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 |
|---|---|---|---|---|---|---|---|---|
| 2603-YDL158C | YDL158C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 2604-YDL159W_NumOfGenes_3 | YDL159W | STE7 | mitogen-activated protein kinase kinase STE7 | Signal transducing MAP kinase kinase; involved in pheromone response where it phosphorylates Fus3p; involved in the pseudohyphal/invasive growth pathway where it phosphorylates of Kss1p; phosphorylated by Ste11p; degraded by ubiquitin pathway | Core | NA | NA | NA |
| 2605-YDL159W-A | YDL159W-A | NA | YDL159W-B | Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species | Core | NA | NA | NA |
| 2606-YDL160C | YDL160C | DHH1 | DExD/H-box ATP-dependent RNA helicase DHH1 | Cytoplasmic DEAD-box helicase, stimulates mRNA decapping; coordinates distinct steps in mRNA function and decay, interacting with both decapping and deadenylase complexes; role in translational repression, mRNA decay, and possibly mRNA export; interacts and cooperates with Ngr1p to promote specific mRNA decay; ATP- and RNA-bound form promotes processing body (PB) assembly, while ATPase stimulation by Not1p promotes PB disassembly; forms cytoplasmic foci on replication stress | Accessory | Ancestral | NA | NA |
| 2607-YDL160C-A | YDL160C-A | MHF2 | NA | Component of the heterotetrameric MHF histone-fold complex; in humans the MHF complex interacts with both DNA and Mph1p ortholog FANCM to stabilize and remodel blocked replication forks and repair damaged DNA; mhf2 srs2 double mutants are MMS hypersensitive; orthologous to human centromere constitutive-associated network (CCAN) subunit CENP-X, also known as MHF2 | Accessory | Ancestral | NA | NA |
| 2608-YDL161W | YDL161W | ENT1 | epsin | Epsin-like protein involved in endocytosis and actin patch assembly; functionally redundant with Ent2p; binds clathrin via a clathrin-binding domain motif at C-terminus; relocalizes from bud neck to cytoplasm upon DNA replication stress; ENT1 has a paralog, ENT2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2609-YDL162C | YDL162C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ENT1/YDL161W, a verified gene involved in endocytosis and actin cortical patch assembly | Accessory | Ancestral | NA | NA |
| 2610-YDL164C_NumOfGenes_2 | YDL164C | CDC9 | DNA ligase (ATP) CDC9|MMS8 | DNA ligase I found in nucleus and mitochondria; essential enzyme that joins Okazaki fragments during DNA replication; also acts in ribonucleotide excision repair, base excision repair, and recombination; DNA ligase I mutants trigger ubiquitination of PCNA at K107, facilitating Rad59p-mediated bypass of unligated Okazaki fragments; human homolog LIG1 can complement yeast cdc9 temperature-sensitive mutant at restrictive temperature | Accessory | Ancestral | NA | NA |
| 2611-YDL165W | YDL165W | CDC36 | CCR4-NOT core subunit CDC36|NOT2|DNA19 | Component of the CCR4-NOT core complex, involved in mRNA decapping; this complex has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs through deadenylation; basal transcription factor | Accessory | Ancestral | NA | NA |
| 2612-YDL166C | YDL166C | FAP7 | nucleoside-triphosphatase | Essential NTPase required for small ribosome subunit synthesis; mediates processing of the 20S pre-rRNA at site D in the cytoplasm but associates only transiently with 43S preribosomes via Rps14p; complex with Rps14 is conserved between humans, yeast, and arches; may be the endonuclease for site D; depletion leads to accumulation of pre-40S ribosomes in 80S-like ribosomes; human TAF9 functionally complements the lethality of the null mutation | Accessory | Ancestral | NA | NA |
| 2613-YDL167C | YDL167C | NRP1 | NA | Putative RNA binding protein of unknown function; localizes to stress granules induced by glucose deprivation; predicted to be involved in ribosome biogenesis | Accessory | Ancestral | NA | NA |
| 2614-YDL168W | YDL168W | SFA1 | bifunctional alcohol dehydrogenase/S-(hydroxymethyl)glutathione dehydrogenase|ADH5 | Bifunctional alcohol dehydrogenase and formaldehyde dehydrogenase; formaldehyde dehydrogenase activity is glutathione-dependent; functions in formaldehyde detoxification and formation of long chain and complex alcohols, regulated by Hog1p-Sko1p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2615-YDL169C | YDL169C | UGX2 | NA | Protein of unknown function; transcript accumulates in response to any combination of stress conditions | Core | NA | NA | NA |
| 2616-YDL170W | YDL170W | UGA3 | NA | Transcriptional activator for GABA-dependent induction of GABA genes; binds to DNA elements found in the promoters of target genes and increases their expression in the presence of GABA (gamma-aminobutyrate); zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type; localized to the nucleus; examples of GABA genes include UGA1, UGA2, and UGA4 | Core | NA | NA | NA |
| 2617-YDL171C | YDL171C | GLT1 | glutamate synthase (NADH) | NAD(+)-dependent glutamate synthase (GOGAT); synthesizes glutamate from glutamine and alpha-ketoglutarate; with Gln1p, forms the secondary pathway for glutamate biosynthesis from ammonia; expression regulated by nitrogen source; assembles into filaments as cells approach stationary phase and under cytosolic acidification and starvation conditions | Core | NA | NA | NA |