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 |
|---|---|---|---|---|---|---|---|---|
| 6143-YMR086C-A | YMR086C-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 |
| 6144-YMR086W | YMR086W | SEG1 | NA | Component of eisosome required for proper eisosome assembly; precedes Pil1p/Lsp1p during eisosome formation, controls eisosome length and shape; diffusely distributed, forms heterogeneous patches at plasma membrane in small buds, also found in medium and large buds; expression repressed by cAMP; similar to A. gossypii SEG gene and to S. pombe Sle1p, important for generating eisosomes; SEG1 has a paralog, SEG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6145-YMR087W | YMR087W | NA | putative ADP-ribose 1''-phosphate phosphatase | Putative ADP-ribose-1''-monophosphatase; converts ADP-ribose-1''-monophosphate to ADP-ribose; may have a role in tRNA splicing; contains an A1pp domain | Core | NA | NA | NA |
| 6146-YMR088C | YMR088C | VBA1 | NA | Permease of basic amino acids in the vacuolar membrane | Core | NA | NA | NA |
| 6147-YMR089C | YMR089C | YTA12 | m-AAA protease subunit YTA12|RCA1 | Mitochondrial inner membrane m-AAA protease component; mediates degradation of misfolded or unassembled proteins; also required for correct assembly of mitochondrial enzyme complexes; overexpression of human AFG3L2 complements respiratory defect of yeast afg3 yta12 double null mutation, but overexpression of disease-associated AFG3L2 variants does not; expression of both human SPG7 (paraplegin) and AFG3L2 complements yeast yta12 afg3 double mutation | Core | NA | NA | NA |
| 6148-YMR090W | YMR090W | NA | NA | Putative protein of unknown function; similar to DTDP-glucose 4,6-dehydratases; GFP-fusion protein localizes to the cytoplasm; up-regulated in response to the fungicide mancozeb; not essential for viability | Core | NA | NA | NA |
| 6149-YMR091C | YMR091C | NPL6 | RSC7 | Component of the RSC chromatin remodeling complex; interacts with Rsc3p, Rsc30p, Ldb7p, and Htl1p to form a module important for a broad range of RSC functions | Core | NA | NA | NA |
| 6150-YMR092C | YMR092C | AIP1 | NA | Actin cortical patch component; interacts with the actin depolymerizing factor cofilin; inhibits elongation of aged ADP-actin filaments decorated with cofilin to maintain a high level of assembly-competent actin species; required to restrict cofilin localization to cortical patches; putative regulator of cytokinesis; contains WD repeats; protein increases in abundance and relocalizes from cytoplasm to plasma membrane upon DNA replication stress | Core | NA | NA | NA |
| 6151-YMR093W | YMR093W | UTP15 | snoRNA-binding rRNA-processing protein UTP15 | Nucleolar protein; component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA | Core | NA | NA | NA |
| 6152-YMR094W | YMR094W | CTF13 | CBF3C | Subunit of the CBF3 complex; CBF3 binds to the CDE III element of centromeres, bending the DNA upon binding, and may be involved in sister chromatid cohesion during mitosis | Core | NA | NA | NA |
| 6153-YMR095C | YMR095C | SNO1 | putative pyridoxal 5'-phosphate synthase | Protein of unconfirmed function; involved in pyridoxine metabolism; expression is induced during stationary phase; forms a putative glutamine amidotransferase complex with Snz1p, with Sno1p serving as the glutaminase | Core | NA | NA | NA |
| 6154-YMR096W | YMR096W | SNZ1 | pyridoxine biosynthesis protein SNZ1 | Protein involved in vitamin B6 biosynthesis; member of a stationary phase-induced gene family; coregulated with SNO1; interacts with Sno1p and with Yhr198p, perhaps as a multiprotein complex containing other Snz and Sno proteins | Core | NA | NA | NA |
| 6155-YMR097C | YMR097C | MTG1 | putative GTPase MTG1 | Putative GTPase peripheral to the mitochondrial inner membrane; essential for respiratory competence, likely functions in assembly of the large ribosomal subunit, has homologs in plants and animals | Core | NA | NA | NA |
| 6156-YMR098C | YMR098C | ATP25 | LRC4 | Mitochondrial protein required for the stability of Oli1p (Atp9p) mRNA; also required for the Oli1p ring formation; YMR098C is not an essential gene | Core | NA | NA | NA |
| 6157-YMR099C | YMR099C | NA | glucose-6-phosphate 1-epimerase | Glucose-6-phosphate 1-epimerase (hexose-6-phosphate mutarotase); likely involved in carbohydrate metabolism; GFP-fusion protein localizes to both the nucleus and cytoplasm and is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |