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 |
|---|---|---|---|---|---|---|---|---|
| 5843-YLR386W_NumOfGenes_2 | YLR386W | VAC14 | NA | Enzyme regulator; involved in synthesis of phosphatidylinositol 3,5-bisphosphate, in control of trafficking of some proteins to the vacuole lumen via the MVB, and in maintenance of vacuole size and acidity; binds negative (Fig4p) and positive (Fab1p) regulators of PtdIns(3,5)P(2) to control endolysosome function; similar to mammalian Vac14p | Core | NA | NA | NA |
| 5844-YLR387C_NumOfGenes_2 | YLR387C | REH1 | NA | Cytoplasmic 60S subunit biogenesis factor; associates with pre-60S particles; similar to Rei1p and shares partially redundant function in cytoplasmic 60S subunit maturation; contains dispersed C2H2 zinc finger domains | Accessory | Ancestral | NA | NA |
| 5845-YLR388W_NumOfGenes_2 | YLR388W | RPS29A | uS14|ribosomal 40S subunit protein S29A|S14|YS29|S36A|S29A|YS29A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S29 and bacterial S14; RPS29A has a paralog, RPS29B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5846-YLR389C_NumOfGenes_2 | YLR389C | STE23 | metalloendopeptidase | Metalloprotease; involved in N-terminal processing of pro-a-factor to mature form; expressed in both haploids and diploids; one of two yeast homologs of human insulin-degrading enzyme (hIDE); homolog Axl1p is also involved in processing of pro-a-factor | Core | NA | NA | NA |
| 5847-YLR390W_NumOfGenes_2 | YLR390W | ECM19 | NA | Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 5848-YLR390W-A_NumOfGenes_2 | YLR390W-A | CCW14 | ICWP|YLR391W|SSR1|YLR391W-A | Covalently linked cell wall glycoprotein; present in the inner layer of the cell wall | Core | NA | NA | NA |
| 5849-YLR392C_NumOfGenes_2 | YLR392C | ART10 | NA | Protein of unknown function that contains 2 PY motifs; ubiquinated by Rsp5p; overexpression confers resistance to arsenite; green fluorescent protein (GFP)-fusion protein localizes it to the cytoplasm; non-essential gene | Core | NA | NA | NA |
| 5850-YLR393W_NumOfGenes_2 | YLR393W | ATP10 | NA | Assembly factor for the F0 sector of mitochondrial F1F0 ATP synthase; mitochondrial inner membrane protein; interacts genetically with ATP6 | Core | NA | NA | NA |
| 5851-YLR394W_NumOfGenes_2 | YLR394W | CST9 | SUMO ligase CST9|ZIP3 | SUMO E3 ligase; required for synaptonemal complex formation; localizes to synapsis initiation sites on meiotic chromosomes; associates with centromeres early in meiosis, then with chromosome axes and finally with double-strand break sites that are engaged in repair by crossovers; potential Cdc28p substrate | Core | NA | NA | NA |
| 5852-YLR395C_NumOfGenes_2 | YLR395C | COX8 | cytochrome c oxidase subunit VIII | Subunit VIII of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain | Core | NA | NA | NA |
| 5853-YLR396C_NumOfGenes_2 | YLR396C | VPS33 | tethering complex ATP-binding subunit VPS33|VPT33|VPL25|VAM5|SLP1|PEP14|MET27|CLS14 | ATP-binding protein that is a subunit of the HOPS and CORVET complexes; essential for protein sorting, vesicle docking, and fusion at the vacuole; binds to SNARE domains | Core | NA | NA | NA |
| 5854-YLR397C_NumOfGenes_2 | YLR397C | AFG2 | AAA family ATPase AFG2|DRG1 | ATPase of the CDC48/PAS1/SEC18 (AAA) family, forms a hexameric complex; is essential for pre-60S maturation and release of several preribosome maturation factors; releases Rlp24p from purified pre-60S particles in vitro; target of the ribosomal biosynthesis inhibitor diazaborine; may be involved in degradation of aberrant mRNAs | Core | NA | NA | NA |
| 5855-YLR398C_NumOfGenes_2 | YLR398C | SKI2 | SKI complex RNA helicase subunit SKI2 | Ski complex component and putative RNA helicase; mediates 3'-5' RNA degradation by the cytoplasmic exosome; null mutants have superkiller phenotype of increased viral dsRNAs and are synthetic lethal with mutations in 5'-3' mRNA decay; mutations in the human ortholog, SKIV2L, causes Syndromic diarrhea/Trichohepatoenteric (SD/THE) syndrome | Core | NA | NA | NA |
| 5856-YLR399C_NumOfGenes_3 | YLR399C | BDF1 | chromatin-binding protein BDF1 | Protein involved in transcription initiation; functions at TATA-containing promoters; associates with the basal transcription factor TFIID; contains two bromodomains; corresponds to the C-terminal region of mammalian TAF1; redundant with Bdf2p; BDF1 has a paralog, BDF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5857-YLR400W | YLR400W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |