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 |
|---|---|---|---|---|---|---|---|---|
| 2213-YBR223C_NumOfGenes_2 | YBR223C | TDP1 | tyrosyl-DNA phosphodiesterase 1 | Tyrosyl-DNA phosphodiesterase I; hydrolyzes 3' and 5'-phosphotyrosyl bonds; involved in the repair of DNA lesions created by topo I and topo II; mutations in the human homolog, TDP1, result in the a neurodegenerative disease, spinocerebellar ataxia with axonal neuropathy (SCAN1); yeast cells and human rhabdomyosarcoma lines that overexpress TDP1 both exhibit elevated dosage chromosomal instability (dCIN) | Core | NA | NA | NA |
| 2214-YBR224W | YBR224W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene TDP1 | Core | NA | NA | NA |
| 2215-YBR225W | YBR225W | NA | NA | Putative protein of unknown function; non-essential gene identified in a screen for mutants affected in mannosylphophorylation of cell wall components | Core | NA | NA | NA |
| 2216-YBR226C | YBR226C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YBR225W | Accessory | Ancestral | NA | NA |
| 2217-YBR227C | YBR227C | MCX1 | NA | Non-proteolytic ATPase of the AAA family; stimulates incorporation of the pyridoxal phosphate cofactor into Hem1p (5-aminolevulinic acid synthase); localized to the mitochondrial matrix; ortholog of vertebrate CLPX, which promotes erythropoiesis | Core | NA | NA | NA |
| 2218-YBR228W | YBR228W | SLX1 | endonuclease | Endonuclease involved in DNA recombination and repair; subunit of a complex, with Slx4p, that hydrolyzes 5' branches from duplex DNA in response to stalled or converging replication forks; function overlaps with that of Sgs1p-Top3p | Core | NA | NA | NA |
| 2219-YBR229C | YBR229C | ROT2 | glucan 1,3-alpha-glucosidase ROT2|GLS2 | Glucosidase II catalytic subunit; required to trim the final glucose in N-linked glycans; required for normal cell wall synthesis; mutations in rot2 suppress tor2 mutations, and are synthetically lethal with rot1 mutations | Core | NA | NA | NA |
| 2220-YBR230C | YBR230C | OM14 | NA | Mitochondrial outer membrane receptor for cytosolic ribosomes; integral protein of the outer membrane that interacts with the nascent chain-associated complex (NAC) bound to ribosomes, contributing to co-translational mitochondrial import; interacts with porin (Por1p) and Om45p; abundance is decreased in cells grown in glucose relative to other carbon sources | Core | NA | NA | NA |
| 2221-YBR230W-A | YBR230W-A | NA | NA | Putative protein of unknown function; YBR230W-A has a paralog, COQ8, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2222-YBR231C | YBR231C | SWC5 | AOR1 | Component of the SWR1 complex; complex exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2223-YBR233W_NumOfGenes_2 | YBR233W | PBP2 | HEK1 | RNA binding protein; has similarity to mammalian heterogeneous nuclear RNP K protein, involved in the regulation of telomere position effect and telomere length; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2224-YBR233W-A | YBR233W-A | DAD3 | NA | Essential subunit of the Dam1 complex (aka DASH complex); complex couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; is transferred to the kinetochore prior to mitosis | Core | NA | NA | NA |
| 2225-YBR234C | YBR234C | ARC40 | NA | Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches | Core | NA | NA | NA |
| 2226-YBR235W | YBR235W | VHC1 | NA | Vacuolar membrane cation-chloride cotransporter (CCC); likely mediates K+ and Cl- cotransport into the vacuole; has a role in potassium homeostasis and salt tolerance; localizes to sites of contact between the vacuole and mitochondria (vCLAMPs); similar to mammalian electroneutral Na(+)-(K+)-C1- cotransporter family | Core | NA | NA | NA |
| 2227-YBR236C | YBR236C | ABD1 | mRNA (guanine-N7)-methyltransferase | Methyltransferase; catalyzes the transfer of a methyl group from S-adenosylmethionine to the GpppN terminus of capped mRNA; nuclear protein that relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |