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 |
|---|---|---|---|---|---|---|---|---|
| 5138-YKL066W | YKL066W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; partially overlaps the verified gene YNK1 | Core | NA | NA | NA |
| 5139-YKL067W | YKL067W | YNK1 | nucleoside diphosphate kinase|NDK1 | Nucleoside diphosphate kinase; catalyzes the transfer of gamma phosphates from nucleoside triphosphates, usually ATP, to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5140-YKL068W | YKL068W | NUP100 | FG-nucleoporin NUP100|[NUP100+]|NSP100 | FG-nucleoporin component of central core of the nuclear pore complex; contributes directly to nucleocytoplasmic transport and maintenance of the nuclear pore complex (NPC) permeability barrier and is involved in gene tethering at the nuclear periphery; NUP100 has a paralog, NUP116, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5141-YKL068W-A | YKL068W-A | NA | NA | Putative protein of unknown function; identified by homology to <i>Ashbya gossypii</i> | Core | NA | NA | NA |
| 5142-YKL069W_NumOfGenes_2 | YKL069W | NA | L-methionine (R)-S-oxide reductase|fRMsr|YKG9 | Methionine-R-sulfoxide reductase; reduces the R enantiomer of free Met-SO, in contrast to Ycl033Cp which reduces Met-R-SO in a peptide linkage; has a role in protection against oxidative stress; relative distribution to the nucleus increases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5143-YKL070W | YKL070W | NA | NA | Putative protein of unknown function; expression induced in cells treated with mycotoxins patulin or citrinin; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 5144-YKL071W_NumOfGenes_2 | YKL071W | NA | NA | Putative protein of unknown function; expression induced in cells treated with the mycotoxin patulin, and also the quinone methide triterpene celastrol; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
| 5145-YKL072W | YKL072W | STB6 | NA | Protein that binds Sin3p in a two-hybrid assay; STB6 has a paralog, STB2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5146-YKL073W | YKL073W | LHS1 | Hsp70 family chaperone LHS1|SSI1|CER1 | Molecular chaperone of the endoplasmic reticulum lumen; involved in polypeptide translocation and folding; nucleotide exchange factor for the ER lumenal Hsp70 chaperone Kar2p; regulated by the unfolded protein response pathway | Core | NA | NA | NA |
| 5147-YKL074C | YKL074C | MUD2 | NA | Protein involved in early pre-mRNA splicing; component of the pre-mRNA-U1 snRNP complex, the commitment complex; interacts with Msl5p/BBP splicing factor and Sub2p; similar to metazoan splicing factor U2AF65 | Core | NA | NA | NA |
| 5148-YKL075C | YKL075C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; proposed to be involved in resistance to streptozotocin and camptothecin | Core | NA | NA | NA |
| 5149-YKL076C | YKL076C | PSY1 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; 69% of ORF overlaps the uncharacterized ORF YKL075C | Accessory | Ancestral | NA | NA |
| 5150-YKL077W | YKL077W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole | Core | NA | NA | NA |
| 5151-YKL078W | YKL078W | DHR2 | RNA helicase | Predominantly nucleolar DEAH-box ATP-dependent RNA helicase; required for 18S rRNA synthesis | Core | NA | NA | NA |
| 5152-YKL079W | YKL079W | SMY1 | NA | Kinesin-like myosin passenger-protein; interacts with Myo2p and enhances its interaction with Sec4p during transport of secretory vesicles; controls actin cable structure and dynamics | Core | NA | NA | NA |