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 |
|---|---|---|---|---|---|---|---|---|
| 2078-YBR095C | YBR095C | RXT2 | RAF60 | Component of the histone deacetylase Rpd3L complex; possibly involved in cell fusion and invasive growth; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2079-YBR096W | YBR096W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the ER | Core | NA | NA | NA |
| 2080-YBR097W | YBR097W | VPS15 | ubiquitin-binding serine/threonine protein kinase VPS15|VPT15|VPS40|VPL19|VAC4|GRD8 | Serine/threonine protein kinase involved in vacuolar protein sorting; functions as a membrane-associated complex with Vps34p; active form recruits Vps34p to the Golgi membrane; interacts with the GDP-bound form of Gpa1p; myristoylated; a fraction is localized, with Vps34p, to nuclear pores at nucleus-vacuole junctions and may facilitate transcription elongation for genes positioned at the nuclear periphery | Core | NA | NA | NA |
| 2081-YBR098W_NumOfGenes_2 | YBR098W | MMS4 | YBR100W|SLX2 | Subunit of structure-specific Mms4p-Mus81p endonuclease; cleaves branched DNA; involved in recombination, DNA repair, and joint molecule formation/resolution during meiotic recombination; phosphorylation of the non-catalytic subunit Mms4p by Cdc28p and Cdc5p during mitotic cell cycle activates the function of Mms4p-Mus81p | Core | NA | NA | NA |
| 2082-YBR101C | YBR101C | FES1 | NA | Hsp70 (Ssa1p) nucleotide exchange factor; required for the release of misfolded proteins from the Hsp70 system to the Ub-proteasome machinery for destruction; cytosolic homolog of Sil1p, which is the nucleotide exchange factor for BiP (Kar2p) in the endoplasmic reticulum; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2083-YBR102C | YBR102C | EXO84 | exocyst subunit EXO84|USA3 | Exocyst subunit with dual roles in exocytosis and spliceosome assembly; subunit of the the exocyst complex which mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis at the plasma membrane (PM) prior to SNARE-mediated fusion; required for exocyst assembly and targeting the complex to specific sites on the bud tip PM; associates the U1 snRNP; role in pre-mRNA splicing and prespliceosome formation; possible Cdc28 substrate | Core | NA | NA | NA |
| 2084-YBR103C-A | YBR103C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; identified by homology to related yeast | Core | NA | NA | NA |
| 2085-YBR103W | YBR103W | SIF2 | EMB1 | WD40 repeat-containing subunit of Set3C histone deacetylase complex; complex represses early/middle sporulation genes; antagonizes telomeric silencing; binds specifically to the Sir4p N-terminus | Core | NA | NA | NA |
| 2086-YBR104W | YBR104W | YMC2 | organic acid transporter | Putative mitochondrial inner membrane transporter; proposed role in oleate metabolism and glutamate biosynthesis; member of the mitochondrial carrier (MCF) family; YMC2 has a paralog, YMC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2087-YBR105C | YBR105C | VID24 | glucose-induced degradation complex subunit VID24|GID4 | GID Complex regulatory subunit; binds GID Complex in response to glucose through interactions with complex member Vid28p; regulates fructose-1,6-bisphosphatase (FBPase) targeting to the vacuole; promotes proteasome-dependent catabolite degradation of FBPase; peripheral membrane protein located at Vid (vacuole import and degradation) vesicles | Core | NA | NA | NA |
| 2088-YBR106W | YBR106W | PHO88 | SND3 | Protein involved in SRP-independent targeting of substrates to the ER; component of an alternative ER targeting pathway that has partial functional redundancy with the GET pathway; preference for substrates with downstream transmembrane domains; interacts with Snd1p, Env10p/Snd2p, and Sec61p-translocon subunits; can compensate for loss of SRP; role in phosphate transport, interacting with pho88, and in the maturation of secretory proteins | Core | NA | NA | NA |
| 2089-YBR107C | YBR107C | IML3 | MCM19 | Outer kinetochore protein and component of the Ctf19 complex; involved in the establishment of pericentromeric cohesion during mitosis; prevents non-disjunction of sister chromatids during meiosis II; forms a stable complex with Chl4p; required for localization of Sgo1p to pericentric sites during meiosis I; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-L and fission yeast fta1 | Core | NA | NA | NA |
| 2090-YBR108W | YBR108W | AIM3 | NA | Protein that inhibits barbed-end actin filament elongation; interacts with Rvs167p; null mutant is viable and displays elevated frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 2091-YBR109C | YBR109C | CMD1 | calmodulin|CaM | Calmodulin; Ca2+ binding protein that regulates Ca2+ independent processes (mitosis, bud growth, actin organization, endocytosis, etc.) and Ca2+ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin; binds to the Hog1p MAPK in response to hyperosmotic stress; potentiates membrane tubulation and constriction mediated by the Rvs161p-Rvs167p complex; human CALM1 or CALM2 functionally complement repression induced inviability | Core | NA | NA | NA |
| 2092-YBR109W-A | YBR109W-A | NA | NA | Putative protein of unknown function; questionable ORF from MIPS | Core | NA | NA | NA |