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 |
|---|---|---|---|---|---|---|---|---|
| 2003-YBR022W | YBR022W | POA1 | ADP-ribose 1''-phosphate phosphatase | Phosphatase that is highly specific for ADP-ribose 1''-phosphate; a tRNA splicing metabolite; may have a role in regulation of tRNA splicing | Core | NA | NA | NA |
| 2004-YBR023C | YBR023C | CHS3 | chitin synthase CHS3|KTI2|DIT101|CSD2|CAL1 | Chitin synthase III; catalyzes the transfer of N-acetylglucosamine (GlcNAc) to chitin; required for synthesis of the majority of cell wall chitin, the chitin ring during bud emergence, and spore wall chitosan; contains overlapping di-leucine and di-acidic signals that mediate, respectively, intracellular trafficking by AP-1 and trafficking to plasma membrane by exomer complex; requires AP-3 complex for its intracellular retention | Core | NA | NA | NA |
| 2005-YBR024W | YBR024W | SCO2 | putative thioredoxin peroxidase SCO2 | Protein anchored to mitochondrial inner membrane; may have a redundant function with Sco1p in delivery of copper to cytochrome c oxidase; interacts with Cox2p; SCO2 has a paralog, SCO1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2006-YBR025C | YBR025C | OLA1 | Obg-like ATPase | P-loop ATPase with similarity to human OLA1 and bacterial YchF; identified as specifically interacting with the proteasome; null mutant displays increased translation rate and increased readthrough of premature stop codons; protein abundance increases in response to hydrogen peroxide and to DNA replication stress | Core | NA | NA | NA |
| 2007-YBR026C | YBR026C | ETR1 | MRF1'|MRF1 | 2-enoyl thioester reductase; member of the medium chain dehydrogenase/reductase family; localized to mitochondria, where it has a probable role in fatty acid synthesis; human MECR functionally complements the respiratory growth defect of the null mutant | Core | NA | NA | NA |
| 2008-YBR027C | YBR027C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YBR027C is not an essential gene | Core | NA | NA | NA |
| 2009-YBR028C | YBR028C | YPK3 | putative protein kinase YPK3 | AGC kinase; phosphorylated by cAMP-dependent protein kinase (PKA) in a TORC1-dependent manner; directly phosphorylated by TORC1; phosphorylates ribosomal protein Rps6a/b (S6), in a TORC-dependent manner; undergoes autophosphorylation | Core | NA | NA | NA |
| 2010-YBR029C | YBR029C | CDS1 | phosphatidate cytidylyltransferase|CDG1 | Phosphatidate cytidylyltransferase (CDP-diglyceride synthetase); an enzyme that catalyzes that conversion of CTP + phosphate into diphosphate + CDP-diaclglyerol, a critical step in the synthesis of all major yeast phospholipids; human homolog CDS1 can complement yeast cds1 null mutant | Core | NA | NA | NA |
| 2011-YBR030W | YBR030W | RKM3 | protein-lysine N-methyltransferase | Ribosomal lysine methyltransferase; specific for monomethylation of Rpl42ap and Rpl42bp (lysine 40); nuclear SET domain containing protein; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2012-YBR032W | YBR032W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YBR032W is not an essential gene | Core | NA | NA | NA |
| 2013-YBR033W | YBR033W | EDS1 | NA | Putative zinc cluster protein, predicted to be a transcription factor; not an essential gene; EDS1 has a paralog, RGT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2014-YBR034C | YBR034C | HMT1 | protein-arginine omega-N methyltransferase HMT1|RMT1|ODP1|HCP1 | Nuclear SAM-dependent mono- and asymmetric methyltransferase; modifies hnRNPs, including Npl3p and Hrp1p, affecting their activity and nuclear export; methylates U1 snRNP protein Snp1p, ribosomal protein Rps2p, and histones H3 and H4; interacts genetically with genes encoding components of Rpd3(L) and this interaction is important for Rpd3 recruitment to the subtelomeric region | Core | NA | NA | NA |
| 2015-YBR035C | YBR035C | PDX3 | pyridoxamine-phosphate oxidase PDX3 | Pyridoxine (pyridoxamine) phosphate oxidase; has homologs in E. coli and Myxococcus xanthus; transcription is under the general control of nitrogen metabolism | Core | NA | NA | NA |
| 2016-YBR036C | YBR036C | CSG2 | mannosylinositol phosphorylceramide synthase regulatory subunit|CLS2 | Endoplasmic reticulum membrane protein; required for mannosylation of inositolphosphorylceramide and for growth at high calcium concentrations; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 2017-YBR037C | YBR037C | SCO1 | Cu-binding protein SCO1|PET161 | Copper-binding protein of mitochondrial inner membrane; required for cytochrome c oxidase activity and respiration; may function to deliver copper to cytochrome c oxidase; similar to thioredoxins; SCO1 has a paralog, SCO2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |