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 |
|---|---|---|---|---|---|---|---|---|
| 3998-YGR099W | YGR099W | TEL2 | NA | Subunit of the ASTRA complex, involved in chromatin remodeling; subunit of the telomere cap complex DNA-binding protein specific to single-stranded yeast telomeric DNA repeats, required for telomere length regulation and telomere position effect; involved in the stability or biogenesis of PIKKs such as TORC1 | Core | NA | NA | NA |
| 3999-YGR100W | YGR100W | MDR1 | GYP2|MIC1 | Cytoplasmic GTPase-activating protein; activates Ypt/Rab transport GTPases Ypt6p, Ypt31p and Sec4p; involved in recycling of internalized proteins and regulation of Golgi secretory function | Core | NA | NA | NA |
| 4000-YGR101W | YGR101W | PCP1 | rhomboid protease PCP1|RBD1|MDM37 | Mitochondrial serine protease; required for the processing of various mitochondrial proteins and maintenance of mitochondrial DNA and morphology; belongs to the rhomboid-GlpG superfamily of intramembrane peptidases | Core | NA | NA | NA |
| 4001-YGR102C | YGR102C | GTF1 | glutamyl-tRNA(Gln) amidotransferase subunit F | Subunit of the trimeric GatFAB AmidoTransferase(AdT) complex; involved in the formation of Q-tRNAQ; transposon insertion mutant is salt sensitive and null mutant has growth defects; non-tagged protein is detected in purified mitochondria | Core | NA | NA | NA |
| 4002-YGR103W | YGR103W | NOP7 | mRNA-binding ribosome synthesis protein NOP7|YPH1 | Component of several different pre-ribosomal particles; forms a complex with Ytm1p and Erb1p that is required for maturation of the large ribosomal subunit; required for exit from G<sub>0</sub> and the initiation of cell proliferation | Core | NA | NA | NA |
| 4003-YGR104C | YGR104C | SRB5 | MED18 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation; required for proper termination of transcription for some genes; involved in telomere maintenance | Core | NA | NA | NA |
| 4004-YGR105W | YGR105W | VMA21 | NA | Integral membrane protein required for V-ATPase function; not an actual component of the vacuolar H+-ATPase (V-ATPase) complex; diverged ortholog of human XMEA (X-linked Myopathy with Excessive Autophagy); functions in the assembly of the V-ATPase; localized to the yeast endoplasmic reticulum (ER) | Core | NA | NA | NA |
| 4005-YGR106C | YGR106C | VOA1 | NA | ER protein that functions in assembly of the V0 sector of V-ATPase; functions with other assembly factors; null mutation enhances the vacuolar ATPase (V-ATPase) deficiency of a vma21 mutant impaired in endoplasmic reticulum (ER) retrieval | Core | NA | NA | NA |
| 4006-YGR107W | YGR107W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4007-YGR108W | YGR108W | CLB1 | B-type cyclin CLB1|SCB1 | B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome; CLB1 has a paralog, CLB2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4008-YGR109C | YGR109C | CLB6 | B-type cyclin CLB6 | B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1; CLB6 has a paralog, CLB5, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4009-YGR110W | YGR110W | CLD1 | carboxylic ester hydrolase | Mitochondrial cardiolipin-specific phospholipase; functions upstream of Taz1p to generate monolyso-cardiolipin; transcription increases upon genotoxic stress; involved in restricting Ty1 transposition; has homology to mammalian CGI-58 | Core | NA | NA | NA |
| 4010-YGR111W | YGR111W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus | Core | NA | NA | NA |
| 4011-YGR112W | YGR112W | SHY1 | NA | Mitochondrial inner membrane protein required for complex IV assembly; associates with complex IV assembly intermediates and complex III/complex IV supercomplexes; similar to human SURF1 involved in Leigh Syndrome; complex IV is also known as cytochrome c oxidase | Core | NA | NA | NA |
| 4012-YGR113W | YGR113W | DAM1 | NA | Essential subunit of the Dam1 complex (aka DASH complex); cooperates with Duo1p to connect the DASH complex with the microtubules (MT); couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; Ipl1p target for regulating kinetochore-MT attachments | Core | NA | NA | NA |