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 |
|---|---|---|---|---|---|---|---|---|
| 2123-YBR139W | YBR139W | NA | carboxypeptidase C | Putative serine type carboxypeptidase; role in phytochelatin synthesis; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner | Core | NA | NA | NA |
| 2124-YBR140C | YBR140C | IRA1 | GTPase-activating protein IRA1|PPD1|GLC1 | GTPase-activating protein; negatively regulates RAS by converting it from GTP- to the GDP-bound inactive form, required for reducing cAMP levels under nutrient limiting conditions, mediates membrane association of adenylate cyclase; mutations cause catalase T deficiency, defective glycogen synthesis and defective trehalose accumulation; IRA1 has a paralog, IRA2, that arose from the whole genome duplication; defects in human homolog NF1 are associated with neurofibromatosis | Core | NA | NA | NA |
| 2125-YBR141C_NumOfGenes_2 | YBR141C | BMT2 | 25S rRNA (adenine2142-N1)-methyltransferase | Nucleolar S-adenosylmethionine-dependent rRNA methyltransferase; methylates adenine (m1A) of the large subunit (LSU) rRNA at position 2142; belongs to Rossmann fold superfamily; green fluorescent protein (GFP)-fusion protein localizes to the nucleolus; YBR141C is not an essential gene | Core | NA | NA | NA |
| 2126-YBR142W | YBR142W | MAK5 | putative ATP-dependent RNA helicase | Essential nucleolar protein; putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits | Core | NA | NA | NA |
| 2127-YBR143C | YBR143C | SUP45 | translation termination factor eRF1|eRF1|SUP47|SUP1|SAL4 | Polypeptide release factor (eRF1) in translation termination; mutant form acts as a recessive omnipotent suppressor; methylated by Mtq2p-Trm112p in ternary complex eRF1-eRF3-GTP; mutation of methylation site confers resistance to zymocin; has a role in cytokinesis through interaction with Mlc1p | Core | NA | NA | NA |
| 2128-YBR144C | YBR144C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YBR144C is not an essential gene | Core | NA | NA | NA |
| 2129-YBR145W | YBR145W | ADH5 | alcohol dehydrogenase ADH5 | Alcohol dehydrogenase isoenzyme V; involved in ethanol production; ADH5 has a paralog, ADH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2130-YBR146W | YBR146W | MRPS9 | mitochondrial 37S ribosomal protein MRPS9 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 2131-YBR147W | YBR147W | RTC2 | cationic amino acid transporter|YPQ3|RRT11 | Putative vacuolar membrane transporter for cationic amino acids; likely contributes to amino acid homeostasis by exporting cationic amino acids from the vacuole; positive regulation by Lys14p suggests that lysine may be the primary substrate; member of the PQ-loop family, with seven transmembrane domains; similar to mammalian PQLC2 vacuolar transporter; RTC2 has a paralog, YPQ1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2132-YBR148W | YBR148W | YSW1 | NA | Protein required for normal prospore membrane formation; interacts with Gip1p, which is the meiosis-specific regulatory subunit of the Glc7p protein phosphatase; expressed specifically in spores and localizes to the prospore membrane; YSW1 has a paralog, SPO21, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2133-YBR149W | YBR149W | ARA1 | D-arabinose 1-dehydrogenase (NAD(P)(+)) ARA1 | NADP+ dependent arabinose dehydrogenase; involved in carbohydrate metabolism; purified as homodimer; naturally occurs with a N-terminus degradation product | Core | NA | NA | NA |
| 2134-YBR150C | YBR150C | TBS1 | NA | Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; TBS1 has a paralog, HAL9, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2135-YBR151W | YBR151W | APD1 | NA | Protein of unknown function; required for normal localization of actin patches and for normal tolerance of sodium ions and hydrogen peroxide; localizes to both cytoplasm and nucleus | Accessory | Ancestral | NA | NA |
| 2136-YBR152W | YBR152W | SPP381 | U4/U6-U5 snRNP complex subunit SPP381 | mRNA splicing factor, component of U4/U6.U5 tri-snRNP; interacts genetically and physically with Prp38p; relocalizes to the cytosol in response to hypoxia | Accessory | Unknown | NA | NA |
| 2137-YBR153W | YBR153W | RIB7 | 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase | Diaminohydroxyphoshoribosylaminopyrimidine deaminase; catalyzes the second step of the riboflavin biosynthesis pathway | Accessory | Ancestral | NA | NA |