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 |
|---|---|---|---|---|---|---|---|---|
| 1763-snap_masked-CPN_4-15749 | NA | NA | NA | NA | Accessory | Introgression | S. paradoxus | NA |
| 1764-snap_masked-CPG_1-7550 | NA | NA | NA | NA | Accessory | Introgression | S. paradoxus | NA |
| 1765-snap_masked-CPQ_4-15088 | NA | NA | NA | NA | Accessory | Introgression | S. paradoxus | NA |
| 1766-snap_masked-AEF_8-5136 | NA | NA | NA | NA | Accessory | Ancestral | NA | NA |
| 1767-snap_masked-BCA_3-8244 | NA | NA | NA | NA | Accessory | Unknown | NA | NA |
| 1768-YAL001C | YAL001C | TFC3 | transcription factor TFIIIC subunit TFC3|tau 138|TSV115|FUN24 | Subunit of RNA polymerase III transcription initiation factor complex; part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding; largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC) | Core | NA | NA | NA |
| 1769-YAL002W | YAL002W | VPS8 | CORVET complex membrane-binding subunit VPS8|VPL8|VPT8|FUN15 | Membrane-binding component of the CORVET complex; involved in endosomal vesicle tethering and fusion in the endosome to vacuole protein targeting pathway; interacts with Vps21p; contains RING finger motif | Core | NA | NA | NA |
| 1770-YAL003W | YAL003W | EFB1 | translation elongation factor 1 subunit beta|EF-1beta|eEF1Balpha|TEF5 | Translation elongation factor 1 beta; stimulates nucleotide exchange to regenerate EF-1 alpha-GTP for the next elongation cycle; part of the EF-1 complex, which facilitates binding of aminoacyl-tRNA to the ribosomal A site; human homolog EEF1B2 can complement yeast efb1 mutants | Core | NA | NA | NA |
| 1771-YAL005C_NumOfGenes_3 | YAL005C | SSA1 | Hsp70 family ATPase SSA1|YG100 | ATPase involved in protein folding and NLS-directed nuclear transport; member of HSP70 family; required for ubiquitin-dependent degradation of short-lived proteins; forms chaperone complex with Ydj1p; localized to nucleus, cytoplasm, cell wall; 98% identical to paralog Ssa2p with different functional specificity in propagation of yeast [URE3] prions, vacuolar-mediated degradations of gluconeogenesis enzymes; general targeting factor of Hsp104p to prion fibrils | Core | NA | NA | NA |
| 1772-YAL007C | YAL007C | ERP2 | NA | Member of the p24 family involved in ER to Golgi transport; similar to Emp24p and Erv25p; role in misfolded protein quality control; forms a heterotrimeric complex with Erp1p, Emp24p, and Erv25p; localized to COPII-coated vesicles; ERP2 has a paralog, ERP4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1773-YAL008W | YAL008W | FUN14 | MCP3 | Integral mitochondrial outer membrane (MOM) protein; dosage suppressor of an MDM10 null that reduces ERMES-related phenotypes, such as alterations in mitochondrial morphology, protein complex assembly, and lipid profile; dosage suppressor of MDM12, MDM34, and MMM1 null mutant growth defects; novel mechanism of MOM import involving Tom70p, the TOM complex, and the TIM23 complex, requiring mitochondrial membrane potential and processing by the IMP complex for correct biogenesis | Accessory | Ancestral | NA | NA |
| 1774-YAL009W | YAL009W | SPO7 | Nem1-Spo7 phosphatase regulatory subunit SPO7 | Putative regulatory subunit of Nem1p-Spo7p phosphatase holoenzyme; regulates nuclear growth by controlling phospholipid biosynthesis, required for normal nuclear envelope morphology, premeiotic replication, and sporulation | Core | NA | NA | NA |
| 1775-YAL010C | YAL010C | MDM10 | FUN37 | Subunit of both the ERMES and the SAM complex; component of ERMES complex which acts as a molecular tether between the mitochondria and the ER, necessary for efficient phospholipid exchange between organelles and for mitophagy; SAM/TOB complex component that functions in the assembly of outer membrane beta-barrel proteins; involved in mitochondrial inheritance and morphology; ERMES complex is often co-localized with peroxisomes and concentrated areas of pyruvate dehydrogenase | Core | NA | NA | NA |
| 1776-YAL011W | YAL011W | SWC3 | SWC1 | Protein of unknown function; component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; required for formation of nuclear-associated array of smooth endoplasmic reticulum known as karmellae | Core | NA | NA | NA |
| 1777-YAL012W | YAL012W | CYS3 | cystathionine gamma-lyase CYS3|STR1|FUN35|CYI1 | Cystathionine gamma-lyase; catalyzes one of the two reactions involved in the transsulfuration pathway that yields cysteine from homocysteine with the intermediary formation of cystathionine; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |