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 |
|---|---|---|---|---|---|---|---|---|
| 2258-YBR267W_NumOfGenes_2 | YBR267W | REI1 | NA | Cytoplasmic pre-60S factor; required for the correct recycling of shuttling factors Alb1, Arx1 and Tif6 at the end of the ribosomal large subunit biogenesis; involved in bud growth in the mitotic signaling network | Core | NA | NA | NA |
| 2259-YBR268W | YBR268W | MRPL37 | mitochondrial 54S ribosomal protein YmL37|YmL37 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 2260-YBR269C | YBR269C | SDH8 | FMP21 | Protein required for assembly of succinate dehydrogenase; interacts with flavinylated Sdh1p and may function as a chaperone for free Sdh1p, protecting its FAD cofactor from redox reactions before assembly of the complex; soluble protein of the mitochondrial matrix; respiratory defect of null mutant is functionally complemented by Drosophila and human orthologs | Core | NA | NA | NA |
| 2261-YBR270C | YBR270C | BIT2 | NA | Subunit of TORC2 membrane-associated complex; involved in regulation of actin cytoskeletal dynamics during polarized growth and cell wall integrity; interacts with Slm1p and Slm2p, homologous PH domain-containing TORC2 substrates; BIT2 has a paralog, BIT61, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2262-YBR271W | YBR271W | EFM2 | S-adenosylmethionine-dependent methyltransferase | S-adenosylmethionine-dependent methyltransferase; seven-beta-strand lysine methyltransferase which dimethylates translation elongation factor EF2 (Eft1p and Eft2p) at lysine 613 and methylates EF3 (Yef3p) at lysine 187; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; involved in regulation of translational termination; predicted involvement in ribosome biogenesis | Core | NA | NA | NA |
| 2263-YBR272C | YBR272C | HSM3 | NA | Evolutionarily conserved 19S regulatory particle assembly-chaperone; involved in the assembly of the base subcomplex of the 19S proteasomal regulatory particle (RP); involved in DNA mismatch repair during slow growth; weak similarity to Msh1p; structural study suggests Hsm3p is a scaffold protein for Rpt1p-Rpt2p complex formation; ortholog of human 19S subunit S5b | Core | NA | NA | NA |
| 2264-YBR273C | YBR273C | UBX7 | CUI3 | UBX (ubiquitin regulatory X) domain-containing protein; interacts with Cdc48p; UBX7 has a paralog, UBX6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2265-YBR274W | YBR274W | CHK1 | serine/threonine protein kinase CHK1 | Serine/threonine kinase and DNA damage checkpoint effector; mediates cell cycle arrest via phosphorylation of Pds1p; phosphorylated by checkpoint signal transducer Mec1p; homolog of S. pombe and mammalian Chk1 checkpoint kinase | Core | NA | NA | NA |
| 2266-YBR275C | YBR275C | RIF1 | DNA-binding protein RIF1 | Protein that binds to the Rap1p C-terminus; acts synergistically with Rif2p to help control telomere length and establish telomeric silencing; involved in control of DNA replication; contributes to resection of DNA double strand breaks (DSBs); deletion results in telomere elongation | Core | NA | NA | NA |
| 2267-YBR276C | YBR276C | PPS1 | tyrosine/serine/threonine protein phosphatase PPS1 | Protein phosphatase; has specificity for serine, threonine, and tyrosine residues; has a role in the DNA synthesis phase of the cell cycle | Core | NA | NA | NA |
| 2268-YBR278W_NumOfGenes_2 | YBR278W | DPB3 | DNA polymerase epsilon noncatalytic subunit | Third-largest subunit of DNA polymerase II (DNA polymerase epsilon); required to maintain fidelity of chromosomal replication and also for inheritance of telomeric silencing; stabilizes the interaction of Pol epsilon with primer-template DNA, positively affecting the processivity of the polymerase and exonuclease activities of Pol epsilon; mRNA abundance peaks at the G1/S boundary of the cell cycle; DPB3 has a paralog, DLS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2269-YBR279W | YBR279W | PAF1 | NA | Component of the Paf1p complex involved in transcription elongation; binds to and modulates the activity of RNA polymerases I and II; required for expression of a subset of genes, including cell cycle-regulated genes; involved in SER3 repression by helping to maintain SRG1 transcription-dependent nucleosome occupancy; homolog of human PD2/hPAF1 | Core | NA | NA | NA |
| 2270-YBR280C | YBR280C | SAF1 | SCF ubiquitin ligase complex subunit SAF1 | F-Box protein involved in proteasome-dependent degradation of Aah1p; involved in proteasome-dependent degradation of Aah1p during entry of cells into quiescence; interacts with Skp1 | Core | NA | NA | NA |
| 2271-YBR281C | YBR281C | DUG2 | glutamine amidotransferase subunit DUG2 | Component of glutamine amidotransferase (GATase II); forms a complex with Dug3p to degrade glutathione (GSH) and other peptides containing a gamma-glu-X bond in an alternative pathway to GSH degradation by gamma-glutamyl transpeptidase (Ecm38p) | Core | NA | NA | NA |
| 2272-YBR282W | YBR282W | MRPL27 | mitochondrial 54S ribosomal protein YmL27|YmL27 | Mitochondrial ribosomal protein of the large subunit; homolog of human Bcl-2 interacting protein BMRP | Core | NA | NA | NA |