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 |
|---|---|---|---|---|---|---|---|---|
| 3473-YER144C | YER144C | UBP5 | putative ubiquitin-specific protease UBP5 | Putative ubiquitin-specific protease; concentrates at the bud neck; UBP5 has a paralog, DOA4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3474-YER145C | YER145C | FTR1 | high-affinity iron permease FTR1 | High affinity iron permease; involved in the transport of iron across the plasma membrane; forms complex with Fet3p; expression is regulated by iron; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3475-YER146W_NumOfGenes_2 | YER146W | LSM5 | RNA-binding protein LSM5 | 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 | Core | NA | NA | NA |
| 3476-YER147C | YER147C | SCC4 | cohesin-loading factor complex subunit SCC4 | Subunit of cohesin loading factor (Scc2p-Scc4p); complex is required for the loading of cohesin complexes onto chromosomes; involved in establishing sister chromatid cohesion during double-strand break repair via phosphorylated histone H2AX | Core | NA | NA | NA |
| 3477-YER148W_NumOfGenes_2 | YER148W | SPT15 | TATA-binding protein|TBP|TBP1|BTF1 | TATA-binding protein (TBP); general transcription factor that interacts with other factors to form the preinitiation complex at promoters; essential for viability, highly conserved; yeast gene can complement mutations in human homolog TBP | Core | NA | NA | NA |
| 3478-YER149C_NumOfGenes_2 | YER149C | PEA2 | PPF2|DFG9 | Coiled-coil 12S polarisome subunit; required for polarity establishment, apical bud growth, shmoo formation, filamentous differentiation; involved in Bni1p localization at sites of polarized growth, controlling polarized assembly of actin cables; role in apical growth affects diploid-specific bipolar bud site selection; retains Slt2p at bud tip to regulate ER inheritance; role in Ca2+ influx, cell fusion; S288C allele encoding Leu409 rather than Met linked with non-invasion | Core | NA | NA | NA |
| 3479-YER150W | YER150W | SPI1 | NA | GPI-anchored cell wall protein involved in weak acid resistance; basal expression requires Msn2p/Msn4p; expression is induced under conditions of stress and during the diauxic shift; SPI1 has a paralog, SED1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3480-YER151C | YER151C | UBP3 | mRNA-binding ubiquitin-specific protease UBP3|BLM3 | Ubiquitin-specific protease involved in transport and osmotic response; negatively regulates Ras/PKA signaling; interacts with Bre5p to coregulate anterograde, retrograde transport between ER and Golgi; involved in transcription elongation in response to osmostress through phosphorylation at Ser695 by Hog1p; inhibitor of gene silencing; role in ribophagy; cleaves ubiquitin fusions but not polyubiquitin; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3481-YER152C_NumOfGenes_2 | YER152C | NA | 2-aminoadipate transaminase | Protein with 2-aminoadipate transaminase activity; shares amino acid similarity with the aminotransferases Aro8p and Aro9p; YER152C is not an essential gene | Core | NA | NA | NA |
| 3482-YER153C | YER153C | PET122 | NA | Mitochondrial translational activator specific for the COX3 mRNA; acts together with Pet54p and Pet494p; located in the mitochondrial inner membrane | Core | NA | NA | NA |
| 3483-YER154W | YER154W | OXA1 | membrane insertase OXA1|PET1402 | Mitochondrial inner membrane insertase; mediates the insertion of both mitochondrial- and nuclear-encoded proteins from the matrix into the inner membrane; also has a role in insertion of carrier proteins into the inner membrane; acts as a voltage-gated ion channel, activated by substrate peptides; interacts with mitochondrial ribosomes; conserved from bacteria to animals | Core | NA | NA | NA |
| 3484-YER155C | YER155C | BEM2 | TSL1|SUP9|IPL2 | Rho GTPase activating protein (RhoGAP); involved in the control of cytoskeleton organization and cellular morphogenesis; required for bud emergence; potential GAP for Rho4p | Core | NA | NA | NA |
| 3485-YER156C | YER156C | NA | NA | Putative protein of unknown function; interacts with Hsp82p and copurifies with Ipl1p; expression is copper responsive and downregulated in strains deleted for MAC1, a copper-responsive transcription factor; similarity to mammalian MYG1 | Core | NA | NA | NA |
| 3486-YER157W | YER157W | COG3 | Golgi transport complex subunit COG3|SEC34|GRD20 | Essential component of the conserved oligomeric Golgi complex; a cytosolic tethering complex (Cog1p through Cog8p) that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments | Core | NA | NA | NA |
| 3487-YER158C | YER158C | NA | NA | Protein of unknown function; potentially phosphorylated by Cdc28p; YER158C has a paralog, AFR1, that arose from the whole genome duplication | Core | NA | NA | NA |