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 |
|---|---|---|---|---|---|---|---|---|
| 3113-YDR422C | YDR422C | SIP1 | NA | Alternate beta-subunit of the Snf1p kinase complex; may confer substrate specificity; vacuolar protein containing KIS (Kinase-Interacting Sequence) and ASC (Association with Snf1 kinase Complex) domains involved in protein interactions | Core | NA | NA | NA |
| 3114-YDR423C | YDR423C | CAD1 | YAP2 | AP-1-like basic leucine zipper (bZIP) transcriptional activator; involved in stress responses, iron metabolism, and pleiotropic drug resistance; controls a set of genes involved in stabilizing proteins; binds consensus sequence TTACTAA; CAD1 has a paralog, YAP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3115-YDR424C | YDR424C | DYN2 | dynein light chain|SLC1 | Cytoplasmic light chain dynein, microtubule motor protein; required for intracellular transport and cell division; involved in mitotic spindle positioning; forms complex with dynein intermediate chain Pac11p that promotes Dyn1p homodimerization, potentiates motor processivity; Dyn2p-Pac11p complex important for interaction of dynein motor complex with dynactin complex; acts as molecular glue to dimerize, stabilize Nup82-Nsp1-Nup159 complex module of cytoplasmic pore filaments | Core | NA | NA | NA |
| 3116-YDR425W_NumOfGenes_2 | YDR425W | SNX41 | NA | Sorting nexin; involved in the retrieval of late-Golgi SNAREs from the post-Golgi endosome to the trans-Golgi network; interacts with Snx4p | Core | NA | NA | NA |
| 3117-YDR427W | YDR427W | RPN9 | proteasome regulatory particle lid subunit RPN9|NAS7 | Non-ATPase regulatory subunit of the 26S proteasome; similar to putative proteasomal subunits in other species; null mutant is temperature sensitive and exhibits cell cycle and proteasome assembly defects; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3118-YDR428C | YDR428C | BNA7 | arylformamidase | Formylkynurenine formamidase; involved in the de novo biosynthesis of NAD from tryptophan via kynurenine | Core | NA | NA | NA |
| 3119-YDR429C | YDR429C | TIF35 | translation initiation factor eIF3 core subunit g | eIF3g subunit of the eukaryotic translation initiation factor 3 (eIF3); subunit of the core complex of eIF3; is essential for translation; stimulates resumption of ribosomal scanning during translation reinitiation; eIF3 is also involved in programmed stop codon readthrough | Core | NA | NA | NA |
| 3120-YDR430C | YDR430C | CYM1 | MOP112 | Lysine-specific metalloprotease of the pitrilysin family; metalloprotease of the intermembrane space; degrades proteins and presequence peptides cleaved from imported proteins; required for normal mitochondrial morphology | Core | NA | NA | NA |
| 3121-YDR431W | YDR431W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 3122-YDR432W_NumOfGenes_2 | YDR432W | NPL3 | mRNA-binding protein NPL3|NAB1|NOP3|MTS1|MTR13 | RNA-binding protein; promotes elongation, regulates termination, and carries poly(A) mRNA from nucleus to cytoplasm; represses translation initiation by binding eIF4G; required for pre-mRNA splicing; interacts with E3 ubiquitin ligase Bre1p, linking histone ubiquitination to mRNA processing; may have role in telomere maintenance; dissociation from mRNAs promoted by Mtr10p; phosphorylated by Sky1p in cytoplasm; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3123-YDR434W | YDR434W | GPI17 | GPI-anchor transamidase GPI17 | Transmembrane protein; subunit of the glycosylphosphatidylinositol transamidase complex that adds GPIs to newly synthesized proteins; human PIG-S homolog | Core | NA | NA | NA |
| 3124-YDR435C | YDR435C | PPM1 | leucine carboxy methyltransferase | Carboxyl methyltransferase; methylates the C terminus of the protein phosphatase 2A catalytic subunit (Pph21p or Pph22p), which is important for complex formation with regulatory subunits; required for methionine to inhibit autophagy and promote growth | Core | NA | NA | NA |
| 3125-YDR436W | YDR436W | PPZ2 | salt homeostasis regulator | Serine/threonine protein phosphatase Z, isoform of Ppz1p; involved in regulation of potassium transport, which affects osmotic stability, cell cycle progression, and halotolerance | Core | NA | NA | NA |
| 3126-YDR437W | YDR437W | GPI19 | phosphatidylinositol N-acetylglucosaminyltransferase GPI19 | Subunit of GPI-GlcNAc transferase involved in synthesis of GlcNAc-PI; N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI) is the first intermediate in glycosylphosphatidylinositol (GPI) anchor synthesis; shares similarity with mammalian PIG-P | Core | NA | NA | NA |
| 3127-YDR438W | YDR438W | THI74 | NA | Mitochondrial transporter repressible by thiamine; THI74 has a paralog, YML018C, that arose from the whole genome duplication; shows sequence homology to human gene SLC35F3, a thiamine transporter implicated in hypertension | Core | NA | NA | NA |