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 |
|---|---|---|---|---|---|---|---|---|
| 5213-YKL140W | YKL140W | TGL1 | YKL5 | Steryl ester hydrolase; one of three gene products (Yeh1p, Yeh2p, Tgl1p) responsible for steryl ester hydrolase activity and involved in sterol homeostasis; localized to lipid particle membranes | Core | NA | NA | NA |
| 5214-YKL141W | YKL141W | SDH3 | succinate dehydrogenase cytochrome b subunit SDH3|YKL4|CYB3 | Subunit of succinate dehydrogenase and of TIM22 translocase; functions as cytochrome b subunit of succinate dehydrogenase, which couples oxidation of succinate to transfer of electrons to ubiquinone as part of the TCA cycle and the mitochondrial respiratory chain; also required for mitochondrial inner membrane protein import as part of the TIM22 complex; SDH3 has a paralog, SHH3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5215-YKL142W | YKL142W | MRP8 | YKL3 | Protein of unknown function; undergoes sumoylation; transcription induced under cell wall stress; protein levels are reduced under anaerobic conditions; protein abundance increases in response to DNA replication stress; originally thought to be a mitochondrial ribosomal protein based on sequence analysis | Core | NA | NA | NA |
| 5216-YKL143W | YKL143W | LTV1 | YKL2 | Component of the GSE complex; GSE is required for proper sorting of amino acid permease Gap1p; required for ribosomal small subunit export from nucleus; required for growth at low temperature | Core | NA | NA | NA |
| 5217-YKL144C | YKL144C | RPC25 | DNA-directed RNA polymerase III subunit RPC25|C25|YKL1 | RNA polymerase III subunit C25; required for transcription initiation; forms a heterodimer with Rpc17p; paralog of Rpb7p | Core | NA | NA | NA |
| 5218-YKL145W_NumOfGenes_2 | YKL145W | RPT1 | proteasome regulatory particle base subunit RPT1|YTA3|CIM5 | ATPase of the 19S regulatory particle of the 26S proteasome; one of six ATPases of the regulatory particle; involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and Ubr1p; mutant has aneuploidy tolerance | Core | NA | NA | NA |
| 5219-YKL146W | YKL146W | AVT3 | NA | Vacuolar transporter; exports large neutral amino acids from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters | Core | NA | NA | NA |
| 5220-YKL147C | YKL147C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; partially overlaps the verified gene AVT3 | Accessory | Ancestral | NA | NA |
| 5221-YKL148C | YKL148C | SDH1 | succinate dehydrogenase flavoprotein subunit SDH1|SDHA | Flavoprotein subunit of succinate dehydrogenase; couples the oxidation of succinate to the transfer of electrons to ubiquinone as part of the TCA cycle and the mitochondrial respiratory chain; FAD binding to Sdh1p is required for the assembly of the succinate dehydrogenase subunits; mutations in human ortholog SDHA are associated with Leigh syndrome | Core | NA | NA | NA |
| 5222-YKL149C | YKL149C | DBR1 | RNA lariat debranching enzyme|PRP26 | RNA lariat debranching enzyme; catalyzes debranching of lariat introns formed during pre-mRNA splicing; required for efficient Ty1 transposition; knockdown of human homolog Dbr1 rescues toxicity of RNA-binding proteins TDP-43 and FUS which are implicated in amyotrophic lateral sclerosis (ALS), suggests potential therapeutic target for ALS and related TDP-43 proteinopathies; human homolog DBR1 can complement yeast dbr1 null mutant | Core | NA | NA | NA |
| 5223-YKL150W | YKL150W | MCR1 | cytochrome-b5 reductase | Mitochondrial NADH-cytochrome b5 reductase; involved in ergosterol biosynthesis | Core | NA | NA | NA |
| 5224-YKL151C | YKL151C | NNR2 | NADHX dehydratase | Widely-conserved NADHX dehydratase; converts (S)-NADHX to NADH in ATP-dependent manner; YKL151C promoter contains STREs (stress response elements) and expression is induced by heat shock or methyl methanesulfonate; downstream intergenic region drives antisense expression and mediates coordinated regulation of YKL151C and GPM1 phosphoglycerate mutase; protein abundance increases in response to DNA replication stress; homolog of Carkd in mammals and C-terminus of YjeF in E.coli | Core | NA | NA | NA |
| 5225-YKL152C_NumOfGenes_2 | YKL152C | GPM1 | phosphoglycerate mutase GPM1 | Tetrameric phosphoglycerate mutase; mediates the conversion of 3-phosphoglycerate to 2-phosphoglycerate during glycolysis and the reverse reaction during gluconeogenesis | Core | NA | NA | NA |
| 5226-YKL154W | YKL154W | SRP102 | Signal recognition particle receptor subunit beta | Signal recognition particle (SRP) receptor beta subunit; involved in SRP-dependent protein targeting; anchors the alpha subunit, Srp101p to the ER membrane | Core | NA | NA | NA |
| 5227-YKL155C | YKL155C | RSM22 | mitochondrial 37S ribosomal protein RSM22 | Mitochondrial ribosomal protein of the small subunit; also predicted to be an S-adenosylmethionine-dependent RNA methyltransferase | Core | NA | NA | NA |