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 |
|---|---|---|---|---|---|---|---|---|
| 1883-YBL013W | YBL013W | FMT1 | methionyl-tRNA formyltransferase | Methionyl-tRNA formyltransferase; catalyzes the formylation of initiator Met-tRNA in mitochondria; potential Cdc28p substrate | Core | NA | NA | NA |
| 1884-YBL014C | YBL014C | RRN6 | NA | Component of the core factor (CF) rDNA transcription factor complex; CF is required for transcription of 35S rRNA genes by RNA polymerase I and is composed of Rrn6p, Rrn7p, and Rrn11p | Core | NA | NA | NA |
| 1885-YBL015W | YBL015W | ACH1 | acetyl-CoA hydrolase | Protein with CoA transferase activity; particularly for CoASH transfer from succinyl-CoA to acetate; has minor acetyl-CoA-hydrolase activity; phosphorylated; required for acetate utilization and for diploid pseudohyphal growth | Accessory | Ancestral | NA | NA |
| 1886-YBL016W | YBL016W | FUS3 | mitogen-activated serine/threonine-protein kinase FUS3|DAC2 | Mitogen-activated serine/threonine protein kinase involved in mating; phosphoactivated by Ste7p; substrates include Ste12p, Far1p, Bni1p, Sst2p; inhibits invasive growth during mating by phosphorylating Tec1p, promoting its; inhibits recruitment of Ste5p, Cdc42p-mediated asymmetry and mating morphogenesis | Core | NA | NA | NA |
| 1887-YBL017C_NumOfGenes_2 | YBL017C | PEP1 | type I sorting receptor|VPT1|VPS10 | Type I transmembrane sorting receptor for multiple vacuolar hydrolases; cycles between the late-Golgi and prevacuolar endosome-like compartments | Core | NA | NA | NA |
| 1888-YBL018C | YBL018C | POP8 | ribonuclease P | Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 1889-YBL019W | YBL019W | APN2 | DNA-(apurinic or apyrimidinic site) lyase APN2|ETH1 | Class II abasic (AP) endonuclease involved in repair of DNA damage; homolog of human HAP1 and E. coli exoIII | Core | NA | NA | NA |
| 1890-YBL020W | YBL020W | RFT1 | glycolipid translocation protein | Membrane protein required for translocation of Man5GlcNac2-PP-Dol; required for translocation of Man5GlcNac2-PP-Dol from the cytoplasmic side to the lumenal side of the ER membrane but is not the flippase; mutation is suppressed by expression of human p53 protein; essential gene | Core | NA | NA | NA |
| 1891-YBL021C | YBL021C | HAP3 | NA | Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex; complex is heme-activated and glucose-repressed; complex is a transcriptional activator and global regulator of respiratory gene expression; contains sequences contributing to both complex assembly and DNA binding | Core | NA | NA | NA |
| 1892-YBL022C | YBL022C | PIM1 | ATP-dependent Lon protease PIM1|LON1 | ATP-dependent Lon protease; involved in degradation of misfolded proteins in mitochondria; required for biogenesis and maintenance of mitochondria | Core | NA | NA | NA |
| 1893-YBL023C_NumOfGenes_2 | YBL023C | MCM2 | MCM DNA helicase complex subunit MCM2 | Protein involved in DNA replication; component of the Mcm2-7 hexameric helicase complex that binds chromatin as a part of the pre-replicative complex; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 1894-YBL024W_NumOfGenes_2 | YBL024W | NCL1 | tRNA (cytosine-C5-)-methyltransferase|TRM4 | S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase; methylates cytosine to m5C at several positions in tRNAs and intron-containing pre-tRNAs; increases proportion of tRNALeu(CAA) with m5C at wobble position in response to hydrogen peroxide, causing selective translation of mRNA from genes enriched in TTG codon; loss of NCL1 confers hypersensitivity to oxidative stress; similar to Nop2p and human proliferation associated nucleolar protein p120 | Core | NA | NA | NA |
| 1895-YBL025W_NumOfGenes_2 | YBL025W | RRN10 | NA | Protein involved in promoting high level transcription of rDNA; subunit of UAF (upstream activation factor) for RNA polymerase I | Core | NA | NA | NA |
| 1896-YBL026W_NumOfGenes_2 | YBL026W | LSM2 | Sm-like protein LSM2|SNP3|SMX5 | Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 1897-YBL027W_NumOfGenes_2 | YBL027W | RPL19B | eL19|ribosomal 60S subunit protein L19B|L19e|rpl5L|YL14|L23B|L19B | Ribosomal 60S subunit protein L19B; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal; homologous to mammalian ribosomal protein L19, no bacterial homolog; RPL19B has a paralog, RPL19A, that arose from the whole genome duplication | Core | NA | NA | NA |