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 |
|---|---|---|---|---|---|---|---|---|
| 2618-YDL173W_NumOfGenes_2 | YDL173W | PAR32 | NA | Protein of unknown function; hyperphosphorylated upon rapamycin treatment in a Tap42p-dependent manner; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; PAR32 is not an essential gene | Core | NA | NA | NA |
| 2619-YDL174C | YDL174C | DLD1 | D-lactate dehydrogenase | Major mitochondrial D-lactate dehydrogenase; oxidizes D-lactate to pyruvate, transcription is heme-dependent, repressed by glucose, and derepressed in ethanol or lactate; located in the mitochondrial inner membrane | Core | NA | NA | NA |
| 2620-YDL175C | YDL175C | AIR2 | TRAMP complex RNA-binding subunit | RNA-binding subunit of the TRAMP nuclear RNA surveillance complex; involved in nuclear RNA processing and degradation; involved in TRAMP complex assembly as a bridge between Mtr4p and Trf4p; stimulates the poly(A) polymerase activity of Pap2p in vitro; has 5 zinc knuckle motifs; AIR2 has a paralog, AIR1, that arose from the whole genome duplication; Air2p and Air1p have nonredundant roles in regulation of substrate specificity of the exosome | Core | NA | NA | NA |
| 2621-YDL176W | YDL176W | NA | NA | Protein of unknown function; predicted by computational methods to be involved in fructose-1,6-bisphosphatase (Fbp1p) degradation; interacts with components of the GID complex; YDL176W is not an essential gene | Core | NA | NA | NA |
| 2622-YDL177C | YDL177C | NA | NA | Putative protein of unknown function; similar to the mouse IMPACT gene; YDL177C is not an essential gene | Core | NA | NA | NA |
| 2623-YDL178W | YDL178W | DLD2 | D-lactate dehydrogenase|AIP2 | D-2-hydroxyglutarate dehydrogenase, and minor D-lactate dehydrogenase; mitochondrial matrix protein that oxidizes D-2-hydroxyglutarate (D-2HG), an oncometabolite, to alpha-ketoglutarate with a minor role in lactate catabolism; located in the mitochondrial matrix | Core | NA | NA | NA |
| 2624-YDL179W | YDL179W | PCL9 | NA | Cyclin; forms a functional kinase complex with Pho85p cyclin-dependent kinase (Cdk), expressed in late M/early G1 phase, activated by Swi5p; PCL9 has a paralog, PCL2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2625-YDL180W | YDL180W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole | Core | NA | NA | NA |
| 2626-YDL181W | YDL181W | INH1 | ATPase inhibitor | Protein that inhibits ATP hydrolysis by the F1F0-ATP synthase; inhibitory function is enhanced by stabilizing proteins Stf1p and Stf2p; has a calmodulin-binding motif and binds calmodulin in vitro; INH1 has a paralog, STF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2627-YDL182W_NumOfGenes_2 | YDL182W | LYS20 | homocitrate synthase LYS20 | Homocitrate synthase isozyme and functions in DNA repair; catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, which is the first step in the lysine biosynthesis pathway; LYS20 has a paralog, LYS21, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2628-YDL183C | YDL183C | NA | MKR1 | Protein that may form an active mitochondrial KHE system; mitochondrial inner-membrane protein; non-essential gene; KHE system stands for K+/H+ exchanger system | Core | NA | NA | NA |
| 2629-YDL185C-A | YDL185C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDL185W; identified by homology with hemiascomycetous yeast species | Core | NA | NA | NA |
| 2630-YDL185W | YDL185W | VMA1 | H(+)-transporting V1 sector ATPase subunit A|TFP1|CLS8 | Subunit A of the V1 peripheral membrane domain of V-ATPase; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease; the V1 peripheral membrane domain of the vacuolar H+-ATPase (V-ATPase) has eight subunits; involved in methionine restriction extension of chronological lifespan in an autophagy-dependent manner | Core | NA | NA | NA |
| 2631-YDL186W | YDL186W | NA | NA | Putative protein of unknown function; YDL186W is not an essential gene | Core | NA | NA | NA |
| 2632-YDL187C | YDL187C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |