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 |
|---|---|---|---|---|---|---|---|---|
| 5123-YKL053C-A | YKL053C-A | MDM35 | NA | Mitochondrial intermembrane space protein; forms complex with Ups2p that transfers phosphatidylserine from outer membrane to inner membrane for phosphatidylethanolamine synthesis; mutation affects mitochondrial distribution and morphology; contains twin cysteine-x9-cysteine motifs; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5124-YKL053W | YKL053W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified ORF ASK1 | Accessory | Ancestral | NA | NA |
| 5125-YKL054C | YKL054C | DEF1 | DNA damage-responsive RNA polymerase-degradation factor DEF1|VID31 | RNAPII degradation factor; forms a complex with Rad26p in chromatin, enables ubiquitination and proteolysis of RNAPII present in an elongation complex; mutant is deficient in Zip1p loading onto chromosomes during meiosis | Core | NA | NA | NA |
| 5126-YKL055C | YKL055C | OAR1 | 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) | Mitochondrial 3-oxoacyl-[acyl-carrier-protein] reductase; may comprise a type II mitochondrial fatty acid synthase along with Mct1p; human homolog CBR4 complements yeast null mutant | Core | NA | NA | NA |
| 5127-YKL056C | YKL056C | TMA19 | MMI1|RBF18 | Protein that associates with ribosomes; homolog of translationally controlled tumor protein; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and relocates to the mitochondrial outer surface upon oxidative stress | Core | NA | NA | NA |
| 5128-YKL057C | YKL057C | NUP120 | RAT2 | Subunit of the Nup84p subcomplex of the nuclear pore complex (NPC); contributes to nucleocytoplasmic transport and NPC biogenesis and is involved in establishment of a normal nucleocytoplasmic concentration gradient of the GTPase Gsp1p; also plays roles in several processes that may require localization of genes or chromosomes at the nuclear periphery, including double-strand break repair, transcription and chromatin silencing; homologous to human NUP160 | Core | NA | NA | NA |
| 5129-YKL058W | YKL058W | TOA2 | transcription initiation factor IIA subunit gamma | TFIIA small subunit; involved in transcriptional activation, acts as antirepressor or as coactivator; required, along with Toa1p, for ribosomal protein gene transcription in vivo; homologous to smallest subunit of human and Drosophila TFIIA; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5130-YKL059C | YKL059C | MPE1 | cleavage polyadenylation factor subunit MPE1 | Essential conserved subunit of CPF cleavage and polyadenylation factor; plays a role in 3' end formation of mRNA via the specific cleavage and polyadenylation of pre-mRNA; contains a ubiquitin-like (UBL) domain, a RNA-binding zinc knuckle motif and a RING finger domain; both the zinc knuckle and RING finger are required for pre-mRNA binding; possible role in ubiquitination of Pap1p; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 5131-YKL060C | YKL060C | FBA1 | fructose-bisphosphate aldolase FBA1|LOT1 | Fructose 1,6-bisphosphate aldolase; required for glycolysis and gluconeogenesis; catalyzes conversion of fructose 1,6 bisphosphate to glyceraldehyde-3-P and dihydroxyacetone-P; locates to mitochondrial outer surface upon oxidative stress; N-terminally propionylated in vivo | Core | NA | NA | NA |
| 5132-YKL061W | YKL061W | BLI1 | NA | Subunit of the BLOC-1 complex involved in endosomal maturation; interacts with Msb3p; green fluorescent protein (GFP)-fusion protein localizes to the endosome | Core | NA | NA | NA |
| 5133-YKL062W | YKL062W | MSN4 | stress-responsive transcriptional activator MSN4 | Stress-responsive transcriptional activator; activated in stochastic pulses of nuclear localization in response to various stress conditions; binds DNA at stress response elements of responsive genes, inducing gene expression; involved in diauxic shift | Core | NA | NA | NA |
| 5134-YKL063C | YKL063C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the Golgi | Core | NA | NA | NA |
| 5135-YKL064W | YKL064W | MNR2 | putative Mg(2+) transporter MNR2 | Vacuolar membrane protein required for magnesium homeostasis; putative magnesium transporter; has similarity to Alr1p and Alr2p, which mediate influx of Mg2+ and other divalent cations; localizes to sites of contact between the vacuole and mitochondria (vCLAMPs) | Core | NA | NA | NA |
| 5136-YKL065C | YKL065C | YET1 | NA | Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein; YET1 has a paralog, YET2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5137-YKL065W-A | YKL065W-A | NA | NA | Putative protein of unknown function; SWAT-GFP fusion protein localizes to the endoplasmic reticulum (ER) while mCherry fusion localizes to both the ER and vacuole | Core | NA | NA | NA |