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 |
|---|---|---|---|---|---|---|---|---|
| 4133-YGR234W | YGR234W | YHB1 | flavohemoglobin|YHB4 | Nitric oxide oxidoreductase; flavohemoglobin that plays role in oxidative and nitrosative stress responses; protects against nitration of cellular targets and against cell growth inhibition under aerobic or anaerobic conditions; yeast flavohemoglobin Yhb1p and human homolog neuroglobin NGB protect cells against alpha-synuclein cytotoxicity and aggregate formation; protein increases in abundance, relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Core | NA | NA | NA |
| 4134-YGR235C | YGR235C | MIC26 | MOS2|MCS29|MIO27 | Component of the MICOS complex; MICOS (formerly MINOS or MitOS) is a mitochondrial inner membrane complex that extends into the intermembrane space and has a role in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane; Mic26p is a non-essential component of the complex | Accessory | Ancestral | NA | NA |
| 4135-YGR236C | YGR236C | SPG1 | NA | Protein required for high temperature survival during stationary phase; not required for growth on nonfermentable carbon sources; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 4136-YGR237C | YGR237C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Accessory | Ancestral | NA | NA |
| 4137-YGR238C | YGR238C | KEL2 | NA | Protein that negatively regulates mitotic exit; forms a complex with Kel1p and Bud14p that regulates Bnr1p (formin) to affect actin cable assembly, cytokinesis, and polarized growth; functions in a complex with Kel1p, interacts with Tem1p and Lte1p; localizes to regions of polarized growth; potential Cdc28p substrate | Accessory | Ancestral | NA | NA |
| 4138-YGR239C | YGR239C | PEX21 | NA | Peroxin required for peroxisomal matrix protein targeting; acts on proteins containing the PTS2 targeting sequence; interacts with Pex7p; constitutively expressed; partially redundant with Pex18p; required for import of the Gpd1p-Pnc1p heterodimer in which only Gpd1p has a peroxisomal targeting signal; relative distribution to cytoplasmic foci increases upon DNA replication stress | Core | NA | NA | NA |
| 4139-YGR240C | YGR240C | PFK1 | 6-phosphofructokinase subunit alpha | Alpha subunit of heterooctameric phosphofructokinase; involved in glycolysis, indispensable for anaerobic growth, activated by fructose-2,6-bisphosphate and AMP, mutation inhibits glucose induction of cell cycle-related genes | Core | NA | NA | NA |
| 4140-YGR240C-A | YGR240C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 4141-YGR241C | YGR241C | YAP1802 | NA | Protein of the AP180 family, involved in clathrin cage assembly; binds Pan1p and clathrin; YAP1802 has a paralog, YAP1801, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4142-YGR242W | YGR242W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF YAP1802/YGR241C | Accessory | Ancestral | NA | NA |
| 4143-YGR243W | YGR243W | MPC3 | mitochondrial pyruvate carrier|FMP43 | Highly conserved subunit of the mitochondrial pyruvate carrier (MPC); expressed during growth on nonfermentable carbon sources, and heterodimerizes with Mpc1p to form the respiratory isoform of MPC; MPC localizes to the mitochondrial inner membrane and mediates pyruvate uptake; MPC3 paralog, MPC2, heterodimerizes with Mpc1p to form the fermentative MPC isoform; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4144-YGR244C | YGR244C | LSC2 | succinate--CoA ligase (GDP-forming) subunit beta | Beta subunit of succinyl-CoA ligase; succinyl-CoA ligase is a mitochondrial enzyme of the TCA cycle that catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate | Core | NA | NA | NA |
| 4145-YGR245C | YGR245C | SDA1 | NA | Protein required for actin organization and passage through Start; highly conserved nuclear protein; required for actin cytoskeleton organization; plays a critical role in G1 events; binds Nap1p; involved in 60S ribosome biogenesis | Core | NA | NA | NA |
| 4146-YGR246C | YGR246C | BRF1 | transcription factor TFIIIB subunit BRF1|TFIIIB70|TDS4|PCF4 | TFIIIB B-related factor; one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB; mutations in human homolog are associated with autosomal recessive cerebellar-facial-dental syndrome | Core | NA | NA | NA |
| 4147-YGR247W | YGR247W | CPD1 | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | Cyclic nucleotide phosphodiesterase; hydrolyzes ADP-ribose 1'', 2''-cyclic phosphate to ADP-ribose 1''-phosphate; may have a role in tRNA splicing; no detectable phenotype is conferred by null mutation or by overexpression; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |