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 |
|---|---|---|---|---|---|---|---|---|
| 5798-YLR342W | YLR342W | FKS1 | 1,3-beta-D-glucan synthase|PBR1|GSC1|ETG1|CWH53|CND1 | Catalytic subunit of 1,3-beta-D-glucan synthase; functionally redundant with alternate catalytic subunit Gsc2p; binds to regulatory subunit Rho1p; involved in cell wall synthesis and maintenance; localizes to sites of cell wall remodeling; FKS1 has a paralog, GSC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5799-YLR342W-A | YLR342W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5800-YLR343W | YLR343W | GAS2 | 1,3-beta-glucanosyltransferase | 1,3-beta-glucanosyltransferase; involved with Gas4p in spore wall assembly; has similarity to Gas1p | Core | NA | NA | NA |
| 5801-YLR344W | YLR344W | RPL26A | uL24|ribosomal 60S subunit protein L26A|L24|YL33|L33A|L26A | Ribosomal 60S subunit protein L26A; binds to 5.8S rRNA; non-essential even when paralog is also deleted; deletion has minimal affections on ribosome biosynthesis; homologous to mammalian ribosomal protein L26 and bacterial L24; RPL26A has a paralog, RPL26B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5802-YLR345W | YLR345W | NA | bifunctional fructose-2,6-bisphosphate 2-phosphatase/6-phosphofructo-2-kinase | Similar to 6-phosphofructo-2-kinase enzymes; mRNA expression is repressed by the Rfx1p-Tup1p-Ssn6p repressor complex; YLR345W is not an essential gene | Core | NA | NA | NA |
| 5803-YLR346C | YLR346C | CIS1 | NA | Protein of unknown function found in mitochondria; expression is regulated by transcription factors involved in pleiotropic drug resistance, Pdr1p and Yrr1p; not an essential gene; YLR346C has a paralog, YGR035C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5804-YLR347C_NumOfGenes_2 | YLR347C | KAP95 | karyopherin beta|RSL1 | Karyopherin beta; forms a complex with Srp1p/Kap60p; interacts with nucleoporins to mediate nuclear import of NLS-containing cargo proteins via the nuclear pore complex; regulates PC biosynthesis; GDP-to-GTP exchange factor for Gsp1p | Core | NA | NA | NA |
| 5805-YLR348C | YLR348C | DIC1 | NA | Mitochondrial dicarboxylate carrier; integral membrane protein, catalyzes a dicarboxylate-phosphate exchange across the inner mitochondrial membrane, transports cytoplasmic dicarboxylates into the mitochondrial matrix | Core | NA | NA | NA |
| 5806-YLR349W | YLR349W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps the verified ORF DIC1/YLR348C | Accessory | Ancestral | NA | NA |
| 5807-YLR350W | YLR350W | ORM2 | sphingolipid homeostasis protein ORM2 | Protein that mediates sphingolipid homeostasis; evolutionarily conserved, required for resistance to agents that induce unfolded protein response; Orm1p and Orm2p together control membrane biogenesis by coordinating lipid homeostasis with protein quality control; protein abundance increases in response to DNA replication stress; ORM2 has a paralog, ORM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5808-YLR351C | YLR351C | NIT3 | putative hydrolase | Nit protein; one of two proteins in S. cerevisiae with similarity to the Nit domain of NitFhit from fly and worm and to the mouse and human Nit protein which interacts with the Fhit tumor suppressor; nitrilase superfamily member | Core | NA | NA | NA |
| 5809-YLR352W | YLR352W | NA | NA | Putative protein of unknown function with similarity to F-box proteins; interacts with Skp1p and Cdc53p; YLR352W is not an essential gene | Core | NA | NA | NA |
| 5810-YLR353W | YLR353W | BUD8 | NA | Protein involved in bud-site selection; diploid mutants display a unipolar budding pattern instead of the wild-type bipolar pattern, and bud at the proximal pole; BUD8 has a paralog, BUD9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5811-YLR354C | YLR354C | TAL1 | sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate transaldolase TAL1 | Transaldolase, enzyme in the non-oxidative pentose phosphate pathway; converts sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to erythrose 4-phosphate and fructose 6-phosphate; TAL1 has a paralog, NQM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5812-YLR355C | YLR355C | ILV5 | ketol-acid reductoisomerase | Acetohydroxyacid reductoisomerase and mtDNA binding protein; involved in branched-chain amino acid biosynthesis and maintenance of wild-type mitochondrial DNA; found in mitochondrial nucleoids | Core | NA | NA | NA |