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 |
|---|---|---|---|---|---|---|---|---|
| 2648-YDL203C | YDL203C | ACK1 | NA | Protein that functions in the cell wall integrity pathway; functions upstream of Pkc1p; GFP-fusion protein expression is induced in response to the DNA-damaging agent MMS; non-tagged Ack1p is detected in purified mitochondria | Core | NA | NA | NA |
| 2649-YDL204W | YDL204W | RTN2 | NA | Reticulon protein; involved in nuclear pore assembly and maintenance of tubular ER morphology; promotes membrane curvature; regulates the ER asymmetry-induced inheritance block during ER stress; role in ER-derived peroxisomal biogenesis; interacts with Sec6p, Yip3p, and Sbh1p; less abundant than RTN1; member of RTNLA (reticulon-like A) subfamily; protein increases in abundance and relocalizes to plasma membrane upon DNA replication stress | Core | NA | NA | NA |
| 2650-YDL205C | YDL205C | HEM3 | hydroxymethylbilane synthase|OLE2 | Porphobilinogen deaminase; catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in heme biosynthesis; localizes to the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p, but not by levels of heme; human homolog HMBS can complement yeast mutant and allow growth of haploid null after sporulation of a heterozygous diploid | Core | NA | NA | NA |
| 2651-YDL206W | YDL206W | NA | NA | Putative protein of unknown function; YDL206W is not an essential protein | Core | NA | NA | NA |
| 2652-YDL207W | YDL207W | GLE1 | nucleoporin GLE1|NLE2|BRR3|RSS1 | Cytoplasmic nucleoporin required for polyadenylated mRNA export; contains a nuclear export signal; when bound to inositol hexakisphosphate (IP6), functions as an activator for the Dbp5p ATPase activity at the nuclear pore complex during mRNA export; mediates translation initiation; required for efficient translation termination | Core | NA | NA | NA |
| 2653-YDL208W | YDL208W | NHP2 | snoRNA-binding protein NHP2 | Protein related to mammalian high mobility group (HMG) proteins; nuclear protein; essential for function of H/ACA-type snoRNPs, which are involved in 18S rRNA processing | Core | NA | NA | NA |
| 2654-YDL209C | YDL209C | CWC2 | NTC40 | Member of the NineTeen Complex (NTC); this complex contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs; binds directly to U6 snRNA; similar to S. pombe Cwf2 | Core | NA | NA | NA |
| 2655-YDL210W | YDL210W | UGA4 | NA | GABA (gamma-aminobutyrate) permease; serves as a GABA transport protein involved in the utilization of GABA as a nitrogen source; catalyzes the transport of putrescine and delta-aminolevulinic acid (ALA); localized to the vacuolar membrane | Core | NA | NA | NA |
| 2656-YDL211C | YDL211C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YDL211C has a paralog, TDA7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2657-YDL212W | YDL212W | SHR3 | APF1 | Endoplasmic reticulum packaging chaperone; required for incorporation of amino acid permeases into COPII coated vesicles for transport to the cell surface | Core | NA | NA | NA |
| 2658-YDL213C | YDL213C | NOP6 | NA | rRNA-binding protein required for 40S ribosomal subunit biogenesis; contains an RNA recognition motif (RRM); hydrophilin essential to overcome the stress of the desiccation-rehydration process; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes | Core | NA | NA | NA |
| 2659-YDL214C | YDL214C | PRR2 | serine/threonine protein kinase PRR2 | Serine/threonine protein kinase; inhibits pheromone induced signalling downstream of MAPK, possibly at the level of the Ste12p transcription factor; mutant has increased aneuploidy tolerance; PRR2 has a paralog, NPR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2660-YDL215C | YDL215C | GDH2 | glutamate dehydrogenase (NAD(+))|GDHB|GDH-B | NAD(+)-dependent glutamate dehydrogenase; degrades glutamate to ammonia and alpha-ketoglutarate; expression sensitive to nitrogen catabolite repression and intracellular ammonia levels; genetically interacts with GDH3 by suppressing stress-induced apoptosis | Core | NA | NA | NA |
| 2661-YDL216C | YDL216C | RRI1 | COP9 signalosome catalytic subunit RRI1|JAB1|CSN5 | Catalytic subunit of the COP9 signalosome (CSN) complex; acts as an isopeptidase in cleaving the ubiquitin-like protein Nedd8 from SCF ubiquitin ligases; metalloendopeptidase involved in the adaptation to pheromone signaling; involved in modulation of genes controlling amino acid and lipid metabolism, and ergosterol biosynthesis | Core | NA | NA | NA |
| 2662-YDL217C | YDL217C | TIM22 | translocation channel protein TIM22 | Essential core component of the mitochondrial TIM22 complex; involved in insertion of polytopic proteins into the inner membrane; forms the channel through which proteins are imported | Core | NA | NA | NA |