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 |
|---|---|---|---|---|---|---|---|---|
| 2483-YDL032W | YDL032W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene SLM3/YDL033C; YDL032W is not an essential gene | Accessory | Ancestral | NA | NA |
| 2484-YDL033C | YDL033C | SLM3 | tRNA-5-taurinomethyluridine 2-sulfurtransferase|MTU1|MTO2 | tRNA-specific 2-thiouridylase; responsible for 2-thiolation of the wobble base of mitochondrial tRNAs; human homolog TRMU is implicated in myoclonus epilepsy associated with ragged red fibers (MERRF), and can complement yeast null mutant | Core | NA | NA | NA |
| 2485-YDL035C_NumOfGenes_2 | YDL035C | GPR1 | NA | Plasma membrane G protein coupled receptor (GPCR); interacts with the heterotrimeric G protein alpha subunit, Gpa2p, and with Plc1p; sensor that integrates nutritional signals with the modulation of cell fate via PKA and cAMP synthesis | Core | NA | NA | NA |
| 2486-YDL036C | YDL036C | PUS9 | pseudouridine synthase PUS9 | Mitochondrial tRNA:pseudouridine synthase; catalyzes the formation of pseudouridine at position 32 in mitochondrial tRNAs; contains an N-terminal mitochondrial targeting sequence; PUS9 has a paralog, RIB2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2487-YDL037C | YDL037C | BSC1 | NA | Protein of unconfirmed function; similar to cell surface flocculin Flo11p; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression; in W303 strain one continuous open reading frame comprising of YDL037C, the intergenic region and YDL039C encodes the gene IMI1 | Core | NA | NA | NA |
| 2488-YDL039C | YDL039C | PRM7 | pheromone-regulated protein PRM7|YDL038C | Pheromone-regulated protein; predicted to have one transmembrane segment; promoter contains Gcn4p binding elements; in W303 strain one continuous open reading frame comprising of YDL037C, the intergenic region and YDL039C encodes the IMI1 | Core | NA | NA | NA |
| 2489-YDL040C | YDL040C | NAT1 | peptide alpha-N-acetyltransferase complex A subunit NAT1|NAA15|AAA1 | Subunit of protein N-terminal acetyltransferase NatA; NatA comprised of Nat1p, Ard1p, and Nat5p; N-terminally acetylates many proteins to influence multiple processes such as cell cycle progression, heat-shock resistance, mating, sporulation, telomeric silencing and early stages of mitophagy; orthologous to human NAA15; expression of both human NAA10 and NAA15 functionally complements ard1 nat1 double mutant although single mutations are not complemented by their orthologs | Core | NA | NA | NA |
| 2490-YDL042C_NumOfGenes_2 | YDL042C | SIR2 | NAD-dependent histone deacetylase SIR2|MAR1 | Conserved NAD+ dependent histone deacetylase of the Sirtuin family; deacetylation targets are primarily nuclear proteins; required for telomere hypercluster formation in quiescent yeast cells; involved in regulation of lifespan; plays roles in silencing at HML, HMR, telomeres, and rDNA; negatively regulates initiation of DNA replication; functions as regulator of autophagy like mammalian homolog SIRT1, and also of mitophagy | Core | NA | NA | NA |
| 2491-YDL043C | YDL043C | PRP11 | RNA11 | Subunit of the SF3a splicing factor complex; required for spliceosome assembly | Core | NA | NA | NA |
| 2492-YDL044C | YDL044C | MTF2 | NAM1 | Mitochondrial protein that interacts with mitochondrial RNA polymerase; interacts with an N-terminal region of mitochondrial RNA polymerase (Rpo41p) and couples RNA processing and translation to transcription | Core | NA | NA | NA |
| 2493-YDL045C | YDL045C | FAD1 | FMN adenylyltransferase | Flavin adenine dinucleotide (FAD) synthetase; performs the second step in synthesis of FAD from riboflavin; mutation is functionally complemented by human FLAD1 | Core | NA | NA | NA |
| 2494-YDL045W-A | YDL045W-A | MRP10 | mitochondrial 37S ribosomal protein YmS-T|YmS-T | Mitochondrial ribosomal protein of the small subunit; contains twin cysteine-x9-cysteine motifs; oxidized by Mia40p during import into mitochondria | Core | NA | NA | NA |
| 2495-YDL046W | YDL046W | NPC2 | sterol transporter | Sterol transport protein and functional homolog of human NPC2/He1; human NPC2 is a cholesterol-binding protein whose deficiency causes Niemann-Pick type C2 disease involving retention of cholesterol in lysosomes; yeast NPC2 can complement mutations in human NPC2 | Core | NA | NA | NA |
| 2496-YDL047W | YDL047W | SIT4 | type 2A-related serine/threonine-protein phosphatase SIT4|PPH1 | Ceramide-activated, type 2A-related serine-threonine phosphatase; functions in G1/S transition of mitotic cycle; controls lifespan, mitochondrial function, cell cycle progression by regulating HXK2 phosphorylation; regulator of COPII coat dephosphorylation; required for ER to Golgi traffic; interacts with Hrr25p kinase; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization; similar to human PP6 | Core | NA | NA | NA |
| 2497-YDL048C | YDL048C | STP4 | NA | Protein containing a Kruppel-type zinc-finger domain; similar to Stp1p, Stp2p; predicted transcription factor; relative distribution to the nucleus increases upon DNA replication stress; STP4 has a paralog, STP3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |