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 |
|---|---|---|---|---|---|---|---|---|
| 6128-YMR071C | YMR071C | TVP18 | NA | Integral membrane protein; localized to late Golgi vesicles along with the v-SNARE Tlg2p; may interact with ribosomes, based on co-purification experiments; may have a role in intracellular sterol transport | Core | NA | NA | NA |
| 6129-YMR072W | YMR072W | ABF2 | DNA-binding protein ABF2|mtTFA|HM|p19 | Mitochondrial DNA-binding protein; involved in mitochondrial DNA replication and recombination, member of HMG1 DNA-binding protein family; activity may be regulated by protein kinase A phosphorylation; ABF2 has a paralog, IXR1, that arose from the whole genome duplication; human homolog TFAM can complement yeast abf2 mutant, rescuing the loss-of-mitochondrial DNA phenotype in a yeast abf2 strain | Core | NA | NA | NA |
| 6130-YMR073C | YMR073C | IRC21 | NA | Protein of unknown function; may be involved in resistance to carboplatin and cisplatin; null mutant displays increase in spontaneous Rad52p foci; contains a lipid-binding domain and binds cardiolipin in a large-scale study | Core | NA | NA | NA |
| 6131-YMR074C | YMR074C | SDD2 | NA | Protein with homology to human PDCD5; PDCD5 is involved in programmed cell death; N-terminal region forms a conserved triple-helix bundle structure; overproduction suppresses lethality due to expression of the dominant PET9 allele AAC2-A128P; overexpression promotes H2O2-induced apoptosis; YMR074C is not an essential gene; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6132-YMR075W_NumOfGenes_2 | YMR075W | RCO1 | NA | Essential component of the Rpd3S histone deacetylase complex; interacts with Eaf3p | Core | NA | NA | NA |
| 6133-YMR076C | YMR076C | PDS5 | NA | Cohesion maintenance factor; involved in sister chromatid condensation and cohesion; colocalizes with cohesin on chromosomes; performs its cohesin maintenance function in pre-anaphase cells by protecting the integrity of the cohesion complex; also required during meiosis; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6134-YMR077C | YMR077C | VPS20 | ESCRT-III subunit protein VPS20|VPL10|VPT20|CHM6 | Myristoylated subunit of the ESCRT-III complex; the endosomal sorting complex required for transport of transmembrane proteins into the multivesicular body pathway to the lysosomal/vacuolar lumen; cytoplasmic protein recruited to endosomal membranes | Core | NA | NA | NA |
| 6135-YMR078C | YMR078C | CTF18 | CHL12 | Subunit of a complex with Ctf8p; shares some subunits with Replication Factor C and is required for sister chromatid cohesion; may have overlapping functions with Rad24p in the DNA damage replication checkpoint | Core | NA | NA | NA |
| 6136-YMR079W | YMR079W | SEC14 | phosphatidylinositol/phosphatidylcholine transfer protein SEC14|PIT1 | Phosphatidylinositol/phosphatidylcholine transfer protein; involved in regulating PtdIns, PtdCho, and ceramide metabolism, products of which regulate intracellular transport and UPR; has a role in localization of lipid raft proteins; functionally homologous to mammalian PITPs; SEC14 has a paralog, YKL091C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6137-YMR080C | YMR080C | NAM7 | SUT2|ATP-dependent RNA helicase NAM7|SUP113|UPF1|MOF4|IFS2 | ATP-dependent RNA helicase of the SFI superfamily; involved in nonsense mediated mRNA decay; required for efficient translation termination at nonsense codons and targeting of NMD substrates to P-bodies; binds to the small ribosomal subunit via an interaction with Rps26; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 6138-YMR081C | YMR081C | ISF1 | MBR3 | Serine-rich, hydrophilic protein; overexpression suppresses growth defects of hap2, hap3, and hap4 mutants; expression is under glucose control; cotranscribed with NAM7 in a cyp1 mutant; ISF1 has a paralog, MBR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6139-YMR082C | YMR082C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR082C is not an essential gene | Core | NA | NA | NA |
| 6140-YMR083W | YMR083W | ADH3 | alcohol dehydrogenase ADH3 | Mitochondrial alcohol dehydrogenase isozyme III; involved in the shuttling of mitochondrial NADH to the cytosol under anaerobic conditions and ethanol production | Core | NA | NA | NA |
| 6141-YMR084W | YMR084W | NA | putative glutamine--fructose-6-phosphate transaminase | Putative protein of unknown function; YMR084W and adjacent ORF YMR085W are merged in related strains, and together are paralogous to glutamine-fructose-6-phosphate amidotransferase GFA1 | Core | NA | NA | NA |
| 6142-YMR085W | YMR085W | NA | NA | Putative protein of unknown function; YMR085W and adjacent ORF YMR084W are merged in related strains, and together are paralogous to glutamine-fructose-6-phosphate amidotransferase GFA1 | Core | NA | NA | NA |