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 |
|---|---|---|---|---|---|---|---|---|
| 6038-YML114C | YML114C | TAF8 | TafII65|TAF65 | TFIID subunit (65 kDa); involved in RNA polymerase II transcription initiation | Core | NA | NA | NA |
| 6039-YML115C | YML115C | VAN1 | LDB13|VRG8|VRG7 | Component of the mannan polymerase I; complex contains Van1p and Mnn9p and is involved in the first steps of mannan synthesis; mutants are vanadate-resistant | Core | NA | NA | NA |
| 6040-YML116W | YML116W | ATR1 | borate transporter|SNQ1 | Multidrug efflux pump of the major facilitator superfamily; required for resistance to aminotriazole and 4-nitroquinoline-N-oxide; ATR1 has a paralog, YMR279C, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6041-YML116W-A | YML116W-A | NA | YML117W-A | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 6042-YML117W | YML117W | NAB6 | NA | Putative RNA-binding protein; associates with mRNAs encoding cell wall proteins in high-throughput studies; deletion mutants display increased sensitivity to some cell wall disrupting agents; expression negatively regulated by cAMP | Core | NA | NA | NA |
| 6043-YML118W | YML118W | NGL3 | 3'-5' poly(A) RNA exonuclease | 3'-5' exonuclease specific for poly-A RNAs; has a domain similar to a magnesium-dependent endonuclease motif in mRNA deadenylase Ccr4p; similar to Ngl1p; NGL3 has a paralog, NGL2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6044-YML119W | YML119W | NA | NA | Putative protein of unknown function; YML119W is not an essential gene; potential Cdc28p substrate | Core | NA | NA | NA |
| 6045-YML120C | YML120C | NDI1 | NADH-ubiquinone reductase (H(+)-translocating) NDI1 | NADH:ubiquinone oxidoreductase; transfers electrons from NADH to ubiquinone in respiratory chain but does not pump protons, in contrast to higher eukaryotic multisubunit respiratory complex I; upon apoptotic stress, is activated in mitochondria by N-terminal cleavage, then translocates to cytoplasm to induce apoptosis; homolog of human AIFM2; yeast NDI1 complements several phenotypes of human cell line with mutated MT-ND4, implicated in Leber hereditary optic neuropathy | Core | NA | NA | NA |
| 6046-YML121W | YML121W | GTR1 | Rag GTPase GTR1 | Subunit of a TORC1-stimulating GTPase complex; subunit of the heterodimeric Gtr1-Gtr2 GTPase complex that stimulates TORC1 in response to amino acid stimulation; tethered to the vacuolar membrane as part of the EGOC, a complex required for sorting of Gap1p and microautophagy; involved in phosphate transport and telomeric chromatin silencing; activated by the the Iml1p (GAP) subunit of the SEACIT complex; similar to human RagA and RagB | Core | NA | NA | NA |
| 6047-YML122C | YML122C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YML122C is not an essential gene | Core | NA | NA | NA |
| 6048-YML123C | YML123C | PHO84 | phosphate transporter PHO84|phoT | High-affinity inorganic phosphate (Pi) transporter; also low-affinity manganese transporter; regulated by Pho4p and Spt7p; mutation confers resistance to arsenate; exit from the ER during maturation requires Pho86p; cells overexpressing Pho84p accumulate heavy metals but do not develop symptoms of metal toxicity | Core | NA | NA | NA |
| 6049-YML124C | YML124C | TUB3 | alpha-tubulin TUB3 | Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules; expressed at lower level than Tub1p; TUB3 has a paralog, TUB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6050-YML125C | YML125C | PGA3 | cytochrome-b5 reductase|NQR1 | Putative cytochrome b5 reductase, localized to the plasma membrane; may be involved in regulation of lifespan; required for maturation of Gas1p and Pho8p, proposed to be involved in protein trafficking; PGA3 has a paralog, AIM33, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6051-YML126C | YML126C | ERG13 | hydroxymethylglutaryl-CoA synthase|HMGS | 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase; catalyzes the formation of HMG-CoA from acetyl-CoA and acetoacetyl-CoA; involved in the second step in mevalonate biosynthesis | Core | NA | NA | NA |
| 6052-YML127W | YML127W | RSC9 | NA | Component of the RSC chromatin remodeling complex; DNA-binding protein involved in the synthesis of rRNA and in transcriptional repression and activation of genes regulated by the Target of Rapamycin (TOR) pathway | Core | NA | NA | NA |