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 |
|---|---|---|---|---|---|---|---|---|
| 4958-YJR051W | YJR051W | OSM1 | fumarate reductase|FRDS2 | Fumarate reductase, catalyzes the reduction of fumarate to succinate; required for the reoxidation of intracellular NADH under anaerobic conditions; mutations cause osmotic sensitivity; has two translation start sites, one at the annotated start codon which produces an ER-targeted form required for anaerobic growth, and one at codon 32 which produces a mitochondrially-targeted form; OSM1 has a paralog, FRD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4959-YJR052W | YJR052W | RAD7 | UV-damaged DNA-binding protein RAD7 | Nucleotide excision repair (NER) protein; binds damaged DNA during NER; binds DNA in an ATP-dependent manner (with Rad16p) during NER; required for repair of non-transcribed chromatin; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex | Core | NA | NA | NA |
| 4960-YJR053W | YJR053W | BFA1 | IBD1 | Subunit of a two-component GTPase-activating protein, Bfa1p-Bub2p; contributes to GAP activity, inactivating Tem1 by stimulating GTP hydrolysis following damage or misalignment of the mitotic spindle; functions as a guanine-nucleotide exchange inhibitor (GDI) for Tem1p; involved in multiple cell cycle checkpoint pathways that control mitotic exit; required when telomeres are damaged, but not for all types of chromosomal DNA damage; phosphorylated by the Polo-like kinase Cdc5p | Core | NA | NA | NA |
| 4961-YJR054W | YJR054W | KCH1 | ERM6 | Potassium transporter that mediates K+ influx; activates high-affinity Ca2+ influx system (HACS) during mating pheromone response; expression up-regulated in response to alpha factor; localized to sites of polarized growth; member of a fungal-specific gene family; potential Cdc28p substrate; KCH1 has a paralog, PRM6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4962-YJR055W | YJR055W | HIT1 | NA | Protein involved in C/D snoRNP assembly; regulates abundance of Rsa1p; required for growth at high temperature; similar to human ZNHIT3 | Core | NA | NA | NA |
| 4963-YJR056C | YJR056C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 4964-YJR057W | YJR057W | CDC8 | bifunctional thymidylate/uridylate kinase | Thymidylate and uridylate kinase; functions in de novo biosynthesis of pyrimidine deoxyribonucleotides; converts dTMP to dTDP and dUMP to dUTP; essential for mitotic and meiotic DNA replication; homologous to S. pombe tmp1; human homolog DTYMK can complement yeast cdc8 null mutant | Core | NA | NA | NA |
| 4965-YJR058C | YJR058C | APS2 | YAP17 | Small subunit of the clathrin-associated adaptor complex AP-2; AP-2 is involved in protein sorting at the plasma membrane; related to the sigma subunit of the mammalian plasma membrane clathrin-associated protein (AP-2) complex | Core | NA | NA | NA |
| 4966-YJR059W | YJR059W | PTK2 | protein kinase PTK2|STK2 | Serine/threonine protein kinase; involved in regulation of ion transport across plasma membrane; carboxyl terminus is essential for glucose-dependent Pma1p activation via phosphorylation of Pma1p-Ser899; enhances spermine uptake; PTK2 has a paralog, PTK1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4967-YJR060W | YJR060W | CBF1 | GFII|CP1|CPF1|CEP1 | Basic helix-loop-helix (bHLH) protein; forms homodimer to bind E-box consensus sequence CACGTG present at MET gene promoters and centromere DNA element I (CDEI); affects nucleosome positioning at this motif; associates with other transcription factors such as Met4p and Isw1p to mediate transcriptional activation or repression; associates with kinetochore proteins, required for chromosome segregation; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4968-YJR061W | YJR061W | NA | NA | Putative protein of unknown function; non-essential gene; transcription repressed by Rm101p; YJR061W has a paralog, MNN4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4969-YJR062C | YJR062C | NTA1 | amidase|DEA1 | Amidase; removes the amide group from N-terminal asparagine and glutamine residues to generate proteins with N-terminal aspartate and glutamate residues that are targets of ubiquitin-mediated degradation | Core | NA | NA | NA |
| 4970-YJR063W_NumOfGenes_2 | YJR063W | RPA12 | DNA-directed RNA polymerase I core subunit RPA12|A12.2|RRN4 | RNA polymerase I subunit A12.2; contains two zinc binding domains, and the N terminal domain is responsible for anchoring to the RNA pol I complex; physically interacts with transcriptional activator Msn4p, to regulate transcription of AYR1, a gene involved in lipid metabolism | Core | NA | NA | NA |
| 4971-YJR064W | YJR064W | CCT5 | chaperonin-containing T-complex subunit CCT5|TCP5 | Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivo | Core | NA | NA | NA |
| 4972-YJR065C_NumOfGenes_2 | YJR065C | ARP3 | actin-related protein 3|ACT4 | Essential component of the Arp2/3 complex; Arp2/3 is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity | Core | NA | NA | NA |