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 |
|---|---|---|---|---|---|---|---|---|
| 5828-YLR371W_NumOfGenes_2 | YLR371W | ROM2 | Rho family guanine nucleotide exchange factor ROM2 | Guanine nucleotide exchange factor (GEF) for Rho1p and Rho2p; mutations are synthetically lethal with mutations in rom1, which also encodes a GEF; Rom2p localization to the bud surface is dependent on Ack1p; ROM2 has a paralog, ROM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5829-YLR372W_NumOfGenes_2 | YLR372W | ELO3 | SUR4|fatty acid elongase ELO3|APA1|VBM1|SRE1 | Elongase; involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis; lethality of the elo2 elo3 double null mutation is functionally complemented by human ELOVL1 and weakly complemented by human ELOVL3 or ELOV7 | Core | NA | NA | NA |
| 5830-YLR373C_NumOfGenes_2 | YLR373C | VID22 | NA | Glycosylated integral membrane protein localized to plasma membrane; plays a role in fructose-1,6-bisphosphatase (FBPase) degradation; involved in FBPase transport from the cytosol to Vid (vacuole import and degradation) vesicles; VID22 has a paralog, ENV11, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5831-YLR374C | YLR374C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF STP3/YLR375W | Core | NA | NA | NA |
| 5832-YLR375W_NumOfGenes_2 | YLR375W | STP3 | NA | Zinc-finger protein of unknown function; possibly involved in pre-tRNA splicing and in uptake of branched-chain amino acids; STP3 has a paralog, STP4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5833-YLR376C_NumOfGenes_2 | YLR376C | PSY3 | NA | Component of Shu complex (aka PCSS complex); Shu complex also includes Shu1, Csm2, Shu2, and promotes error-free DNA repair; promotes Rad51p filament assembly; Shu complex mediates inhibition of Srs2p function; Psy3p and Csm2p contain similar DNA-binding regions which work together to form a single DNA binding site; deletion of PSY3 results in a mutator phenotype; deletion increases sensitivity to anticancer drugs oxaliplatin and cisplatin but not mitomycin C | Core | NA | NA | NA |
| 5834-YLR377C_NumOfGenes_2 | YLR377C | FBP1 | fructose 1,6-bisphosphate 1-phosphatase|ACN8 | Fructose-1,6-bisphosphatase; key regulatory enzyme in the gluconeogenesis pathway, required for glucose metabolism; undergoes either proteasome-mediated or autophagy-mediated degradation depending on growth conditions; glucose starvation results in redistribution to the periplasm; interacts with Vid30p | Core | NA | NA | NA |
| 5835-YLR378C_NumOfGenes_2 | YLR378C | SEC61 | translocon subunit SEC61 | Conserved ER protein translocation channel; essential subunit of Sec61 complex (Sec61p, Sbh1p, and Sss1p); forms channel for SRP-dependent protein import; with Sec63 complex allows SRP-independent protein import into ER; involved in posttranslational soluble protein import into the ER, ERAD of soluble substrates, and misfolded soluble protein export from the ER | Core | NA | NA | NA |
| 5836-YLR379W | YLR379W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the essential ORF SEC61/YLR378C | Accessory | Ancestral | NA | NA |
| 5837-YLR380W_NumOfGenes_2 | YLR380W | CSR1 | SFH2 | Phosphatidylinositol transfer protein; has a potential role in regulating lipid and fatty acid metabolism under heme-depleted conditions; interacts specifically with thioredoxin peroxidase; may have a role in oxidative stress resistance; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5838-YLR381W_NumOfGenes_2 | YLR381W | CTF3 | CHL3 | Outer kinetochore protein that forms a complex with Mcm16p and Mcm22p; may bind the kinetochore to spindle microtubules; required for the spindle assembly checkpoint; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-I and fission yeast mis6 | Core | NA | NA | NA |
| 5839-YLR382C_NumOfGenes_2 | YLR382C | NAM2 | leucine--tRNA ligase NAM2|LeuRS|MSL1 | Mitochondrial leucyl-tRNA synthetase; also has direct role in splicing of several mitochondrial group I introns; indirectly required for mitochondrial genome maintenance; human homolog LARS2 can complement yeast null mutant, and is implicated in Perrault syndrome | Core | NA | NA | NA |
| 5840-YLR383W_NumOfGenes_2 | YLR383W | SMC6 | DNA repair protein SMC6|RHC18 | Component of the SMC5-SMC6 complex; this complex plays a key role in the removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair; homologous to S. pombe rad18 | Core | NA | NA | NA |
| 5841-YLR384C_NumOfGenes_2 | YLR384C | IKI3 | Elongator subunit IKI3|KTI7|TOT1|ELP1 | Subunit of Elongator complex; Elongator is required for modification of wobble nucleosides in tRNA; maintains structural integrity of Elongator; homolog of human IKAP, mutations in which cause familial dysautonomia (FD) | Core | NA | NA | NA |
| 5842-YLR385C_NumOfGenes_2 | YLR385C | SWC7 | AWS1 | Protein of unknown function; component of the Swr1p complex that incorporates Htz1p into chromatin | Core | NA | NA | NA |