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 |
|---|---|---|---|---|---|---|---|---|
| 3353-YER039C-A | YER039C-A | NA | NA | Putative protein of unknown function; YER039C-A is not an essential gene | Core | NA | NA | NA |
| 3354-YER040W | YER040W | GLN3 | nitrogen-responsive transcriptional regulator GLN3 | Transcriptional activator of genes regulated by nitrogen catabolite repression; localization and activity regulated by quality of nitrogen source and Ure2p | Core | NA | NA | NA |
| 3355-YER041W | YER041W | YEN1 | crossover junction endodeoxyribonuclease | Holliday junction resolvase; promotes template switching during break-induced replication (BIR), causing non-reciprocal translocations (NRTs); localization is cell-cycle dependent and regulated by Cdc28p phosphorylation; homolog of human GEN1; similar to S. cerevisiae endonuclease Rth1p | Core | NA | NA | NA |
| 3356-YER042W | YER042W | MXR1 | peptide-methionine-S-sulfoxide reductase|msrA | Methionine-S-sulfoxide reductase; involved in the response to oxidative stress; protects iron-sulfur clusters from oxidative inactivation along with MXR2; involved in the regulation of lifespan; reduced activity of human homolog implicated in Alzheimer disease | Core | NA | NA | NA |
| 3357-YER043C | YER043C | SAH1 | adenosylhomocysteinase | S-adenosyl-L-homocysteine hydrolase; catabolizes S-adenosyl-L-homocysteine which is formed after donation of the activated methyl group of S-adenosyl-L-methionine (AdoMet) to an acceptor; regulates cellular lipid homoeostasis by regulating phosphatidylcholine(PC)synthesis and triacylglycerol (TG) levels | Core | NA | NA | NA |
| 3358-YER044C | YER044C | ERG28 | BUD18 | Endoplasmic reticulum membrane protein; may facilitate protein-protein interactions between the Erg26p dehydrogenase and the Erg27p 3-ketoreductase and/or tether these enzymes to the ER, also interacts with Erg6p | Core | NA | NA | NA |
| 3359-YER044C-A | YER044C-A | MEI4 | NA | Meiosis-specific protein involved in forming DSBs; involved in double-strand break (DSBs) formation during meiotic recombination; required for chromosome synapsis and production of viable spores | Core | NA | NA | NA |
| 3360-YER045C | YER045C | ACA1 | NA | ATF/CREB family basic leucine zipper (bZIP) transcription factor; binds as a homodimer to the ATF/CREB consensus sequence TGACGTCA; important for carbon source utilization; target genes include GRE2 and COS8; ACA1 has a paralog, CST6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3361-YER046W_NumOfGenes_2 | YER046W | SPO73 | NA | Meiosis-specific protein required for prospore membrane morphogenesis; required for the proper shape of the prospore membrane (PSM) and for spore wall formation; functions cooperatively with SPO71 in PSM elongation; physically interacts with Spo71p; genetically antagonistic to SPO1, similar to SPO71; localizes to the PSM; required for spore wall formation during sporulation; dispensable for both nuclear divisions during meiosis; dysferlin domain-only protein | Core | NA | NA | NA |
| 3362-YER046W-A | YER046W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF SAP1/YER047C | Accessory | Ancestral | NA | NA |
| 3363-YER047C | YER047C | SAP1 | putative AAA family ATPase SAP1 | Putative ATPase of the AAA family; interacts with the Sin1p transcriptional repressor in the two-hybrid system | Core | NA | NA | NA |
| 3364-YER048C | YER048C | CAJ1 | NA | Nuclear type II J heat shock protein of the E. coli dnaJ family; contains a leucine zipper-like motif, binds to non-native substrates for presentation to Ssa3p, may function during protein translocation, assembly and disassembly | Core | NA | NA | NA |
| 3365-YER048W-A | YER048W-A | ISD11 | NA | Cysteine desulfurase (Nfs1p) activator; essential for the formation of the persulfide intermediate at the desulfurase active site during pyridoxal phosphate-dependent desulfuration of cysteine; required for mitochondrial iron-sulfur cluster biosynthesis; exclusive to eukaryotes, implicated as eukaryotic supplement to the bacterium-derived Fe-S cluster (ISC) assembly apparatus; involved in regulation of iron metabolism; member of the LYR protein family | Core | NA | NA | NA |
| 3366-YER049W | YER049W | TPA1 | oxidative DNA demethylase | Fe(II)/2-oxoglutarate-dependent dioxygenase family member; catalyzes the repair of methyl-base lesions in both ss and dsDNA by oxidative demethylation; Poly(rA)-binding protein involved in mRNA poly(A) tail length and mRNA stability; role in translation termination efficiency; interacts with Sup45p (eRF1), Sup35p (eRF3) and Pab1p; similar to human prolyl 4-hydroxylase OGFOD1; binds Fe(II) and 2-oxoglutarate | Core | NA | NA | NA |
| 3367-YER050C | YER050C | RSM18 | mitochondrial 37S ribosomal protein RSM18 | Mitochondrial ribosomal protein of the small subunit; has similarity to E. coli S18 ribosomal protein | Core | NA | NA | NA |