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 |
|---|---|---|---|---|---|---|---|---|
| 3878-YGL239C | YGL239C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene CSE1 | Accessory | Ancestral | NA | NA |
| 3879-YGL240W | YGL240W | DOC1 | anaphase promoting complex subunit DOC1|APC10 | Processivity factor; required for the ubiquitination activity of the anaphase promoting complex (APC), mediates the activity of the APC by contributing to substrate recognition; involved in cyclin proteolysis; contains a conserved DOC1 homology domain | Core | NA | NA | NA |
| 3880-YGL241W | YGL241W | KAP114 | NA | Karyopherin, responsible for nuclear import of specific proteins; cargoes include Spt15p, Sua7p, histones H2A and H2B, and Nap1p; amino terminus shows similarity to those of other importins, particularly Cse1p; localization is primarily nuclear; function is regulated by sumoylation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3881-YGL242C | YGL242C | NA | NA | Protein of unknown function; N-terminally propionylated in vivo; deletion mutant is viable | Core | NA | NA | NA |
| 3882-YGL243W | YGL243W | TAD1 | tRNA-specific adenosine deaminase | tRNA-specific adenosine deaminase; deaminates adenosine-37 to inosine in tRNA-Ala | Core | NA | NA | NA |
| 3883-YGL244W | YGL244W | RTF1 | CSL3 | Subunit of RNAPII-associated chromatin remodeling Paf1 complex; regulates gene expression by directing cotranscriptional histone modification, influences transcription and chromatin structure through several independent functional domains; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay | Core | NA | NA | NA |
| 3884-YGL245W | YGL245W | GUS1 | glutamate--tRNA ligase GUS1|GluRS|GSN1 | Glutamyl-tRNA synthetase (GluRS); forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3885-YGL246C | YGL246C | RAI1 | decapping nuclease | Nuclear protein with decapping endonuclease activity; targets mRNAs with unmethylated 7-methylguanosine cap structures and 5'-triphosphates; binds to and stabilizes the exoribonuclease Rat1p; required for pre-rRNA processing; relocalizes to the cytosol in response to hypoxia; homologous to human DOM3Z | Core | NA | NA | NA |
| 3886-YGL247W | YGL247W | BRR6 | NA | Essential nuclear envelope integral membrane protein; interacts and functions with Apq12p and Brl1p in lipid homeostasis; mutants are defective in nuclear pore complex biogenesis, nuclear envelope morphology, mRNA nuclear export, and are sensitive to sterol biosynthesis inhibitors and membrane fluidizing agents; exhibits synthetic lethal genetic interactions with genes involved in lipid metabolism; homologous to Brl1p | Core | NA | NA | NA |
| 3887-YGL248W | YGL248W | PDE1 | 3',5'-cyclic-nucleotide phosphodiesterase PDE1 | Low-affinity cyclic AMP phosphodiesterase; controls glucose and intracellular acidification-induced cAMP signaling, target of the cAMP-protein kinase A (PKA) pathway; glucose induces transcription and inhibits translation | Core | NA | NA | NA |
| 3888-YGL249W | YGL249W | ZIP2 | NA | Meiosis-specific protein; involved in normal synaptonemal complex formation and pairing between homologous chromosomes during meiosis; relocalizes from mitochondrion to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 3889-YGL250W | YGL250W | RMR1 | NA | Protein required for meiotic recombination and gene conversion; null mutant displays reduced PIS1 expression and growth defects on non-fermentable carbon sources and minimal media; GFP-fusion protein localizes to both cytoplasm and nucleus | Core | NA | NA | NA |
| 3890-YGL251C | YGL251C | HFM1 | MER3 | Meiosis specific DNA helicase; involved in the conversion of double-stranded breaks to later recombination intermediates and in crossover control; catalyzes the unwinding of Holliday junctions; has ssDNA and dsDNA stimulated ATPase activity | Core | NA | NA | NA |
| 3891-YGL252C | YGL252C | RTG2 | NA | Sensor of mitochondrial dysfunction; regulates the subcellular location of Rtg1p and Rtg3p, transcriptional activators of the retrograde (RTG) and TOR pathways; Rtg2p is inhibited by the phosphorylated form of Mks1p | Core | NA | NA | NA |
| 3892-YGL253W_NumOfGenes_2 | YGL253W | HXK2 | hexokinase 2|SCI2|HKB|HEX1 | Hexokinase isoenzyme 2; phosphorylates glucose in cytosol; predominant hexokinase during growth on glucose; represses expression of HXK1, GLK1, induces expression of its own gene; antiapoptotic; phosphorylation/dephosphorylation at Ser14 by kinase Snf1p, phosphatase Glc7p-Reg1p regulates nucleocytoplasmic shuttling of Hxk2p; functions downstream of Sit4p in control of cell cycle, mitochondrial function, oxidative stress resistance, chronological lifespan; has paralog HXK1 | Core | NA | NA | NA |