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 |
|---|---|---|---|---|---|---|---|---|
| 6023-YML100W | YML100W | TSL1 | trehalose 6-phosphate synthase/phosphatase complex subunit | Large subunit of trehalose 6-phosphate synthase/phosphatase complex; Tps1p-Tps2p complex converts uridine-5'-diphosphoglucose and glucose 6-phosphate to trehalose; contributes to survival to acute lethal heat stress; mutant has aneuploidy tolerance; protein abundance increases in response to DNA replication stress; TSL1 has a paralog, TPS3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6024-YML100W-A | YML100W-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Core | NA | NA | NA |
| 6025-YML101C | YML101C | CUE4 | NA | Protein of unknown function; has a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitination; CUE4 has a paralog, CUE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6026-YML102W_NumOfGenes_2 | YML102W | CAC2 | NA | Subunit of chromatin assembly factor I (CAF-1), with Rlf2p and Msi1p; chromatin assembly by CAF-1 is important for multiple processes including silencing at telomeres, mating type loci, and rDNA; maintenance of kinetochore structure, deactivation of the DNA damage checkpoint after DNA repair, chromatin dynamics during transcription; and repression of divergent transcription; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6027-YML103C | YML103C | NUP188 | NA | Subunit of the inner ring of the nuclear pore complex (NPC); contributes to NPC organization and nucleocytoplasmic transport; homologous to human NUP188 | Core | NA | NA | NA |
| 6028-YML104C | YML104C | MDM1 | NA | PtdIns-3-P binding protein that tethers the ER to vacuoles at NVJs; anchored in the ER membrane at nucleus-vacuole junctions and binds phosphatidylinositol 3-phosphate (PtdIns-3-P) in the vacuolar membrane via its Phox homology (PX) domain; expressed predominantly in late G1 to early S phase of the cell cycle; mutation affects nuclear and mitochondrial transmission to daughter buds; similar to 4 human genes, one of which (SNX14) is associated with neurological disease | Core | NA | NA | NA |
| 6029-YML105C | YML105C | SEC65 | RNA-binding signal recognition particle subunit SEC65 | Subunit of the signal recognition particle (SRP); involved in protein targeting to the ER; interacts with Srp54p; homolog of mammalian SRP19 | Core | NA | NA | NA |
| 6030-YML106W | YML106W | URA5 | orotate phosphoribosyltransferase URA5|PYR5 | Major orotate phosphoribosyltransferase (OPRTase) isozyme; catalyzes the fifth enzymatic step in de novo biosynthesis of pyrimidines, converting orotate into orotidine-5'-phosphate; URA5 has a paralog, URA10, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6031-YML107C | YML107C | PML39 | NA | Protein required for nuclear retention of unspliced pre-mRNAs; required along with Mlp1p and Pml1p; anchored to nuclear pore complex via Mlp1p and Mlp2p; found with the subset of nuclear pores farthest from the nucleolus; may interact with ribosomes | Core | NA | NA | NA |
| 6032-YML108W | YML108W | NA | NA | Protein of unknown function; structure defines a new subfamily of the split beta-alpha-beta sandwiches; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YML108W is not an essential gene; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 6033-YML109W | YML109W | ZDS2 | CES4 | Protein with a role in regulating Swe1p-dependent polarized growth; involved in maintenance of Cdc55p in the cytoplasm where it promotes mitotic entry; interacts with silencing proteins at the telomere; implicated in the mitotic exit network through regulation of Cdc14p localization; ZDS2 has a paralog, ZDS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6034-YML110C | YML110C | COQ5 | 2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase|DBI56 | 2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase; involved in ubiquinone (Coenzyme Q) biosynthesis; localizes to the matrix face of the mitochondrial inner membrane in a large complex with other ubiquinone biosynthetic enzymes; respiratory defect of the null mutant is partially complemented by human COQ5 | Core | NA | NA | NA |
| 6035-YML111W | YML111W | BUL2 | ubiquitin-ubiquitin ligase BUL2 | Component of the Rsp5p E3-ubiquitin ligase complex; involved in intracellular amino acid permease sorting, functions in heat shock element mediated gene expression, essential for growth in stress conditions; BUL2 has a paralog, BUL1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6036-YML112W | YML112W | CTK3 | NA | Gamma subunit of C-terminal domain kinase I; CTDK-I phosphorylates RNA polymerase II subunit Rpo21p to affect transcription and pre-mRNA 3' end processing, and also phosphorylates ribosomal protein Rps2p to increase translational fidelity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6037-YML113W | YML113W | DAT1 | NA | DNA binding protein that recognizes oligo(dA).oligo(dT) tracts; Arg side chain in its N-terminal pentad Gly-Arg-Lys-Pro-Gly repeat is required for DNA-binding; relocalizes to the cytosol in response to hypoxia; not essential for viability | Core | NA | NA | NA |