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 |
|---|---|---|---|---|---|---|---|---|
| 1913-YBL041W_NumOfGenes_2 | YBL041W | PRE7 | proteasome core particle subunit beta 6|PRS3 | Beta 6 subunit of the 20S proteasome | Core | NA | NA | NA |
| 1914-YBL042C_NumOfGenes_2 | YBL042C | FUI1 | uridine permease | High affinity uridine permease, localizes to the plasma membrane; also mediates low but significant transport of the cytotoxic nucleoside analog 5-fluorouridine; not involved in uracil transport; relative distribution to the vacuole increases upon DNA replication stress | Core | NA | NA | NA |
| 1915-YBL043W_NumOfGenes_2 | YBL043W | ECM13 | NA | Non-essential protein of unknown function; induced by treatment with 8-methoxypsoralen and UVA irradiation; ECM13 has a paralog, YJR115W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1916-YBL044W | YBL044W | NA | NA | Putative protein of unknown function; YBL044W is not an essential protein | Core | NA | NA | NA |
| 1917-YBL045C_NumOfGenes_2 | YBL045C | COR1 | ubiquinol--cytochrome-c reductase subunit COR1|QCR1 | Core subunit of the ubiquinol-cytochrome c reductase complex; the ubiquinol-cytochrome c reductase complex (bc1 complex) is a component of the mitochondrial inner membrane electron transport chain | Core | NA | NA | NA |
| 1918-YBL046W_NumOfGenes_2 | YBL046W | PSY4 | HSM6 | Regulatory subunit of protein phosphatase PP4; presence of Psy4p in the PP4 complex (along with catalytic subunit Pph3p and Psy2p) is required for dephosphorylation of the histone variant H2AX, but not for dephosphorylation of Rad53p, during recovery from the DNA damage checkpoint; localization is cell-cycle dependent and regulated by Cdc28p phosphorylation; required for cisplatin resistance; homolog of mammalian R2 | Core | NA | NA | NA |
| 1919-YBL047C_NumOfGenes_2 | YBL047C | EDE1 | BUD15 | Scaffold protein involved in the formation of early endocytic sites; putative regulator of cytokinesis; homo-oligomerization is required for localization to and organization of endocytic sites; has a network of interactions with other endocytic proteins; binds membranes in a ubiquitin-dependent manner; may also bind ubiquitinated membrane-associated proteins; interacts with Cmk2 and functions upstream of CMK2 in regulating non-apoptotic cell death; homolog of mammalian Eps15 | Core | NA | NA | NA |
| 1920-YBL048W | YBL048W | RRT1 | NA | Protein of unknown function; identified in a screen for mutants with increased levels of rDNA transcription; dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 1921-YBL049W_NumOfGenes_2 | YBL049W | MOH1 | NA | Protein of unknown function, essential for stationary phase survival; not required for growth on nonfermentable carbon sources; possibly linked with vacuolar transport | Core | NA | NA | NA |
| 1922-YBL050W_NumOfGenes_2 | YBL050W | SEC17 | RNS3 | Alpha-SNAP cochaperone; SNARE-complex adaptor for Sec18 (NSF) during the disassembly of postfusion cis-SNARE complexes; stimulates the ATPase activity of Sec18p; peripheral membrane protein required for vesicular transport between ER and Golgi, the 'priming' step in homotypic vacuole fusion, and autophagy; similar to mammalian alpha-SNAP | Core | NA | NA | NA |
| 1923-YBL051C_NumOfGenes_2 | YBL051C | PIN4 | MDT1 | Protein involved in G2/M phase progression and response to DNA damage; interacts with Rad53p; contains an RNA recognition motif, a nuclear localization signal, and several SQ/TQ cluster domains; hyperphosphorylated in response to DNA damage | Core | NA | NA | NA |
| 1924-YBL052C_NumOfGenes_3 | YBL052C | SAS3 | KAT6 | Histone acetyltransferase catalytic subunit of NuA3 complex; acetylates histone H3, involved in transcriptional silencing; homolog of the mammalian MOZ proto-oncogene; mutant has aneuploidy tolerance; sas3gcn5 double mutation is lethal | Core | NA | NA | NA |
| 1925-YBL054W_NumOfGenes_2 | YBL054W | TOD6 | PBF1 | PAC motif binding protein involved in rRNA and ribosome biogenesis; subunit of the RPD3L histone deacetylase complex; Myb-like HTH transcription factor; hypophosphorylated by rapamycin treatment in a Sch9p-dependent manner; activated in stochastic pulses of nuclear localization | Accessory | Ancestral | NA | NA |
| 1926-YBL055C_NumOfGenes_2 | YBL055C | NA | 3'-5'-exodeoxyribonuclease|Tat-D | 3'-->5' exonuclease and endonuclease with a possible role in apoptosis; has similarity to mammalian and C. elegans apoptotic nucleases | Core | NA | NA | NA |
| 1927-YBL056W_NumOfGenes_2 | YBL056W | PTC3 | type 2C protein phosphatase PTC3 | Type 2C protein phosphatase (PP2C); dephosphorylates Hog1p (see also Ptc2p) to limit maximal kinase activity induced by osmotic stress; dephosphorylates T169 phosphorylated Cdc28p (see also Ptc2p); role in DNA damage checkpoint inactivation; PTC3 has a paralog, PTC2, that arose from the whole genome duplication | Core | NA | NA | NA |