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 |
|---|---|---|---|---|---|---|---|---|
| 3278-YEL043W | YEL043W | NA | NA | Predicted cytoskeleton protein involved in intracellular signaling; based on quantitative analysis of protein-protein interaction maps; may interact with ribosomes, based on co-purification studies; contains fibronectin type III domain fold | Core | NA | NA | NA |
| 3279-YEL044W | YEL044W | IES6 | NA | Component of the INO80 chromatin remodeling complex; critical for INO80 function; involved in regulation of chromosome segregation and maintenance of normal centromeric chromatin structure; human ortholog INO80C is a member of the human INO80 complex; implicated in DNA repair based on genetic interactions with RAD52 epistasis genes | Core | NA | NA | NA |
| 3280-YEL045C | YEL045C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; deletion gives MMS sensitivity, growth defect under alkaline conditions, less than optimal growth upon citric acid stress | Core | NA | NA | NA |
| 3281-YEL046C | YEL046C | GLY1 | threonine aldolase GLY1 | Threonine aldolase; catalyzes the cleavage of L-allo-threonine and L-threonine to glycine; involved in glycine biosynthesis | Core | NA | NA | NA |
| 3282-YEL047C | YEL047C | FRD1 | fumarate reductase|FRDS1 | Soluble fumarate reductase; required with isoenzyme Osm1p for anaerobic growth; may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in purified mitochondria in high-throughput studies; similar to Arxula adeninovorans fumarate reductase; protein abundance increases in response to DNA replication stress; FRD1 has a paralog, OSM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3283-YEL048C | YEL048C | TCA17 | NA | Component of transport protein particle (TRAPP) complex II; TRAPPII is a multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating intra-Golgi and endosome-Golgi traffic; promotes association of TRAPPII-specific subunits with the TRAPP core complex; sedlin related; human Sedlin mutations cause SEDT, a skeletal disorder | Core | NA | NA | NA |
| 3284-YEL050C_NumOfGenes_2 | YEL050C | RML2 | mitochondrial 54S ribosomal protein RML2 | Mitochondrial ribosomal protein of the large subunit (L2); has similarity to E. coli L2 ribosomal protein; mutant allele (fat21) causes inability to utilize oleate, and induce oleic acid oxidation; may interfere with activity of the Adr1p transcription factor | Core | NA | NA | NA |
| 3285-YEL050W-A | YEL050W-A | NA | NA | Dubious open reading frame unlikely to encode a functional protein; identified by fungal homology and RT-PCR | Accessory | Ancestral | NA | NA |
| 3286-YEL051W_NumOfGenes_2 | YEL051W | VMA8 | H(+)-transporting V1 sector ATPase subunit D | Subunit D of the V1 peripheral membrane domain of V-ATPase; part of the electrogenic proton pump found throughout the endomembrane system; plays a role in the coupling of proton transport and ATP hydrolysis; the V1 peripheral membrane domain of the vacuolar H+-ATPase (V-ATPase) has eight subunits | Core | NA | NA | NA |
| 3287-YEL052W_NumOfGenes_2 | YEL052W | AFG1 | NA | Protein that may act as a chaperone for cytochrome c oxidase subunits; conserved protein; may act as a chaperone in the degradation of misfolded or unassembled cytochrome c oxidase subunits; localized to matrix face of the mitochondrial inner membrane; member of the AAA family but lacks a protease domain | Core | NA | NA | NA |
| 3288-YEL053C_NumOfGenes_2 | YEL053C | MAK10 | NAA35 | Non-catalytic subunit of the NatC N-terminal acetyltransferase; required for replication of dsRNA virus; expression is glucose-repressible; human NatC ortholog, Naa35, requires co-expression of the human catalytic subunit, Naa30, to functionally complement the null allele | Core | NA | NA | NA |
| 3289-YEL054C_NumOfGenes_3 | YEL054C | RPL12A | uL11|ribosomal 60S subunit protein L12A|L11|YL23|L15A|L12A | Ribosomal 60S subunit protein L12A; rpl12a rpl12b double mutant exhibits slow growth and slow translation; homologous to mammalian ribosomal protein L12 and bacterial L11; RPL12A has a paralog, RPL12B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3290-YEL055C_NumOfGenes_2 | YEL055C | POL5 | DNA-directed DNA polymerase | DNA Polymerase phi; has sequence similarity to the human MybBP1A and weak sequence similarity to B-type DNA polymerases, not required for chromosomal DNA replication; required for the synthesis of rRNA | Core | NA | NA | NA |
| 3291-YEL056W_NumOfGenes_2 | YEL056W | HAT2 | NA | Subunit of the Hat1p-Hat2p histone acetyltransferase complex; required for high affinity binding of the complex to free histone H4, thereby enhancing Hat1p activity; similar to human RbAp46 and 48; has a role in telomeric silencing | Core | NA | NA | NA |
| 3292-YEL057C_NumOfGenes_2 | YEL057C | SDD1 | NA | Protein of unknown function; overproduction suppresses lethality due to expression of the dominant PET9 allele AAC2-A128P; may have a role in telomere maintenance; target of UME6 regulation | Core | NA | NA | NA |