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 |
|---|---|---|---|---|---|---|---|---|
| 7343-YOR386W_NumOfGenes_2 | YOR386W | PHR1 | deoxyribodipyrimidine photo-lyase PHR1 | DNA photolyase involved in photoreactivation; repairs pyrimidine dimers in the presence of visible light; induced by DNA damage; regulated by transcriptional repressor Rph1p | Accessory | Ancestral | NA | NA |
| 7344-YOR387C_NumOfGenes_4 | YOR387C | NA | NA | Putative protein of unknown function; regulated by the metal-responsive Aft1p transcription factor; highly inducible in zinc-depleted conditions; localizes to the soluble fraction; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively; YOR387C has a paralog, VEL1, that arose from a single-locus duplication | Accessory | Ancestral | NA | NA |
| 7345-YOR388C_NumOfGenes_3 | YOR388C | FDH1 | formate dehydrogenase (NAD+) | NAD(+)-dependent formate dehydrogenase; may protect cells from exogenous formate | Core | NA | NA | NA |
| 7346-YOR389W_NumOfGenes_4 | YOR389W | NA | NA | Putative protein of unknown function; expression regulated by copper levels | Core | NA | NA | NA |
| 7347-YOR392W | YOR392W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; gene expression induced by heat | Accessory | Unknown | NA | NA |
| 7348-YOR394C-A | YOR394C-A | NA | NA | Protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Accessory | Unknown | NA | NA |
| 7349-YOR394W_NumOfGenes_7 | YOR394W | PAU21 | seripauperin PAU21 | Protein of unknown function; member of the seripauperin multigene family encoded mainly in subtelomeric regions; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the cytosol; identical to Pau22p; encodes two proteins that are translated from 2 different start codons | Accessory | Ancestral | NA | NA |
| 7350-YPL001W | YPL001W | HAT1 | histone acetyltransferase catalytic subunit HAT1|KAT1 | Catalytic subunit of the Hat1p-Hat2p histone acetyltransferase complex; uses the cofactor acetyl coenzyme A to acetylate free nuclear and cytoplasmic histone H4; involved in telomeric silencing and DNA double-strand break repair | Core | NA | NA | NA |
| 7351-YPL002C | YPL002C | SNF8 | ESCRT-II subunit protein SNF8|VPL14|VPS22 | Component of the ESCRT-II complex; ESCRT-II is involved in ubiquitin-dependent sorting of proteins into the endosome; appears to be functionally related to SNF7; involved in glucose derepression | Core | NA | NA | NA |
| 7352-YPL003W | YPL003W | ULA1 | ENR2 | Protein that activates Rub1p (NEDD8) before neddylation; acts together with Uba3p; may play a role in protein degradation | Core | NA | NA | NA |
| 7353-YPL004C | YPL004C | LSP1 | lipid-binding protein LSP1 | Eisosome core component; eisosomes are large immobile patch structures at the cell cortex associated with endocytosis; phosphorylated on Thr233 upon Pkc1p hyperactivation in a Slt2p MAPK-dependent fashion; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; member of the BAR domain family | Core | NA | NA | NA |
| 7354-YPL005W | YPL005W | AEP3 | NA | Peripheral mitochondrial inner membrane protein; may facilitate use of unformylated tRNA-Met in mitochondrial translation initiation; stabilizes the bicistronic AAP1-ATP6 mRNA | Core | NA | NA | NA |
| 7355-YPL006W | YPL006W | NCR1 | sphingolipid transporter | Vacuolar membrane protein; transits through the biosynthetic vacuolar protein sorting pathway, involved in sphingolipid metabolism; cells lacking Ncr1p exhibit high levels of long chain bases (LCB), similar to the accumulation of high amounts of lipids observed in patients with Neimann-Pick C, a disease caused by loss-of-function mutations in NPC1, the functional ortholog of Ncr1p | Core | NA | NA | NA |
| 7356-YPL007C | YPL007C | TFC8 | transcription factor TFIIIC subunit TFC8|tau 60 | Subunit of RNA polymerase III transcription initiation factor complex; one of six subunits of RNA polymerase III transcription initiation factor complex (TFIIIC); part of TFIIIC TauB domain that binds BoxB promoter sites of tRNA and other genes; linker between TauB and TauA domains; human homolog is TFIIIC-90 | Core | NA | NA | NA |
| 7357-YPL008W | YPL008W | CHL1 | MCM12|LPA9|CTF1 | Probable DNA helicase; involved in sister-chromatid cohesion and genome integrity and interstrand cross-link repair; interacts with ECO1 and CTF18; mutants are defective in silencing, rDNA recombination, aging and the heat shock response; FANCJ-like helicase family member; mutations in the human homolog, DDX11/ChLR1, cause Warsaw breakage syndrome | Core | NA | NA | NA |