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 |
|---|---|---|---|---|---|---|---|---|
| 4928-YJR014W | YJR014W | TMA22 | RBF22 | Protein of unknown function; associates with ribosomes and has a putative RNA binding domain; interacts with Tma20p; similar to human GRAP and human DRP1, which interacts with human Tma20p homolog MCT-1; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4929-YJR015W | YJR015W | NA | NA | Putative protein of unknown function; localizes to endoplasmic reticulum and cytoplasm; predicted to encode a membrane transporter based on phylogenetic analysis; not an essential gene; YJR015W has a paralog, SNG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4930-YJR016C | YJR016C | ILV3 | dihydroxy-acid dehydratase ILV3 | Dihydroxyacid dehydratase; catalyzes third step in the common pathway leading to biosynthesis of branched-chain amino acids | Core | NA | NA | NA |
| 4931-YJR017C | YJR017C | ESS1 | peptidylprolyl isomerase ESS1|PIN1|PTF1 | Peptidylprolyl-cis/trans-isomerase (PPIase); specific for phosphorylated S/T residues N-terminal to proline; regulates phosphorylation of RNAPII large subunit (Rpo21p) C-terminal domain (CTD) at Ser7; associates with phospho-Ser5 form of RNAPII in vivo; present along entire coding length of genes; represses initiation of CUTs; required for efficient termination of mRNA transcription, trimethylation of histone H3; human ortholog PIN1 can complement yeast null and ts mutants | Accessory | Ancestral | NA | NA |
| 4932-YJR018W | YJR018W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4933-YJR019C_NumOfGenes_2 | YJR019C | TES1 | PTE1 | Peroxisomal acyl-CoA thioesterase; likely to be involved in fatty acid oxidation rather than fatty acid synthesis; conserved protein also found in human peroxisomes; TES1 mRNA levels increase during growth on fatty acids | Core | NA | NA | NA |
| 4934-YJR021C | YJR021C | REC107 | MER2 | Protein involved in early stages of meiotic recombination; involved in coordination between the initiation of recombination and the first division of meiosis; part of a complex (Rec107p-Mei4p-Rec114p) required for ds break formation | Core | NA | NA | NA |
| 4935-YJR022W_NumOfGenes_2 | YJR022W | LSM8 | U4/U6-U5 snRNP complex subunit LSM8 | Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA | Core | NA | NA | NA |
| 4936-YJR024C | YJR024C | MDE1 | methylthioribulose 1-phosphate dehydratase MDE1 | 5'-methylthioribulose-1-phosphate dehydratase; acts in the methionine salvage pathway; potential Smt3p sumoylation substrate; expression downregulated by caspofungin and deletion mutant is caspofungin resistant | Core | NA | NA | NA |
| 4937-YJR025C | YJR025C | BNA1 | 3-hydroxyanthranilate 3,4-dioxygenase|HAD1 | 3-hydroxyanthranilic acid dioxygenase; required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p | Core | NA | NA | NA |
| 4938-YJR030C | YJR030C | RBH2 | RBH2 | Putative protein of unknown function; expression repressed in carbon limited vs carbon replete chemostat cultures; non-essential gene; contains a PH-like domain; RBH2 has a paralog, RBH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4939-YJR031C | YJR031C | GEA1 | Arf family guanine nucleotide exchange factor GEA1 | Guanine nucleotide exchange factor for ADP ribosylation factors (ARFs); involved in vesicular transport between the Golgi and ER, Golgi organization, and actin cytoskeleton organization; GEA1 has a paralog, GEA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4940-YJR032W | YJR032W | CPR7 | peptidylprolyl isomerase CPR7 | Peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; binds to Hsp82p and contributes to chaperone activity; plays a role in determining prion variants | Core | NA | NA | NA |
| 4941-YJR033C | YJR033C | RAV1 | SOI3 | Subunit of RAVE complex (Rav1p, Rav2p, Skp1p); the RAVE complex promotes assembly of the V-ATPase holoenzyme; required for transport between the early and late endosome/PVC and for localization of TGN membrane proteins; potential Cdc28p substrate | Core | NA | NA | NA |
| 4942-YJR034W | YJR034W | PET191 | NA | Protein required for assembly of cytochrome c oxidase; exists as an oligomer; described as both an integral mitochondrial inner membrane protein facing the intermembrane space (IMS) and as a soluble IMS protein; contains a twin Cx9C motif; imported into the IMS via the MIA import machinery | Core | NA | NA | NA |