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 |
|---|---|---|---|---|---|---|---|---|
| 3323-YER012W | YER012W | PRE1 | proteasome core particle subunit beta 4 | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle | Core | NA | NA | NA |
| 3324-YER013W | YER013W | PRP22 | DEAH-box ATP-dependent RNA helicase PRP22 | DEAH-box RNA-dependent ATPase/ATP-dependent RNA helicase; associates with lariat intermediates before the second catalytic step of splicing; mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes; required for proofreading the exon ligation reaction | Core | NA | NA | NA |
| 3325-YER014C-A | YER014C-A | BUD25 | NA | Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern | Accessory | Ancestral | NA | NA |
| 3326-YER014W | YER014W | HEM14 | oxygen-dependent protoporphyrinogen oxidase | Protoporphyrinogen oxidase; a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX; inhibited by diphenyl ether-type herbicides | Core | NA | NA | NA |
| 3327-YER015W | YER015W | FAA2 | medium-chain fatty acid-CoA ligase FAA2|FAM1 | Medium chain fatty acyl-CoA synthetase; activates imported fatty acids; accepts a wide range of fatty acid chain lengths with a preference for medium chains, C9:0-C13:0; localized to the peroxisome; comparative analysis suggests that a mitochondrially targeted form may result from translation starting at a non-canonical codon upstream of the annotated start codon | Core | NA | NA | NA |
| 3328-YER016W | YER016W | BIM1 | microtubule-binding protein BIM1|EB1|YEB1 | Microtubule plus end-tracking protein; together with Kar9p makes up the cortical microtubule capture site and delays the exit from mitosis when the spindle is oriented abnormally; homolog of human end binding protein 1 (EB1) | Core | NA | NA | NA |
| 3329-YER017C | YER017C | AFG3 | AAA family ATPase AFG3|YTA10 | Mitochondrial inner membrane m-AAA protease component; mediates degradation of misfolded or unassembled proteins; also required for correct assembly of mitochondrial enzyme complexes; involved in cytoplasmic mRNA translation and aging; expression of human homolog AFG3L2 can complement yeast yta12 afg3 double mutant | Accessory | Ancestral | NA | NA |
| 3330-YER018C | YER018C | SPC25 | kinetochore-associated Ndc80 complex subunit SPC25 | Component of the kinetochore-associated Ndc80 complex; involved in chromosome segregation, spindle checkpoint activity, and kinetochore clustering; evolutionarily conserved; other members include Ndc80p, Nuf2p, Spc24p, and Spc25p | Core | NA | NA | NA |
| 3331-YER019C-A | YER019C-A | SBH2 | Arf family guanine nucleotide exchange factor SBH2|SEB2 | Ssh1p-Sss1p-Sbh2p complex component; involved in protein translocation into the endoplasmic reticulum; SBH2 has a paralog, SBH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3332-YER019W | YER019W | ISC1 | inositol phosphosphingolipid phospholipase | Inositol phosphosphingolipid phospholipase C; mitochondrial membrane localized; hydrolyzes complex sphingolipids to produce ceramide; activates genes required for non-fermentable carbon source metabolism during diauxic shift; activated by phosphatidylserine, cardiolipin, and phosphatidylglycerol; mediates Na+ and Li+ halotolerance; ortholog of mammalian neutral sphingomyelinase type 2 | Core | NA | NA | NA |
| 3333-YER020W | YER020W | GPA2 | guanine nucleotide-binding protein subunit alpha|SSP101 | Nucleotide binding alpha subunit of the heterotrimeric G protein; interacts with the receptor Gpr1p, has signaling role in response to nutrients; required for the recruitment of Ras-GTP at the plasma membrane and in the nucleus | Core | NA | NA | NA |
| 3334-YER021W | YER021W | RPN3 | proteasome regulatory particle lid subunit RPN3|SUN2 | Essential non-ATPase regulatory subunit of the 26S proteasome lid; similar to the p58 subunit of the human 26S proteasome; temperature-sensitive alleles cause metaphase arrest, suggesting a role for the proteasome in cell cycle control | Core | NA | NA | NA |
| 3335-YER022W | YER022W | SRB4 | MED17 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for basal RNA polymerase II transcription; homozygosity of the human MED17 L371P mutation is associated with infantile cerebral and cerebellar atrophy with poor myelination | Core | NA | NA | NA |
| 3336-YER023W_NumOfGenes_2 | YER023W | PRO3 | pyrroline-5-carboxylate reductase|ORE2 | Delta 1-pyrroline-5-carboxylate reductase; catalyzes the last step in proline biosynthesis | Core | NA | NA | NA |
| 3337-YER024W | YER024W | YAT2 | carnitine O-acetyltransferase YAT2 | Carnitine acetyltransferase; has similarity to Yat1p, which is a carnitine acetyltransferase associated with the mitochondrial outer membrane | Core | NA | NA | NA |