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 |
|---|---|---|---|---|---|---|---|---|
| 4418-YHR159W | YHR159W | TDA11 | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; potential Cdc28p substrate; null mutant is sensitive to expression of the top1-T722A allele | Core | NA | NA | NA |
| 4419-YHR160C | YHR160C | PEX18 | NA | Peroxin; required for targeting of peroxisomal matrix proteins containing PTS2; interacts with Pex7p; partially redundant with Pex21p; primarily responsible for peroxisomal import during growth on oleate, and expression is induced during oleate growth | Core | NA | NA | NA |
| 4420-YHR161C | YHR161C | YAP1801 | NA | Protein of the AP180 family, involved in clathrin cage assembly; binds Pan1p and clathrin; YAP1801 has a paralog, YAP1802, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4421-YHR162W | YHR162W | MPC2 | mitochondrial pyruvate carrier | Highly conserved subunit of the mitochondrial pyruvate carrier (MPC); expressed during growth on fermentable carbon sources, and heterodimerizes with Mpc1p to form the fermentative isoform of MPC; MPC localizes to the mitochondrial inner membrane and mediates pyruvate uptake; MPC2 paralog, MPC3, heterodimerizes with Mpc1p to form the respiratory MPC isoform | Core | NA | NA | NA |
| 4422-YHR163W | YHR163W | SOL3 | 6-phosphogluconolactonase SOL3 | 6-phosphogluconolactonase; catalyzes the second step of the pentose phosphate pathway; weak multicopy suppressor of los1-1 mutation; homologous to Sol2p and Sol1p; SOL3 has a paralog, SOL4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4423-YHR164C | YHR164C | DNA2 | bifunctional ATP-dependent DNA helicase/ssDNA endodeoxyribonuclease DNA2|WEB2 | Tripartite DNA replication factor; single-stranded DNA-dependent ATPase, ATP-dependent nuclease, helicase; tracking protein for flap cleavage during Okazaki fragment maturation; involved in DNA repair/processing of meiotic DNA double strand breaks; component of telomeric chromatin with cell-cycle dependent localization; required for telomerase-dependent telomere synthesis; forms nuclear foci upon DNA replication stress; human homolog DNA2 complements yeast dna2 mutant | Core | NA | NA | NA |
| 4424-YHR165C_NumOfGenes_2 | YHR165C | PRP8 | U4/U6-U5 snRNP complex subunit PRP8|USA2|SLT21|RNA8|DNA39|DBF3 | Component of U4/U6-U5 snRNP complex; involved in second catalytic step of splicing; participates in spliceosomal assembly through its interaction with U1 snRNA; largest and most evolutionarily conserved protein of the spliceosome; mutations in human ortholog, PRPF8, cause Retinitis pigmentosa and missplicing in Myelodysplastic syndrome; mouse ortholog interacts with androgen receptor and may have a role in prostate cancer | Core | NA | NA | NA |
| 4425-YHR166C | YHR166C | CDC23 | anaphase promoting complex subunit CDC23 | Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C); APC/C is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition | Core | NA | NA | NA |
| 4426-YHR167W | YHR167W | THP2 | NA | Subunit of the THO and TREX complexes; THO connects transcription elongation and mitotic recombination, and TREX is recruited to activated genes and couples transcription to mRNA export; involved in telomere maintenance | Core | NA | NA | NA |
| 4427-YHR168W | YHR168W | MTG2 | putative GTPase MTG2 | Putative GTPase; member of the Obg family; peripheral protein of the mitochondrial inner membrane that associates with the large ribosomal subunit; required for mitochondrial translation, possibly via a role in ribosome assembly | Core | NA | NA | NA |
| 4428-YHR169W | YHR169W | DBP8 | ATP-dependent RNA helicase DBP8 | ATPase, putative RNA helicase of the DEAD-box family; component of 90S preribosome complex involved in production of 18S rRNA and assembly of 40S small ribosomal subunit; ATPase activity stimulated by association with Esf2p | Core | NA | NA | NA |
| 4429-YHR170W | YHR170W | NMD3 | ribosome-binding protein NMD3|SRC5 | Protein involved in nuclear export of the large ribosomal subunit; acts as a Crm1p-dependent adapter protein for export of nascent ribosomal subunits through the nuclear pore complex | Core | NA | NA | NA |
| 4430-YHR171W | YHR171W | ATG7 | APG11|APG7|CVT2 | Autophagy-related protein and dual specificity member of the E1 family; mediates the attachment of Atg12p to Atg5p and Atg8p to phosphatidylethanolamine which are required steps in autophagosome formation; E1 enzymes are also known as ubiquitin-activating enzymes; involved in methionine restriction extension of chronological lifespan in an autophagy-dependent manner | Core | NA | NA | NA |
| 4431-YHR172W | YHR172W | SPC97 | NA | Component of the microtubule-nucleating Tub4p (gamma-tubulin) complex; interacts with Spc110p at the spindle pole body (SPB) inner plaque and with Spc72p at the SPB outer plaque | Core | NA | NA | NA |
| 4432-YHR173C | YHR173C | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels; SWAT-GFP and mCherry fusion proteins localize to the vacuole | Core | NA | NA | NA |