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 |
|---|---|---|---|---|---|---|---|---|
| 2243-YBR252W | YBR252W | DUT1 | bifunctional dITP/dUTP diphosphatase | Deoxyuridine triphosphate diphosphatase (dUTPase); catalyzes hydrolysis of dUTP to dUMP and PPi, thereby preventing incorporation of uracil into DNA during replication; critical for the maintenance of genetic stability; also has diphosphatase activity on deoxyinosine triphosphate; human homolog DUT allows growth of yeast haploid dut1 null mutant after sporulation of heterozygous diploid | Core | NA | NA | NA |
| 2244-YBR253W | YBR253W | SRB6 | MED22 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation | Core | NA | NA | NA |
| 2245-YBR254C | YBR254C | TRS20 | TRAPP subunit TRS20 | Core component of transport protein particle (TRAPP) complexes I-III; TRAPPs are multimeric guanine nucleotide-exchange factors for GTPase Ypt1p, regulating ER-Golgi traffic (TRAPPI), intra-Golgi traffic (TRAPPII), endosome-Golgi traffic (TRAPPII and III) and autophagy (TRAPPIII); mutation leads to defects in endocytic recycling, block in sporulation/meiosis; mutations in human homolog TRAPPC2 cause spondyloepiphyseal dysplasia tarda, TRAPPC2 can complement yeast null mutant | Core | NA | NA | NA |
| 2246-YBR255C-A | YBR255C-A | RCF3 | NA | Putative protein of unknown function; may interact with respiratory chain complexes III (ubiquinol-cytochrome c reductase) or IV (cytochrome c oxidase); identified by sequence comparison with hemiascomycetous yeast species | Core | NA | NA | NA |
| 2247-YBR255W | YBR255W | MTC4 | NA | Protein of unknown function; required for normal growth rate at 15 degrees C; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; mtc4 is synthetically sick with cdc13-1 | Core | NA | NA | NA |
| 2248-YBR256C | YBR256C | RIB5 | riboflavin synthase | Riboflavin synthase; catalyzes the last step of the riboflavin biosynthesis pathway | Core | NA | NA | NA |
| 2249-YBR257W | YBR257W | POP4 | RNase P/RNase MRP complex subunit | Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; binds to the RPR1 RNA subunit in RNase P | Core | NA | NA | NA |
| 2250-YBR258C | YBR258C | SHG1 | CPS15 | Subunit of the COMPASS (Set1C) complex; COMPASS methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres | Core | NA | NA | NA |
| 2251-YBR259W | YBR259W | NA | NA | Protein of unknown function; YBR259W is not an essential gene; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 2252-YBR260C | YBR260C | RGD1 | NA | GTPase-activating protein (RhoGAP) for Rho3p and Rho4p; possibly involved in control of actin cytoskeleton organization | Core | NA | NA | NA |
| 2253-YBR261C | YBR261C | TAE1 | N-terminal protein methyltransferase|NTM1 | AdoMet-dependent proline methyltransferase; catalyzes the dimethylation of ribosomal proteins Rpl12 and Rps25 at N-terminal proline residues; has a role in protein synthesis; fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 2254-YBR262C | YBR262C | MIC12 | AIM5|MCS12|FMP51 | Component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; forms a subcomplex with Mic10p and Mic27p whose assembly and stability requires cardiolipin | Core | NA | NA | NA |
| 2255-YBR263W | YBR263W | SHM1 | glycine hydroxymethyltransferase SHM1|TMP3|SHMT1 | Mitochondrial serine hydroxymethyltransferase; converts serine to glycine plus 5,10 methylenetetrahydrofolate; involved in generating precursors for purine, pyrimidine, amino acid, and lipid biosynthesis; reverse reaction generates serine | Core | NA | NA | NA |
| 2256-YBR264C | YBR264C | YPT10 | Rab family GTPase YPT10 | Rab family GTP-binding protein; contains the PEST signal sequence specific for proteolytic enzymes; may be involved in vesicular transport; overexpression leads to accumulation of Golgi-like cisternae with budding vesicles | Core | NA | NA | NA |
| 2257-YBR265W | YBR265W | TSC10 | 3-dehydrosphinganine reductase | 3-ketosphinganine reductase; catalyzes the second step in phytosphingosine synthesis; essential for growth in the absence of exogenous dihydrosphingosine or phytosphingosine; localized to lipid droplets; member of short chain dehydrogenase/reductase protein family | Core | NA | NA | NA |