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 |
|---|---|---|---|---|---|---|---|---|
| 5183-YKL108W | YKL108W | SLD2 | DRC1 | Single-stranded DNA origin-binding and annealing protein; required for initiation of DNA replication; phosphorylated in S phase by cyclin-dependent kinases (Cdks), promoting origin binding, DNA replication and Dpb11p complex formation; component of the preloading complex; binds the Mcm2-7p complex to prevent inappropriate Mcm2-7p interaction with the GINS complex in G1; required for S phase checkpoint; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 5184-YKL109W | YKL109W | HAP4 | transcription factor HAP4 | Transcription factor; subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; provides the principal activation function of the complex; involved in diauxic shift | Core | NA | NA | NA |
| 5185-YKL110C | YKL110C | KTI12 | TOT4 | Protein that plays a role in modification of tRNA wobble nucleosides; protein plays role in tRNA wobble nucleoside modification with Elongator complex; involved in sensitivity to G1 arrest induced by zymocin; interacts with chromatin throughout the genome; also interacts with Cdc19p | Core | NA | NA | NA |
| 5186-YKL112W_NumOfGenes_2 | YKL112W | ABF1 | GFI|SBF-B|DNA-binding protein ABF1|SBF1|REB2|OBF1|BAF1 | DNA binding protein with possible chromatin-reorganizing activity; involved in transcriptional activation, gene silencing, and DNA replication and repair | Core | NA | NA | NA |
| 5187-YKL113C | YKL113C | RAD27 | multifunctional nuclease RAD27|FEN1|RTH1|ERC11 | 5' to 3' exonuclease, 5' flap endonuclease; required for Okazaki fragment processing and maturation, for long-patch base-excision repair and large loop repair (LLR), ribonucleotide excision repair; member of the S. pombe RAD2/FEN1 family; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 5188-YKL114C | YKL114C | APN1 | DNA-(apurinic or apyrimidinic site) lyase APN1 | Major apurinic/apyrimidinic endonuclease; 3'-repair diesterase; involved in repair of DNA damage by oxidation and alkylating agents; also functions as a 3'-5' exonuclease to repair 7,8-dihydro-8-oxodeoxyguanosine; genetically interacts with NTG1 to maintain mitochondrial genome integrity | Core | NA | NA | NA |
| 5189-YKL115C | YKL115C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene PRR1 | Core | NA | NA | NA |
| 5190-YKL116C | YKL116C | PRR1 | serine/threonine protein kinase PRR1 | Serine/threonine protein kinase; inhibits pheromone induced signaling downstream of MAPK, possibly at the level of the Ste12p transcription factor | Core | NA | NA | NA |
| 5191-YKL117W_NumOfGenes_2 | YKL117W | SBA1 | Hsp90 cochaperone SBA1|CST18 | Co-chaperone that binds and regulates Hsp90 family chaperones; plays a role in determining prion variants; important for pp60v-src activity in yeast; homologous to the mammalian p23 proteins, and like p23 can regulate telomerase activity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5192-YKL118W | YKL118W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene VPH2 | Core | NA | NA | NA |
| 5193-YKL119C | YKL119C | VPH2 | VMA12|CLS10 | Integral membrane protein required for V-ATPase function; not an actual component of the vacuolar H+-ATPase (V-ATPase) complex; functions in the assembly of the V-ATPase; localized to the endoplasmic reticulum (ER); involved in methionine restriction extension of chronological lifespan in an autophagy-dependent manner | Core | NA | NA | NA |
| 5194-YKL120W | YKL120W | OAC1 | NA | Mitochondrial inner membrane transporter; transports oxaloacetate, sulfate, thiosulfate, and isopropylmalate; member of the mitochondrial carrier family | Core | NA | NA | NA |
| 5195-YKL121W | YKL121W | DGR2 | NA | Protein of unknown function; null mutant is resistant to 2-deoxy-D-glucose and displays abnormally elongated buds; DGR2 has a paralog, YMR102C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5196-YKL122C | YKL122C | SRP21 | signal recognition particle subunit SRP21 | Subunit of the signal recognition particle (SRP); SRP functions in protein targeting to the endoplasmic reticulum membrane; not found in mammalian SRP; forms a pre-SRP structure in the nucleolus that is translocated to the cytoplasm | Core | NA | NA | NA |
| 5197-YKL124W_NumOfGenes_2 | YKL124W | SSH4 | MLF4 | Specificity factor required for Rsp5p-dependent ubiquitination; also required for sorting of cargo proteins at the multivesicular body; identified as a high-copy suppressor of a SHR3 deletion, increasing steady-state levels of amino acid permeases | Core | NA | NA | NA |