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 |
|---|---|---|---|---|---|---|---|---|
| 7613-YPL266W | YPL266W | DIM1 | putative dimethyladenosine transferase|CDH1 | Essential 18S rRNA dimethylase (dimethyladenosine transferase); responsible for conserved m6(2)Am6(2)A dimethylation in 3'-terminal loop of 18S rRNA, part of 90S and 40S pre-particles in nucleolus, involved in pre-ribosomal RNA processing; human homolog DIMT1 complements yeast dim1 mutant | Core | NA | NA | NA |
| 7614-YPL267W | YPL267W | ACM1 | NA | Pseudosubstrate inhibitor of the APC/C; suppresses APC/C [Cdh1]-mediated proteolysis of mitotic cyclins; associates with Cdh1p, Bmh1p and Bmh2p; cell cycle regulated protein; the anaphase-promoting complex/cyclosome is also known as APC/C | Core | NA | NA | NA |
| 7615-YPL268W | YPL268W | PLC1 | phosphatidylinositol phospholipase C | Phospholipase C; hydrolyzes phosphatidylinositol 4,5-biphosphate (PIP2) to generate the signaling molecules inositol 1,4,5-triphosphate (IP3) and 1,2-diacylglycerol (DAG); involved in regulating many cellular processes; Plc1p and inositol polyphosphates are required for acetyl-CoA homeostasis which regulates global histone acetylation | Core | NA | NA | NA |
| 7616-YPL269W | YPL269W | KAR9 | NA | Spindle positioning factor; orients astral microtubules, connecting them to actin cables at the cortex with Bim1p and Myo2, resulting in proper spindle positioning; targeted for StuBL-dependent degradation at kinetochores by Slx5p-Slx8p, ensuring chromosome transmission fidelity and correct spindle positioning; role in karyogamy; localizes to the shmoo tip, the growing bud-tip, the nucleus, the kinetochore, the spindle and microtubules; homolog of adenomatous polyposis coli | Core | NA | NA | NA |
| 7617-YPL270W | YPL270W | MDL2 | ATP-binding cassette permease MDL2 | Mitochondrial inner membrane half-type ABC transporter; required for respiratory growth at high temperature; localizes to vacuole membrane in response to H2O2; similar to human TAP1 and TAP2 implicated in bare lymphocyte syndrome and Wegener-like granulomatosis | Core | NA | NA | NA |
| 7618-YPL271W | YPL271W | ATP15 | F1F0 ATP synthase subunit epsilon|ATPEPSILON | Epsilon subunit of the F1 sector of mitochondrial F1F0 ATP synthase; which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; F1 translationally regulates ATP6 and ATP8 expression to achieve a balanced output of ATP synthase genes encoded in nucleus and mitochondria; phosphorylated | Core | NA | NA | NA |
| 7619-YPL272C | YPL272C | PBI1 | NA | Putative protein of unknown function; gene expression induced in response to ketoconazole; YPL272C is not an essential gene | Core | NA | NA | NA |
| 7620-YPL273W_NumOfGenes_2 | YPL273W | SAM4 | S-adenosylmethionine-homocysteine S-methyltransferase SAM4 | S-adenosylmethionine-homocysteine methyltransferase; functions along with Mht1p in the conversion of S-adenosylmethionine (AdoMet) to methionine to control the methionine/AdoMet ratio; SAM4 has a paralog, YMR321C, that arose from a single-locus duplication | Core | NA | NA | NA |
| 7621-YPL274W | YPL274W | SAM3 | bifunctional polyamine/amino acid permease SAM3 | High-affinity S-adenosylmethionine permease; required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p | Core | NA | NA | NA |
| 7622-YPL279C_NumOfGenes_2 | YPL279C | FEX2 | fluoride transporter | Protein involved in fluoride export; nearly identical to FEX1, and deletion of both proteins results in a large increase in fluoride sensitivity compared with the single mutant; contains two FEX domains connected by a linker; part of a widespread family of conserved fluoride export proteins | Core | NA | NA | NA |
| 7623-YPL280W_NumOfGenes_3 | YPL280W | HSP32 | glutathione-independent methylglyoxalase family protein | Possible chaperone and cysteine protease; required for transcriptional reprogramming during the diauxic shift and for survival in stationary phase; similar to E. coli Hsp31 and S. cerevisiae Hsp31p, Hsp33p, and Sno4p; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease and cancer | Accessory | Ancestral | NA | NA |
| 7624-YPL281C_NumOfGenes_3 | YPL281C | ERR2 | phosphopyruvate hydratase ERR2 | Enolase, a phosphopyruvate hydratase; catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate; complements the growth defect of an ENO1 ENO2 double mutant | Accessory | Ancestral | NA | NA |
| 7625-YPR001W | YPR001W | CIT3 | citrate (Si)-synthase CIT3 | Dual specificity mitochondrial citrate and methylcitrate synthase; catalyzes the condensation of acetyl-CoA and oxaloacetate to form citrate and that of propionyl-CoA and oxaloacetate to form 2-methylcitrate | Core | NA | NA | NA |
| 7626-YPR002W | YPR002W | PDH1 | putative 2-methylcitrate dehydratase | Putative 2-methylcitrate dehydratase; mitochondrial protein that participates in respiration; induced by diauxic shift; homologous to E. coli PrpD, may take part in the conversion of 2-methylcitrate to 2-methylisocitrate | Core | NA | NA | NA |
| 7627-YPR003C | YPR003C | NA | NA | Putative sulfate permease; physically interacts with Hsp82p; green fluorescent protein (GFP)-fusion protein localizes to the ER; YPR003C is not an essential gene | Core | NA | NA | NA |