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 |
|---|---|---|---|---|---|---|---|---|
| 3833-YGL191W | YGL191W | COX13 | cytochrome c oxidase subunit VIa | Subunit VIa of cytochrome c oxidase; present in a subclass of cytochrome c oxidase complexes that may have a role in mimimizing generation of reactive oxygen species; not essential for cytochrome c oxidase activity but may modulate activity in response to ATP; required for assembly of Rcf2p into cytochrome c oxidase - cytochrome bc1 supercomplexes | Core | NA | NA | NA |
| 3834-YGL192W | YGL192W | IME4 | mRNA (N6-adenosine)-methyltransferase|SPO8 | mRNA N6-adenosine methyltransferase required for entry into meiosis; mediates N6-adenosine methylation of bulk mRNA during the induction of sporulation which includes the meiotic regulators IME1, IME2 and IME4 itself; repressed in haploids via production of antisense IME4 transcripts; transcribed in diploid cells where antisense transcription is repressed; orthologous to human METTL3 (MT-A70) | Core | NA | NA | NA |
| 3835-YGL193C | YGL193C | NA | NA | Haploid-specific gene repressed by a1-alpha2; turned off in sir3 null strains, absence enhances the sensitivity of rad52-327 cells to campothecin almost 100-fold | Core | NA | NA | NA |
| 3836-YGL194C | YGL194C | HOS2 | histone deacetylase HOS2|RTL1 | Histone deacetylase and subunit of Set3 and Rpd3L complexes; required for gene activation via specific deacetylation of lysines in H3 and H4 histone tails; subunit of the Set3 complex, a meiotic-specific repressor of sporulation specific genes that contains deacetylase activity; co-localizes with Cmr1p in nuclear foci in response to DNA damage by MMS | Core | NA | NA | NA |
| 3837-YGL194C-A | YGL194C-A | NA | NA | Putative protein of unknown function; identified based on comparisons of the genome sequences of six Saccharomyces species; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum | Core | NA | NA | NA |
| 3838-YGL195W | YGL195W | GCN1 | AAS103|NDR1 | Positive regulator of the Gcn2p kinase activity; forms a complex with Gcn20p; proposed to stimulate Gcn2p activation by an uncharged tRNA | Core | NA | NA | NA |
| 3839-YGL196W | YGL196W | DSD1 | D-serine ammonia-lyase DSD1 | D-serine dehydratase (aka D-serine ammonia-lyase); converts D-serine to pyruvate and ammonia by a reaction dependent on pyridoxal 5'-phosphate and zinc; may play a role in D-serine detoxification; L-serine is not a substrate | Core | NA | NA | NA |
| 3840-YGL197W | YGL197W | MDS3 | NA | Putative component of the TOR regulatory pathway; negative regulator of early meiotic gene expression; required, with Pmd1p, for growth under alkaline conditions; has an N-terminal kelch-like domain; MDS3 has a paralog, PMD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3841-YGL198W_NumOfGenes_2 | YGL198W | YIP4 | NA | Protein that interacts with Rab GTPases; localized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests a possible role in vesicle-mediated transport | Core | NA | NA | NA |
| 3842-YGL200C | YGL200C | EMP24 | BST2 | Component of the p24 complex; role in misfolded protein quality control; binds to GPI anchor proteins and mediates their efficient transport from the ER to the Golgi; integral membrane protein that associates with endoplasmic reticulum-derived COPII-coated vesicles | Core | NA | NA | NA |
| 3843-YGL201C | YGL201C | MCM6 | MCM DNA helicase complex subunit MCM6 | Protein involved in DNA replication; component of the Mcm2-7 hexameric helicase complex that binds chromatin as a part of the pre-replicative complex; forms a subcomplex with Mcm4p and Mcm7p | Core | NA | NA | NA |
| 3844-YGL202W | YGL202W | ARO8 | bifunctional 2-aminoadipate transaminase/aromatic-amino-acid:2-oxoglutarate transaminase | Aromatic aminotransferase I; expression is regulated by general control of amino acid biosynthesis | Core | NA | NA | NA |
| 3845-YGL203C | YGL203C | KEX1 | serine-type carboxypeptidase | Cell death protease essential for hypochlorite-induced apoptosis; involved in the processing of killer toxin and alpha factor precursor; cleaves Lys and Arg residues from the C-terminus of peptides and proteins | Core | Ancestral | NA | NA |
| 3846-YGL204C | YGL204C | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum | Core | Unknown | NA | NA |
| 3847-YGL205W | YGL205W | POX1 | acyl-CoA oxidase|FOX1 | Fatty-acyl coenzyme A oxidase; involved in the fatty acid beta-oxidation pathway; localized to the peroxisomal matrix | Core | NA | NA | NA |