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 |
|---|---|---|---|---|---|---|---|---|
| 5408-YLL008W | YLL008W | DRS1 | putative ATP-dependent RNA helicase | Nucleolar DEAD-box protein required for ribosome assembly and function; including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles | Core | NA | NA | NA |
| 5409-YLL009C | YLL009C | COX17 | copper metallochaperone COX17 | Copper metallochaperone that transfers copper to Sco1p and Cox11p; eventual delivery to cytochrome c oxidase; contains twin cysteine-x9-cysteine motifs; interacts with the MICOS complex, and interaction is promoted by copper ions; human homolog COX17 partially complements yeast null mutant | Core | NA | NA | NA |
| 5410-YLL010C | YLL010C | PSR1 | phosphatase | Plasma membrane associated protein phosphatase; involved in the general stress response; required along with binding partner Whi2p for full activation of STRE-mediated gene expression, possibly through dephosphorylation of Msn2p; PSR1 has a paralog, PSR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5411-YLL011W | YLL011W | SOF1 | rRNA-processing protein SOF1 | Protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p; essential gene | Core | NA | NA | NA |
| 5412-YLL012W | YLL012W | YEH1 | sterol esterase | Steryl ester hydrolase; one of three gene products (Yeh1p, Yeh2p, Tgl1p) responsible for steryl ester hydrolase activity and involved in sterol homeostasis; localized to lipid particle membranes; YEH1 has a paralog, YEH2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5413-YLL013C | YLL013C | PUF3 | mRNA-binding protein PUF3 | Protein of the mitochondrial outer surface; links the Arp2/3 complex with the mitochore during anterograde mitochondrial movement; also binds to and promotes degradation of mRNAs for select nuclear-encoded mitochondrial proteins | Core | NA | NA | NA |
| 5414-YLL014W | YLL014W | EMC6 | NA | Member of conserved ER transmembrane complex; required for efficient folding of proteins in the ER; null mutant displays induction of the unfolded protein response; homologous to worm F33D4.7/EMC-6, fly CG11781, human TMEM93 | Core | NA | NA | NA |
| 5415-YLL015W | YLL015W | BPT1 | ATP-binding cassette bilirubin transporter BPT1 | ABC type transmembrane transporter of MRP/CFTR family; found in vacuolar membrane, involved in the transport of unconjugated bilirubin and in heavy metal detoxification via glutathione conjugates, along with Ycf1p | Core | NA | NA | NA |
| 5416-YLL016W | YLL016W | SDC25 | Ras family guanine nucleotide exchange factor SDC25 | Non-essential Ras guanine nucleotide exchange factor (GEF); localized to the membrane; expressed in poor nutrient conditions and on nonfermentable carbon sources; contains a stop codon in S288C, full-length gene includes YLL017W; SDC25 has a paralog, CDC25, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5417-YLL017W_NumOfGenes_2 | YLL017W | NA | Ras family guanine nucleotide exchange factor SDC25|SDC25 | Non-essential Ras guanine nucleotide exchange factor (GEF); localized to the membrane; expressed in poor nutrient conditions and on nonfermentable carbon sources; contains a stop codon in S288C, full-length gene includes YLL016W; SDC25 has a paralog, CDC25, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5418-YLL018C | YLL018C | DPS1 | aspartate--tRNA ligase DPS1|AspRS | Aspartyl-tRNA synthetase, primarily cytoplasmic; homodimeric enzyme that catalyzes the specific aspartylation of tRNA(Asp); class II aminoacyl tRNA synthetase; binding to its own mRNA may confer autoregulation; shares five highly conserved amino acids with human that when mutated cause leukoencephalopathy characterized by hypomyelination with brain stem and spinal cord involvement and leg spasticity (HBSL) | Core | NA | NA | NA |
| 5419-YLL018C-A | YLL018C-A | COX19 | NA | Protein required for cytochrome c oxidase assembly; located in the cytosol and mitochondrial intermembrane space; putative copper metallochaperone that delivers copper to cytochrome c oxidase; contains twin cysteine-x9-cysteine motifs | Core | NA | NA | NA |
| 5420-YLL019C_NumOfGenes_2 | YLL019C | KNS1 | serine/threonine protein kinase KNS1|L124 | Protein kinase involved in negative regulation of PolIII transcription; effector kinase of the TOR signaling pathway and phosphorylates Rpc53p to regulate ribosome and tRNA biosynthesis; member of the LAMMER family of protein kinases, which are serine/threonine kinases also capable of phosphorylating tyrosine residues; capable of autophosphorylation | Core | NA | NA | NA |
| 5421-YLL020C | YLL020C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene KNS1 | Accessory | Ancestral | NA | NA |
| 5422-YLL021W | YLL021W | SPA2 | PPF1|PEA1|FUS6 | Component of the polarisome; functions in actin cytoskeletal organization during polarized growth; acts as a scaffold for Mkk1p and Mpk1p cell wall integrity signaling components; potential Cdc28p substrate; coding sequence contains length polymorphisms in different strains; SPA2 has a paralog, SPH1, that arose from the whole genome duplication | Core | NA | NA | NA |