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 |
|---|---|---|---|---|---|---|---|---|
| 2513-YDL065C | YDL065C | PEX19 | PAS12 | Chaperone and import receptor for newly-synthesized class I PMPs; binds peroxisomal membrane proteins (PMPs) in the cytoplasm and delivers them to the peroxisome for subsequent insertion into the peroxisomal membrane; interacts with Myo2p and contributes to peroxisome partitioning | Core | NA | NA | NA |
| 2514-YDL066W | YDL066W | IDP1 | isocitrate dehydrogenase (NADP(+)) IDP1 | Mitochondrial NADP-specific isocitrate dehydrogenase; catalyzes the oxidation of isocitrate to alpha-ketoglutarate; not required for mitochondrial respiration and may function to divert alpha-ketoglutarate to biosynthetic processes | Core | NA | NA | NA |
| 2515-YDL067C | YDL067C | COX9 | cytochrome c oxidase subunit VIIa | Subunit VIIa of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain | Core | NA | NA | NA |
| 2516-YDL069C_NumOfGenes_2 | YDL069C | CBS1 | NA | Mitochondrial translational activator of the COB mRNA; membrane protein that interacts with translating ribosomes, acts on the COB mRNA 5'-untranslated leader | Core | NA | NA | NA |
| 2517-YDL070W | YDL070W | BDF2 | NA | Protein involved in transcription initiation; acts at TATA-containing promoters; associates with the basal transcription factor TFIID; contains two bromodomains; corresponds to the C-terminal region of mammalian TAF1; redundant with Bdf1p; protein abundance increases in response to DNA replication stress; BDF2 has a paralog, BDF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2518-YDL071C | YDL071C | NA | IRC1 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF BDF2/YDL070W | Core | NA | NA | NA |
| 2519-YDL072C | YDL072C | YET3 | NA | Protein of unknown function; YET3 null mutant decreases the level of secreted invertase; homolog of human BAP31 protein; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 2520-YDL073W | YDL073W | AHK1 | NA | Scaffold protein in the HKR1 sub-branch of the Hog1p-signaling pathway; physically interacts with the cytoplasmic domain of Hkr1p, and with Sho1p, Pbs2p, and Ste11p; prevents cross-talk signaling from Hkr1p of the osmotic stress MAPK cascade to the Kss1p MAPK cascade; non-essential gene | Accessory | Ancestral | NA | NA |
| 2521-YDL074C_NumOfGenes_2 | YDL074C | BRE1 | E3 ubiquitin-protein ligase BRE1 | E3 ubiquitin ligase; forms heterodimer with Rad6p to regulate K63 polyubiquitination in response to oxidative stress and to monoubiquinate histone H2B-K123, which is required for the subsequent methylation of histone H3-K4 and H3-K79; required for DSBR, transcription, silencing, and checkpoint control; interacts with RNA-binding protein Npl3p, linking histone ubiquitination to mRNA processing; Bre1p-dependent histone ubiquitination promotes pre-mRNA splicing | Core | NA | NA | NA |
| 2522-YDL075W | YDL075W | RPL31A | eL31|ribosomal 60S subunit protein L31A|L31e|YL28|L34A|L31A|RPL34 | Ribosomal 60S subunit protein L31A; associates with karyopherin Sxm1p; loss of both Rpl31p and Rpl39p confers lethality; homologous to mammalian ribosomal protein L31, no bacterial homolog; RPL31A has a paralog, RPL31B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2523-YDL076C | YDL076C | RXT3 | NA | Component of the Rpd3L histone deacetylase complex; involved in histone deacetylation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2524-YDL077C | YDL077C | VAM6 | VPS39|VPL22|VPL18|CVT4 | Guanine nucleotide exchange factor for the GTPase Gtr1p; subunit of the HOPS endocytic tethering complex; vacuole membrane protein; functions as a Rab GTPase effector, interacting with both GTP- and GDP-bound conformations of Ypt7p; facilitates tethering and promotes membrane fusion events at the late endosome and vacuole; required for both membrane and protein trafficking; component of vacuole-mitochondrion contacts (vCLAMPs) important for lipid transfer between organelles | Core | NA | NA | NA |
| 2525-YDL078C | YDL078C | MDH3 | malate dehydrogenase MDH3 | Peroxisomal malate dehydrogenase; catalyzes interconversion of malate and oxaloacetate; involved in the glyoxylate cycle | Core | NA | NA | NA |
| 2526-YDL079C | YDL079C | MRK1 | putative serine/threonine protein kinase MRK1 | Glycogen synthase kinase 3 (GSK-3) homolog; one of four GSK-3 homologs in S. cerevisiae that function to activate Msn2p-dependent transcription of stress responsive genes and that function in protein degradation; MRK1 has a paralog, RIM11, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2527-YDL080C | YDL080C | THI3 | branched-chain-2-oxoacid decarboxylase THI3|KID1 | Regulatory protein that binds Pdc2p and Thi2p transcription factors; activates thiamine biosynthesis transcription factors Pdc2p and Thi2p by binding to them, but releases and de-activates them upon binding to thiamine pyrophosphate (TPP), the end product of the pathway; has similarity to decarboxylases but enzymatic activity is not detected | Core | NA | NA | NA |