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 |
|---|---|---|---|---|---|---|---|---|
| 2873-YDR181C | YDR181C | SAS4 | NA | Subunit of the SAS complex (Sas2p, Sas4p, Sas5p); acetylates free histones and nucleosomes and regulates transcriptional silencing; required for the HAT activity of Sas2p | Core | NA | NA | NA |
| 2874-YDR182W | YDR182W | CDC1 | putative lipid phosphatase CDC1|ESP2|DSR1|DSC1 | Putative mannose-ethanolamine phosphate phosphodiesterase; involved in GPI-anchor remodeling prior to the attachment of cell wall proteins to beta 1,3-glucan, removing ethanolamine phosphate from the first mannose of GPI anchors; mutants display elevated Ca2+-dependent signaling resulting in secondary actin polarization and Golgi inheritance defects; enzyme is Mn2+-dependent; mutants have cell division cycle defect and fragile cell walls | Core | NA | NA | NA |
| 2875-YDR182W-A | YDR182W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 2876-YDR183C-A | YDR183C-A | NA | NA | Dubious open reading frame unlikely to encode a functional protein; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 2877-YDR183W | YDR183W | PLP1 | NA | Protein that interacts with CCT (chaperonin containing TCP-1) complex; has a role in actin and tubulin folding; has weak similarity to phosducins, which are G-protein regulators | Core | NA | NA | NA |
| 2878-YDR184C | YDR184C | ATC1 | LIC4 | Nuclear protein; possibly involved in regulation of cation stress responses and/or in the establishment of bipolar budding pattern; relative distribution to the nucleus decreases upon DNA replication stress | Core | NA | NA | NA |
| 2879-YDR185C | YDR185C | UPS3 | GEP2 | Mitochondrial protein of unknown function; similar to Ups1p and Ups2p which are involved in regulation of mitochondrial cardiolipin and phosphatidylethanolamine levels; null is viable but interacts synthetically with ups1 and ups2 mutations; UPS3 has a paralog, UPS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2880-YDR186C | YDR186C | SND1 | NA | Protein involved in SRP-independent targeting of substrates to the ER; component of an alternative ER targeting pathway that has partial functional redundancy with the GET pathway; preference for substrates with downstream transmembrane domains; interacts with Env10p/Snd2p and Pho88p/Snd3p; can compensate for loss of SRP; may interact with ribosomes, based on co-purification experiments; GFP-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 2881-YDR187C | YDR187C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified, essential ORF CCT6/YDR188W | Accessory | Ancestral | NA | NA |
| 2882-YDR188W | YDR188W | CCT6 | chaperonin-containing T-complex subunit CCT6|TCP20|TCP6|HTR3 | Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, essential protein that is required for the assembly of actin and tubulins in vivo; contains an ATP-binding motif | Core | NA | NA | NA |
| 2883-YDR189W | YDR189W | SLY1 | syntaxin-binding protein | Hydrophilic protein involved in ER/Golgi vesicle trafficking; SM (Sec1/Munc-18) family protein that binds the tSNARE Sed5p and stimulates its assembly into a trans-SNARE membrane-protein complex | Core | NA | NA | NA |
| 2884-YDR190C | YDR190C | RVB1 | RuvB family ATP-dependent DNA helicase pontin|TIP49|TIH1|TIP49A | ATP-dependent DNA helicase, also known as pontin; member of the AAA+ and RuvB-like protein families; similar to Rvb2p; conserved component of multiple complexes including the INO80 complex, the Swr1 complex, and the R2TP complex (Rvb1-Rvb2-Tah1-Pih1); involved in multiple processes such as chromatin remodeling, box C/D snoRNP assembly, and RNA polymerase II assembly | Core | NA | NA | NA |
| 2885-YDR191W | YDR191W | HST4 | NAD-dependent histone deacetylase HST4 | NAD(+)-dependent protein deacetylase; deacetylation targets are primarily mitochondrial proteins; involved along with Hst3p in silencing at telomeres, cell cycle progression, radiation resistance, genomic stability and short-chain fatty acid metabolism; accumulates in mitochondria in response to biotin starvation and may link biotin metabolism with energy homeostasis; member of the Sir2 family and may be the functional equivalent of human SIRT3 | Core | NA | NA | NA |
| 2886-YDR192C_NumOfGenes_2 | YDR192C | NUP42 | FG-nucleoporin NUP42|UIP1|RIP1 | FG-nucleoporin component of central core of the nuclear pore complex; also part of the nuclear pore complex (NPC) cytoplasmic filaments; contributes directly to nucleocytoplasmic transport and maintenance of the NPC permeability barrier and is involved in gene tethering at the nuclear periphery; interacts with Gle1p | Core | NA | NA | NA |
| 2887-YDR194C | YDR194C | MSS116 | ATP-dependent RNA helicase | Mitochondrial transcription elongation factor; DEAD-box protein; required for efficient splicing of mitochondrial Group I and II introns; non-polar RNA helicase that also facilities strand annealing; promotes RNA folding by stabilizing an early assembly intermediate | Core | NA | NA | NA |