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 |
|---|---|---|---|---|---|---|---|---|
| 6458-YNL067W | YNL067W | RPL9B | uS4|uL6|ribosomal 60S subunit protein L9B|L6|rp24|YL11|L9B|L8B | Ribosomal 60S subunit protein L9B; homologous to mammalian ribosomal protein L9 and bacterial L6; RPL9B has a paralog, RPL9A, that arose from a single-locus duplication | Core | NA | NA | NA |
| 6459-YNL067W-A | YNL067W-A | NA | YNL067W-B | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6460-YNL067W-B | YNL067W-B | NA | YNL067W-A | Putative protein of unknown function | Core | NA | NA | NA |
| 6461-YNL068C | YNL068C | FKH2 | forkhead family transcription factor FKH2 | Forkhead family transcription factor; rate-limiting activator of replication origins; evolutionarily conserved regulator of lifespan; binds multiple chromosomal elements with distinct specificities, cell cycle dynamics; positively regulates transcriptional elongation; facilitates clustering, activation of early-firing replication origins; negative role in chromatin silencing at HML and HMR; major role in expression of G2/M phase genes; relocalizes to cytosol under hypoxia | Core | NA | NA | NA |
| 6462-YNL069C | YNL069C | RPL16B | uL13|ribosomal 60S subunit protein L16B|L13|rp23|YL15|L21B|L16B|RP23 | Ribosomal 60S subunit protein L16B; N-terminally acetylated, binds 5.8 S rRNA; transcriptionally regulated by Rap1p; homologous to mammalian ribosomal protein L13A and bacterial L13; RPL16B has a paralog, RPL16A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6463-YNL070W | YNL070W | TOM7 | YOK22|MOM7 | Component of the TOM (translocase of outer membrane) complex; responsible for recognition and initial import steps for all mitochondrially directed proteins; promotes assembly and stability of the TOM complex | Core | NA | NA | NA |
| 6464-YNL071W | YNL071W | LAT1 | dihydrolipoyllysine-residue acetyltransferase|PDA2|ODP2 | Dihydrolipoamide acetyltransferase component (E2) of the PDC; the pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA | Core | NA | NA | NA |
| 6465-YNL072W | YNL072W | RNH201 | ribonuclease H2 catalytic subunit RNH201|Rnh2A|RNH35 | Ribonuclease H2 catalytic subunit; removes RNA primers during Okazaki fragment synthesis and errant ribonucleotides misincorporated during DNA replication; role in ribonucleotide excision repair; homolog of RNAse HI; related to human AGS4 which causes Aicardi-Goutieres syndrome | Core | NA | NA | NA |
| 6466-YNL073W | YNL073W | MSK1 | lysine--tRNA ligase MSK1 | Mitochondrial lysine-tRNA synthetase; required for import of both aminoacylated and deacylated forms of tRNA(Lys) into mitochondria and for aminoacylation of mitochondrially encoded tRNA(Lys) | Core | NA | NA | NA |
| 6467-YNL074C | YNL074C | MLF3 | YMK1 | Serine-rich protein of unknown function; predicted to be palmitoylated; overproduction suppresses growth inhibition caused by exposure to immunosuppressant leflunomide; MLF3 has a paralog, VHS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6468-YNL075W | YNL075W | IMP4 | snoRNA-binding rRNA-processing protein IMP4 | Component of the SSU processome; SSU processome is required for pre-18S rRNA processing; interacts with Mpp10p; member of a superfamily of proteins that contain a sigma(70)-like motif and associate with RNAs | Core | NA | NA | NA |
| 6469-YNL076W | YNL076W | MKS1 | LYS80 | Pleiotropic negative transcriptional regulator; involved in Ras-CAMP and lysine biosynthetic pathways and nitrogen regulation; involved in retrograde (RTG) mitochondria-to-nucleus signaling | Core | NA | NA | NA |
| 6470-YNL077W | YNL077W | APJ1 | NA | Chaperone with a role in SUMO-mediated protein degradation; member of the DnaJ-like family; conserved across eukaryotes; overexpression interferes with propagation of the [Psi+] prion; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 6471-YNL078W | YNL078W | NIS1 | JIP1 | Protein localized in the bud neck at G2/M phase; physically interacts with septins; possibly involved in a mitotic signaling network | Core | NA | NA | NA |
| 6472-YNL079C | YNL079C | TPM1 | tropomyosin TPM1 | Major isoform of tropomyosin; binds to and stabilizes actin cables and filaments, which direct polarized cell growth and the distribution of several organelles; acetylated by the NatB complex and acetylated form binds actin most efficiently; TPM1 has a paralog, TPM2, that arose from the whole genome duplication | Core | NA | NA | NA |