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 |
|---|---|---|---|---|---|---|---|---|
| 6758-YNR038W | YNR038W | DBP6 | putative ATP-dependent RNA helicase DBP6 | Essential protein involved in ribosome biogenesis; putative ATP-dependent RNA helicase of the DEAD-box protein family; human homolog DDX51 complements yeast dbp6 mutant | Core | NA | NA | NA |
| 6759-YNR039C | YNR039C | ZRG17 | Zn(2+) transporter ZRG17 | Endoplasmic reticulum zinc transporter; part of a heterodimeric transporter with Msc2p that transfers zinc from the cytosol to the ER lumen; member of the cation diffusion facilitator family of efflux pumps; zinc-regulated directly through Zap1p; transcription induced under conditions of zinc deficiency | Core | NA | NA | NA |
| 6760-YNR040W | YNR040W | NA | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 6761-YNR041C_NumOfGenes_2 | YNR041C | COQ2 | 4-hydroxybenzoate octaprenyltransferase | Para hydroxybenzoate polyprenyl transferase; catalyzes the second step in ubiquinone (coenzyme Q) biosynthesis; human COQ2, mutations in which are implicated in an increased risk of mutiple-system atrophy, can complement a yeast coq2 null mutant | Core | NA | NA | NA |
| 6762-YNR043W | YNR043W | MVD1 | diphosphomevalonate decarboxylase MVD1|ERG19 | Mevalonate pyrophosphate decarboxylase; essential enzyme involved in the biosynthesis of isoprenoids and sterols, including ergosterol; acts as a homodimer | Core | NA | NA | NA |
| 6763-YNR044W | YNR044W | AGA1 | NA | Anchorage subunit of a-agglutinin of a-cells; highly O-glycosylated protein with N-terminal secretion signal and C-terminal signal for addition of GPI anchor to cell wall, linked to adhesion subunit Aga2p via two disulfide bonds; AGA1 has a paralog, FIG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6764-YNR045W | YNR045W | PET494 | NA | Mitochondrial translational activator specific for the COX3 mRNA; acts together with Pet54p and Pet122p; located in the mitochondrial inner membrane | Core | NA | NA | NA |
| 6765-YNR046W | YNR046W | TRM112 | RNA methylation protein TRM112 | Protein involved in methylation of tRNA, rRNA, and translation factors; also involved in ribosome biogenesis; subunit of tRNA methyltransferase (MTase) complexes in combination with Trm9p and Trm11p; N7-methylates G1575 of 18S rRNA as complex with Bud23p; subunit of complex with Mtq2p that methylates Sup45p (eRF1) in the ternary complex eRF1-eRF3-GTP; relative distribution to the nucleus increases upon DNA replication stress; functional homolog of human TRMT112 | Core | NA | NA | NA |
| 6766-YNR047W | YNR047W | FPK1 | serine/threonine protein kinase FPK1 | Ser/Thr protein kinase; phosphorylates several aminophospholipid translocase family members, regulating phospholipid translocation and membrane asymmetry; phosphorylates and inhibits upstream inhibitory kinase, Ypk1p; localizes to the cytoplasm, early endosome/TGN compartments and thplasma membrane; localizes to the shmoo tip where it has a redundant role in the cellular response to mating pheromone; FPK1 has a paralog, KIN82, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6767-YNR048W | YNR048W | NA | putative aminophospholipid translocase regulatory protein|CRF1 | Potential noncatalytic subunit for phospholipid translocase Dnf3p; YNR048W has a paralog, CDC50, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6768-YNR049C | YNR049C | MSO1 | NA | Lipid-interacting protein in SNARE complex assembly machinery; acts at late step in secretion; interacts with membranes through two distinct binding sites; shows genetic and physical interactions with Sec1p; required for prospore membrane formation during sporulation; N-terminus closely associates with plasma membrane, C-terminus colocalizes with Sec4p on intracellular membranes; relocalizes from bud neck to nucleus upon DNA replication stress | Core | NA | NA | NA |
| 6769-YNR050C | YNR050C | LYS9 | saccharopine dehydrogenase (NADP+, L-glutamate-forming)|LYS13 | Saccharopine dehydrogenase (NADP+, L-glutamate-forming); catalyzes the formation of saccharopine from alpha-aminoadipate 6-semialdehyde, the seventh step in lysine biosynthesis pathway; exhibits genetic and physical interactions with TRM112 | Core | NA | NA | NA |
| 6770-YNR051C | YNR051C | BRE5 | NA | Ubiquitin protease cofactor; forms deubiquitination complex with Ubp3p that coregulates anterograde and retrograde transport between the endoplasmic reticulum and Golgi compartments; null is sensitive to brefeldin A | Core | NA | NA | NA |
| 6771-YNR052C | YNR052C | POP2 | CCR4-NOT core DEDD family RNase subunit POP2|CAF1 | RNase of the DEDD superfamily; subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation | Core | NA | NA | NA |
| 6772-YNR053C | YNR053C | NOG2 | putative GTPase NOG2|NUG2 | Putative GTPase; associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation; recruited by ribosomal proteins L17, L35, and L37 to assembling ribosomes after 27SB pre-rRNA is generated, immediately preceding removal of ITS2 | Core | NA | NA | NA |