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 |
|---|---|---|---|---|---|---|---|---|
| 5768-YLR308W | YLR308W | CDA2 | chitin deacetylase CDA2 | Chitin deacetylase; together with Cda1p involved in the biosynthesis ascospore wall component, chitosan; required for proper rigidity of the ascospore wall | Core | NA | NA | NA |
| 5769-YLR309C | YLR309C | IMH1 | SYS3 | Protein involved in vesicular transport; mediates transport between an endosomal compartment and the Golgi, contains a Golgi-localization (GRIP) domain that interacts with activated Arl1p-GTP to localize Imh1p to the Golgi | Core | NA | NA | NA |
| 5770-YLR310C | YLR310C | CDC25 | Ras family guanine nucleotide exchange factor CDC25|CDC25'|CTN1 | Membrane bound guanine nucleotide exchange factor; also known as a GEF or GDP-release factor; indirectly regulates adenylate cyclase through activation of Ras1p and Ras2p by stimulating the exchange of GDP for GTP; required for progression through G1; thermosensitivity of the cdc25-5 mutant is functionally complemented by human RASGRF1 or by a fragment of human SOS1 comprising the CDC25-related catalytic domain | Core | NA | NA | NA |
| 5771-YLR311C | YLR311C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5772-YLR312C | YLR312C | ATG39 | QNQ1 | Autophagy receptor with a role in degradation of the ER and nucleus; involved specifically in autophagy of perinuclear endoplasmic reticulum in response to nitrogen starvation or rapamycin treatment; localizes to the perinuclear ER | Core | NA | NA | NA |
| 5773-YLR312W-A | YLR312W-A | MRPL15 | mitochondrial 54S ribosomal protein YmL15|YmL15 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 5774-YLR313C | YLR313C | SPH1 | YLR312C-B | Protein involved in shmoo formation and bipolar bud site selection; localizes to sites of polarized growth in a cell cycle dependent- and Spa2p-dependent manner, interacts with MAPKKs Mkk1p, Mkk2p, and Ste7p; SPH1 has a paralog, SPA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5775-YLR314C | YLR314C | CDC3 | septin CDC3 | Component of the septin ring that is required for cytokinesis; septins are GTP-binding proteins that assemble with other septins into rod-like complexes that can associate with other rods to form filament polymers; septin rings at the mother-bud neck act as scaffolds for recruiting factors needed for cell division and as barriers to prevent diffusion of specific proteins between mother and daughter cells | Core | NA | NA | NA |
| 5776-YLR315W | YLR315W | NKP2 | NA | Central kinetochore protein and subunit of the Ctf19 complex; mutants have elevated rates of chromosome loss; orthologous to fission yeast kinetochore protein cnl2 | Core | NA | NA | NA |
| 5777-YLR316C_NumOfGenes_2 | YLR316C | TAD3 | NA | Subunit of tRNA-specific adenosine-34 deaminase; forms a heterodimer with Tad2p that converts adenosine to inosine at the wobble position of several tRNAs | Core | NA | NA | NA |
| 5778-YLR318W | YLR318W | EST2 | TERT | Reverse transcriptase subunit of the telomerase holoenzyme; essential for telomerase core catalytic activity, involved in other aspects of telomerase assembly and function; mutations in human homolog are associated with aplastic anemia | Core | NA | NA | NA |
| 5779-YLR319C | YLR319C | BUD6 | AIP3 | Actin- and formin-interacting protein; participates in actin cable assembly and organization as a nucleation-promoting factor (NPF) for formins Bni1p and Bnr1p; a triple helical coiled-coil domain in the C-terminal region interacts with Bni1p; involved in polarized cell growth; isolated as bipolar budding mutant; potential Cdc28p substrate | Core | NA | NA | NA |
| 5780-YLR320W | YLR320W | MMS22 | SLM2 | Subunit of E3 ubiquitin ligase complex involved in replication repair; stabilizes protein components of the replication fork, such as the fork-pausing complex and leading strand polymerase, preventing fork collapse and promoting efficient recovery during replication stress; required for accurate meiotic chromosome segregation | Core | NA | NA | NA |
| 5781-YLR321C_NumOfGenes_2 | YLR321C | SFH1 | NA | Component of the RSC chromatin remodeling complex; essential gene required for cell cycle progression and maintenance of proper ploidy; phosphorylated in the G1 phase of the cell cycle; Snf5p paralog; hSNF5 tumor suppressor ortholog | Core | NA | NA | NA |
| 5782-YLR323C | YLR323C | CWC24 | U2-type spliceosomal complex subunit CWC24 | General splicing factor; required for stable U2 snRNP binding to primary transcripts; essential for the first step of splicing; component of the pre-catalytic spliceosome complex containing Cef1p; similar to S. pombe Cwf24p | Core | NA | NA | NA |