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 |
|---|---|---|---|---|---|---|---|---|
| 6593-YNL201C_NumOfGenes_2 | YNL201C | PSY2 | NA | Subunit of protein phosphatase PP4 complex; Pph3p and Psy2p form the active complex, Psy4p may provide additional substrate specificity; regulates recovery from the DNA damage checkpoint, the gene conversion- and single-strand annealing-mediated pathways of meiotic double-strand break repair and efficient Non-Homologous End-Joining (NHEJ) pathway; Pph3p and Psy2p localize to foci on meiotic chromosomes; putative homolog of mammalian R3 | Core | NA | NA | NA |
| 6594-YNL202W_NumOfGenes_3 | YNL202W | SPS19 | SPX19 | Peroxisomal 2,4-dienoyl-CoA reductase; auxiliary enzyme of fatty acid beta-oxidation; homodimeric enzyme required for growth and sporulation on petroselineate medium; expression induced during late sporulation and in the presence of oleate | Core | NA | NA | NA |
| 6595-YNL204C_NumOfGenes_2 | YNL204C | SPS18 | SPX18 | Protein of unknown function, contains a putative zinc-binding domain; expressed during sporulation; SPS18 has a paralog, GCS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6596-YNL205C | YNL205C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 6597-YNL206C_NumOfGenes_2 | YNL206C | RTT106 | NA | Histone chaperone; involved in regulation of chromatin structure in both transcribed and silenced chromosomal regions; affects transcriptional elongation; has a role in regulation of Ty1 transposition; interacts physically and functionally with Chromatin Assembly Factor-1 (CAF-1) | Core | NA | NA | NA |
| 6598-YNL207W_NumOfGenes_2 | YNL207W | RIO2 | protein kinase RIO2 | Essential serine kinase involved in the processing of 20S pre-rRNA; involved in the processing of the 20S pre-rRNA into mature 18S rRNA; has similarity to Rio1p | Core | NA | NA | NA |
| 6599-YNL208W | YNL208W | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in purified mitochondria in high-throughput studies; potential orthologs found in other fungi | Core | NA | NA | NA |
| 6600-YNL210W | YNL210W | MER1 | NA | mRNA-binding protein required for meiosis-specific mRNA splicing; required for chromosome pairing and meiotic recombination; Mer1p regulon embraces four essential meiotic pre-mRNAs: REC107, HFM1, AMA1 and SPO22 | Core | NA | NA | NA |
| 6601-YNL211C | YNL211C | MRX7 | NA | Protein that associates with mitochondrial ribosome; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YNL211C is not an essential gene | Core | NA | NA | NA |
| 6602-YNL212W | YNL212W | VID27 | NA | Cytoplasmic protein of unknown function; possibly involved in vacuolar protein degradation; not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase); null mutants exhibit normal growth; contains two PH-like domains | Core | NA | NA | NA |
| 6603-YNL213C | YNL213C | RRG9 | NA | Protein of unknown function; null mutant lacks mitochondrial DNA and cannot grow on glycerol; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6604-YNL214W | YNL214W | PEX17 | PAS9 | Membrane peroxin of the peroxisomal importomer complex; complex facilitates the import of peroxisomal matrix proteins; required for peroxisome biogenesis | Core | NA | NA | NA |
| 6605-YNL215W | YNL215W | IES2 | NA | Protein that associates with the INO80 chromatin remodeling complex; associates with the INO80 complex under low-salt conditions; essential for growth under anaerobic conditions; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6606-YNL216W | YNL216W | RAP1 | DNA-binding transcription factor RAP1|TUF1|TBA1|GRF1 | Essential DNA-binding transcription regulator that binds many loci; involved in transcription activation, repression, chromatin silencing, telomere length maintenance; relocalizes to cytosol under hypoxia; conserved protein with N-terminal BRCT domain, central region with homology to Myb DNA binding domain, and C-terminal Rap1-specific protein-interaction domain (RCT domain); recruits Sir complex to telomeric DNA; present in quiescent cell telomere hyperclusters | Core | NA | NA | NA |
| 6607-YNL217W | YNL217W | NA | putative serine/threonine-protein phosphatase | Putative protein of unknown function; weak sequence similarity to bis (5'-nucleotidyl)-tetraphosphatases; (GFP)-fusion protein localizes to the vacuole; null mutant is highly sensitive to azaserine and resistant to sodium-O-vandate | Core | NA | NA | NA |