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 |
|---|---|---|---|---|---|---|---|---|
| 7538-YPL189C-A | YPL189C-A | COA2 | NA | Cytochrome oxidase assembly factor; null mutation results in respiratory deficiency with specific loss of cytochrome oxidase activity; functions downstream of assembly factors Mss51p and Coa1p and interacts with assembly factor Shy1p | Core | NA | NA | NA |
| 7539-YPL189W | YPL189W | GUP2 | putative O-acyltransferase | Probable membrane protein; possible role in proton symport of glycerol; member of the MBOAT family of putative membrane-bound O-acyltransferases; homolog of the mammalian Hedgehog pathway modulator HHAT; GUP2 has a paralog, GUP1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7540-YPL190C | YPL190C | NAB3 | HMD1 | RNA-binding protein, subunit of Nrd1 complex (Nrd1p-Nab3p-Sen1p); complex interacts with exosome to mediate 3'-end formation of some mRNAs, snRNAs, snoRNAs, and CUTs; required for termination of non-poly(A) transcripts and efficient splicing; Nrd1-Nab3 pathway appears to have a role in rapid suppression of some genes when cells are shifted to poor growth conditions, indicating role for Nrd1-Nab3 in regulating cellular response to nutrient availability | Core | NA | NA | NA |
| 7541-YPL191C | YPL191C | NA | NA | Protein of unknown function; diploid deletion strain exhibits high budding index; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL191C has a paralog, YGL082W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7542-YPL192C | YPL192C | PRM3 | pheromone-regulated protein PRM3 | Protein required for nuclear envelope fusion during karyogamy; pheromone-regulated; peripheral protein of the nuclear membrane; interacts with Kar5p at the spindle pole body | Core | NA | NA | NA |
| 7543-YPL193W | YPL193W | RSA1 | NA | Protein involved in the assembly of 60S ribosomal subunits; functionally interacts with Dbp6p; functions in a late nucleoplasmic step of the assembly | Core | NA | NA | NA |
| 7544-YPL194W | YPL194W | DDC1 | NA | DNA damage checkpoint protein; part of a PCNA-like complex required for DNA damage response, required for pachytene checkpoint to inhibit cell cycle in response to unrepaired recombination intermediates; potential Cdc28p substrate; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 7545-YPL195W | YPL195W | APL5 | YKS4 | Delta adaptin-like subunit of the clathrin associated protein complex; functions in transport of alkaline phosphatase to the vacuole via the alternate pathway; suppressor of loss of casein kinase 1 function; the clathrin associated protein complex is also known as AP-3 | Core | NA | NA | NA |
| 7546-YPL196W | YPL196W | OXR1 | NA | Protein of unknown function required for oxidative damage resistance; required for normal levels of resistance to oxidative damage; null mutants are sensitive to hydrogen peroxide; member of a conserved family of proteins found in eukaryotes | Core | NA | NA | NA |
| 7547-YPL198W_NumOfGenes_3 | YPL198W | RPL7B | uL30|ribosomal 60S subunit protein L7B|YL8|L7B|L6B|L30|rp11 | Ribosomal 60S subunit protein L7B; required for processing of 27SA3 pre-rRNA to 27SB pre-rRNA during assembly of large ribosomal subunit; depletion leads to a turnover of pre-rRNA; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2); binds to Domain II of 25S and 5.8S rRNAs; homologous to mammalian ribosomal protein L7 and bacterial L30; RPL7B has a paralog, RPL7A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7548-YPL199C | YPL199C | NA | NA | Putative protein of unknown function; predicted to be palmitoylated | Core | NA | NA | NA |
| 7549-YPL200W | YPL200W | CSM4 | NA | Protein required for accurate chromosome segregation during meiosis; involved in meiotic telomere clustering (bouquet formation) and telomere-led rapid prophase movements; functions with meiosis-specific telomere-binding protein Ndj1p; CSM4 has a paralog, MPS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7550-YPL201C | YPL201C | YIG1 | NA | Protein that interacts with glycerol 3-phosphatase; plays a role in anaerobic glycerol production; localizes to the nucleus and cytosol | Core | NA | NA | NA |
| 7551-YPL202C | YPL202C | AFT2 | NA | Iron-regulated transcriptional activator; activates genes involved in intracellular iron use and required for iron homeostasis and resistance to oxidative stress; AFT2 has a paralog, AFT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7552-YPL203W | YPL203W | TPK2 | cAMP-dependent protein kinase catalytic subunit TPK2|PKA3|YKR1|PKA2 | cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; partially redundant with Tpk1p and Tpk3p; localizes to P-bodies during stationary phase; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |