034W-A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2421-YCR076C | YCR076C | FUB1 | NA | Proteasome-binding protein; interacts physically with multiple subunits of the 20S proteasome and genetically with genes encoding 20S core particle and 19S regulatory particle subunits; exhibits boundary activity which blocks the propagation of heterochromatic silencing; contains a PI31 proteasome regulator domain and sequence similarity with human PSMF1, a proteasome inhibitor; not an essential gene | Core | NA | NA | NA |
| 2422-YCR077C | YCR077C | PAT1 | MRT1 | Deadenylation-dependent mRNA-decapping factor; also required for faithful chromosome transmission, maintenance of rDNA locus stability, and protection of mRNA 3'-UTRs from trimming; associated with topoisomerase II; binds to mRNAs under glucose starvation, most often in the 3' UTR; functionally linked to Pab1p; forms cytoplasmic foci upon DNA replication stress; phosphorylation by PKA inhibits P body foci formation | Accessory | Ancestral | NA | NA |