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 |
|---|---|---|---|---|---|---|---|---|
| 3983-YGR083C | YGR083C | GCD2 | translation initiation factor eIF2B subunit delta|GCD12 | Delta subunit of the translation initiation factor eIF2B; the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a negative regulator of GCN4 expression | Core | NA | NA | NA |
| 3984-YGR084C | YGR084C | MRP13 | mitochondrial 37S ribosomal protein YmS-A | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 3985-YGR086C | YGR086C | PIL1 | lipid-binding protein PIL1 | Eisosome core component; eisosomes are large immobile cell cortex structures associated with endocytosis; detected in phosphorylated state in mitochondria; phosphorylated on Thr233 upon Pkc1p hyperactivation in a Slt2p MAPK-dependent fashion; null mutant shows activation of Pkc1p/Ypk1p stress resistance pathways; member of BAR domain family; protein increases in abundance and relocalizes from plasma membrane to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3986-YGR087C | YGR087C | PDC6 | indolepyruvate decarboxylase 6 | Minor isoform of pyruvate decarboxylase; decarboxylates pyruvate to acetaldehyde, involved in amino acid catabolism; transcription is glucose- and ethanol-dependent, and is strongly induced during sulfur limitation | Core | NA | NA | NA |
| 3987-YGR088W | YGR088W | CTT1 | catalase T|SPS101 | Cytosolic catalase T; has a role in protection from oxidative damage by hydrogen peroxide | Core | NA | NA | NA |
| 3988-YGR089W | YGR089W | NNF2 | NA | Protein that exhibits physical and genetic interactions with Rpb8p; Rpb8p is a subunit of RNA polymerases I, II, and III; computational analysis of large-scale protein-protein interaction data suggests a role in chromosome segregation | Core | NA | NA | NA |
| 3989-YGR090W | YGR090W | UTP22 | rRNA-processing protein UTP22 | Component of the small-subunit processome; required for nuclear export of tRNAs; may facilitate binding of Utp8p to aminoacylated tRNAs and their delivery to Los1p for export; conserved from yeast to mammals | Core | NA | NA | NA |
| 3990-YGR091W | YGR091W | PRP31 | U4/U6-U5 snRNP complex subunit PRP31 | Splicing factor; component of the U4/U6-U5 snRNP complex | Core | NA | NA | NA |
| 3991-YGR092W | YGR092W | DBF2 | serine/threonine-protein kinase DBF2 | Ser/Thr kinase involved in transcription and stress response; functions as part of a network of genes in exit from mitosis; localization is cell cycle regulated; activated by Cdc15p during the exit from mitosis; also plays a role in regulating the stability of SWI5 and CLB2 mRNAs; phosphorylates Chs2p to regulate primary septum formation and Hof1p to regulate cytokinesis; DBF2 has a paralog, DBF20, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3992-YGR093W | YGR093W | DRN1 | NA | Splicing factor that modulates turnover of branched RNAs by Dbr1p; interacts with spliceosomal components and branched RNA splicing products; enhances Dbr1p debranching in vitro; conserved protein with domain organization identical from yeast to human; N-terminal homology to Dbr1p N-terminus, but Dbr1p catalytic residues not conserved; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 3993-YGR094W | YGR094W | VAS1 | valine--tRNA ligase | Mitochondrial and cytoplasmic valyl-tRNA synthetase; human homolog VARS2 implicated in mitochondrial diseases, can partially complement yeast null mutant | Core | NA | NA | NA |
| 3994-YGR095C | YGR095C | RRP46 | exosome non-catalytic core subunit RRP46 | Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp46p (EXOSC5) | Core | NA | NA | NA |
| 3995-YGR096W | YGR096W | TPC1 | thiamine transporter TPC1 | Mitochondrial membrane transporter; mediates uptake of the essential cofactor thiamine pyrophosphate (ThPP) into mitochondria; expression appears to be regulated by carbon source; member of the mitochondrial carrier family | Core | NA | NA | NA |
| 3996-YGR097W | YGR097W | ASK10 | RGC2 | Regulator of the Fps1p glycerol channel; under nonstress conditions, binds to Fps1p to positively regulate glycerol transport; under osmotic stress, multiple phosphorylation by Hog1p causes Ask10p to dissociate from Fps1p; forms homodimers and heterodimerizes with paralog Rgc1p; phosphorylated in response to oxidative stress; has a role in destruction of Ssn8p; associates with RNA polymerase II holoenzyme | Core | NA | NA | NA |
| 3997-YGR098C | YGR098C | ESP1 | separase | Separase, a caspase-like cysteine protease; promotes sister chromatid separation by mediating dissociation of the cohesin Scc1p from chromatin; inhibits protein phosphatase 2A-Cdc55p to promote mitotic exit; inhibited by Pds1p; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |