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 |
|---|---|---|---|---|---|---|---|---|
| 5033-YJR127C | YJR127C | RSF2 | ZMS1 | Zinc-finger protein; involved in transcriptional control of both nuclear and mitochondrial genes, many of which specify products required for glycerol-based growth, respiration, and other functions; RSF2 has a paralog, TDA9, that arose from the whole genome duplication; relocalizes from nucleus to cytoplasm upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5034-YJR128W | YJR128W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; partially overlaps the verified ORF RSF2 | Accessory | Ancestral | NA | NA |
| 5035-YJR129C | YJR129C | EFM3 | protein-lysine N-methyltransferase | S-adenosylmethionine-dependent methyltransferase; seven-beta-strand lysine methyltransferase which trimethylates translation elongation factor EF2 (Eft1p and Eft2p) at lysine 509; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; ortholog of human gene FAM86A | Accessory | Ancestral | NA | NA |
| 5036-YJR130C | YJR130C | STR2 | cystathionine gamma-synthase | Cystathionine gamma-synthase, converts cysteine into cystathionine; STR2 has a paralog, YML082W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5037-YJR131W | YJR131W | MNS1 | mannosyl-oligosaccharide 1,2-alpha-mannosidase | Alpha-1,2-mannosidase; involved in ER-associated protein degradation (ERAD); catalyzes the removal of one mannose residue from a glycosylated protein, converting the modification from Man9GlcNAc to Man8GlcNAc; catalyzes the last step in glycoprotein maturation in the ER and is critical for ER protein degradation | Accessory | Ancestral | NA | NA |
| 5038-YJR132W | YJR132W | NMD5 | KAP119 | Karyopherin; a carrier protein involved in nuclear import of proteins; importin beta homolog | Core | NA | NA | NA |
| 5039-YJR133W | YJR133W | XPT1 | xanthine phosphoribosyltransferase | Xanthine-guanine phosphoribosyl transferase; required for xanthine utilization and for optimal utilization of guanine | Core | NA | NA | NA |
| 5040-YJR134C | YJR134C | SGM1 | NA | Protein of unknown function; required for wild-type growth rate on galactose and mannose; localizes to COPI coated vesicles and the Golgi apparatus | Core | NA | NA | NA |
| 5041-YJR135C | YJR135C | MCM22 | NA | Outer kinetochore protein and component of the Ctf3 subcomplex; binds to centromeric DNA in a Ctf19p-dependent manner; involved in chromosome segregation and minichromosome maintenance; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-K and fission yeast sim4 | Core | NA | NA | NA |
| 5042-YJR135W-A | YJR135W-A | TIM8 | protein transporter TIM8 | Mitochondrial intermembrane space protein; forms a complex with Tim13p that delivers a subset of hydrophobic proteins to the TIM22 complex for inner membrane insertion; homolog of human TIMM8A, implicated in Mohr-Tranebjaerg syndrome, also known as deafness-dystonia-optic neuronopathy (DDON) syndrome; human TIMM8A can complement yeast null mutant | Core | NA | NA | NA |
| 5043-YJR136C | YJR136C | TTI2 | NA | Subunit of the ASTRA complex, involved in chromatin remodeling; telomere length regulator involved in the stability or biogenesis of PIKKs such as TORC1; involved in the cellular stress response; similar to S. pombe Tti2p; may interact with Rsm23p; GFP-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 5044-YJR137C | YJR137C | MET5 | sulfite reductase (NADPH) subunit beta|ECM17 | Sulfite reductase beta subunit; involved in amino acid biosynthesis, transcription repressed by methionine | Core | NA | NA | NA |
| 5045-YJR138W | YJR138W | IML1 | SEA1 | GTPase-activating protein (GAP) subunit of the Iml1p/SEACIT complex; SEACIT (Iml1p-Npr2p-Npr3p) is a subcomplex of the SEA complex, a coatomer-related complex that associates dynamically with the vacuole; Iml1p functions in the SEACIT complex as a GAP for the Rag family GTPase Gtr1p (EGOC subunit), resulting in the inhibition of TORC1 signaling in response to amino acid deprivation; the Iml1p/SEACIT complex is required for non-nitrogen-starvation (NNS)-induced autophagy | Core | NA | NA | NA |
| 5046-YJR139C | YJR139C | HOM6 | homoserine dehydrogenase|THR6 | Homoserine dehydrogenase (L-homoserine:NADP oxidoreductase); dimeric enzyme that catalyzes the third step in the common pathway for methionine and threonine biosynthesis; enzyme has nucleotide-binding, dimerization and catalytic regions | Core | NA | NA | NA |
| 5047-YJR140C_NumOfGenes_2 | YJR140C | HIR3 | HPC1 | Subunit of the HIR complex; a nucleosome assembly complex involved in regulation of histone gene transcription; involved in position-dependent gene silencing and nucleosome reassembly; ortholog of human CABIN1 protein | Core | NA | NA | NA |