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 |
|---|---|---|---|---|---|---|---|---|
| 3053-YDR362C | YDR362C | TFC6 | transcription factor TFIIIC subunit TFC6|tau 91 | Subunit of RNA polymerase III transcription initiation factor complex; one of six subunits of RNA polymerase III transcription initiation factor complex (TFIIIC); part of TFIIIC TauB domain that binds BoxB promoter sites of tRNA and other genes; cooperates with Tfc3p in DNA binding; human homolog is TFIIIC-110 | Core | NA | NA | NA |
| 3054-YDR363W | YDR363W | ESC2 | NA | Sumo-like domain protein; prevents accumulation of toxic intermediates during replication-associated recombinational repair; roles in silencing, lifespan, chromatid cohesion and the intra-S-phase DNA damage checkpoint; RENi family member | Core | NA | NA | NA |
| 3055-YDR363W-A | YDR363W-A | SEM1 | proteasome regulatory particle lid subunit SEM1|HOD1|DSS1 | 19S proteasome regulatory particle lid subcomplex component; role in Ub-dependent proteolysis and proteasome stability; involved in TREX-2 mediated mRNA export, and in the prevention of transcription-associated genome instability; ubiquitinated by Nedd4-like E3-ligase, Rsp5p; human ortholog DSS1, a BRCA1 binding protein implicated in cancer, complements the yeast null; drives trinucleotide repeat expansion; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3056-YDR364C | YDR364C | CDC40 | SLU4|SLT15|PRP17 | Pre-mRNA splicing factor; important for catalytic step II of pre-mRNA splicing and plays a role in cell cycle progression, particularly at the G1/S phase transition; required for DNA synthesis during mitosis and meiosis; has WD repeats; thermosensitivity of the cdc40 null mutant is functionally complemented by a chimeric construct containing the N-terminal 156 amino acids of yeast Cdc40p fused to the C-terminal two thirds (297 amino acids) of human CDC40 | Core | NA | NA | NA |
| 3057-YDR365C | YDR365C | ESF1 | NA | Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels | Core | NA | NA | NA |
| 3058-YDR367W | YDR367W | KEI1 | NA | Component of inositol phosphorylceramide (IPC) synthase; forms a complex with Aur1p and regulates its activity; required for IPC synthase complex localization to the Golgi; post-translationally processed by Kex2p; KEI1 is an essential gene | Core | NA | NA | NA |
| 3059-YDR368W | YDR368W | YPR1 | trifunctional aldehyde reductase/carbonyl reductase (NADPH)/glucose 1-dehydrogenase (NADP(+)) YPR1 | NADPH-dependent aldo-keto reductase; reduces multiple substrates including 2-methylbutyraldehyde and D,L-glyceraldehyde, expression is induced by osmotic and oxidative stress; functionally redundant with other aldo-keto reductases; protein abundance increases in response to DNA replication stress; YPR1 has a paralog, GCY1, that arose from the whole genome duplication; human homolog AKR1B1 can complement yeast null mutant | Core | NA | NA | NA |
| 3060-YDR369C | YDR369C | XRS2 | NA | Protein required for DNA repair; component of the Mre11 complex, which is involved in double strand breaks, meiotic recombination, telomere maintenance, and checkpoint signaling | Core | NA | NA | NA |
| 3061-YDR370C | YDR370C | DXO1 | NA | mRNA 5'-end-capping quality-control protein; has distributive, 5'-3' exoRNase activity; similar to Rai1p; | Core | NA | NA | NA |
| 3062-YDR371W_NumOfGenes_2 | YDR371W | CTS2 | putative chitinase | Putative chitinase; functionally complements A. gossypii cts2 mutant sporulation defect | Core | NA | NA | NA |
| 3063-YDR372C | YDR372C | VPS74 | MNN3|API1 | Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor; interacts with the cytosolic domains of cis and medial glycosyltransferases, and in the PtdIns4P-bound state mediates the targeting of these enzymes to the Golgi; interacts with the catalytic domain of Sac1p, the major cellular PtdIns4P phosphatase, to direct dephosphosphorylation of the Golgi pool of PtdIns4P; tetramerization required for function; ortholog of human GOLPH3/GPP34/GMx33 | Core | NA | NA | NA |
| 3064-YDR373W | YDR373W | FRQ1 | frequenin | N-myristoylated calcium-binding protein; may have a role in intracellular signaling through its regulation of the phosphatidylinositol 4-kinase Pik1p; member of the recoverin/frequenin branch of the EF-hand superfamily; human NCS1 functionally complements the heat sensitivity of a frq1 ts mutant | Core | NA | NA | NA |
| 3065-YDR374C | YDR374C | PHO92 | mRNA-binding phosphate metabolism regulator | Posttranscriptional regulator of phosphate metabolism; facilitates PHO4 mRNA degradation by interacting with Pop2p; regulates PHO4 mRNA stability by binding to PHO4's 3'UTR in a phosphate-dependent manner; contains highly conserved YTH (YT521-B Homology) domain that exhibits RNA-binding activity; human homolog YTHDF2 can complement yeast null mutant | Core | NA | NA | NA |
| 3066-YDR374W-A | YDR374W-A | WIP1 | NA | Kinetochore localized protein of unknown function; interacts with Cnn1p (CENP-T); orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-W and fission yeast new1 | Core | NA | NA | NA |
| 3067-YDR375C | YDR375C | BCS1 | bifunctional AAA family ATPase chaperone/translocase BCS1 | Protein translocase and chaperone required for Complex III assembly; member of the AAA ATPase family; forms a homo-oligomeric complex in the mitochondrial inner membrane that translocates the C-terminal domain of Rip1p from the matrix across the inner membrane and delivers it to an assembly intermediate of respiratory Complex III; also required for assembly of the Qcr10p subunit; mutation is functionally complemented by human homolog BCS1L, linked to neonatal diseases | Core | NA | NA | NA |