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 |
|---|---|---|---|---|---|---|---|---|
| 6218-YMR156C | YMR156C | TPP1 | polynucleotide 3'-phosphatase | DNA 3'-phosphatase; functions in repair of endogenous damage of double-stranded DNA, activity is specific for removal of 3' phosphates at strand breaks; similar to the l-2-haloacid dehalogenase superfamily; homolog of human polynucleotide kinase/3'-phosphatase | Core | NA | NA | NA |
| 6219-YMR157C | YMR157C | AIM36 | FMP39 | Protein of unknown function; null mutant displays reduced respiratory growth and elevated frequency of mitochondrial genome loss; the authentic, non-tagged protein is detected in purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6220-YMR158C-A | YMR158C-A | NA | YMR158C-B | Putative protein of unknown function; may contain a lipid attachment site; YMR158C-A is not an essential gene | Core | NA | NA | NA |
| 6221-YMR158W | YMR158W | MRPS8 | mitochondrial 37S ribosomal protein MRPS8 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 6222-YMR159C_NumOfGenes_2 | YMR159C | ATG16 | APG15|APG16|CVT11|SAP18 | Conserved protein involved in autophagy; interacts with Atg12p-Atg5p conjugates to form Atg12p-Atg5p-Atg16p multimers, which binds to membranes and localizes to the pre-autophagosomal structure and are required for autophagy; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 6223-YMR160W | YMR160W | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of the vacuole; mutant has enhanced sensitivity to overexpression of mutant huntingtin; YMR160W is not an essential gene; relative distribution within the vacuolar membrane changes upon DNA replication stress | Core | NA | NA | NA |
| 6224-YMR161W | YMR161W | HLJ1 | type I HSP40 co-chaperone HLJ1 | Co-chaperone for Hsp40p; anchored in the ER membrane; with its homolog Ydj1p promotes ER-associated protein degradation (ERAD) of integral membrane substrates; similar to E. coli DnaJ | Core | NA | NA | NA |
| 6225-YMR162C | YMR162C | DNF3 | aminophospholipid-translocating P4-type ATPase DNF3 | Trans-golgi network aminophospholipid translocase (flippase); type 4 P-type ATPase; involved in phospholipid translocation, contributing to the maintenance of membrane lipid asymmetry in post-Golgi secretory vesicles; role in protein trafficking between the Golgi and endosomal system; localizes to the trans-Golgi network; localizes to the shmoo tip where it has a redundant role in the cellular response to mating pheromone | Core | NA | NA | NA |
| 6226-YMR163C | YMR163C | INP2 | NA | Peroxisome-specific receptor important for peroxisome inheritance; co-fractionates with peroxisome membranes and co-localizes with peroxisomes in vivo; physically interacts with the myosin V motor Myo2p; INP2 is not an essential gene | Core | NA | NA | NA |
| 6227-YMR164C | YMR164C | MSS11 | NA | Transcription factor; involved in regulation of invasive growth and starch degradation; controls the activation of FLO11 and STA2 in response to nutritional signals; forms a heterodimer with Flo8p that interacts with the Swi/Snf complex during transcriptional activation of FLO1, FLO11, and STA1 | Core | NA | NA | NA |
| 6228-YMR165C | YMR165C | PAH1 | phosphatidate phosphatase PAH1|SMP2 | Mg2+-dependent phosphatidate (PA) phosphatase; dephosphorylates PA to yield diacylglycerol; regulates phospholipid synthesis, nuclear/ER membrane growth, lipid droplet formation, triacylglycerol synthesis, vacuolar homeostasis and cell wall integrity; phosphorylated by Pho85p/Pho80p, Cdc28p/Cyclin B, PKA, PKC, and CKII, regulating activity, localization, and proteosomal degradation; homolog of mammalian lipins 1 and 2; human homologs LPIN1, LPIN2, LPIN3 complement the null | Accessory | Ancestral | NA | NA |
| 6229-YMR166C | YMR166C | MME1 | NA | Transporter of the mitochondrial inner membrane that exports magnesium; involved in mitochondrial Mg2+ homeostasis; has similarity to human mitochondrial ATP-Mg/Pi carriers | Core | NA | NA | NA |
| 6230-YMR167W | YMR167W | MLH1 | mismatch repair ATPase MLH1|PMS2 | Protein required for mismatch repair in mitosis and meiosis; also required for crossing over during meiosis; forms a complex with Pms1p and Msh2p-Msh3p during mismatch repair; human homolog is associated with hereditary non-polyposis colon cancer | Core | NA | NA | NA |
| 6231-YMR168C | YMR168C | CEP3 | CSL1|CBF3B|CBF3 | Essential kinetochore protein; component of the CBF3 complex that binds the CDEIII region of the centromere; contains an N-terminal Zn2Cys6 type zinc finger domain, a C-terminal acidic domain, and a putative coiled coil dimerization domain | Core | NA | NA | NA |
| 6232-YMR169C | YMR169C | ALD3 | aldehyde dehydrogenase (NAD(+)) ALD3 | Cytoplasmic aldehyde dehydrogenase; involved in beta-alanine synthesis; uses NAD+ as the preferred coenzyme; very similar to Ald2p; expression is induced by stress and repressed by glucose | Accessory | Ancestral | NA | NA |