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 |
|---|---|---|---|---|---|---|---|---|
| 6293-YMR226C | YMR226C | NA | oxidoreductase|TMA29 | NADP(+)-dependent serine dehydrogenase and carbonyl reductase; acts on serine, L-allo-threonine, and other 3-hydroxy acids; green fluorescent protein fusion protein localizes to the cytoplasm and nucleus; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |
| 6294-YMR227C | YMR227C | TAF7 | TafII67|TAF67 | TFIID subunit (67 kDa); involved in RNA polymerase II transcription initiation | Core | NA | NA | NA |
| 6295-YMR228W | YMR228W | MTF1 | RNA polymerase specificity factor | Mitochondrial RNA polymerase specificity factor; has structural similarity to S-adenosylmethionine-dependent methyltransferases and functional similarity to bacterial sigma-factors; Mtf1p interacts with and stabilizes the Rpo41p-promoter complex, enhancing DNA bending and melting to facilitate pre-initiation open complex formation | Core | NA | NA | NA |
| 6296-YMR229C | YMR229C | RRP5 | NA | RNA binding protein involved in synthesis of 18S and 5.8S rRNAs; component of ribosomal small subunit (SSU) processome and 90S preribosome; required for pre-rRNA packaging and compaction of processome into dense terminal balls; part of Mak21p-Noc2p-Rrp5p module that associates with nascent pre-rRNA during transcription with role in biogenesis of large ribosomal subunit; binds single stranded tracts of U's; relocalizes from nucleolus to nucleus upon DNA replication stress | Core | NA | NA | NA |
| 6297-YMR230W | YMR230W | RPS10B | eS10|ribosomal 40S subunit protein S10B|S10e|S10B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S10, no bacterial homolog; RPS10B has a paralog, RPS10A, that arose from the whole genome duplication; mutations in the human homolog associated with Diamond-Blackfan anemia | Core | NA | NA | NA |
| 6298-YMR230W-A | YMR230W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6299-YMR231W | YMR231W | PEP5 | tethering complex subunit PEP5|VPT11|VPS11|VPL9|VAM1|END1 | Histone E3 ligase, component of CORVET membrane tethering complex; peripheral vacuolar membrane protein required for protein trafficking and vacuole biogenesis; interacts with Pep7p; involved in ubiquitination and degradation of excess histones | Core | NA | NA | NA |
| 6300-YMR232W | YMR232W | FUS2 | NA | Cell fusion regulator; cytoplasmic protein localized to shmoo tip; required for alignment of parental nuclei before nuclear fusion during mating; contains a Dbl-homology domain; binds specifically with activated Cdc42p | Core | NA | NA | NA |
| 6301-YMR233W | YMR233W | TRI1 | NA | Non-essential sumoylated protein of unknown function; similar to components of human SWI/SNF complex including SMRD3; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm, nucleus and nucleolus; TRI1 has a paralog, UAF30, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6302-YMR234W | YMR234W | RNH1 | RNA-DNA hybrid ribonuclease | Ribonuclease H1; able to bind double-stranded RNAs and RNA-DNA hybrids; associates with RNAse polymerase I. | Core | NA | NA | NA |
| 6303-YMR235C | YMR235C | RNA1 | GTPase-activating protein RNA1 | GTPase activating protein (GAP) for Gsp1p; involved in nuclear transport | Core | NA | NA | NA |
| 6304-YMR236W | YMR236W | TAF9 | chromatin modification protein|TafII17|TAF17 | Subunit (17 kDa) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3 | Core | NA | NA | NA |
| 6305-YMR237W | YMR237W | BCH1 | exomer complex subunit | Member of the ChAPs family (Chs5p-Arf1p-binding proteins); members include Bch1p, Bch2p, Bud7p, and Chs6p; ChAPs family proteins form the exomer complex with Chs5p to mediate export of specific cargo proteins from the Golgi to the plasma membrane; interacts selectively with the activated, GTP-bound form of Arf1p; may interact with ribosomes; protein abundance increases and forms cytoplasmic foci in response to DNA replication stress | Core | NA | NA | NA |
| 6306-YMR238W | YMR238W | DFG5 | putative mannan endo-1,6-alpha-mannosidase | Putative mannosidase; essential glycosylphosphatidylinositol (GPI)-anchored membrane protein required for cell wall biogenesis in bud formation, involved in filamentous growth, homologous to Dcw1p | Core | NA | NA | NA |
| 6307-YMR239C | YMR239C | RNT1 | ribonuclease III | Nuclear dsRNA-specific ribonuclease (RNase III); involved in rDNA transcription, rRNA processing and U2 snRNA 3' end formation by cleavage of a stem-loop structure at the 3' end of U2 snRNA; involved in polyadenylation-independent transcription termination; involved in the cell wall stress response, regulating the degradation of cell wall integrity and morphogenesis checkpoint genes | Core | NA | NA | NA |