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 |
|---|---|---|---|---|---|---|---|---|
| 7658-YPR032W | YPR032W | SRO7 | Rab GTPase-binding protein SRO7|SOP1|SNI1 | Effector of Rab GTPase Sec4p; forms a complex with Sec4p and t-SNARE Sec9p; involved in exocytosis and docking and fusion of post-Golgi vesicles with plasma membrane; regulates cell proliferation and colony development via the Rho1-Tor1 pathway; homolog of Drosophila lgl tumor suppressor; SRO7 has a paralog, SRO77, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7659-YPR033C | YPR033C | HTS1 | TS4572|histidine--tRNA ligase|TSM4572 | Cytoplasmic and mitochondrial histidine tRNA synthetase; efficient mitochondrial localization requires both a presequence and an amino-terminal sequence; mutations in human ortholog HARS2 are associated with Perrault syndrome | Core | NA | NA | NA |
| 7660-YPR034W | YPR034W | ARP7 | RSC11|SWP61 | Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation | Core | NA | NA | NA |
| 7661-YPR035W | YPR035W | GLN1 | glutamate--ammonia ligase | Glutamine synthetase (GS); synthesizes glutamine from glutamate and ammonia; with Glt1p, forms the secondary pathway for glutamate biosynthesis from ammonia; expression regulated by nitrogen source and by amino acid limitation; forms filaments of back-to-back stacks of cylindrical homo-decamers at low pH, leading to enzymatic inactivation and storage during states of advanced cellular starvation; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 7662-YPR036W | YPR036W | VMA13 | H(+)-transporting V1 sector ATPase subunit H|CLS11 | Subunit H of the V1 peripheral membrane domain of V-ATPase; part of the electrogenic proton pump found throughout the endomembrane system; serves as an activator or a structural stabilizer of the V-ATPase; the V1 peripheral membrane domain of the vacuolar H+-ATPase (V-ATPase) has eight subunits | Core | NA | NA | NA |
| 7663-YPR036W-A | YPR036W-A | SPO24 | NA | Small (67 amino acids) protein involved in sporulation; localizes to the prospore membrane; phosphorylated during meiosis; a longer, 5'-extended mRNA is also transcribed beginning in mid-meiosis, regulated by two MSEs (middle sporulation elements), and includes an uORF of 15 codons in its 5'-UTR; evidence transcription is regulated by Pdr1p | Core | NA | NA | NA |
| 7664-YPR037C | YPR037C | ERV2 | flavin-linked sulfhydryl oxidase | Flavin-linked sulfhydryl oxidase localized to the ER lumen; involved in disulfide bond formation within the endoplasmic reticulum (ER) | Core | NA | NA | NA |
| 7665-YPR038W | YPR038W | IRC16 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene YPR037C; null mutant displays increased levels of spontaneous Rad52p foci | Accessory | Ancestral | NA | NA |
| 7666-YPR039W | YPR039W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified non essential genes ERV2/YPR037C and TIP41/YPR040W | Accessory | Ancestral | NA | NA |
| 7667-YPR040W | YPR040W | TIP41 | NA | Protein that interacts with Tap42p, which regulates PP2A; component of the TOR (target of rapamycin) signaling pathway; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7668-YPR041W | YPR041W | TIF5 | translation initiation factor eIF5|SUI5 | Translation initiation factor eIF5; functions both as a GTPase-activating protein to mediate hydrolysis of ribosome-bound GTP and as a GDP dissociation inhibitor to prevent recycling of eIF2 | Core | NA | NA | NA |
| 7669-YPR042C | YPR042C | PUF2 | NA | PUF family mRNA-binding protein; Pumilio homology domain confers RNA binding activity; preferentially binds mRNAs encoding membrane-associated proteins; binding site composed of two UAAU tetranucleotides, separated by a 3-nt linker; PUF2 has a paralog, JSN1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7670-YPR043W_NumOfGenes_2 | YPR043W | RPL43A | eL43|ribosomal 60S subunit protein L43A|L43e|L43A | Ribosomal 60S subunit protein L43A; null mutation confers a dominant lethal phenotype; homologous to mammalian ribosomal protein L37A, no bacterial homolog; RPL43A has a paralog, RPL43B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7671-YPR045C | YPR045C | THP3 | MNI2 | Protein that may have a role in transcription elongation; forms a complex with Csn12p that is recruited to transcribed genes; possibly involved in splicing based on pre-mRNA accumulation defect for many intron-containing genes | Core | NA | NA | NA |
| 7672-YPR046W | YPR046W | MCM16 | NA | Component of the Ctf19 complex and the COMA subcomplex; involved in kinetochore-microtubule mediated chromosome segregation; binds to centromere DNA; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-H and fission yeast fta3 | Core | NA | NA | NA |