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 |
|---|---|---|---|---|---|---|---|---|
| 2978-YDR288W | YDR288W | NSE3 | Smc5-Smc6 complex subunit NSE3 | Component of the SMC5-SMC6 complex; this complex plays a key role in the removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2979-YDR289C | YDR289C | RTT103 | NA | Protein involved in transcription termination by RNA polymerase II; interacts with exonuclease Rat1p and Rai1p; has an RPR domain (carboxy-terminal domain interacting domain); also involved in regulation of Ty1 transposition | Core | NA | NA | NA |
| 2980-YDR290W | YDR290W | NA | SWS1 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RTT103 | Accessory | Ancestral | NA | NA |
| 2981-YDR291W | YDR291W | HRQ1 | ATP-dependent 3'-5' DNA helicase | 3'-5' DNA helicase that has DNA strand annealing activity; helicase activity is stimulated by fork structure and 3'-tail length of substrates; acts with Rad4p in nucleotide-excision repair; belongs to the widely conserved RecQ family of proteins which are involved in maintaining genomic integrity; similar to the human RecQ4p implicated in Rothmund-Thomson syndrome (RTS) | Core | NA | NA | NA |
| 2982-YDR292C | YDR292C | SRP101 | Signal recognition particle receptor subunit alpha | Signal recognition particle (SRP) receptor alpha subunit; contain GTPase domains; involved in SRP-dependent protein targeting; interacts with the beta subunit, Srp102p | Core | NA | NA | NA |
| 2983-YDR293C | YDR293C | SSD1 | mRNA-binding translational repressor SSD1|SRK1|RLT1|MCS1|CLA1 | Translational repressor with a role in polar growth and wall integrity; regulated by Cbk1p phosphorylation to effect bud-specific translational control and localization of specific mRNAs; interacts with TOR pathway components; contains a functional N-terminal nuclear localization sequence and nucleocytoplasmic shuttling appears to be critical to Ssd1p function | Core | NA | NA | NA |
| 2984-YDR294C | YDR294C | DPL1 | sphinganine-1-phosphate aldolase DPL1|BST1 | Dihydrosphingosine phosphate lyase; regulates intracellular levels of sphingolipid long-chain base phosphates (LCBPs), degrades phosphorylated long chain bases, prefers C16 dihydrosphingosine-l-phosphate as a substrate | Core | NA | NA | NA |
| 2985-YDR295C | YDR295C | HDA2 | PLO2 | Subunit of the HDA1 histone deacetylase complex; possibly tetrameric trichostatin A-sensitive class II histone deacetylase complex contains Hda1p homodimer and an Hda2p-Hda3p heterodimer; involved in telomere maintenance; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 2986-YDR296W | YDR296W | MHR1 | XTC1 | Mitochondrial ribosomal protein of the large subunit; also involved in homologous recombination in mitochondria; required for recombination-dependent mtDNA partitioning; involved in stimulation of mitochondrial DNA replication in response to oxidative stress | Core | NA | NA | NA |
| 2987-YDR297W | YDR297W | SUR2 | sphingosine hydroxylase|SYR2 | Sphinganine C4-hydroxylase; catalyses the conversion of sphinganine to phytosphingosine in sphingolipid biosyntheis | Core | NA | NA | NA |
| 2988-YDR298C | YDR298C | ATP5 | F1F0 ATP synthase subunit 5|OSC1 | Subunit 5 of the stator stalk of mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; homologous to bovine subunit OSCP (oligomycin sensitivity-conferring protein); phosphorylated | Core | NA | NA | NA |
| 2989-YDR299W | YDR299W | BFR2 | rRNA-processing protein BFR2 | Component of the SSU and 90S preribosomes; involved in pre-18S rRNA processing; binds to U3 snoRNA and Mpp10p; multicopy suppressor of sensitivity to Brefeldin A; expression is induced during lag phase and also by cold shock | Core | NA | NA | NA |
| 2990-YDR300C | YDR300C | PRO1 | glutamate 5-kinase | Gamma-glutamyl kinase; catalyzes the first step in proline biosynthesis; required for nitrogen starvation-induced ribophagy but not for nonselective autophagy; PRO1 has a paralog, YHR033W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2991-YDR301W | YDR301W | CFT1 | YHH1 | RNA-binding subunit of the mRNA cleavage and polyadenylation factor; involved in poly(A) site recognition and required for both pre-mRNA cleavage and polyadenylation, 51% sequence similarity with mammalian AAUAA-binding subunit of CPSF | Core | NA | NA | NA |
| 2992-YDR302W | YDR302W | GPI11 | mannose-ethanolamine phosphotransferase GPI11 | ER membrane protein involved in a late step of GPI anchor assembly; involved in the addition of phosphoethanolamine to the multiply mannosylated glycosylphosphatidylinositol (GPI) intermediate; human PIG-Fp is a functional homolog | Core | NA | NA | NA |