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 |
|---|---|---|---|---|---|---|---|---|
| 4553-YIL070C | YIL070C | MAM33 | NA | Specific translational activator for the mitochondrial COX1 mRNA; acidic protein of the mitochondrial matrix; related to the human complement receptor gC1q-R | Core | NA | NA | NA |
| 4554-YIL071C_NumOfGenes_2 | YIL071C | PCI8 | YIL071W|CSN11|YIH1 | Possible shared subunit of Cop9 signalosome (CSN) and eIF3; binds eIF3b subunit Prt1p, has possible dual functions in transcriptional and translational control, contains a PCI (Proteasome-COP9 signalosome (CSN)-eIF3) domain | Core | NA | NA | NA |
| 4555-YIL072W | YIL072W | HOP1 | NA | Meiosis-specific protein required for chromosome synapsis; displays Red1p dependent localization to the unsynapsed axial-lateral elements of the synaptonemal complex; required for chiasma formation; in vitro, displays the ability to promote intra- and intermolecular synapsis between double-stranded DNA molecules and to fold DNA into rigid protein-DNA filaments | Core | NA | NA | NA |
| 4556-YIL073C | YIL073C | SPO22 | ZIP4 | Meiosis-specific protein essential for chromosome synapsis; involved in completion of nuclear divisions during meiosis; induced early in meiosis | Core | NA | NA | NA |
| 4557-YIL074C | YIL074C | SER33 | phosphoglycerate dehydrogenase SER33 | 3-phosphoglycerate dehydrogenase and alpha-ketoglutarate reductase; 3PG dehydrogenase that catalyzes the first step in serine and glycine biosynthesis; also functions as an alpha-ketoglutarate reductase, converting alpha-ketoglutarate to D-2-hydroxyglutarate (D-2HG); localizes to the cytoplasm; SER33 has a paralog, SER3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4558-YIL075C | YIL075C | RPN2 | proteasome regulatory particle base subunit RPN2|SEN3 | Subunit of the 26S proteasome; substrate of the N-acetyltransferase Nat1p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4559-YIL076W | YIL076W | SEC28 | coatomer subunit epsilon|ANU2 | Epsilon-COP subunit of the coatomer; regulates retrograde Golgi-to-ER protein traffic; stabilizes Cop1p, the alpha-COP and the coatomer complex; non-essential for cell growth; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4560-YIL077C | YIL077C | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO) | Core | NA | NA | NA |
| 4561-YIL078W | YIL078W | THS1 | threonine--tRNA ligase THS1 | Threonyl-tRNA synthetase; essential cytoplasmic protein; human homolog TARS can complement yeast null mutant | Core | NA | NA | NA |
| 4562-YIL079C | YIL079C | AIR1 | TRAMP complex RNA-binding subunit | Zinc knuckle protein; involved in nuclear RNA processing and degradation as a component of the TRAMP complex; stimulates the poly(A) polymerase activity of Pap2p in vitro; AIR1 has a paralog, AIR2, that arose from the whole genome duplication; although Air1p and Air2p are homologous TRAMP subunits, they have nonredundant roles in regulation of substrate specificity of the exosome | Core | NA | NA | NA |
| 4563-YIL083C | YIL083C | CAB2 | phosphopantothenate--cysteine ligase CAB2 | Subunit of the CoA-Synthesizing Protein Complex (CoA-SPC); subunits of this complex are: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p; probable phosphopantothenoylcysteine synthetase (PPCS), which catalyzes the second step of coenzyme A biosynthesis from pantothenate; null mutant lethality is complemented by human homolog PPCS and by E. coli coaBC (encoding a bifunctional enzyme with PPCS activity) | Core | NA | NA | NA |
| 4564-YIL084C | YIL084C | SDS3 | NA | Component of the Rpd3L histone deacetylase complex; required for its structural integrity and catalytic activity, involved in transcriptional silencing and required for sporulation; relocalizes to the cytosol in response to hypoxia; cells defective in SDS3 display pleiotropic phenotypes | Core | NA | NA | NA |
| 4565-YIL085C | YIL085C | KTR7 | putative mannosyltransferase | Putative mannosyltransferase involved in protein glycosylation; member of the KRE2/MNT1 mannosyltransferase family; KTR7 has a paralog, KTR5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4566-YIL086C | YIL086C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4567-YIL087C | YIL087C | AIM19 | LRC2 | Protein of unknown function; mitochondrial protein that physically interacts with Tim23p; null mutant displays reduced respiratory growth | Core | NA | NA | NA |