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 |
|---|---|---|---|---|---|---|---|---|
| 4673-YIR018W | YIR018W | YAP5 | NA | Basic leucine zipper (bZIP) iron-sensing transcription factor; involved in diauxic shift; YAP5 has a paralog, YAP7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4674-YIR019C_NumOfGenes_5 | YIR019C | FLO11 | MUC1|STA4 | GPI-anchored cell surface glycoprotein (flocculin); required for pseudohyphal and invasive growth, flocculation, and biofilm formation; major determinant of colony morphology; transcription regulated by the MAPK pathway (Ste12p and Tec1p) and the cAMP pathway (Flo8p); required for formation of fibrous interconnections between cells of a wild strain; role in co-flocculation with other yeast species; cleaved and shed from cells, contributing to their surface properties | Accessory | Unknown | S. paradoxus | NA |
| 4675-YIR020C_NumOfGenes_2 | YIR020C | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data; SWAT-GFP fusion protein localizes to the endoplasmic reticulum | Core | NA | NA | NA |
| 4676-YIR020W-A | YIR020W-A | NA | YIR020W-B | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4677-YIR021W_NumOfGenes_2 | YIR021W | MRS1 | PET157 | Splicing protein; required for splicing of two mitochondrial group I introns (BI3 in COB and AI5beta in COX1); forms a splicing complex, containing four subunits of Mrs1p and two subunits of the BI3-encoded maturase, that binds to the BI3 RNA; MRS1 has a paralog, CCE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4678-YIR021W-A | YIR021W-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 4679-YIR022W | YIR022W | SEC11 | signal peptidase complex catalytic subunit SEC11 | 18kDa catalytic subunit of the Signal Peptidase Complex (SPC); the Signal Peptidase Complex cleaves the signal sequence of proteins targeted to the endoplasmic reticulum; other members are Spc1p, Spc2p, Spc3p, and Sec11p | Core | NA | NA | NA |
| 4680-YIR023W_NumOfGenes_2 | YIR023W | DAL81 | DURL|UGA35 | Positive regulator of genes in multiple nitrogen degradation pathways; contains DNA binding domain but does not appear to bind the dodecanucleotide sequence present in the promoter region of many genes involved in allantoin catabolism | Core | NA | NA | NA |
| 4681-YIR024C | YIR024C | INA22 | GIF1 | F1F0 ATP synthase peripheral stalk assembly factor; subunit of the matrix-exposed inner mitochondrial membrane localized INA complex (Ina22p-Ina17p) involved in assembly of the F1F0 peripheral stalk; co-purifies with Aim43p, ATP synthase subunits, and cytochrome bc1 complex assembly factors; interacts with Arh1p, a mitochondrial oxidoreductase; deletion mutant has a respiratory growth defect | Core | NA | NA | NA |
| 4682-YIR025W | YIR025W | MND2 | NA | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); necessary for maintaining sister chromatid cohesion in prophase I of meiosis by inhibiting premature ubiquitination and subsequent degradation of substrates by the APC(Ama1) ubiquitin ligase | Core | NA | NA | NA |
| 4683-YIR026C | YIR026C | YVH1 | tyrosine protein phosphatase YVH1 | Dual specificity protein phosphatase; regulates growth, sporulation, and glycogen accumulation in a cAMP-dependent protein kinase cascade dependent manner; mutants are defective in 60S ribosome assembly; positively regulates pre-autophagosomal structure (PAS) formation upon nitrogen starvation or rapamycin treatment | Core | NA | NA | NA |
| 4684-YIR027C | YIR027C | DAL1 | allantoinase | Allantoinase; converts allantoin to allantoate in the first step of allantoin degradation; expression sensitive to nitrogen catabolite repression | Core | NA | NA | NA |
| 4685-YIR028W | YIR028W | DAL4 | allantoin permease | Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation | Core | NA | NA | NA |
| 4686-YIR029W | YIR029W | DAL2 | allantoicase|ALC1 | Allantoicase; converts allantoate to urea and ureidoglycolate in the second step of allantoin degradation; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation | Core | NA | NA | NA |
| 4687-YIR030C | YIR030C | DCG1 | NA | Protein of unknown function; expression is sensitive to nitrogen catabolite repression and regulated by Dal80p; contains transmembrane domain | Core | NA | NA | NA |