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 |
|---|---|---|---|---|---|---|---|---|
| 3428-YER099C_NumOfGenes_2 | YER099C | PRS2 | ribose phosphate diphosphokinase subunit PRS2 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, synthesizes PRPP; which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes; PRS2 has a paralog, PRS4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3429-YER100W_NumOfGenes_2 | YER100W | UBC6 | E2 ubiquitin-conjugating protein UBC6|DOA2 | Ubiquitin-conjugating enzyme involved in ERAD; located at the cytosolic side of the ER membrane; tail region contains a transmembrane segment at the C-terminus; substrate of the ubiquitin-proteasome pathway; ER-associated protein degradation is also known as ERAD | Core | NA | NA | NA |
| 3430-YER101C_NumOfGenes_2 | YER101C | AST2 | NA | Lipid raft associated protein; overexpression restores Pma1p localization to lipid rafts which is required for targeting of Pma1p to the plasma membrane; sometimes classified in the medium-chain dehydrogenase/reductases (MDRs) superfamily; AST2 has a paralog, AST1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3431-YER102W_NumOfGenes_2 | YER102W | RPS8B | eS8|ribosomal 40S subunit protein S8B|S8e|rp19|YS9|S8B|S14B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S8, no bacterial homolog; RPS8B has a paralog, RPS8A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3432-YER103W | YER103W | SSA4 | Hsp70 family chaperone SSA4|YG107 | Heat shock protein that is highly induced upon stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the HSP70 family; cytoplasmic protein that concentrates in nuclei upon starvation; SSA4 has a paralog, SSA3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3433-YER104W | YER104W | RTT105 | NA | Protein with a role in regulation of Ty1 transposition | Core | NA | NA | NA |
| 3434-YER105C | YER105C | NUP157 | NA | Subunit of the inner ring of the nuclear pore complex (NPC); contributes to NPC assembly and tethering of DNA to the nuclear periphery; both Nup170p and NUP157p are similar to human Nup155p; NUP157 has a paralog, NUP170, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3435-YER106W | YER106W | MAM1 | NA | Monopolin; meiosis-specific kinetochore-associated protein involved in monopolar attachment of sister kinetochores to the meiotic spindle; subunit of monopolin, a complex that prevents biorientation of sister kinetochores to ensure homolog biorientation during meiosis I; regulates the conformation, enzyme kinetics and substrate specificity of the Dsn1p kinase, Hrr1p; expressed only during the first meiotic division | Core | NA | NA | NA |
| 3436-YER107C | YER107C | GLE2 | RNA export factor GLE2|RAE1 | RNA export factor associated with the nuclear pore complex (NPC); associates with NUP116p; required for polyadenylated RNA export but not for protein import; homologous to S. pombe Rae1p and human RAE1 | Core | NA | NA | NA |
| 3437-YER107W-A | YER107W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified ORF GLE2/YER107C | Core | NA | NA | NA |
| 3438-YER109C | YER109C | FLO8 | transcription factor FLO8|STA10|YER108C|PHD5 | Transcription factor; required for flocculation, diploid filamentous growth, and haploid invasive growth; forms a heterodimer with Mss1p that interacts with the Swi/Snf complex during transcriptional activation of FLO1, FLO11, and STA1; S. cerevisiae genome reference strain S288C contains an internal in-frame stop at codon 142, which in other strains encodes tryptophan | Core | NA | NA | NA |
| 3439-YER110C | YER110C | KAP123 | YRB4 | Karyopherin beta; mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1 | Core | NA | NA | NA |
| 3440-YER111C | YER111C | SWI4 | SBF complex DNA-binding subunit SWI4|ART1 | DNA binding component of the SBF complex (Swi4p-Swi6p); a transcriptional activator that in concert with MBF (Mbp1-Swi6p) regulates late G1-specific transcription of targets including cyclins and genes required for DNA synthesis and repair; Slt2p-independent regulator of cold growth; acetylation at two sites, K1016 and K1066, regulates interaction with Swi6p | Core | NA | NA | NA |
| 3441-YER112W | YER112W | LSM4 | U6 snRNA complex subunit LSM4|USS1|SDB23 | Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA; forms cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 3442-YER113C | YER113C | TMN3 | NA | Protein with a role in cellular adhesion and filamentous growth; similar to Emp70p and Tmn2p; member of Transmembrane Nine family with 9 transmembrane segments; localizes to Golgi; induced by 8-methoxypsoralen plus UVA irradiation | Core | NA | NA | NA |