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 |
|---|---|---|---|---|---|---|---|---|
| 6773-YNR054C | YNR054C | ESF2 | RNA-binding ATPase activator ESF2|ABT1 | Essential nucleolar protein involved in pre-18S rRNA processing; binds to RNA and stimulates ATPase activity of Dbp8; involved in assembly of the small subunit (SSU) processome | Core | NA | NA | NA |
| 6774-YNR055C | YNR055C | HOL1 | NA | Putative transporter in the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; mutations in membrane-spanning domains permit cation and histidinol uptake | Core | NA | NA | NA |
| 6775-YNR056C | YNR056C | BIO5 | NA | Putative transmembrane protein involved in the biotin biosynthesis; responsible for uptake of 7-keto 8-aminopelargonic acid; BIO5 is in a cluster of 3 genes (BIO3, BIO4, and BIO5) that mediate biotin synthesis | Core | NA | NA | NA |
| 6776-YNR057C | YNR057C | BIO4 | dethiobiotin synthase | Dethiobiotin synthetase; catalyzes the third step in the biotin biosynthesis pathway; BIO4 is in a cluster of 3 genes (BIO3, BIO4, and BIO5) that mediate biotin synthesis; BIO3 and BIO4 were acquired by horizontal gene transfer (HGT) from bacteria; expression appears to be repressed at low iron levels | Core | NA | NA | NA |
| 6777-YNR058W | YNR058W | BIO3 | adenosylmethionine-8-amino-7-oxononanoate transaminase | 7,8-diamino-pelargonic acid aminotransferase (DAPA); catalyzes the second step in the biotin biosynthesis pathway; BIO3 is in a cluster of 3 genes (BIO3, BIO4, and BIO5) that mediate biotin synthesis; BIO3 and BIO4 were acquired by horizontal gene transfer (HGT) from bacteria | Core | NA | NA | NA |
| 6778-YNR059W | YNR059W | MNT4 | putative alpha-1,3-mannosyltransferase | Putative alpha-1,3-mannosyltransferase; not required for protein O-glycosylation; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Accessory | Ancestral | NA | NA |
| 6779-YNR060W | YNR060W | FRE4 | ferric-chelate reductase | Ferric reductase; reduces a specific subset of siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels | Accessory | Ancestral | NA | NA |
| 6780-YNR061C | YNR061C | NA | NA | Protein of unknown function; relocalizes from vacuole to cytoplasm upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 6781-YNR062C | YNR062C | NA | NA | Putative membrane protein of unknown function | Accessory | Ancestral | NA | NA |
| 6782-YNR063W | YNR063W | NA | NA | Putative zinc-cluster protein of unknown function | Accessory | Ancestral | NA | NA |
| 6783-YNR064C | YNR064C | NA | epoxide hydrolase | Epoxide hydrolase; member of the alpha/beta hydrolase fold family; may have a role in detoxification of epoxides | Accessory | Ancestral | NA | NA |
| 6784-YNR065C | YNR065C | NA | YSN1 | Protein of unknown function; protein-protein interactions suggest a possible role in actin patch formation; YNR065C is not an essential gene | Accessory | Unknown | S. paradoxus | NA |
| 6785-YNR066C | YNR066C | NA | NA | Putative membrane-localized protein of unknown function | Accessory | Ancestral | NA | NA |
| 6786-YNR067C_NumOfGenes_2 | YNR067C | DSE4 | endo-1,3(4)-beta-glucanase|ENG1 | Daughter cell-specific secreted protein with similarity to glucanases; degrades cell wall from the daughter side causing daughter to separate from mother | Accessory | Ancestral | NA | NA |
| 6787-YNR068C_NumOfGenes_2 | YNR068C | NA | BUL3 | Putative protein of unknown function; exhibits homology to C-terminal end of Bul1p; expressed as a readthrough product of BSC5, the readthrough locus being termed BUL3; the BUL3 readthrough product is involved in ubiquitin-mediated sorting of plasma membrane proteins and interacts with WW domains of Rsp5p in vitro, but in a functionally different way than the non-readthrough form | Accessory | Ancestral | NA | NA |