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 |
|---|---|---|---|---|---|---|---|---|
| 3083-YDR389W | YDR389W | SAC7 | NA | GTPase activating protein (GAP) for Rho1p; regulator of a Tor2p-mediated, Rho1p GTPase switch that controls organization of the actin cytoskeleton; negative regulator of the RHO1-PKC1-MAPK cell integrity (CWI) and membrane fluidity homeostasis signaling pathways; potential Cdc28p substrate; SAC7 has a paralog, BAG7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3084-YDR390C | YDR390C | UBA2 | E1 ubiquitin-activating protein UBA2|UAL1 | Subunit of heterodimeric nuclear SUMO activating enzyme E1 with Aos1p; activates Smt3p (SUMO) before its conjugation to proteins (sumoylation), which may play a role in protein targeting; essential for viability | Accessory | Ancestral | NA | NA |
| 3085-YDR391C | YDR391C | NA | NA | Putative protein of unknown function; possibly involved in zinc homeostasis; Bdf1p-dependent transcription induced by salt stress; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus | Accessory | Ancestral | NA | NA |
| 3086-YDR392W | YDR392W | SPT3 | transcriptional regulator SPT3 | Subunit of the SAGA and SAGA-like transcriptional regulatory complexes; interacts with Spt15p to activate transcription of some RNA polymerase II-dependent genes, also functions to inhibit transcription at some promoters; relocalizes to the cytosol in response to hypoxia | Accessory | Ancestral | NA | NA |
| 3087-YDR393W | YDR393W | SHE9 | MDM33 | Protein required for normal mitochondrial morphology; mitochondrial inner membrane protein; may be involved in fission of the inner membrane; forms a homo-oligomeric complex | Accessory | Ancestral | NA | NA |
| 3088-YDR394W | YDR394W | RPT3 | proteasome regulatory particle base subunit RPT3|YTA2|YNT1 | ATPase of the 19S regulatory particle of the 26S proteasome; one of ATPases of the regulatory particle; involved in the degradation of ubiquitinated substrates; substrate of N-acetyltransferase B | Core | NA | NA | NA |
| 3089-YDR395W | YDR395W | SXM1 | KAP108 | Nuclear transport factor (karyopherin); involved in protein transport between the cytoplasm and nucleoplasm; similar to Nmd5p, Cse1p, Lph2p, and the human cellular apoptosis susceptibility protein, CAS1 | Core | NA | NA | NA |
| 3090-YDR397C_NumOfGenes_2 | YDR397C | NCB2 | negative cofactor 2 transcription regulator complex subunit NCB2|YDR1 | Subunit of a heterodimeric NC2 transcription regulator complex; complex binds to TBP and can repress transcription by preventing preinitiation complex assembly or stimulate activated transcription; homologous to human NC2beta; complex also includes Bur6p | Core | NA | NA | NA |
| 3091-YDR398W | YDR398W | UTP5 | NA | Subunit of U3-containing Small Subunit (SSU) processome complex; involved in production of 18S rRNA and assembly of small ribosomal subunit | Accessory | Ancestral | NA | NA |
| 3092-YDR399W | YDR399W | HPT1 | hypoxanthine phosphoribosyltransferase|HGPRTase|HPRT|BRA6 | Dimeric hypoxanthine-guanine phosphoribosyltransferase; catalyzes the transfer of the phosphoribosyl portion of 5-phosphoribosyl-alpha-1-pyrophosphate to a purine base (either guanine or hypoxanthine) to form pyrophosphate and a purine nucleotide (either guanosine monophosphate or inosine monophosphate); mutations in the human homolog HPRT1 can cause Lesch-Nyhan syndrome and Kelley-Seegmiller syndrome | Accessory | Ancestral | NA | NA |
| 3093-YDR400W | YDR400W | URH1 | trifunctional uridine nucleosidase/nicotinamide riboside hydrolase/nicotinic acid riboside hydrolase | Uridine nucleosidase (uridine-cytidine N-ribohydrolase); cleaves N-glycosidic bonds in nucleosides; involved in the pyrimidine salvage and nicotinamide riboside salvage pathways | Accessory | Ancestral | NA | NA |
| 3094-YDR402C_NumOfGenes_2 | YDR402C | DIT2 | putative cytochrome P450|CYP56 | N-formyltyrosine oxidase; sporulation-specific microsomal enzyme involved in the production of N,N-bisformyl dityrosine required for spore wall maturation, homologous to cytochrome P-450s; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and vacuole respectively | Accessory | Ancestral | NA | NA |
| 3095-YDR403W | YDR403W | DIT1 | NA | Sporulation-specific enzyme required for spore wall maturation; involved in the production of a soluble LL-dityrosine-containing precursor of the spore wall; transcripts accumulate at the time of prospore enclosure | Core | NA | NA | NA |
| 3096-YDR404C | YDR404C | RPB7 | DNA-directed RNA polymerase II subunit RPB7|B16 | RNA polymerase II subunit B16; forms dissociable heterodimer with Rpb4p; Rpb4/7 dissociates from RNAPII as Ser2 CTD phosphorylation increases; Rpb4/7 regulates cellular lifespan via mRNA decay process; involved in recruitment of 3'-end processing factors to transcribing RNA polymerase II complex, export of mRNA to cytoplasm under stress conditions; also involved in translation initiation | Core | NA | NA | NA |
| 3097-YDR405W | YDR405W | MRP20 | mitochondrial 54S ribosomal protein YmL41|YmL41|MRPL41 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |