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 |
|---|---|---|---|---|---|---|---|---|
| 4973-YJR066W | YJR066W | TOR1 | phosphatidylinositol kinase-related protein kinase TOR1|DRR1 | PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis; TOR1 has a paralog, TOR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4974-YJR067C | YJR067C | YAE1 | NA | Protein that forms a complex with Lto1p and Rli1p; essential for growth under standard (aerobic) conditions but not under anaerobic conditions; may have a role in protection of ribosomal assembly and function from damage due to reactive oxygen species | Core | NA | NA | NA |
| 4975-YJR068W | YJR068W | RFC2 | replication factor C subunit 2 | Subunit of heteropentameric Replication factor C (RF-C); RF-C is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon | Core | NA | NA | NA |
| 4976-YJR069C | YJR069C | HAM1 | nucleoside triphosphate pyrophosphohydrolase HAM1 | Nucleoside triphosphate pyrophosphohydrolase; active against various substrates including ITP, dITP and XTP; mediates exclusion of non canonical purines, pyrimidines from dNTP pools; functions with YJL055W to mediate resistance to 5-FU; specifically reduces the incorporation of 5-FU into RNA without affecting uptake or incorporation of uracil into RNA; protein abundance increases in response to DNA replication stress; yeast HAM1 can complement knockdown of human homolog ITPA | Core | NA | NA | NA |
| 4977-YJR070C | YJR070C | LIA1 | MMD1 | Deoxyhypusine hydroxylase; HEAT-repeat containing metalloenzyme that catalyzes hypusine formation; binds to and is required for the modification of Hyp2p (eIF5A); complements S. pombe mmd1 mutants defective in mitochondrial positioning; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4978-YJR071W | YJR071W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4979-YJR072C | YJR072C | NPA3 | GTPase NPA3|GPN1|EPA1 | Member of the conserved GPN-loop GTPase family; has a role in transport of RNA polymerase II to the nucleus; exhibits GTP-dependent binding to PolII; has ATPase activity; involved in sister chromatid cohesion; phosphorylated by the Pcl1p-Pho85p kinase complex; human homolog XAB1 interacts with human RNA polymerase II; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4980-YJR073C | YJR073C | OPI3 | bifunctional phosphatidyl-N-methylethanolamine N-methyltransferase/phosphatidyl-N-dimethylethanolamine N-methyltransferase|PEM2 | Methylene-fatty-acyl-phospholipid synthase; catalyzes the last two steps in phosphatidylcholine biosynthesis; also known as phospholipid methyltransferase | Core | NA | NA | NA |
| 4981-YJR074W | YJR074W | MOG1 | Ran GTPase-binding protein MOG1 | Conserved nuclear protein that interacts with GTP-Gsp1p; stimulates nucleotide release from Gsp1p; involved in nuclear protein import; nucleotide release is inhibited by Yrb1p | Core | NA | NA | NA |
| 4982-YJR075W | YJR075W | HOC1 | alpha-1,6-mannosyltransferase | Alpha-1,6-mannosyltransferase; involved in cell wall mannan biosynthesis; subunit of a Golgi-localized complex that also contains Anp1p, Mnn9p, Mnn11p, and Mnn10p; identified as a suppressor of a cell lysis sensitive pkc1-371 allele | Core | NA | NA | NA |
| 4983-YJR076C | YJR076C | CDC11 | septin CDC11|PSL9 | Component of the septin ring that is required for cytokinesis; present at the ends of rod-like septin hetero-oligomers; C-terminal extension is important for recruitment of Bni5p to the mother-bud neck, which in turn is required for Myo1p recruitment and cytokinesis; septin rings at the mother-bud neck act as scaffolds for recruiting cell division factors and as barriers to prevent diffusion of specific proteins between mother and daughter cells | Core | NA | NA | NA |
| 4984-YJR077C | YJR077C | MIR1 | PTP | Mitochondrial phosphate carrier; imports inorganic phosphate into mitochondria; functionally redundant with Pic2p but more abundant than Pic2p under normal conditions; phosphorylated | Core | NA | NA | NA |
| 4985-YJR078W | YJR078W | BNA2 | dioxygenase BNA2 | Tryptophan 2,3-dioxygenase or indoleamine 2,3-dioxygenase; required for de novo biosynthesis of NAD from tryptophan via kynurenine; interacts genetically with telomere capping gene CDC13; regulated by Hst1p and Aftp | Core | NA | NA | NA |
| 4986-YJR079W_NumOfGenes_2 | YJR079W | NA | NA | Putative protein of unknown function; mutation results in impaired mitochondrial respiration | Core | NA | NA | NA |
| 4987-YJR082C | YJR082C | EAF6 | NA | Subunit of the NuA4 acetyltransferase complex; this complex acetylates histone H4 and NuA3 acetyltransferase complex that acetylates histone H3 | Core | NA | NA | NA |