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 |
|---|---|---|---|---|---|---|---|---|
| 4163-YGR264C | YGR264C | MES1 | methionine--tRNA ligase MES1|MetRS|MESI | Methionyl-tRNA synthetase; forms a complex with glutamyl-tRNA synthetase (Gus1p) and Arc1p, which increases the catalytic efficiency of both tRNA synthetases; also has a role in nuclear export of tRNAs; mutations in human ortholog MARS are associated with pediatric pulmonary alveolar proteinosis | Core | NA | NA | NA |
| 4164-YGR265W | YGR265W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF MES1/YGR264C, which encodes methionyl-tRNA synthetase | Core | NA | NA | NA |
| 4165-YGR266W | YGR266W | NA | NA | Protein of unknown function; predicted to contain a single transmembrane domain; mutant has increased aneuploidy tolerance; localized to both the mitochondrial outer membrane and the plasma membrane; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4166-YGR267C | YGR267C | FOL2 | GTP cyclohydrolase I | GTP-cyclohydrolase I, catalyzes first step in folic acid biosynthesis; human homolog GCH1 is implicated in dopa-responsive dystonia (DRD), and can complement yeast null mutant | Core | NA | NA | NA |
| 4167-YGR268C | YGR268C | HUA1 | NA | Cytoplasmic protein containing a zinc finger domain; sequence similarity to that of Type I J-proteins; computational analysis of large-scale protein-protein interaction data suggests a possible role in actin patch assembly | Core | NA | NA | NA |
| 4168-YGR269W | YGR269W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF HUA1/YGR268C | Core | NA | NA | NA |
| 4169-YGR270W_NumOfGenes_2 | YGR270W | YTA7 | NA | Protein that localizes to chromatin; has a role in regulation of histone gene expression; has a bromodomain-like region that interacts with the N-terminal tail of histone H3, and an ATPase domain; relocalizes to the cytosol in response to hypoxia; potentially phosphorylated by Cdc28p | Core | NA | NA | NA |
| 4170-YGR271C-A | YGR271C-A | EFG1 | YGR272C | Essential protein required for maturation of 18S rRNA; null mutant is sensitive to hydroxyurea and is delayed in recovering from alpha-factor arrest; green fluorescent protein (GFP)-fusion protein localizes to the nucleolus | Core | NA | NA | NA |
| 4171-YGR271W | YGR271W | SLH1 | putative RNA helicase | Putative RNA helicase related to Ski2p; involved in translation inhibition of non-poly(A) mRNAs; required for repressing propagation of dsRNA viruses | Core | NA | NA | NA |
| 4172-YGR273C | YGR273C | NA | IBI1 | Putative protein of unknown function; expression downregulated by treatment with 8-methoxypsoralen plus UVA irradiation; not an essential gene; YGR273C has a paralog, YMR295C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4173-YGR274C | YGR274C | TAF1 | KAT4|TafII145|TafII130|TAF145|TAF130 | TFIID subunit, involved in RNA pol II transcription initiation; possesses in vitro histone acetyltransferase activity but its role in vivo appears to be minor; involved in promoter binding and G1/S progression; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 4174-YGR275W | YGR275W | RTT102 | NA | Component of both the SWI/SNF and RSC chromatin remodeling complexes; suggested role in chromosome maintenance; possible weak regulator of Ty1 transposition; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4175-YGR276C | YGR276C | RNH70 | RNA82|REX1 | 3'-5' exoribonuclease; required for maturation of 3' ends of 5S rRNA and tRNA-Arg3 from dicistronic transcripts | Core | NA | NA | NA |
| 4176-YGR277C | YGR277C | CAB4 | putative pantetheine-phosphate adenylyltransferase | Subunit of the CoA-Synthesizing Protein Complex (CoA-SPC); subunits of this complex are: Cab2p, Cab3p, Cab4p, Cab5p, Sis2p and Vhs3p; probable pantetheine-phosphate adenylyltransferase (PPAT); PPAT catalyzes the fourth step in the biosynthesis of coenzyme A from pantothenate; null mutant lethality is complemented by E. coli coaD (encoding PPAT) and by human COASY | Core | NA | NA | NA |
| 4177-YGR278W | YGR278W | CWC22 | U2-type spliceosomal complex subunit CWC22 | Spliceosome-associated protein that is required for pre-mRNA splicing; necessary for Prp2p function at the first catalytic step of splicing; has similarity to S. pombe Cwf22p; CWC22 is an essential protein | Core | NA | NA | NA |