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 |
|---|---|---|---|---|---|---|---|---|
| 3728-YGL083W | YGL083W | SCY1 | NA | Putative kinase; suppressor of GTPase mutant; similar to bovine rhodopsin kinase; may have a role in intracellular sterol transport | Core | NA | NA | NA |
| 3729-YGL084C | YGL084C | GUP1 | O-acyltransferase | Plasma membrane protein involved in remodeling GPI anchors; member of the MBOAT family of putative membrane-bound O-acyltransferases; role in misfolded protein quality control; proposed to be involved in glycerol transport; homolog of the mammalian Hedgehog pathway modulator HHATL; GUP1 has a paralog, GUP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3730-YGL085W | YGL085W | LCL3 | NA | Putative protein of unknown function; mutant has long chronological lifespan; has homology to Staphylococcus aureus nuclease; GFP-fusion protein localizes to mitochondria; is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 3731-YGL086W | YGL086W | MAD1 | coiled-coil domain-containing protein MAD1 | Coiled-coil protein involved in spindle-assembly checkpoint; required for inhibition of karyopherin/importin Pse1p (aka Kap121p) upon spindle assembly checkpoint arrest; phosphorylated by Mps1p upon checkpoint activation which leads to inhibition of anaphase promoting complex activity; forms a complex with Mad2p; gene dosage imbalance between MAD1 and MAD2 leads to chromosome instability | Core | NA | NA | NA |
| 3732-YGL087C | YGL087C | MMS2 | E2 ubiquitin-conjugating protein MMS2 | Ubiquitin-conjugating enzyme variant; involved in error-free postreplication repair; forms a heteromeric complex with Ubc13p, an active ubiquitin-conjugating enzyme; cooperates with chromatin-associated RING finger proteins, Rad18p and Rad5p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3733-YGL088W | YGL088W | NA | NA | Putative protein of unknown function; conserved across S. cerevisiae strains; partially overlaps snR10, a snoRNA required for preRNA processing | Core | NA | NA | NA |
| 3734-YGL089C | YGL089C | MF(ALPHA)2 | NA | Mating pheromone alpha-factor, made by alpha cells; interacts with mating type a cells to induce cell cycle arrest and other responses leading to mating; also encoded by MF(ALPHA)1, which is more highly expressed; binds copper(II) ions | Core | NA | NA | NA |
| 3735-YGL090W | YGL090W | LIF1 | NA | Component of the DNA ligase IV complex; this complex mediates nonhomologous end joining in DNA double-strand break repair; physically interacts with Dnl4p and Nej1p; homologous to mammalian XRCC4 protein | Core | NA | NA | NA |
| 3736-YGL091C | YGL091C | NBP35 | Fe-S cluster-binding ATPase | Essential cytoplasmic iron-sulfur cluster binding protein; forms a complex with Cfd1p that is involved in iron-sulfur protein assembly in the cytosol; similar to P-loop NTPases | Core | NA | NA | NA |
| 3737-YGL092W | YGL092W | NUP145 | nucleocytoplasmic transporter NUP145|RAT10 | Essential protein with distinct roles in two nuclear pore subcomplexes; catalyzes its own proteolytic cleavage in vivo to generate a C-terminal fragment that is a structural component of the Nup84p subcomplex (with roles in NPC biogenesis and localization of genes to the nuclear periphery), and an N-terminal fragment that is one of several FG-nucleoporins within the NPC central core directly responsible for nucleocytoplasmic transport; homologous to human NUP98 | Core | NA | NA | NA |
| 3738-YGL093W | YGL093W | SPC105 | NA | Subunit of a kinetochore-microtubule binding complex; complex bridges centromeric heterochromatin and kinetochore MAPs and motors; required for sister chromatid bi-orientation and kinetochore binding of SAC components; complex also includes Kre28p; modified by sumoylation | Core | NA | NA | NA |
| 3739-YGL094C | YGL094C | PAN2 | poly(A)-specific ribonuclease | Catalytic subunit of the Pan2p-Pan3p poly(A)-ribonuclease complex; complex acts to control poly(A) tail length and regulate the stoichiometry and activity of postreplication repair complexes | Core | NA | NA | NA |
| 3740-YGL095C | YGL095C | VPS45 | VPL28|STT10 | Protein of the Sec1p/Munc-18 family; essential for vacuolar protein sorting; required for the function of Pep12p and the early endosome/late Golgi SNARE Tlg2p; essential for fusion of Golgi-derived vesicles with the prevacuolar compartment | Core | NA | NA | NA |
| 3741-YGL096W_NumOfGenes_2 | YGL096W | TOS8 | NA | Homeodomain-containing protein and putative transcription factor; found associated with chromatin; target of SBF transcription factor; induced during meiosis and under cell-damaging conditions; TOS8 has a paralog, CUP9, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3742-YGL097W | YGL097W | SRM1 | Ran guanyl-nucleotide exchange factor|TSM437|PRP20|MTR1 | Nucleotide exchange factor for Gsp1p; localizes to the nucleus, required for nucleocytoplasmic trafficking of macromolecules; suppressor of the pheromone response pathway; potentially phosphorylated by Cdc28p; human homolog of the RAN GEF, RCC1, can complement a temperature sensitive point mutant | Accessory | Ancestral | NA | NA |