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 |
|---|---|---|---|---|---|---|---|---|
| 4403-YHR143W-A | YHR143W-A | RPC10 | DNA-directed RNA polymerase core subunit RPC10|ABC10-alpha|RPB12 | RNA polymerase subunit ABC10-alpha, found in RNA pol I, II, and III; relocalizes from nucleolus to cytoplasm upon DNA replication stress | Core | NA | NA | NA |
| 4404-YHR144C | YHR144C | DCD1 | deoxycytidine monophosphate deaminase | Deoxycytidine monophosphate (dCMP) deaminase; involved in dUMP and dTMP biosynthesis; expression is NOT cell cycle regulated | Core | NA | NA | NA |
| 4405-YHR146W | YHR146W | CRP1 | NA | Protein that binds to cruciform DNA structures; CRP1 has a paralog, MDG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4406-YHR147C | YHR147C | MRPL6 | mitochondrial 54S ribosomal protein YmL16|YmL16 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 4407-YHR148W | YHR148W | IMP3 | snoRNA-binding rRNA-processing protein IMP3 | Component of the SSU processome; SSU processome is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA | Core | NA | NA | NA |
| 4408-YHR149C | YHR149C | SKG6 | NA | Integral membrane protein; localizes primarily to growing sites such as the bud tip or the cell periphery; potential Cdc28p substrate; Skg6p interacts with Zds1p and Zds2p; SKG6 has a paralog, TOS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4409-YHR150W | YHR150W | PEX28 | NA | Peroxisomal integral membrane peroxin; involved in the regulation of peroxisomal size, number and distribution; genetic interactions suggest that Pex28p and Pex29p act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p | Core | NA | NA | NA |
| 4410-YHR151C | YHR151C | MTC6 | NA | Protein of unknown function; mtc6 is synthetically sick with cdc13-1; SWAT-GFP and mCherry fusion proteins localize to the vacuole while SWAT-GFP fusion also localizes to the endoplasmic reticulum | Core | NA | NA | NA |
| 4411-YHR152W | YHR152W | SPO12 | SDB21 | Nucleolar protein of unknown function; positive regulator of mitotic exit; involved in regulating release of Cdc14p from the nucleolus in early anaphase, may play similar role in meiosis; SPO12 has a paralog, BNS1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4412-YHR153C | YHR153C | SPO16 | NA | Meiosis-specific protein involved in synaptonemal complex assembly; implicated in regulation of crossover formation; required for sporulation | Core | NA | NA | NA |
| 4413-YHR154W | YHR154W | RTT107 | ESC4 | Protein implicated in Mms22-dependent DNA repair during S phase; involved in recruiting the SMC5/6 complex to double-strand breaks; DNA damage induces phosphorylation by Mec1p at one or more SQ/TQ motifs; interacts with Mms22p and Slx4p; has four BRCT domains; has a role in regulation of Ty1 transposition; relative distribution to nuclear foci increases upon DNA replication stress | Core | NA | NA | NA |
| 4414-YHR155W | YHR155W | LAM1 | YSP1 | Putative sterol transfer protein; localizes to puncta in the cortical ER; probable role in retrograde transport of sterols from the plasma membrane to the ER; one of six StART-like domain-containing proteins in yeast that may be involved in sterol transfer between intracellular membranes; conserved across eukaryotes; contains GRAM, StART-like (VASt) and two PH-like domains | Core | NA | NA | NA |
| 4415-YHR156C | YHR156C | LIN1 | U5 snRNP complex subunit LIN1|SNU40 | Non-essential component of U5 snRNP; nuclear protein; physically interacts with Irr1p of cohesin complex; may link together proteins involved in chromosome segregation, mRNA splicing and DNA replication | Core | NA | NA | NA |
| 4416-YHR157W | YHR157W | REC104 | NA | Protein involved in early stages of meiotic recombination; required for meiotic crossing over; forms a complex with Rec102p and Spo11p necessary during the initiation of recombination | Core | NA | NA | NA |
| 4417-YHR158C | YHR158C | KEL1 | NA | Protein required for proper cell fusion and cell morphology; forms a complex with Bud14p and Kel2p that regulates Bnr1p (formin) to affect actin cable assembly, cytokinesis, and polarized growth; functions in a complex with Kel2p to negatively regulate mitotic exit, interacts with Tem1p and Lte1p; localizes to regions of polarized growth; potential Cdc28p substrate | Core | NA | NA | NA |