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 |
|---|---|---|---|---|---|---|---|---|
| 2918-YDR226W | YDR226W | ADK1 | adenylate kinase ADK1|AKY2|AKY1 | Adenylate kinase, required for purine metabolism; localized to the cytoplasm and the mitochondria; lacks cleavable signal sequence; protein abundance increases in response to DNA replication stress; mutations affecting Adk1p catalytic activity deregulate expression of phosphate utilization genes PHO5 and PHO84; human homolog AK1 can complement yeast adk1 mutant | Accessory | Ancestral | NA | NA |
| 2919-YDR227W | YDR227W | SIR4 | chromatin-silencing protein SIR4|UTH2|STE9|ASD1 | SIR protein involved in assembly of silent chromatin domains; silent information regulator (SIR) along with SIR2 and SIR3; involved in assembly of silent chromatin domains at telomeres and the silent mating-type loci; some alleles of SIR4 prolong lifespan; required for telomere hypercluster formation in quiescent yeast cells | Accessory | Ancestral | NA | NA |
| 2920-YDR228C | YDR228C | PCF11 | NA | mRNA 3' end processing factor; essential component of cleavage and polyadenylation factor IA (CF IA), involved in pre-mRNA 3' end processing and in transcription termination; binds C-terminal domain of largest subunit of RNA pol II (Rpo21p); required for gene looping; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2921-YDR229W | YDR229W | IVY1 | NA | Phospholipid-binding protein that interacts with both Ypt7p and Vps33p; may partially counteract the action of Vps33p and vice versa, localizes to the rim of the vacuole as cells approach stationary phase | Core | NA | NA | NA |
| 2922-YDR231C_NumOfGenes_2 | YDR231C | COX20 | NA | Mitochondrial inner membrane protein; required for proteolytic processing of Cox2p and its assembly into cytochrome c oxidase | Core | NA | NA | NA |
| 2923-YDR232W | YDR232W | HEM1 | 5-aminolevulinate synthase|OLE3|CYD1 | 5-aminolevulinate synthase; catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p; has a pyridoxal phosphate cofactor whose insertion is mediated by Mcx1p | Core | NA | NA | NA |
| 2924-YDR233C | YDR233C | RTN1 | NA | Reticulon protein; involved in nuclear pore assembly and maintenance of tubular ER morphology; promotes membrane curvature; regulates the ER asymmetry-induced inheritance block during ER stress; role in ER-derived peroxisomal biogenesis; increases tubular ER when overexpressed; mutants have reduced phosphatidylserine transfer between the ER and mitochondria; interacts with exocyst subunit Sec6p, Yip3p, and Sbh1p; member of the RTNLA subfamily | Core | NA | NA | NA |
| 2925-YDR234W | YDR234W | LYS4 | homoaconitate hydratase LYS4|LYS3 | Homoaconitase; catalyzes the conversion of homocitrate to homoisocitrate, which is a step in the lysine biosynthesis pathway | Core | NA | NA | NA |
| 2926-YDR235W | YDR235W | PRP42 | mRNA splicing protein PRP42|SNU65|MUD16 | U1 snRNP protein involved in splicing; required for U1 snRNP biogenesis; contains multiple tetriatricopeptide repeats | Core | NA | NA | NA |
| 2927-YDR236C | YDR236C | FMN1 | riboflavin kinase | Riboflavin kinase, produces riboflavin monophosphate (FMN); FMN is a necessary cofactor for many enzymes; predominantly localizes to the microsomal fraction and also found in the mitochondrial inner membrane; human RFK functionally complements the lethality of the null mutation | Core | NA | NA | NA |
| 2928-YDR237W | YDR237W | MRPL7 | mitochondrial 54S ribosomal protein YmL7/YmL5|YmL7|YmL5 | Mitochondrial ribosomal protein of the large subunit; MRPL7 produces both YmL5 and YmL7, which are two different modified forms of the same protein | Core | NA | NA | NA |
| 2929-YDR238C | YDR238C | SEC26 | coatomer subunit beta | Essential beta-coat protein of the COPI coatomer; involved in ER-to-Golgi protein trafficking and maintenance of normal ER morphology; shares 43% sequence identity with mammalian beta-coat protein (beta-COP) | Core | NA | NA | NA |
| 2930-YDR239C | YDR239C | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |
| 2931-YDR240C | YDR240C | SNU56 | MUD10 | Component of U1 snRNP required for mRNA splicing via spliceosome; yeast specific, no metazoan counterpart; interacts with mRNA in commitment complex | Core | NA | NA | NA |
| 2932-YDR241W | YDR241W | BUD26 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; 1% of ORF overlaps the verified gene SNU56; diploid mutant displays a weak budding pattern phenotype in a systematic assay | Core | NA | NA | NA |