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 |
|---|---|---|---|---|---|---|---|---|
| 4208-YHL015W_NumOfGenes_2 | YHL015W | RPS20 | uS10|ribosomal 40S subunit protein S20|S10|URP2 | Protein component of the small (40S) ribosomal subunit; overproduction suppresses mutations affecting RNA polymerase III-dependent transcription; homologous to mammalian ribosomal protein S20 and bacterial S10 | Core | NA | NA | NA |
| 4209-YHL015W-A | YHL015W-A | NA | NA | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 4210-YHL016C_NumOfGenes_2 | YHL016C | DUR3 | NA | Plasma membrane transporter for both urea and polyamines; expression is highly sensitive to nitrogen catabolite repression and induced by allophanate, the last intermediate of the allantoin degradative pathway | Core | NA | NA | NA |
| 4211-YHL017W_NumOfGenes_2 | YHL017W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein co-localizes with clathrin-coated vesicles; YHL017W has a paralog, PTM1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4212-YHL018W_NumOfGenes_2 | YHL018W | NA | 4a-hydroxytetrahydrobiopterin dehydratase | Putative 4a-hydroxytetrahydrobiopterin dehydratase; green fluorescent protein (GFP)-fusion protein localizes to mitochondria and is induced in response to the DNA-damaging agent MMS | Accessory | Ancestral | NA | NA |
| 4213-YHL019C_NumOfGenes_3 | YHL019C | APM2 | NA | Protein of unknown function; homologous to the medium chain of mammalian clathrin-associated protein complex; involved in vesicular transport | Accessory | Ancestral | NA | NA |
| 4214-YHL020C_NumOfGenes_2 | YHL020C | OPI1 | transcriptional regulator OPI1 | Transcriptional regulator of a variety of genes; phosphorylation by protein kinase A stimulates Opi1p function in negative regulation of phospholipid biosynthetic genes; involved in telomere maintenance; null exhibits disrupted mitochondrial metabolism and low cardiolipin content, strongly correlated with overproduction of inositol; binds to phosphatidic acid | Accessory | Ancestral | NA | NA |
| 4215-YHL021C_NumOfGenes_2 | YHL021C | AIM17 | FMP12 | Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays reduced frequency of mitochondrial genome loss | Core | NA | NA | NA |
| 4216-YHL022C_NumOfGenes_2 | YHL022C | SPO11 | NA | Meiosis-specific protein that initiates meiotic recombination; initiates meiotic recombination by catalyzing the formation of double-strand breaks in DNA via a transesterification reaction; required for homologous chromosome pairing and synaptonemal complex formation | Core | NA | NA | NA |
| 4217-YHL023C_NumOfGenes_2 | YHL023C | NPR3 | RMD11 | Subunit of the Iml1p/SEACIT complex; SEACIT (Iml1p-Npr2p-Npr3p) is a subcomplex of SEAC, a coatomer-related complex that associates dynamically with the vacuole; Npr3p may have a structural or regulatory role, supporting Iml1p function as a GAP for the Rag family GTPase Gtr1p, and leading to inhibition of TORC1 signaling in response to amino acid deprivation; SEACIT is required for non-nitrogen-starvation-induced autophagy; null mutant has meiotic defects; human NPRL3 homolog | Core | NA | NA | NA |
| 4218-YHL024W_NumOfGenes_2 | YHL024W | RIM4 | NA | Putative RNA-binding protein; required for the expression of early and middle sporulation genes | Core | NA | NA | NA |
| 4219-YHL025W | YHL025W | SNF6 | NA | Subunit of the SWI/SNF chromatin remodeling complex; involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2p and Snf5p; relocates to the cytosol under hypoxic conditions | Core | NA | NA | NA |
| 4220-YHL026C | YHL026C | NA | NA | Putative protein of unknown function; transcriptionally regulated by Upc2p via an upstream sterol response element; SWAT-GFP fusion protein localizes to the cell periphery, while mCherry fusion localizes to both the cell periphery and vacuole; YHL026C is not an essential gene; in 2005 the start site was moved 141 nt upstream (see Locus History) | Core | NA | NA | NA |
| 4221-YHL027W | YHL027W | RIM101 | alkaline-responsive transcriptional regulator RIM101|RIM1 | Cys2His2 zinc-finger transcriptional repressor; involved in alkaline responsive gene repression as part of adaptation to alkaline conditions; involved in cell wall assembly; required for alkaline pH-stimulated haploid invasive growth and sporulation; activated by alkaline-dependent proteolytic processing which results in removal of the C-terminal tail; similar to A. nidulans PacC | Core | NA | NA | NA |
| 4222-YHL028W | YHL028W | WSC4 | YFW1|YHC8 | Endoplasmic reticulum (ER) membrane protein; involved in the translocation of soluble secretory proteins and insertion of membrane proteins into the ER membrane; may also have a role in the stress response but has only partial functional overlap with WSC1-3 | Core | NA | NA | NA |