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 |
|---|---|---|---|---|---|---|---|---|
| 3218-YDR527W_NumOfGenes_2 | YDR527W | RBA50 | NA | Protein involved in transcription; interacts with RNA polymerase II subunits Rpb2p, Rpb3, and Rpb11p; has similarity to human RPAP1 | Accessory | Ancestral | NA | NA |
| 3219-YDR528W | YDR528W | HLR1 | NA | Protein involved in regulation of cell wall composition and integrity; also involved in cell wall response to osmotic stress; overproduction suppresses a lysis sensitive PKC mutation; HLR1 has a paralog, LRE1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3220-YDR529C | YDR529C | QCR7 | ubiquinol--cytochrome-c reductase subunit 7|UCR7|CRO1|COR4 | Subunit 7 of ubiquinol cytochrome-c reductase (Complex III); Complex III is a component of the mitochondrial inner membrane electron transport chain; oriented facing the mitochondrial matrix; N-terminus appears to play a role in complex assembly | Accessory | Ancestral | NA | NA |
| 3221-YDR530C | YDR530C | APA2 | bifunctional AP-4-A phosphorylase/ADP sulfurylase | Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase II; AP4A phosphorylase involved in catabolism of bis(5'-nucleosidyl) tetraphosphates; APA2 has a paralog, APA1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3222-YDR531W | YDR531W | CAB1 | pantothenate kinase | Pantothenate kinase, ATP:D-pantothenate 4'-phosphotransferase; catalyzes the first committed step in the universal biosynthetic pathway for synthesis of coenzyme A (CoA); transcriptionally regulated by Upc2p via a sterol response element | Accessory | Ancestral | NA | NA |
| 3223-YDR532C | YDR532C | KRE28 | NA | Subunit of a kinetochore-microtubule binding complex; complex bridges centromeric heterochromatin and kinetochore MAPs and motors; required for sister chromatid bi-orientation and kinetochore binding of SAC components; complex also includes Spc105p; modified by sumoylation | Accessory | Ancestral | NA | NA |
| 3224-YDR533C_NumOfGenes_2 | YDR533C | HSP31 | glutathione-independent methylglyoxalase | Methylglyoxalase that converts methylglyoxal to D-lactate; involved in oxidative stress resistance, diauxic shift, and stationary phase survival; has similarity to E. coli Hsp31 and C. albicans Glx3p; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease and cancer; exists as a dimer and contains a putative metal-binding site; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3225-YDR534C_NumOfGenes_2 | YDR534C | FIT1 | NA | Mannoprotein that is incorporated into the cell wall; incorporated via a glycosylphosphatidylinositol (GPI) anchor; involved in the retention of siderophore-iron in the cell wall | Accessory | Ancestral | NA | NA |
| 3226-YDR535C | YDR535C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YDR535C is not an essential gene | Accessory | Unknown | NA | NA |
| 3227-YDR536W | YDR536W | STL1 | glucose-inactivated glycerol proton symporter STL1 | Glycerol proton symporter of the plasma membrane; subject to glucose-induced inactivation, strongly but transiently induced when cells are subjected to osmotic shock | Accessory | Ancestral | NA | NA |
| 3228-YDR538W_NumOfGenes_2 | YDR538W | PAD1 | phenylacrylic acid decarboxylase PAD1|POF1 | Phenylacrylic acid decarboxylase; confers resistance to cinnamic acid, decarboxylates aromatic carboxylic acids to the corresponding vinyl derivatives; also has mRNA binding activity; homolog of E. coli UbiX; co-overproduction of Pad1p and Fdc1p greatly increases cinnamic acid decarboxylase activity | Accessory | Ancestral | NA | NA |
| 3229-YDR539W | YDR539W | FDC1 | putative phenylacrylic acid decarboxylase FDC1 | Ferulic acid decarboxylase, also active on p-coumaric acid; essential for decarboxylation of aromatic carboxylic acids to corresponding vinyl derivatives; co-overproduction of Pad1p and Fdc1p greatly increases cinnamic acid decarboxylase activity; structure implicates Glu285 as the general base in the nonoxidative decarboxylation reaction catalyzed by Fdc1p; homolog of E. coli UbiD; GFP-fusion protein localizes to cytoplasm | Accessory | Ancestral | NA | NA |
| 3230-YDR540C | YDR540C | IRC4 | NA | Protein of unknown function; null mutant displays increased levels of spontaneous Rad52p foci; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus | Accessory | Introgression | S. mikatae | NA |
| 3231-YDR541C | YDR541C | NA | carbonyl reductase (NADPH-dependent) | Aldehyde reductase; substrates include both aromatic and aliphatic aldehydes; uses NADPH as cofactor; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Accessory | Introgression | S. mikatae | NA |
| 3232-YDR544C | YDR544C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. paradoxus | NA |