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 |
|---|---|---|---|---|---|---|---|---|
| 4298-YHR047C | YHR047C | AAP1 | arginine/alanine aminopeptidase|AAP1' | Arginine/alanine amino peptidase; overproduction stimulates glycogen accumulation; AAP1 has a paralog, APE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4299-YHR048W | YHR048W | YHK8 | NA | Presumed antiporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; expression of gene is up-regulated in cells exhibiting reduced susceptibility to azoles | Core | NA | NA | NA |
| 4300-YHR049C-A | YHR049C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4301-YHR049W | YHR049W | FSH1 | putative serine hydrolase | Putative serine hydrolase; localizes to both the nucleus and cytoplasm; sequence is similar to S. cerevisiae Fsh2p and Fsh3p and the human candidate tumor suppressor OVCA2 | Core | NA | NA | NA |
| 4302-YHR050W | YHR050W | SMF2 | divalent metal ion transporter SMF2 | Divalent metal ion transporter involved in manganese homeostasis; has broad specificity for di-valent and tri-valent metals; post-translationally regulated by levels of metal ions; member of the Nramp family of metal transport proteins | Core | NA | NA | NA |
| 4303-YHR050W-A | YHR050W-A | NA | NA | Protein of unknown function; identified by expression profiling and mass spectrometry | Core | NA | NA | NA |
| 4304-YHR051W | YHR051W | COX6 | cytochrome c oxidase subunit VI | Subunit VI of cytochrome c oxidase (Complex IV); Complex IV is the terminal member of the mitochondrial inner membrane electron transport chain; expression is regulated by oxygen levels | Core | NA | NA | NA |
| 4305-YHR052W | YHR052W | CIC1 | NSA3 | Essential protein that interacts with proteasome components; has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles | Core | NA | NA | NA |
| 4306-YHR055C_NumOfGenes_4 | YHR055C | CUP1-2 | metallothionein CUP1|CUP1 | Metallothionein; binds copper and mediates resistance to high concentrations of copper and cadmium; locus is variably amplified in different strains, with two copies, CUP1-1 and CUP1-2, in the genomic sequence reference strain S288C; CUP1-2 has a paralog, CUP1-1, that arose from a segmental duplication | Core | NA | NA | NA |
| 4307-YHR056C_NumOfGenes_3 | YHR056C | RSC30 | NA | Component of the RSC chromatin remodeling complex; non-essential gene required for regulation of ribosomal protein genes and the cell wall/stress response; null mutants are osmosensitive; RSC30 has a paralog, RSC3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4308-YHR057C | YHR057C | CPR2 | peptidylprolyl isomerase CPR2|CYP2 | Peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; potential role in the secretory pathway; seamless-GFP and mCherry fusion proteins localize to the vacuole, while SWAT-GFP fusion localizes to both the endoplasmic reticulum and vacuole; suppresses toxicity of slow-folding human Z-type alpha1-antitrypsin variant associated with liver cirrhosis and emphysema | Accessory | Ancestral | NA | NA |
| 4309-YHR058C | YHR058C | MED6 | mediator complex subunit MED6 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4310-YHR059W | YHR059W | FYV4 | NA | Protein of unknown function; required for survival upon exposure to K1 killer toxin | Core | NA | NA | NA |
| 4311-YHR060W | YHR060W | VMA22 | VPH6|CEV1 | Protein that is required for vacuolar H+-ATPase (V-ATPase) function; peripheral membrane protein; not an actual component of the V-ATPase complex; functions in the assembly of the V-ATPase; localized to the yeast endoplasmic reticulum (ER) | Core | NA | NA | NA |
| 4312-YHR061C | YHR061C | GIC1 | NA | Protein involved in initiation of budding and cellular polarization; interacts with Cdc42p via the Cdc42/Rac-interactive binding (CRIB) domain; relocalizes from bud neck to nucleus upon DNA replication stress; GIC1 has a paralog, GIC2, that arose from the whole genome duplication | Core | NA | NA | NA |