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 |
|---|---|---|---|---|---|---|---|---|
| 4058-YGR159C_NumOfGenes_2 | YGR159C | NSR1 | SHE5 | Nucleolar protein that binds nuclear localization sequences; required for pre-rRNA processing and ribosome biogenesis; binds to single stranded telomeric DNA and mRNA; methylated by Hmt1p; interaction with Top1p and nucleolar localization are negatively regulated by polyphosphorylation | Core | NA | NA | NA |
| 4059-YGR161C | YGR161C | RTS3 | NA | Putative component of the protein phosphatase type 2A complex | Core | NA | NA | NA |
| 4060-YGR161W-C | YGR161W-C | NA | NA | Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species | Core | NA | NA | NA |
| 4061-YGR162W | YGR162W | TIF4631 | translation initiation factor eIF4G|eiF4G1 | Translation initiation factor eIF4G; subunit of the mRNA cap-binding protein complex (eIF4F) that also contains eIF4E (Cdc33p); interacts with Pab1p and with eIF4A (Tif1p); also has a role in biogenesis of the large ribosomal subunit; TIF4631 has a paralog, TIF4632, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4062-YGR163W | YGR163W | GTR2 | NA | Subunit of a TORC1-stimulating GTPase complex; subunit of the Gtr1-Gtr2 GTPase complex that stimulates TORC1 in response to amino acid stimulation; stimulates the GTPase activity of Gtr1p; negatively regulates the Ran/Tc4 GTPase cycle; activates transcription; tethered to the vacuolar membrane as part of the EGO complex (EGOC); required for sorting of Gap1p; activated by the the Lst4p-Lst7p GAP complex; localizes to cytoplasm and to chromatin; homolog of human RagC and | Core | NA | NA | NA |
| 4063-YGR164W | YGR164W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4064-YGR165W | YGR165W | MRPS35 | mitochondrial 37S ribosomal protein MRPS35 | Mitochondrial ribosomal protein of the small subunit; null mutant does not grow on glycerol, is sensitive to 2,4-dichlorophenol, and accumulates large lipid droplets | Core | NA | NA | NA |
| 4065-YGR166W | YGR166W | TRS65 | KRE11 | Component of transport protein particle (TRAPP) complex II; TRAPPII is a multimeric guanine nucleotide-exchange factor for the GTPase Ypt1p, regulating intra-Golgi and endosome-Golgi traffic; role in cell wall beta-glucan biosynthesis and the stress response | Core | NA | NA | NA |
| 4066-YGR167W | YGR167W | CLC1 | SCD4 | Clathrin light chain; subunit of the major coat protein involved in intracellular protein transport and endocytosis; regulates endocytic progression; thought to regulate clathrin function; the clathrin triskelion is a trimeric molecule composed of three heavy chains that radiate from a vertex and three light chains which bind noncovalently near the vertex of the triskelion | Core | NA | NA | NA |
| 4067-YGR168C | YGR168C | NA | NA | Putative protein of unknown function; YGR168C is not an essential gene | Core | NA | NA | NA |
| 4068-YGR169C | YGR169C | PUS6 | pseudouridine synthase PUS6 | tRNA:pseudouridine synthase; catalyzes the conversion of uridine to pseudouridine at position 31 in cytoplasmic and mitochondrial tRNAs; mutation of Asp168 to Ala abolishes enzyme activity; not essential for viability | Core | NA | NA | NA |
| 4069-YGR169C-A | YGR169C-A | LSO2 | YGR169C-C | Protein with a potential role in response to iron deprivation; localizes to nucleus and cytoplasm, and nuclear localization is enhanced under iron-replete conditions; null mutant exhibits slow growth during iron deprivation; LSO2 has a paralog, LSO1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4070-YGR170W | YGR170W | PSD2 | phosphatidylserine decarboxylase 2 | Phosphatidylserine decarboxylase of the Golgi and vacuolar membranes; converts phosphatidylserine to phosphatidylethanolamine; controls vacuolar membrane phospholipid content by regulating phospholipids in compartments that will eventually give rise to the vacuole; loss of Psd2p causes a specific reduction in vacuolar membrane PE levels while total PE levels are not significantly affected | Core | NA | NA | NA |
| 4071-YGR171C | YGR171C | MSM1 | methionine--tRNA ligase MSM1 | Mitochondrial methionyl-tRNA synthetase (MetRS); functions as a monomer in mitochondrial protein synthesis; functions similarly to cytoplasmic MetRS although the cytoplasmic form contains a zinc-binding domain not found in Msm1p | Core | NA | NA | NA |
| 4072-YGR172C | YGR172C | YIP1 | transporter YIP1 | Integral membrane protein; required for the biogenesis of ER-derived COPII transport vesicles; interacts with Yif1p and Yos1p; localizes to the Golgi, the ER, and COPII vesicles; human homolog YIPF5 can complement yeast yip1 mutant | Core | NA | NA | NA |