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 |
|---|---|---|---|---|---|---|---|---|
| 7313-YOR355W | YOR355W | GDS1 | NA | Protein of unknown function; required for growth on glycerol as a carbon source; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 7314-YOR356W | YOR356W | CIR2 | putative electron-transferring-flavoprotein dehydrogenase | Putative ortholog of human ETF-dH; found in a large supramolecular complex with other mitochondrial dehydrogenases; may have a role in oxidative stress response; ETF-dH is also known as electron transfer flavoprotein dehydrogenase | Core | NA | NA | NA |
| 7315-YOR357C | YOR357C | SNX3 | GRD19 | Sorting nexin for late-Golgi enzymes; required to maintain late-Golgi resident enzymes in their proper location by recycling molecules from the prevacuolar compartment; contains a PX domain and sequence similarity to human Snx3p | Core | NA | NA | NA |
| 7316-YOR358W | YOR358W | HAP5 | NA | Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex; complex is heme-activated and glucose repressed; complex is a transcriptional activator and global regulator of respiratory gene expression; required for assembly and DNA binding activity of the complex | Core | NA | NA | NA |
| 7317-YOR359W | YOR359W | VTS1 | NA | Flap-structured DNA-binding and RNA-binding protein; stimulates deadenylation-dependent mRNA degradation mediated by the CCR4-NOT deadenylase complex; member of the Smaug (Smg) family of post-transcriptional regulators which bind RNA through a conserved sterile alpha motif (SAM) domain that interacts with Smg recognition element (SREs) containing transcripts; stimulates Dna2p endonuclease activity | Core | NA | NA | NA |
| 7318-YOR360C | YOR360C | PDE2 | 3',5'-cyclic-nucleotide phosphodiesterase PDE2|SRA5 | High-affinity cyclic AMP phosphodiesterase; component of the cAMP-dependent protein kinase signaling system, protects the cell from extracellular cAMP, contains readthrough motif surrounding termination codon | Core | NA | NA | NA |
| 7319-YOR361C | YOR361C | PRT1 | translation initiation factor eIF3 core subunit b|DNA26|CDC63 | eIF3b subunit of the eukaryotic translation initiation factor 3 (eIF3); subunit of the core complex of eIF3; essential for translation; part of a subcomplex (Prt1p-Rpg1p-Nip1p) that stimulates binding of mRNA and tRNA(i)Met to ribosomes; eIF3 is also involved in programmed stop codon readthrough | Core | NA | NA | NA |
| 7320-YOR362C | YOR362C | PRE10 | proteasome core particle subunit alpha 7 | Alpha 7 subunit of the 20S proteasome; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7321-YOR363C | YOR363C | PIP2 | oleate-activated transcription factor PIP2|OAF2 | Autoregulatory, oleate-activated transcription factor; subunit of a heterodimeric complex with Oaf1p, which binds to oleate-response elements (ORE) in the promoter of genes involved in beta-oxidation of fatty acids, peroxisome organization and biogenesis, activating transcription in the presence of oleate; PIP2 has a paralog, OAF1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7322-YOR365C_NumOfGenes_3 | YOR365C | NA | putative flavin adenine dinucleotide transporter | Putative protein of unknown function; not an essential protein; YOR365C has a paralog, FLC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7323-YOR367W | YOR367W | SCP1 | NA | Component of yeast cortical actin cytoskeleton; binds and cross links actin filaments; originally identified by its homology to calponin (contains a calponin-like repeat) but the Scp1p domain structure is more similar to transgelin | Core | NA | NA | NA |
| 7324-YOR368W | YOR368W | RAD17 | NA | Checkpoint protein; involved in the activation of the DNA damage and meiotic pachytene checkpoints; with Mec3p and Ddc1p, forms a clamp that is loaded onto partial duplex DNA; homolog of human and S. pombe Rad1 and U. maydis Rec1 proteins | Core | NA | NA | NA |
| 7325-YOR369C | YOR369C | RPS12 | eS12|ribosomal 40S subunit protein S12|S12e|S12 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S12, no bacterial homolog | Core | NA | NA | NA |
| 7326-YOR370C | YOR370C | MRS6 | GTPase-activating protein MRS6|MSI4 | Rab escort protein; forms a complex with the Ras-like small GTPase Ypt1p that is required for the prenylation of Ypt1p by protein geranylgeranyltransferase type II (Bet2p-Bet4p); sequence similarity to mammalian choroideraemia gene; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 7327-YOR371C | YOR371C | GPB1 | KRH2 | Multistep regulator of cAMP-PKA signaling; inhibits PKA downstream of Gpa2p and Cyr1p, thereby increasing cAMP dependency; promotes ubiquitin-dependent proteolysis of Ira2p; regulated by G-alpha protein Gpa2p; GPB1 has a paralog, GPB2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |