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 |
|---|---|---|---|---|---|---|---|---|
| 6848-YOL052C | YOL052C | SPE2 | adenosylmethionine decarboxylase SPE2 | S-adenosylmethionine decarboxylase; required for the biosynthesis of spermidine and spermine; cells lacking Spe2p require spermine or spermidine for growth in the presence of oxygen but not when grown anaerobically | Core | NA | NA | NA |
| 6849-YOL052C-A | YOL052C-A | DDR2 | YOL053C-A|DDRA2 | Multi-stress response protein; expression is activated by a variety of xenobiotic agents and environmental or physiological stresses; DDR2 has a paralog, HOR7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6850-YOL053W | YOL053W | AIM39 | NA | Protein of unknown function; null mutant displays elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 6851-YOL054W | YOL054W | PSH1 | ubiquitin-protein ligase PSH1 | E3 ubiquitin ligase targeting centromere-binding protein Cse4p; mediates polyubiquitination and degradation of histone H3 variant Cse4p, preventing its mislocalization to euchromatin independent of Slx5p; ubiquitination of Cse4p may be antagonized by Scm3p | Core | NA | NA | NA |
| 6852-YOL055C | YOL055C | THI20 | trifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase/thiaminase | Trifunctional enzyme of thiamine biosynthesis, degradation and salvage; has hydroxymethylpyrimidine (HMP) kinase, HMP-phosphate (HMP-P) kinase and thiaminase activities; member of a gene family with THI21 and THI22; HMP and HMP-P kinase activity redundant with Thi21p | Core | NA | NA | NA |
| 6853-YOL056W | YOL056W | GPM3 | phosphoglycerate mutase family protein GPM3 | Homolog of Gpm1p phosphoglycerate mutase; converts 3-phosphoglycerate to 2-phosphoglycerate in glycolysis; may be non-functional; GPM3 has a paralog, GPM2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6854-YOL057W | YOL057W | NA | dipeptidyl-peptidase III | Dipeptidyl-peptidase III; cleaves dipeptides from the amino terminus of target proteins; highly active on synthetic substrate Arg-Arg-2-naphthylamide; mammalian ortholog may be a biomarker for some cancers | Core | NA | NA | NA |
| 6855-YOL058W | YOL058W | ARG1 | argininosuccinate synthase|ARG10 | Arginosuccinate synthetase; catalyzes the formation of L-argininosuccinate from citrulline and L-aspartate in the arginine biosynthesis pathway; potential Cdc28p substrate | Core | NA | NA | NA |
| 6856-YOL059W | YOL059W | GPD2 | glycerol-3-phosphate dehydrogenase (NAD(+)) GPD2|GPD3 | NAD-dependent glycerol 3-phosphate dehydrogenase; expression is controlled by an oxygen-independent signaling pathway required to regulate metabolism under anoxic conditions; located in cytosol and mitochondria; constitutively active but is inactivated via phosphorylation by energy-stress responsive kinase SNF1; GPD2 has a paralog, GPD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6857-YOL060C | YOL060C | MAM3 | NA | Protein required for normal mitochondrial morphology; has similarity to hemolysins | Core | NA | NA | NA |
| 6858-YOL061W | YOL061W | PRS5 | ribose phosphate diphosphokinase subunit PRS5 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase; synthesizes PRPP, which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 6859-YOL062C | YOL062C | APM4 | AMP1 | Cargo-binding mu subunit of AP-2; AP-2 is a heterotetrameric endocytic cargo-binding adaptor that facilitates uptake of membrane proteins during clathrin-mediated endocytosis; Apm4p is required for AP-2 function and localization, and binds cell wall stress receptor Mid2p; AP-2 is required for cell polarity responses to pheromone, nutritional status and cell wall damage in S. cerevisiae, and for hyphal growth in C. albicans; AP-2 complex is conserved in mammals | Core | NA | NA | NA |
| 6860-YOL063C | YOL063C | CRT10 | HUS1 | Protein involved in transcriptional regulation of RNR2 and RNR3; expression of the gene is induced by DNA damage and null mutations confer increased resistance to hydroxyurea; N-terminal region has a leucine repeat and a WD40 repeat | Core | NA | NA | NA |
| 6861-YOL064C | YOL064C | MET22 | 3'(2'),5'-bisphosphate nucleotidase|HAL2 | Bisphosphate-3'-nucleotidase; involved in salt tolerance and methionine biogenesis; dephosphorylates 3'-phosphoadenosine-5'-phosphate and 3'-phosphoadenosine-5'-phosphosulfate, intermediates of the sulfate assimilation pathway; human homolog BPNT1 complements yeast null mutant | Core | NA | NA | NA |
| 6862-YOL065C | YOL065C | INP54 | phosphoinositide 5-phosphatase INP54 | Phosphatidylinositol 4,5-bisphosphate 5-phosphatase; role in secretion; localizes to the endoplasmic reticulum via the C-terminal tail; lacks the Sac1 domain and proline-rich region found in the other 3 INP proteins | Core | NA | NA | NA |