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 |
|---|---|---|---|---|---|---|---|---|
| 5663-YLR205C | YLR205C | HMX1 | NA | ER localized heme oxygenase; involved in heme degradation during iron starvation and in the oxidative stress response; expression is regulated by AFT1 and oxidative stress; relocates to the perinuclear region in the presence of oxidants | Accessory | Ancestral | NA | NA |
| 5664-YLR206W | YLR206W | ENT2 | epsin | Epsin-like protein required for endocytosis and actin patch assembly; functionally redundant with Ent1p; contains clathrin-binding motif at C-terminus; ENT2 has a paralog, ENT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5665-YLR207W | YLR207W | HRD3 | ubiquitin ligase complex subunit HRD3 | ER membrane protein that plays a central role in ERAD; forms HRD complex with Hrd1p and ER-associated protein degradation (ERAD) determinants that engages in lumen to cytosol communication and coordination of ERAD events | Core | NA | NA | NA |
| 5666-YLR208W | YLR208W | SEC13 | GTPase-activating protein SEC13|ANU3 | Structural component of 3 complexes; subunit of the Nup84p nuclear pore subcomplex that contributes to nucleocytoplasmic transport and NPC biogenesis; subunit of the COPII vesicle coat required for ER-to-Golgi transport; subunit of SEACAT, a subcomplex of the coatomer-related, vacuolar-associated SEA complex, that inhibits the TORC1 inhibitory role of SEACIT (Iml1p-Npr2p-Npr3p), a GAP for Gtr1p, thereby resulting in activation of TORC1 signaling; human SEC13 homolog | Core | NA | NA | NA |
| 5667-YLR209C | YLR209C | PNP1 | purine-nucleoside phosphorylase | Purine nucleoside phosphorylase; specifically metabolizes inosine and guanosine nucleosides; involved in the nicotinamide riboside salvage pathway | Accessory | Ancestral | NA | NA |
| 5668-YLR210W | YLR210W | CLB4 | B-type cyclin CLB4 | B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the G2/M transition; may be involved in DNA replication and spindle assembly; accumulates during S phase and G2, then targeted for ubiquitin-mediated degradation; CLB4 has a paralog, CLB3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5669-YLR211C | YLR211C | ATG38 | NA | Homodimeric subunit of autophagy-specific PtdIns-3-kinase complex I; required for the integrity of the active PtdIns-3-kinase complex I by maintaining an association between Vps15p-Vps34p and Atg14p-Vps30p subcomplexes; localizes to the pre-autophagosomal structure (PAS) in an Atg14p-dependent manner; ATG38 is non-essential but is required for macroautophagy | Core | NA | NA | NA |
| 5670-YLR212C | YLR212C | TUB4 | gamma-tubulin | Gamma-tubulin; involved in nucleating microtubules from both the cytoplasmic and nuclear faces of the spindle pole body; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5671-YLR213C | YLR213C | CRR1 | putative glycosylase | Putative glycoside hydrolase of the spore wall envelope; required for normal spore wall assembly, possibly for cross-linking between the glucan and chitosan layers; expressed during sporulation | Core | NA | NA | NA |
| 5672-YLR214W | YLR214W | FRE1 | ferric/cupric-chelate reductase | Ferric reductase and cupric reductase; reduces siderophore-bound iron and oxidized copper prior to uptake by transporters; expression induced by low copper and iron levels | Core | NA | NA | NA |
| 5673-YLR215C | YLR215C | CDC123 | cell proliferation protein CDC123 | Assembly factor for the eIF2 translation initiation factor complex; regulates translational initiation; conserved residues of this ATP-Grasp protein that bind to ATP-Mg2+ in the pombe ortholog are required for complex assembly in budding yeast; interaction with eIF2 subunit Gcd11p facilitates complex assembly and activity; required for the START transition and timely progression through G2; regulated by nutrient availability; human ortholog complements the yeast mutant | Core | NA | NA | NA |
| 5674-YLR216C_NumOfGenes_2 | YLR216C | CPR6 | peptidylprolyl isomerase CPR6|CYP40 | Peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; plays a role in determining prion variants; binds to Hsp82p and contributes to chaperone activity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5675-YLR218C | YLR218C | COA4 | CMC3 | Twin Cx(9)C protein involved in cytochrome c oxidase organization; organization includes assembly or stability; localizes to the mitochondrial intermembrane space via the Mia40p-Erv1p system; interacts genetically with CYC1 and with cytochrome c oxidase assembly factors | Core | NA | NA | NA |
| 5676-YLR219W | YLR219W | MSC3 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; msc3 mutants are defective in directing meiotic recombination events to homologous chromatids; potential Cdc28p substrate; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5677-YLR220W | YLR220W | CCC1 | NA | Vacuolar Fe2+/Mn2+ transporter; suppresses respiratory deficit of yfh1 mutants, which lack the ortholog of mammalian frataxin, by preventing mitochondrial iron accumulation; relative distribution to the vacuole decreases upon DNA replication stress | Core | NA | NA | NA |