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 |
|---|---|---|---|---|---|---|---|---|
| 3548-YFL026W | YFL026W | STE2 | alpha-factor pheromone receptor STE2 | Receptor for alpha-factor pheromone; seven transmembrane-domain GPCR that interacts with both pheromone and a heterotrimeric G protein to initiate the signaling response that leads to mating between haploid a and alpha cells | Core | NA | NA | NA |
| 3549-YFL027C | YFL027C | GYP8 | NA | GTPase-activating protein for yeast Rab family members; Ypt1p is the preferred in vitro substrate but also acts on Sec4p, Ypt31p and Ypt32p; involved in the regulation of ER to Golgi vesicle transport | Core | NA | NA | NA |
| 3550-YFL028C | YFL028C | CAF16 | putative ATP-binding cassette family ATPase CAF16 | Part of evolutionarily-conserved CCR4-NOT regulatory complex; contains single ABC-type ATPase domain but no transmembrane domain; interacts with several subunits of Mediator | Core | NA | NA | NA |
| 3551-YFL029C | YFL029C | CAK1 | cyclin-dependent protein kinase-activating kinase CAK1|CIV1 | Cyclin-dependent kinase-activating kinase; required for passage through the cell cycle; phosphorylates and activates Cdc28p; nucleotide-binding pocket differs significantly from those of most other protein kinases | Core | NA | NA | NA |
| 3552-YFL030W | YFL030W | AGX1 | alanine--glyoxylate transaminase | Alanine:glyoxylate aminotransferase (AGT); catalyzes the synthesis of glycine from glyoxylate, which is one of three pathways for glycine biosynthesis in yeast; similar to mammalian and plant alanine:glyoxylate aminotransferases; human homolog AGXT complements yeast null mutant | Core | NA | NA | NA |
| 3553-YFL031W_NumOfGenes_3 | YFL031W | HAC1 | transcription factor HAC1|IRE15|ERN4 | Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog); regulates the unfolded protein response, via UPRE binding, and membrane biogenesis; ER stress-induced splicing pathway facilitates efficient Hac1p synthesis; two functional forms of Hac1p are produced; translation initiation is repressed under non-stress conditions; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3554-YFL032W | YFL032W | 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 HAC1/YFL031W; YFL032W is not an essential gene | Accessory | Unknown | NA | NA |
| 3555-YFL033C_NumOfGenes_2 | YFL033C | RIM15 | protein kinase RIM15|TAK1 | Protein kinase involved in cell proliferation in response to nutrients; glucose-repressible; involved in signal transduction during cell proliferation in response to nutrients, specifically the establishment of stationary phase; identified as a regulator of IME2; phosphorylates Igo1p and Igo2p; substrate of Pho80p-Pho85p kinase | Accessory | Ancestral | NA | NA |
| 3556-YFL034C-A_NumOfGenes_2 | YFL034C-A | RPL22B | eL22|ribosomal 60S subunit protein L22B|L22e|rp4|l1c|YL31|L22B|YFL035C-B | Ribosomal 60S subunit protein L22A; required for translation of long 5' UTR of IME1 mRNA and meiotic entry; homologous to mammalian ribosomal protein L22, no bacterial homolog; RPL22B has a paralog, RPL22A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3557-YFL034C-B_NumOfGenes_2 | YFL034C-B | MOB2 | YFL035C-A|YFL035C | Activator of Cbk1p kinase; component of the RAM signaling network that regulates cellular polarity and morphogenesis; activation of Cbk1p facilitates the Ace2p-dependent daughter cell-specific transcription of genes involved in cell separation; similar to Mob1p | Core | NA | NA | NA |
| 3558-YFL034W_NumOfGenes_2 | YFL034W | MIL1 | NA | Predicted lipase; binds variant medium clathrin chain Apm2p and contributes to its membrane recruitment; putative integral membrane protein that interacts with Rpp0p component of ribosomal stalk | Core | NA | NA | NA |
| 3559-YFL036W_NumOfGenes_2 | YFL036W | RPO41 | DNA-directed RNA polymerase | Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; requires a specificity subunit encoded by MTF1 for promoter recognition; Mtf1p interacts with and stabilizes the Rpo41p-promoter complex, enhancing DNA bending and melting to facilitate pre-initiation open complex formation; Rpo41p also synthesizes RNA primers for mitochondrial DNA replication | Core | NA | NA | NA |
| 3560-YFL037W_NumOfGenes_2 | YFL037W | TUB2 | beta-tubulin|SHE8|ARM10 | Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules; mutation in human ortholog is associated with congenital fibrosis of the extraocular muscles (CFEOM) with polymicrogyria | Core | NA | NA | NA |
| 3561-YFL038C_NumOfGenes_2 | YFL038C | YPT1 | Rab family GTPase YPT1|YP2 | Rab family GTPase; involved in the ER-to-Golgi step of the secretory pathway; complex formation with the Rab escort protein Mrs6p is required for prenylation of Ypt1p by type II protein geranylgeranyltransferase (Bet2p-Bet4p); binds to unspliced HAC1 mRNA; regulates the unfolded protein response (UPR) by promoting the decay of HAC1 RNA; localizes to the early Golgi, the transitional Golgi and ER membranes, pre-autophagosomal structures, and cytoplasmic vesicles | Core | NA | NA | NA |
| 3562-YFL039C_NumOfGenes_2 | YFL039C | ACT1 | actin|ABY1|END7 | Actin; structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions | Core | NA | NA | NA |