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 |
|---|---|---|---|---|---|---|---|---|
| 6098-YMR038C_NumOfGenes_2 | YMR038C | CCS1 | copper chaperone CCS1|LYS7|CCS | Copper chaperone for superoxide dismutase Sod1p; involved in oxidative stress protection; Met-X-Cys-X2-Cys motif within N-terminus is involved in insertion of copper into Sod1p under conditions of copper deprivation; required for regulation of yeast copper genes in response to DNA-damaging agents; protein abundance increases in response to DNA replication stress; human homolog CCS can complement yeast ccs1 null mutant | Accessory | Ancestral | NA | NA |
| 6099-YMR039C | YMR039C | SUB1 | chromatin-binding transcription coactivator SUB1|TSP1 | Transcriptional regulator; facilitates elongation through factors that modify RNAP II; role in peroxide resistance involving Rad2p; role in nonhomologous end-joining (NHEJ) of ds breaks in plasmid DNA, but not chromosomal DNA; role in the hyperosmotic stress response through polymerase recruitment at RNAP II and RNAP III genes; negatively regulates sporulation; protein abundance increases in response to DNA replication stress; functionally complemented by human SUB1 (PC4) | Accessory | Ancestral | NA | NA |
| 6100-YMR040W | YMR040W | YET2 | NA | Protein of unknown function that may interact with ribosomes; based on co-purification experiments; homolog of human BAP31 protein; YET2 has a paralog, YET1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6101-YMR041C | YMR041C | ARA2 | D-arabinose 1-dehydrogenase (NAD(P)(+)) ARA2 | NAD-dependent arabinose dehydrogenase; involved in biosynthesis of dehydro-D-arabinono-1,4-lactone; similar to plant L-galactose dehydrogenase | Accessory | Ancestral | NA | NA |
| 6102-YMR042W | YMR042W | ARG80 | ARGRI|ARGR1 | Transcription factor involved in regulating arginine-responsive genes; acts with Arg81p and Arg82p | Accessory | Ancestral | NA | NA |
| 6103-YMR043W | YMR043W | MCM1 | transcription factor MCM1|FUN80 | Transcription factor; involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes; relocalizes to the cytosol in response to hypoxia | Accessory | Ancestral | NA | NA |
| 6104-YMR044W | YMR044W | IOC4 | NA | Member of a complex (Isw1b) with Isw1p and Ioc2p; interacts directly with H3K36me3 nucleosomes through its PWWP domain to recruit the Isw1b complex to open reading frames in a Set2p-dependent manner; Isw1b exhibits nucleosome-stimulated ATPase activity and acts within coding regions to coordinate transcription elongation with termination and processing | Core | NA | NA | NA |
| 6105-YMR047C | YMR047C | NUP116 | FG-nucleoporin NUP116|NSP116 | FG-nucleoporin component of central core of the nuclear pore complex; contributes directly to nucleocytoplasmic transport and maintenance of the nuclear pore complex (NPC) permeability barrier; forms a stable association with Nup82p, Gle2p and two other FG-nucleoporins (Nsp1p and Nup159p); NUP116 has a paralog, NUP100, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6106-YMR048W | YMR048W | CSM3 | NA | Replication fork associated factor; required for stable replication fork pausing; component of the DNA replication checkpoint pathway; required for accurate chromosome segregation during meiosis; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 6107-YMR049C | YMR049C | ERB1 | NA | Constituent of 66S pre-ribosomal particles; forms a complex with Nop7p and Ytm1p that is required for maturation of the large ribosomal subunit; required for maturation of the 25S and 5.8S ribosomal RNAs; homologous to mammalian Bop1 | Core | NA | NA | NA |
| 6108-YMR052C-A | YMR052C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 6109-YMR052W | YMR052W | FAR3 | NA | Protein of unknown function; involved in recovery from cell cycle arrest in response to pheromone, in a Far1p-independent pathway; interacts with Far7p, Far8p, Far9p, Far10p, and Far11p; localizes to the endoplasmic reticulum; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6110-YMR053C | YMR053C | STB2 | NA | Protein that interacts with Sin3p in a two-hybrid assay; part of a large protein complex with Sin3p and Stb1p; STB2 has a paralog, STB6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6111-YMR054W | YMR054W | STV1 | H(+)-transporting V0 sector ATPase subunit a | Subunit a of the vacuolar-ATPase V0 domain; one of two isoforms (Stv1p and Vph1p); Stv1p is located in V-ATPase complexes of the Golgi and endosomes while Vph1p is located in V-ATPase complexes of the vacuole | Core | NA | NA | NA |
| 6112-YMR055C | YMR055C | BUB2 | PAC7 | Mitotic exit network regulator; forms GTPase-activating Bfa1p-Bub2p complex that binds Tem1p and spindle pole bodies, blocks cell cycle progression before anaphase in response to spindle and kinetochore damage | Core | NA | NA | NA |