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 |
|---|---|---|---|---|---|---|---|---|
| 1823-YAL049C | YAL049C | AIM2 | protein AIM2 | Cytoplasmic protein involved in mitochondrial function or organization; null mutant displays reduced frequency of mitochondrial genome loss; potential Hsp82p interactor | Core | NA | NA | NA |
| 1824-YAL051W | YAL051W | OAF1 | oleate-activated transcription factor OAF1|YAF1 | Oleate-activated transcription factor; subunit of a heterodimeric complex with Pip2p, which binds to oleate-response elements (ORE) in the promoter of genes involved in beta-oxidation of fatty acids, peroxisome organization and biogenesis, activating transcription in the presence of oleate; regulates chromatin silencing at telomeres; involved in diauxic shift; OAF1 has a paralog, PIP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1825-YAL053W | YAL053W | FLC2 | flavin adenine dinucleotide transporter FLC2|HUF2 | Putative calcium channel involved in calcium release under hypotonic stress; required for uptake of FAD into endoplasmic reticulum; involved in cell wall maintenance; FLC2 has a paralog, YOR365C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1826-YAL054C | YAL054C | ACS1 | acetate--CoA ligase 1|FUN44 | Acetyl-coA synthetase isoform; along with Acs2p, acetyl-coA synthetase isoform is the nuclear source of acetyl-coA for histone acetylation; expressed during growth on nonfermentable carbon sources and under aerobic conditions | Core | NA | NA | NA |
| 1827-YAL055W | YAL055W | PEX22 | ubiquitin-protein transferase activating protein PEX22|YAF5 | Putative peroxisomal membrane protein; required for import of peroxisomal proteins; functionally complements a Pichia pastoris pex22 mutation | Core | NA | NA | NA |
| 1828-YAL056W | YAL056W | GPB2 | KRH1 | Multistep regulator of cAMP-PKA signaling; inhibits PKA downstream of Gpa2p and Cyr1p, thereby increasing cAMP dependency; inhibits Ras activity through direct interactions with Ira1p/2p; regulated by G-alpha protein Gpa2p; GPB2 has a paralog, GPB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1829-YAL058W_NumOfGenes_2 | YAL058W | CNE1 | calnexin|FUN48 | Calnexin; integral membrane ER chaperone involved in folding and quality control of glycoproteins; chaperone activity is inhibited by Mpd1p, with which Cne1p interacts; 24% identical to mammalian calnexin; Ca+ binding not yet shown in yeast | Core | NA | NA | NA |
| 1830-YAL059W_NumOfGenes_3 | YAL059W | ECM1 | NA | Pre-ribosomal factor involved in 60S ribosomal protein subunit export; associates with the pre-60S particle; shuttles between the nucleus and cytoplasm | Core | NA | NA | NA |
| 1831-YAL060W | YAL060W | BDH1 | (R,R)-butanediol dehydrogenase|BDH | NAD-dependent (R,R)-butanediol dehydrogenase; catalyzes oxidation of (R,R)-2,3-butanediol to (3R)-acetoin, oxidation of meso-butanediol to (3S)-acetoin, and reduction of acetoin; enhances use of 2,3-butanediol as an aerobic carbon source | Core | NA | NA | NA |
| 1832-YAL061W_NumOfGenes_2 | YAL061W | BDH2 | putative dehydrogenase BDH2 | Putative medium-chain alcohol dehydrogenase with similarity to BDH1; transcription induced by constitutively active PDR1 and PDR3 | Accessory | Ancestral | NA | NA |
| 1833-YAL062W_NumOfGenes_2 | YAL062W | GDH3 | glutamate dehydrogenase (NADP(+)) GDH3|FUN51 | NADP(+)-dependent glutamate dehydrogenase; synthesizes glutamate from ammonia and alpha-ketoglutarate; rate of alpha-ketoglutarate utilization differs from Gdh1p; expression regulated by nitrogen and carbon sources; GDH3 has a paralog, GDH1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 1834-YAL063C | YAL063C | FLO9 | flocculin FLO9 | Lectin-like protein with similarity to Flo1p; thought to be expressed and involved in flocculation | Accessory | Ancestral | NA | NA |
| 1835-YAL063C-A | YAL063C-A | NA | NA | Putative protein of unknown function; identified by expression profiling and mass spectrometry | Accessory | Unknown | NA | NA |
| 1836-YAL064C-A_NumOfGenes_2 | YAL064C-A | TDA8 | YAL065C-A | Putative protein of unknown function; null mutant is sensitive to expression of the top1-T722A allele; not an essential gene | Accessory | Ancestral | NA | NA |
| 1837-YAL064W | YAL064W | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments | Accessory | Unknown | NA | NA |