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 |
|---|---|---|---|---|---|---|---|---|
| 4523-YIL038C | YIL038C | NOT3 | CCR4-NOT core subunit NOT3 | Component of the CCR4-NOT core complex, involved in mRNA decapping; involved in transcription initiation and elongation and in mRNA degradation; conserved lysine in human homolog of Not3p and Not5p is mutated in cancers | Core | NA | NA | NA |
| 4524-YIL039W | YIL039W | TED1 | NA | GPI-glycan remodelase; conserved phosphoesterase domain-containing protein; acts together with Emp24p/Erv25p in cargo exit from the ER; functional ortholog of mammalian GPI-glycan remodelase PGAP5; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO) | Core | NA | NA | NA |
| 4525-YIL040W | YIL040W | APQ12 | NA | Nuclear envelope/ER integral membrane protein; interacts and functions with Brr6p and Brl1p in lipid homeostasis; mutants are defective in nuclear pore complex biogenesis, nuclear envelope morphology, mRNA export from the nucleus and are sensitive to sterol biosynthesis inhibitors and membrane fluidizing agents; exhibits synthetic lethal genetic interactions with genes involved in lipid metabolism | Core | NA | NA | NA |
| 4526-YIL041W | YIL041W | GVP36 | NA | BAR domain protein that localizes to early and late Golgi vesicles; required for adaptation to varying nutrient concentrations, fluid-phase endocytosis, polarization of the actin cytoskeleton, and vacuole biogenesis | Core | NA | NA | NA |
| 4527-YIL042C | YIL042C | PKP1 | protein kinase PKP1 | Mitochondrial protein kinase; involved in negative regulation of pyruvate dehydrogenase complex activity by phosphorylating the ser-133 residue of the Pda1p subunit; acts in concert with kinase Pkp2p and phosphatases Ptc5p and Ptc6p | Core | NA | NA | NA |
| 4528-YIL043C | YIL043C | CBR1 | CBR5 | Cytochrome b reductase; not essential for viability; also detected in mitochondria; mutation in conserved NADH binding domain of the human ortholog results in type I methemoglobinemia | Core | NA | NA | NA |
| 4529-YIL044C | YIL044C | AGE2 | SAT2 | ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector; involved in Trans-Golgi-Network (TGN) transport; contains C2C2H2 cysteine/histidine motif | Core | NA | NA | NA |
| 4530-YIL045W | YIL045W | PIG2 | putative protein phosphatase regulator PIG2 | Putative type-1 protein phosphatase targeting subunit; tethers Glc7p type-1 protein phosphatase to Gsy2p glycogen synthase; PIG2 has a paralog, GIP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4531-YIL046W | YIL046W | MET30 | ubiquitin-binding SDF ubiquitin ligase complex subunit MET30|ZRG11 | F-box protein containing five copies of the WD40 motif; controls cell cycle function, sulfur metabolism, and methionine biosynthesis as part of the ubiquitin ligase complex; interacts with and regulates Met4p, localizes within the nucleus; dissociation of Met30p from SCF complex in response to cadmium stress is regulated by Cdc48p | Accessory | Ancestral | NA | NA |
| 4532-YIL047C_NumOfGenes_2 | YIL047C | SYG1 | NA | Plasma membrane protein of unknown function; truncation and overexpression suppresses lethality of G-alpha protein deficiency | Accessory | Ancestral | NA | NA |
| 4533-YIL048W | YIL048W | NEO1 | putative aminophospholipid-translocating P4-type ATPase NEO1 | Phospholipid translocase (flippase), role in phospholipid asymmetry of plasma membrane; involved in endocytosis, vacuolar biogenesis and Golgi to ER vesicle-mediated transport; localizes to endosomes and the Golgi apparatus | Core | NA | NA | NA |
| 4534-YIL049W | YIL049W | DFG10 | putative polyprenol reductase | Probable polyprenol reductase; catalyzes conversion of polyprenol to dolichol, the precursor for N-glycosylation; involved in filamentous growth; mutations in human homolog SRD5A3 confer CDG (Congenital Disorders of Glycosylation); human SRD5A3 can complement yeast null mutant | Core | NA | NA | NA |
| 4535-YIL050W | YIL050W | PCL7 | NA | Pho85p cyclin of the Pho80p subfamily; forms a functional kinase complex with Pho85p which phosphorylates Mmr1p and is regulated by Pho81p; involved in glycogen metabolism, expression is cell-cycle regulated; PCL7 has a paralog, PCL6, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4536-YIL051C | YIL051C | MMF1 | isoleucine biosynthesis protein MMF1|IBM1 | Mitochondrial protein required for transamination of isoleucine; but not of valine or leucine; may regulate specificity of branched-chain transaminases Bat1p and Bat2p; induction of expression in response to stress is mediated by a Hog1p-regulated antisense RNA and gene looping; interacts genetically with mitochondrial ribosomal protein genes; MMF1 has a paralog, HMF1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4537-YIL052C | YIL052C | RPL34B | eL34|ribosomal 60S subunit protein L34B|L34e|L34B | Ribosomal 60S subunit protein L34B; homologous to mammalian ribosomal protein L34, no bacterial homolog; RPL34B has a paralog, RPL34A, that arose from the whole genome duplication | Core | NA | NA | NA |