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 |
|---|---|---|---|---|---|---|---|---|
| 7163-YOR203W | YOR203W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps 5' end of essential DED1 gene required for translation initiation | Core | NA | NA | NA |
| 7164-YOR204W | YOR204W | DED1 | DEAD-box ATP-dependent RNA helicase DED1|SPP81 | ATP-dependent DEAD (Asp-Glu-Ala-Asp)-box RNA helicase; required for translation initiation of all yeast mRNAs; binds to mRNA cap-associated factors, and binding stimulates Ded1p RNA-dependent ATPase activity; mutation in human homolog DBY is associated with male infertility; human homolog DDX3X complements ded1 null mutation; DED1 has a paralog, DBP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7165-YOR205C | YOR205C | GEP3 | MTG3|AIM40|LRC5|FMP38 | Protein required for mitochondrial ribosome small subunit biogenesis; null mutant is defective in respiration and in maturation of 15S rRNA; protein is localized to the mitochondrial inner membrane; null mutant interacts synthetically with prohibitin (Phb1p) | Core | NA | NA | NA |
| 7166-YOR206W | YOR206W | NOC2 | mRNA-binding ribosome synthesis protein NOC2 | Protein involved in ribosome biogenesis; forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes; forms a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors; acts as part of a Mak21p-Noc2p-Rrp5p module that associates with nascent pre-rRNA during transcription and has a role in bigenesis of the large ribosomal subunit | Core | NA | NA | NA |
| 7167-YOR207C | YOR207C | RET1 | DNA-directed RNA polymerase III core subunit RET1|C128|RPC128|RPC2|PDS2 | Second-largest subunit of RNA polymerase III; RNA polymerase III is responsible for the transcription of tRNA and 5S RNA genes, and other low molecular weight RNAs | Core | NA | NA | NA |
| 7168-YOR208W | YOR208W | PTP2 | tyrosine protein phosphatase PTP2 | Nuclear phosphotyrosine-specific phosphatase involved in osmosensing; involved in the inactivation of mitogen-activated protein kinase (MAPK) during osmolarity sensing; dephosporylates Hog1p MAPK and regulates its localization; with Msg5p co-regulates the calcium signaling pathway | Core | NA | NA | NA |
| 7169-YOR209C | YOR209C | NPT1 | nicotinate phosphoribosyltransferase | Nicotinate phosphoribosyltransferase; acts in the salvage pathway of NAD+ biosynthesis; required for silencing at rDNA and telomeres and has a role in silencing at mating-type loci; localized to the nucleus | Core | NA | NA | NA |
| 7170-YOR210W | YOR210W | RPB10 | DNA-directed RNA polymerase core subunit RPB10|ABC10-beta | RNA polymerase subunit ABC10-beta; common to RNA polymerases I, II, and III | Core | NA | NA | NA |
| 7171-YOR211C | YOR211C | MGM1 | dynamin-related GTPase MGM1|MNA1 | Mitochondrial GTPase, present in complex with Ugo1p and Fzo1p; required for mitochondrial morphology, fusion, and genome maintenance; promotes membrane bending; exists as long and short form with different distributions; ratio of long to short forms is regulated by Psd1p; homolog of human OPA1 involved in autosomal dominant optic atrophy | Core | NA | NA | NA |
| 7172-YOR212W | YOR212W | STE4 | G protein subunit beta|HMD2 | G protein beta subunit; forms a dimer with Ste18p to activate mating signaling pathway, forms heterotrimer with Gpa1p and Ste18p to dampen signaling; pheromone-induced phosphorylation plays critical role in chemotropism; may recruit Rho1p to polarized growth site during mating; contains WD40 repeats | Core | NA | NA | NA |
| 7173-YOR213C | YOR213C | SAS5 | NA | Subunit of the SAS complex (Sas2p, Sas4p, Sas5p); acetylates free histones and nucleosomes and regulates transcriptional silencing; stimulates Sas2p HAT activity | Core | NA | NA | NA |
| 7174-YOR214C | YOR214C | SPR2 | NA | Putative spore wall protein; expression increases during sporulation; not an essential gene; YOR214C has a paralog, SPO19, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7175-YOR215C | YOR215C | AIM41 | NA | Protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays reduced frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 7176-YOR216C | YOR216C | RUD3 | GRP1 | Golgi matrix protein; involved in the structural organization of the cis-Golgi; interacts genetically with COG3 and USO1 | Core | NA | NA | NA |
| 7177-YOR217W_NumOfGenes_2 | YOR217W | RFC1 | replication factor C subunit 1|CDC44 | 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 |