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 |
|---|---|---|---|---|---|---|---|---|
| 7193-YOR234C | YOR234C | RPL33B | eL33|ribosomal 60S subunit protein L33B|L33e|rp47|Yl37|L37B|L33B|RPL37B | Ribosomal 60S subunit protein L33B; rpl33b null mutant exhibits normal growth while rpl33a rpl33b double null mutant is inviable; homologous to mammalian ribosomal protein L35A, no bacterial homolog; RPL33B has a paralog, RPL33A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7194-YOR235W | YOR235W | IRC13 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; null mutant displays increased levels of spontaneous Rad52 foci | Core | NA | NA | NA |
| 7195-YOR236W | YOR236W | DFR1 | dihydrofolate reductase | Dihydrofolate reductase involved in tetrahydrofolate biosynthesis; required for respiratory metabolism; mutation is functionally complemented by human DHFR | Core | NA | NA | NA |
| 7196-YOR237W | YOR237W | HES1 | oxysterol-binding protein related protein HES1|OSH5 | Protein implicated in the regulation of ergosterol biosynthesis; one of a seven member gene family with a common essential function and non-essential unique functions; similar to human oxysterol binding protein (OSBP); SWAT-GFP and mCherry fusion proteins localize to the bud neck and vacuolar membrane; HES1 has a paralog, KES1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7197-YOR238W | YOR238W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 7198-YOR239W | YOR239W | ABP140 | TRM140|YOR240W | AdoMet-dependent tRNA methyltransferase and actin binding protein; C-terminal domain is responsible for 3-methylcytidine modification of residue 32 of the tRNA anticodon loop of tRNA-Thr and tRNA-Ser and contains an S-adenosylmethionine (AdoMet) binding motif; N-terminal actin binding sequence interacts with actin filaments and localizes to actin patches and cables; N- and C-terminal domains are encoded in separate ORFs that are translated into one protein via a +1 frameshift | Core | NA | NA | NA |
| 7199-YOR241W | YOR241W | MET7 | tetrahydrofolate synthase|MET23 | Folylpolyglutamate synthetase; catalyzes extension of the glutamate chains of the folate coenzymes, required for methionine synthesis and for maintenance of mitochondrial DNA; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7200-YOR242C | YOR242C | SSP2 | NA | Sporulation specific protein that localizes to the spore wall; required for sporulation at a point after meiosis II and during spore wall formation; expression controlled by a tightly regulated middle-meiotic promoter that is activated by Ndt80p; translation of SSP2 mRNA is delayed, such that the mRNA is present as nuclear divisions are taking place but is not engaged by ribosomes until relatively late in meiotic development | Core | NA | NA | NA |
| 7201-YOR243C | YOR243C | PUS7 | pseudouridine synthase PUS7 | Pseudouridine synthase; catalyzes pseudouridylation at positions 35 and 56 in U2 snRNA, position 50 in 5S rRNA, position 13 in cytoplasmic tRNAs, and position 35 in pre-tRNA(Tyr); also pseudouridylates some mRNAs; relocates from nucleus to cytoplasm during heat shock and differentially modifies some mRNAs during heat shock; conserved in archaea, vertebrates, and some bacteria | Core | NA | NA | NA |
| 7202-YOR244W | YOR244W | ESA1 | NuA4 histone acetyltransferase complex catalytic subunit ESA1|KAT5|TAS1 | Catalytic subunit of the histone acetyltransferase complex (NuA4); acetylates four conserved internal lysines of histone H4 N-terminal tail and can acetylate histone H2A; master regulator of cellular acetylation balance; required for cell cycle progression and transcriptional silencing at the rDNA locus and regulation of autophagy; human ortholog TIP60/KAT5 is implicated in cancer and other diseases, functionally complements lethality of the esa1 null mutation | Core | NA | NA | NA |
| 7203-YOR245C | YOR245C | DGA1 | diacylglycerol O-acyltransferase | Diacylglycerol acyltransferase; catalyzes the terminal step of triacylglycerol (TAG) formation, acylates diacylglycerol using acyl-CoA as an acyl donor; Lro1p and Dga1p can O-acylate ceramides; localized to lipid particles | Core | NA | NA | NA |
| 7204-YOR246C | YOR246C | ENV9 | NA | Protein proposed to be involved in vacuolar functions; mutant shows defect in CPY processing and defects in vacuolar morphology; has similarity to oxidoreductases, found in lipid particles; required for replication of Brome mosaic virus in S. cerevisiae, a model system for studying replication of positive-strand RNA viruses in their natural hosts | Core | NA | NA | NA |
| 7205-YOR247W_NumOfGenes_2 | YOR247W | SRL1 | NA | Mannoprotein that exhibits a tight association with the cell wall; required for cell wall stability in the absence of GPI-anchored mannoproteins; has a high serine-threonine content; expression is induced in cell wall mutants; SRL1 has a paralog, SVS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7206-YOR249C | YOR249C | APC5 | anaphase promoting complex subunit 5|RMC1 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition; component of the platform domain of the APC/C, based on structural analysis; relative distribution to nuclear foci decreases upon DNA replication stress | Core | NA | NA | NA |
| 7207-YOR250C | YOR250C | CLP1 | cleavage polyadenylation factor subunit CLP1 | Component of the cleavage and polyadenylation factor I (CF I); CF 1, composed of the CF 1A complex (Rna14p, Rna15p, Clp1p, Pcf11p) and Hrp1, is involved in cleavage and polyadenylation of mRNA 3' ends; involved in both the endonucleolyitc cleavage and polyadenylation steps of mRNA 3'-end maturation and in gene looping which affects reinitiation of transcription | Core | NA | NA | NA |