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 |
|---|---|---|---|---|---|---|---|---|
| 4913-YJL222W-B_NumOfGenes_2 | YJL222W-B | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4914-YJR001W | YJR001W | AVT1 | NA | Vacuolar transporter; imports large neutral amino acids into the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters | Core | NA | NA | NA |
| 4915-YJR002W | YJR002W | MPP10 | rRNA-processing protein MPP10 | Component of the SSU processome and 90S preribosome; required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p | Core | NA | NA | NA |
| 4916-YJR003C | YJR003C | MRX12 | NA | Protein that associates with mitochondrial ribosome; detected in highly purified mitochondria in high-throughput studies; predicted to be involved in ribosome biogenesis | Core | NA | NA | NA |
| 4917-YJR004C | YJR004C | SAG1 | AG(ALPHA)1 | Alpha-agglutinin of alpha-cells; binds to Aga1p during agglutination, N-terminal half is homologous to the immunoglobulin superfamily and contains binding site for a-agglutinin, C-terminal half is highly glycosylated and contains GPI anchor | Core | NA | NA | NA |
| 4918-YJR005C-A | YJR005C-A | LSO1 | NA | Protein with a potential role in response to iron deprivation; transcription increases during iron deprivation and during treatment with 2-(6-benzyl-2-pyridyl)quinazoline (BPQ) and copper; regulated by Aft1p and, to a lesser extent, by Aft2p; originally identified as a syntenic homolog of an Ashbya gossypii gene; localizes to nucleus and cytoplasm, and nuclear localization is enhanced under iron-replete conditions | Core | NA | NA | NA |
| 4919-YJR005W | YJR005W | APL1 | YAP80 | Beta-adaptin; large subunit of the clathrin associated protein complex (AP-2); involved in vesicle mediated transport; similar to mammalian beta-chain of the clathrin associated protein complex | Core | NA | NA | NA |
| 4920-YJR006W | YJR006W | POL31 | DNA-directed DNA polymerase delta subunit POL31|HYS2|SDP5|HUS2 | Subunit of DNA polymerase delta (polymerase III); essential for cell viability; involved in DNA replication and DNA repair; forms a complex with Rev3p, Rev7p and Pol32p; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4921-YJR007W | YJR007W | SUI2 | translation initiation factor eIF2 subunit alpha | Alpha subunit of the translation initiation factor eIF2; eIF2 is involved in identification of the start codon; phosphorylation of Ser51 is required for regulation of translation by inhibiting the exchange of GDP for GTP; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4922-YJR008W | YJR008W | MHO1 | NA | Protein of unknown function; inhibits haploid invasive growth when overexpressed; synthetically lethal with phospholipase C (PLC1); expression induced by mild heat-stress on a non-fermentable carbon source, upon entry into stationary phase and upon nitrogen deprivation; repressed by inosine and choline in an Opi1p-dependent manner; highly conserved from bacteria to human; Memo, the human homolog, is an ErbB2 interacting protein with an essential function in cell motility | Core | NA | NA | NA |
| 4923-YJR010C-A | YJR010C-A | SPC1 | signal peptidase complex subunit SPC1 | Subunit of the signal peptidase complex (SPC); SPC cleaves the signal sequence from proteins targeted to the endoplasmic reticulum (ER); homolog of the SPC12 subunit of mammalian signal peptidase complex; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4924-YJR010W | YJR010W | MET3 | sulfate adenylyltransferase | ATP sulfurylase; catalyzes the primary step of intracellular sulfate activation, essential for assimilatory reduction of sulfate to sulfide, involved in methionine metabolism; human homolog PAPSS2 complements yeast null mutant | Core | NA | NA | NA |
| 4925-YJR011C | YJR011C | NA | NA | Putative protein of unknown function; GFP-fusion protein expression is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 4926-YJR012C | YJR012C | NA | NA | Essential protein of unknown function; proposed involvement in transport based on mass spectrometry analysis of copurifying proteins; partially overlaps neighboring ORF, GPI14/YJR013W | Core | NA | NA | NA |
| 4927-YJR013W | YJR013W | GPI14 | glycosylphosphatidylinositol-alpha 1,4 mannosyltransferase I|PMH1 | Glycosylphosphatidylinositol-alpha 1,4 mannosyltransferase I; involved in GPI anchor biosynthesis, requires Pbn1p for function; homolog of mammalian PIG-M | Core | NA | NA | NA |