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 |
|---|---|---|---|---|---|---|---|---|
| 6173-YMR114C | YMR114C | NA | putative peptide hydrolase | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; YMR114C is not an essential gene | Core | NA | NA | NA |
| 6174-YMR115W | YMR115W | MGR3 | FMP24 | Subunit of the mitochondrial (mt) i-AAA protease supercomplex; i-AAA degrades misfolded mitochondrial proteins; forms a subcomplex with Mgr1p that binds to substrates to facilitate proteolysis; required for growth of cells lacking mtDNA | Core | NA | NA | NA |
| 6175-YMR116C | YMR116C | ASC1 | RACK1|guanine nucleotide-binding protein subunit beta|ASU9|NAD1|CPC2 | G-protein beta subunit and guanine dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; required to prevent frameshifting at ribosomes stalled at repeated CGA codons; regulates P-body formation induced by replication stress; represses Gcn4p in the absence of amino acid starvation | Core | NA | NA | NA |
| 6176-YMR117C | YMR117C | SPC24 | kinetochore-associated Ndc80 complex subunit SPC24 | 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 |
| 6177-YMR118C | YMR118C | SHH3 | protein SHH3 | Putative mitochondrial inner membrane protein of unknown function; although similar to paralogous Sdh3p, Shh3p is not a stoichiometric subunit of either succinate dehydrogenase or of the TIM22 translocase; SHH3 has a paralog, SDH3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6178-YMR119W | YMR119W | ASI1 | putative ubiquitin-protein ligase ASI1 | Subunit of the inner nuclear membrane Asi ubiquitin ligase complex; the Asi complex targets both misfolded proteins of the inner nuclear membrane-associated degradation (INMAD) pathway and regulators of sterol biosynthesis for ubiquitin-mediated degradation; acts with Asi2p and Asi3p to ensure the fidelity of SPS-sensor signaling by targeting latent unprocessed forms of Stp1p and Stp2p, maintaining the repressed state of gene expression in the absence of inducing amino acids | Core | NA | NA | NA |
| 6179-YMR119W-A | YMR119W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps 3' end of ORF ASI1/YMR119W | Accessory | Ancestral | NA | NA |
| 6180-YMR120C | YMR120C | ADE17 | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase ADE17 | Enzyme of 'de novo' purine biosynthesis; contains both 5-aminoimidazole-4-carboxamide ribonucleotide transformylase and inosine monophosphate cyclohydrolase activities; ADE17 has a paralog, ADE16, that arose from the whole genome duplication; ade16 ade17 mutants require adenine and histidine | Core | NA | NA | NA |
| 6181-YMR121C | YMR121C | RPL15B | eL15|ribosomal 60S subunit protein L15B|L15e|rp15R|YL10|L15B|L13B | Ribosomal 60S subunit protein L15B; binds to 5.8 S rRNA; homologous to mammalian ribosomal protein L15, no bacterial homolog; RPL15B has a paralog, RPL15A, that arose from the whole genome duplication; relocalizes from nucleus to nucleolus upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 6182-YMR122C | YMR122C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YMR122C is not an essential gene | Accessory | Unknown | NA | NA |
| 6183-YMR122W-A | YMR122W-A | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and endoplasmic reticulum | Core | NA | NA | NA |
| 6184-YMR123W | YMR123W | PKR1 | NA | V-ATPase assembly factor; functions with other V-ATPase assembly factors in the ER to efficiently assemble the V-ATPase membrane sector (V0); protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 6185-YMR124W | YMR124W | EPO1 | NA | Protein involved in septin-ER tethering; interacts with ER membrane protein, Scs2p, and Shs1p, a septin ring component, at bud neck to create ER diffusion barrier; GFP-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; interacts with Crm1p in two-hybrid assay; YMR124W has a paralog, YLR031W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6186-YMR125W | YMR125W | STO1 | SUT1|CBP80|GCR3|CBC1 | Large subunit of the nuclear mRNA cap-binding protein complex; interacts with Npl3p to carry nuclear poly(A)+ mRNA to cytoplasm; also involved in nuclear mRNA degradation and telomere maintenance; orthologous to mammalian CBP80 | Core | NA | NA | NA |
| 6187-YMR126C | YMR126C | DLT1 | NA | Protein of unknown function; mutant sensitive to 6-azauracil (6AU) and mycophenolic acid (MPA) | Core | NA | NA | NA |