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 |
|---|---|---|---|---|---|---|---|---|
| 2933-YDR242W | YDR242W | AMD2 | putative amidase | Putative amidase | Core | NA | NA | NA |
| 2934-YDR243C | YDR243C | PRP28 | mRNA splicing protein PRP28 | RNA binding protein; involved in RNA isomerization at the 5' splice site and for exchange of U6 for U1 snRNA at the 5' splice site; similar to the RNA helicases of the DEAD-box family | Core | NA | NA | NA |
| 2935-YDR244W | YDR244W | PEX5 | PAS10 | Peroxisomal membrane signal receptor for peroxisomal matrix proteins; receptor for the C-terminal tripeptide signal sequence (PTS1) of peroxisomal matrix proteins; required for peroxisomal matrix protein import; also proposed to have PTS1-receptor independent functions | Core | NA | NA | NA |
| 2936-YDR245W | YDR245W | MNN10 | alpha-1,6-mannosyltransferase|REC41|SLC2|BED1 | Subunit of a Golgi mannosyltransferase complex; complex mediates elongation of the polysaccharide mannan backbone; membrane protein of the mannosyltransferase family; other members of the complex are Anp1p, Mnn9p, Mnn11p, and Hoc1p | Core | NA | NA | NA |
| 2937-YDR246W | YDR246W | TRS23 | TRAPP subunit TRS23 | Core component of transport protein particle (TRAPP) complexes I-III; TRAPP complexes are related multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating ER-Golgi traffic (TRAPPI), intra-Golgi traffic (TRAPPII), endosome-Golgi traffic (TRAPPII and III) and autophagy (TRAPPIII); human homolog is TRAPPC4 | Core | NA | NA | NA |
| 2938-YDR246W-A | YDR246W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 2939-YDR247W | YDR247W | VHS1 | putative serine/threonine protein kinase VHS1 | Cytoplasmic serine/threonine protein kinase; identified as a high-copy suppressor of the synthetic lethality of a sis2 sit4 double mutant, suggesting a role in G1/S phase progression; VHS1 has a paralog, SKS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2940-YDR248C | YDR248C | NA | gluconokinase | Putative gluconokinase; sequence similarity to bacterial and human gluconokinase; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; upregulated by deletion of the RNAP-II associated factor, PAF1 | Core | NA | NA | NA |
| 2941-YDR249C | YDR249C | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 2942-YDR250C | YDR250C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 2943-YDR251W | YDR251W | PAM1 | NA | Essential protein of unknown function; exhibits variable expression during colony morphogenesis; overexpression permits survival without protein phosphatase 2A, inhibits growth, and induces a filamentous phenotype; PAM1 has a paralog, SVL3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2944-YDR252W | YDR252W | BTT1 | CCR4-NOT core subunit BTT1 | Heterotrimeric nascent polypeptide-associated complex beta3 subunit; complex binds ribosomes via its beta-subunits in close proximity to nascent polypeptides; interacts with Caf130p of the CCR4-NOT complex; similar to human BTF3; BTT1 has a paralog, EGD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2945-YDR253C | YDR253C | MET32 | NA | Zinc-finger DNA-binding transcription factor; involved in transcriptional regulation of the methionine biosynthetic genes; targets strong transcriptional activator Met4p to promoters of sulfur metabolic genes; feedforward loop exists in the regulation of genes controlled by Met4p and Met32p; lack of such a loop for MET31 may account for the differential actions of Met32p and Met31p; MET32 has a paralog, MET31, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2946-YDR254W | YDR254W | CHL4 | MCM17|CTF17 | Outer kinetochore protein required for chromosome stability; involved in new kinetochore assembly and sister chromatid cohesion; forms a stable complex with Iml3p; peripheral component of the Ctf19 kinetochore complex that interacts with Ctf19p, Ctf3p, and Mif2p; required for the spindle assembly checkpoint; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-N and fission yeast mis15 | Core | NA | NA | NA |
| 2947-YDR255C | YDR255C | RMD5 | ubiquitin-protein ligase RMD5|GID2 | Component of GID Complex that confers ubiquitin ligase (U3) activity; necessary for polyubiquitination and degradation of the gluconeogenic enzyme fructose-1,6-bisphosphatase; forms dimer with Fyv10p that is then recruited to GID Complex by Gid8p; also required for sporulation; conserved protein that has a degenerate RING finger domain | Core | NA | NA | NA |