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 |
|---|---|---|---|---|---|---|---|---|
| 5603-YLR143W | YLR143W | DPH6 | diphthine--ammonia ligase | Diphthamide synthetase; catalyzes the last amidation step of diphthamide biosynthesis using ammonium and ATP; evolutionarily conserved in eukaryotes; dph6 mutants exhibit diphthine accumulation and resistance to sordarin, which is indicative of defects in diphthamide formation on EF2; green fluorescent protein (GFP)-tagged protein localizes to the cytoplasm; DPH6/YLR143W is not an essential gene | Accessory | Ancestral | NA | NA |
| 5604-YLR144C | YLR144C | ACF2 | PCA1|ENG2 | Intracellular beta-1,3-endoglucanase; expression is induced during sporulation; may have a role in cortical actin cytoskeleton assembly; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5605-YLR145W | YLR145W | RMP1 | NA | Subunit of RNase MRP; RNase MRP processes pre-rRNA and has a role in cell cycle-regulated degradation of daughter cell-specific mRNAs; unlike most subunits, not shared between RNase MRP and nuclear RNase P | Accessory | Ancestral | NA | NA |
| 5606-YLR146C | YLR146C | SPE4 | spermine synthase | Spermine synthase; required for the biosynthesis of spermine and also involved in biosynthesis of pantothenic acid | Accessory | Ancestral | NA | NA |
| 5607-YLR146W-A | YLR146W-A | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |
| 5608-YLR147C | YLR147C | SMD3 | mRNA splicing protein SMD3|Sm D3|SLT16 | Core Sm protein Sm D3; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D3 | Accessory | Ancestral | NA | NA |
| 5609-YLR148W | YLR148W | PEP3 | tethering complex subunit PEP3|VPT18|VPS18|VAM8 | Component of CORVET membrane tethering complex; vacuolar peripheral membrane protein that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins, required for vacuolar biogenesis | Accessory | Ancestral | NA | NA |
| 5610-YLR149C | YLR149C | NA | NA | Protein of unknown function; overexpression causes a cell cycle delay or arrest; null mutation results in a decrease in plasma membrane electron transport; YLR149C is not an essential gene; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 5611-YLR149C-A | YLR149C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Introgression | S. paradoxus | NA |
| 5612-YLR150W | YLR150W | STM1 | MPT4 | Protein required for optimal translation under nutrient stress; perturbs association of Yef3p with ribosomes; involved in TOR signaling; binds G4 quadruplex and purine motif triplex nucleic acid; helps maintain telomere structure; protein abundance increases in response to DNA replication stress; serves as a ribosome preservation factor both during quiescence and recovery | Accessory | Ancestral | NA | NA |
| 5613-YLR151C | YLR151C | PCD1 | 8-oxo-dGTP diphosphatase | 8-oxo-dGTP diphosphatase; prevents spontaneous mutagenesis via sanitization of oxidized purine nucleoside triphosphates; can also act as peroxisomal pyrophosphatase with specificity for coenzyme A and CoA derivatives, may function to remove potentially toxic oxidized CoA disulfide from peroxisomes to maintain the capacity for beta-oxidation of fatty acids; nudix hydrolase family member; similar E. coli MutT and human, rat and mouse MTH1 | Accessory | Ancestral | NA | NA |
| 5614-YLR152C | YLR152C | NA | NA | Putative protein of unknown function; YLR152C is not an essential gene | Accessory | Ancestral | NA | NA |
| 5615-YLR153C | YLR153C | ACS2 | acetate--CoA ligase ACS2 | Acetyl-coA synthetase isoform; along with Acs1p, acetyl-coA synthetase isoform is the nuclear source of acetyl-coA for histone acetylation; mutants affect global transcription; required for growth on glucose; expressed under anaerobic conditions | Accessory | Ancestral | NA | NA |
| 5616-YLR154C | YLR154C | RNH203 | Rnh2C | Ribonuclease H2 subunit; required for RNase H2 activity; role in ribonucleotide excision repair; related to human AGS3 that causes Aicardi-Goutieres syndrome | Accessory | Ancestral | NA | NA |
| 5617-YLR154C-H_NumOfGenes_4 | YLR154C-H | NA | NA | Putative protein of unknown function; identified by fungal homology comparisons and RT-PCR; this ORF partially overlaps RDN5-2; YLR154C-H has a paralog, YLR157C-C, that arose from a segmental duplication | Core | NA | NA | NA |