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 |
|---|---|---|---|---|---|---|---|---|
| 3668-YGL021W | YGL021W | ALK1 | protein kinase ALK1 | Protein kinase; along with its paralog, ALK2, required for proper spindle positioning and nuclear segregation following mitotic arrest, proper organization of cell polarity factors in mitosis, proper localization of formins and polarity factors, and survival in cells that activate spindle assembly checkpoint; phosphorylated in response to DNA damage; ALK1 has a paralog, ALK2, that arose from the whole genome duplication; similar to mammalian haspins | Accessory | Ancestral | NA | NA |
| 3669-YGL022W | YGL022W | STT3 | dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 | Subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes asparagine-linked glycosylation of newly synthesized proteins; forms a subcomplex with Ost3p and Ost4p and is directly involved in catalysis | Accessory | Ancestral | NA | NA |
| 3670-YGL023C | YGL023C | PIB2 | NA | Protein of unknown function; contains FYVE domain; similar to Fab1 and Vps27 | Core | NA | NA | NA |
| 3671-YGL024W | YGL024W | NA | SST3 | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially/completely overlaps the verified ORF PGD1/YGL025C | Accessory | Ancestral | NA | NA |
| 3672-YGL025C | YGL025C | PGD1 | MED3|HRS1 | Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for basal and activated transcription; direct target of Cyc8p-Tup1p transcriptional corepressor | Core | NA | NA | NA |
| 3673-YGL026C | YGL026C | TRP5 | tryptophan synthase TRP5 | Tryptophan synthase; catalyzes the last step of tryptophan biosynthesis; regulated by the general control system of amino acid biosynthesis | Core | NA | NA | NA |
| 3674-YGL027C | YGL027C | CWH41 | DER7|GLS1 | Processing alpha glucosidase I; ER type II integral membrane N-glycoprotein involved in assembly of cell wall beta 1,6 glucan and asparagine-linked protein glycosylation; also involved in ER protein quality control and sensing of ER stress | Core | NA | NA | NA |
| 3675-YGL028C | YGL028C | SCW11 | putative glucan endo-1,3-beta-D-glucosidase | Cell wall protein with similarity to glucanases; may play a role in conjugation during mating based on its regulation by Ste12p | Core | NA | NA | NA |
| 3676-YGL029W | YGL029W | CGR1 | NA | Protein involved in nucleolar integrity and processing of pre-rRNA; has a role in processing rRNA for the 60S ribosome subunit; transcript is induced in response to cytotoxic stress but not genotoxic stress; relocalizes from nucleus to nucleolus upon DNA replication stress | Core | NA | NA | NA |
| 3677-YGL030W_NumOfGenes_2 | YGL030W | RPL30 | eL30|ribosomal 60S subunit protein L30|L30e|rp73|YL38|L32|L30 | Ribosomal 60S subunit protein L30; involved in pre-rRNA processing in the nucleolus; autoregulates splicing of its transcript; homologous to mammalian ribosomal protein L30, no bacterial homolog | Core | NA | NA | NA |
| 3678-YGL031C_NumOfGenes_2 | YGL031C | RPL24A | eL24|ribosomal 60S subunit protein L24A|L24e|rp29|YL21|L30A|L24A|RPL30A | Ribosomal 60S subunit protein L24A; not essential for translation but may be required for normal translation rate; homologous to mammalian ribosomal protein L24, no bacterial homolog; RPL24A has a paralog, RPL24B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3679-YGL032C | YGL032C | AGA2 | NA | Adhesion subunit of a-agglutinin of a-cells; C-terminal sequence acts as a ligand for alpha-agglutinin (Sag1p) during agglutination, modified with O-linked oligomannosyl chains, linked to anchorage subunit Aga1p via two disulfide bonds | Core | NA | NA | NA |
| 3680-YGL033W | YGL033W | HOP2 | NA | Meiosis-specific protein that localizes to chromosomes; prevents synapsis between nonhomologous chromosomes and ensures synapsis between homologs; complexes with Mnd1p to promote homolog pairing and meiotic double-strand break repair; heterodimer of Hop2p-Mnd1p stimulates the Dmc1p-mediated strand invasion | Core | NA | NA | NA |
| 3681-YGL034C | YGL034C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YGL034C is not an essential gene | Core | NA | NA | NA |
| 3682-YGL035C | YGL035C | MIG1 | transcription factor MIG1|TDS22|SSN1|CAT4 | Transcription factor involved in glucose repression; sequence specific DNA binding protein containing two Cys2His2 zinc finger motifs; regulated by the SNF1 kinase and the GLC7 phosphatase; regulates filamentous growth along with Mig2p in response to glucose depletion; activated in stochastic pulses of nuclear localization, shuttling between cytosol and nucleus depending on external glucose levels and its phosphorylation state | Core | NA | NA | NA |