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 |
|---|---|---|---|---|---|---|---|---|
| 3533-YFL012W-A | YFL012W-A | NA | YFL013W-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified gene IES1/YFL013C | Accessory | Ancestral | NA | NA |
| 3534-YFL013C_NumOfGenes_2 | YFL013C | IES1 | NA | Subunit of the INO80 chromatin remodeling complex; relocalizes to the cytosol in response to hypoxia | Accessory | Ancestral | NA | NA |
| 3535-YFL014W | YFL014W | HSP12 | lipid-binding protein HSP12|HOR5|GLP1 | Plasma membrane protein involved in maintaining membrane organization; involved in maintaining organization during stress conditions; induced by heat shock, oxidative stress, osmostress, stationary phase, glucose depletion, oleate and alcohol; protein abundance increased in response to DNA replication stress and dietary restriction; regulated by the HOG and Ras-Pka pathways; required for dietary restriction-induced lifespan extension | Accessory | Ancestral | NA | NA |
| 3536-YFL015W-A_NumOfGenes_2 | YFL015W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF YFL015C | Accessory | Ancestral | NA | NA |
| 3537-YFL016C | YFL016C | MDJ1 | NA | Co-chaperone that stimulates HSP70 protein Ssc1p ATPase activity; involved in protein folding/refolding in the mitochodrial matrix; required for proteolysis of misfolded proteins; member of the HSP40 (DnaJ) family of chaperones | Accessory | Ancestral | NA | NA |
| 3538-YFL017C | YFL017C | GNA1 | glucosamine 6-phosphate N-acetyltransferase|PAT1 | Glucosamine-6-phosphate acetyltransferase; evolutionarily conserved; required for multiple cell cycle events including passage through START, DNA synthesis, and mitosis; involved in UDP-N-acetylglucosamine synthesis, forms GlcNAc6P from AcCoA | Accessory | Ancestral | NA | NA |
| 3539-YFL017W-A | YFL017W-A | SMX2 | mRNA splicing protein SMX2|Sm G|SmG|YFL018W-A|SNP2 | Core Sm protein Sm G; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and Smx3p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm G | Accessory | Ancestral | NA | NA |
| 3540-YFL018C | YFL018C | LPD1 | dihydrolipoyl dehydrogenase|HPD1 | Dihydrolipoamide dehydrogenase; the lipoamide dehydrogenase component (E3) of the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase multi-enzyme complexes; PDH complex is concentrated in spots within the mitochondrial matrix, often near the ERMES complex and near peroxisomes; LPD1 has a paralog, IRC15, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3541-YFL019C | YFL019C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; YFL019C is not an essential gene | Accessory | Unknown | NA | NA |
| 3542-YFL020C_NumOfGenes_2 | YFL020C | PAU5 | seripauperin PAU5 | Member of the seripauperin multigene family; encoded mainly in subtelomeric regions; induced during alcoholic fermentation; induced by low temperature and also by anaerobic conditions; negatively regulated by oxygen and repressed by heme | Core | NA | NA | NA |
| 3543-YFL021W_NumOfGenes_2 | YFL021W | GAT1 | MEP80|NIL1 | Transcriptional activator of nitrogen catabolite repression genes; contains a GATA-1-type zinc finger DNA-binding motif; activity and localization regulated by nitrogen limitation and Ure2p; different translational starts produce two major and two minor isoforms that are differentially regulated and localized | Accessory | Ancestral | NA | NA |
| 3544-YFL022C | YFL022C | FRS2 | phenylalanine--tRNA ligase subunit alpha | Alpha subunit of cytoplasmic phenylalanyl-tRNA synthetase; forms a tetramer with Frs1p to form active enzyme; evolutionarily distant from mitochondrial phenylalanyl-tRNA synthetase based on protein sequence, but substrate binding is similar | Accessory | Ancestral | NA | NA |
| 3545-YFL023W_NumOfGenes_2 | YFL023W | BUD27 | URI1 | Unconventional prefoldin protein involved in translation initiation; required for correct assembly of RNAP I, II, and III in an Rpb5p-dependent manner; shuttles between nucleus and cytoplasm; mutants have inappropriate expression of nutrient sensitive genes due to translational derepression of Gcn4p transcription factor; diploid mutants show random budding; ortholog of human URI/RMP | Core | NA | NA | NA |
| 3546-YFL024C | YFL024C | EPL1 | NA | Subunit of NuA4, an essential histone H4/H2A acetyltransferase complex; conserved region at N-terminus is essential for interaction with the NPC (nucleosome core particle); required for autophagy; homologous to Drosophila Enhancer of Polycomb; coding sequence contains length polymorphisms in different strains | Core | NA | NA | NA |
| 3547-YFL025C | YFL025C | BST1 | PER17 | GPI inositol deacylase of the endoplasmic reticulum (ER); negatively regulates COPII vesicle formation; prevents production of vesicles with defective subunits; required for proper discrimination between resident ER proteins and Golgi-bound cargo molecules; functional ortholog of human PGAP1, mutation of which is associated with intellectual disability and encephalopathy | Core | NA | NA | NA |