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 |
|---|---|---|---|---|---|---|---|---|
| 5243-YKL171W | YKL171W | NNK1 | protein kinase NNK1 | Protein kinase; implicated in proteasome function; interacts with TORC1, Ure2 and Gdh2; overexpression leads to hypersensitivity to rapamycin and nuclear accumulation of Gln3; epitope-tagged protein localizes to the cytoplasm | Core | NA | NA | NA |
| 5244-YKL172W | YKL172W | EBP2 | NA | Required for 25S rRNA maturation and 60S ribosomal subunit assembly; localizes to the nucleolus and in foci along nuclear periphery; constituent of 66S pre-ribosomal particles; cooperates with Rrs1p and Mps3p to mediate telomere clustering by binding Sir4p, but is not involved in telomere tethering | Core | NA | NA | NA |
| 5245-YKL173W | YKL173W | SNU114 | U5 snRNP GTPase SNU114|GIN10 | GTPase component of U5 snRNP involved in mRNA splicing via spliceosome; binds directly to U5 snRNA; proposed to be involved in conformational changes of the spliceosome; similarity to ribosomal translocation factor EF-2 | Core | NA | NA | NA |
| 5246-YKL174C | YKL174C | TPO5 | NA | Protein involved in excretion of putrescine and spermidine; putative polyamine transporter in the Golgi or post-Golgi vesicles | Core | NA | NA | NA |
| 5247-YKL175W | YKL175W | ZRT3 | Zn(2+) transporter ZRT3 | Vacuolar membrane zinc transporter; transports zinc from storage in the vacuole to the cytoplasm when needed; transcription is induced under conditions of zinc deficiency | Core | NA | NA | NA |
| 5248-YKL176C | YKL176C | LST4 | NA | Subunit of the Lst4p-Lst7p GTPase activating protein complex for Gtr2p; stimulates the GTPase activity of Rag family GTPase Gtr2p, within the context of the Gtr1p-Gtr2p heterodimer, after amino acid stimulation; required for activation of TORC1 in response to amino acid stimulation; recruited to the vacuolar membrane during amino acid starvation and released from the membrane by TORC1; required for the transport of amino acid permease Gap1p from the Golgi to the cell surface | Core | NA | NA | NA |
| 5249-YKL178C_NumOfGenes_2 | YKL178C | STE3 | DAF2 | Receptor for a factor pheromone; couples to MAP kinase cascade to mediate pheromone response; transcribed in alpha cells and required for mating by alpha cells, ligand bound receptors endocytosed and recycled to the plasma membrane; GPCR | Core | NA | NA | NA |
| 5250-YKL179C | YKL179C | COY1 | NA | Golgi membrane protein with similarity to mammalian CASP; genetic interactions with GOS1 (encoding a Golgi snare protein) suggest a role in Golgi function | Core | NA | NA | NA |
| 5251-YKL180W | YKL180W | RPL17A | uL22|ribosomal 60S subunit protein L17A|L22|YL17|L20A|L17A|RPL17 | Ribosomal 60S subunit protein L17A; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; copurifies with the Dam1 complex (aka DASH complex); homologous to mammalian ribosomal protein L17 and bacterial L22; RPL17A has a paralog, RPL17B, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5252-YKL181W | YKL181W | PRS1 | ribose phosphate diphosphokinase subunit PRS1|PRP1 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase; synthesizes PRPP, which is required for nucleotide, histidine, and tryptophan biosynthesis; plays a key role in cell wall integrity (CWI) pathway; one of five related enzymes, which are active as heteromultimeric complexes; missense mutations in human homolog PRPS1 are associated with neuropathic Arts syndrome and Charcot-Marie Tooth (CMTX5) disease | Core | NA | NA | NA |
| 5253-YKL182W | YKL182W | FAS1 | tetrafunctional fatty acid synthase subunit FAS1 | Beta subunit of fatty acid synthetase; complex catalyzes the synthesis of long-chain saturated fatty acids; contains acetyltransacylase, dehydratase, enoyl reductase, malonyl transacylase, and palmitoyl transacylase activities | Core | NA | NA | NA |
| 5254-YKL183C-A | YKL183C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Accessory | Unknown | NA | NA |
| 5255-YKL183W | YKL183W | LOT5 | NA | Protein of unknown function; gene expression increases in cultures shifted to a lower temperature; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5256-YKL184W | YKL184W | SPE1 | ornithine decarboxylase SPE1|SPE10|ORD1 | Ornithine decarboxylase; catalyzes the first step in polyamine biosynthesis; degraded in a proteasome-dependent manner in the presence of excess polyamines; deletion decreases lifespan, and increases necrotic cell death and ROS generation | Core | NA | NA | NA |
| 5257-YKL185W | YKL185W | ASH1 | DNA-binding transcription repressor ASH1 | Component of the Rpd3L histone deacetylase complex; zinc-finger inhibitor of HO transcription; mRNA is localized and translated in the distal tip of anaphase cells, resulting in accumulation of Ash1p in daughter cell nuclei and inhibition of HO expression; potential Cdc28p substrate | Accessory | Ancestral | NA | NA |