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 |
|---|---|---|---|---|---|---|---|---|
| 5903-YLR445W | YLR445W | GMC2 | NA | Protein involved in meiotic crossing over; component of the Synaptonemal Complex (SC) along with Ecm11p; required for the efficient loading of the SC transverse filament protein, Zip1p; promotes SUMOylation of Ecm11p; mutants are delayed in meiotic nuclear division and are defective in synaptonemal complex assembly; transcription is regulated by Ume6p and induced in response to alpha factor | Core | NA | NA | NA |
| 5904-YLR446W_NumOfGenes_2 | YLR446W | NA | hexokinase | Putative hexokinase; transcript is upregulated during sporulation and the unfolded protein response; YLR446W is not an essential gene | Core | NA | NA | NA |
| 5905-YLR447C_NumOfGenes_2 | YLR447C | VMA6 | H(+)-transporting V0 sector ATPase subunit d | Subunit d of the V0 integral membrane domain of V-ATPase; part of the electrogenic proton pump found in the endomembrane system; required for V1 domain assembly on the vacuolar membrane; the V0 integral membrane domain of vacuolar H+-ATPase (V-ATPase) has five subunits | Core | NA | NA | NA |
| 5906-YLR448W_NumOfGenes_2 | YLR448W | RPL6B | eL6|ribosomal 60S subunit protein L6B|L6e|rp18|YL16|L6B|L17B | Ribosomal 60S subunit protein L6B; binds 5.8S rRNA; homologous to mammalian ribosomal protein L6, no bacterial homolog; RPL6B has a paralog, RPL6A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5907-YLR449W_NumOfGenes_2 | YLR449W | FPR4 | peptidylprolyl isomerase FPR4 | Peptidyl-prolyl cis-trans isomerase (PPIase); nuclear proline isomerase; affects expression of multiple genes via its role in nucleosome assembly; catalyzes isomerization of proline residues in histones H3 and H4, which affects lysine methylation of those histones; PPIase domain acts as a transcriptional repressor when tethered to DNA by lexA, and repressor activity is dependent on PPIase activity; contains a nucleoplasmin-like fold and can form pentamers | Core | NA | NA | NA |
| 5908-YLR450W | YLR450W | HMG2 | hydroxymethylglutaryl-CoA reductase (NADPH) HMG2 | HMG-CoA reductase; converts HMG-CoA to mevalonate, a rate-limiting step in sterol biosynthesis; one of two isozymes; overproduction induces assembly of peripheral ER membrane arrays and short nuclear-associated membrane stacks; forms foci at nuclear periphery upon DNA replication stress; HMG2 has a paralog, HMG1, that arose from the whole genome duplication; human homolog HMGCR can complement yeast hmg2 mutant | Core | NA | NA | NA |
| 5909-YLR451W | YLR451W | LEU3 | leucine-responsive transcriptional regulator LEU3 | Zinc-knuckle transcription factor, repressor and activator; regulates genes involved in branched chain amino acid biosynthesis and ammonia assimilation; acts as a repressor in leucine-replete conditions and as an activator in the presence of alpha-isopropylmalate, an intermediate in leucine biosynthesis that accumulates during leucine starvation | Accessory | Ancestral | NA | NA |
| 5910-YLR452C | YLR452C | SST2 | GTPase-activating protein SST2 | GTPase-activating protein for Gpa1p; regulates desensitization to alpha factor pheromone; also required to prevent receptor-independent signaling of the mating pathway; member of the RGS (regulator of G-protein signaling) family | Accessory | Ancestral | NA | NA |
| 5911-YLR453C | YLR453C | RIF2 | NA | Protein that binds to the Rap1p C-terminus; acts synergistically with Rif1p to help control telomere length and establish telomeric silencing; deletion results in telomere elongation; RIF2 has a paralog, ORC4, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5912-YLR454W | YLR454W | FMP27 | NA | Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |
| 5913-YLR455W | YLR455W | PDP3 | NA | Component of the NuA3b histone acetyltransferase complex; regulates interaction between NuA3b and H3K36me3 at the transcribed regions of genes; contains PWWP domain; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO); protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia | Accessory | Ancestral | NA | NA |
| 5914-YLR456W | YLR456W | NA | pyridoxal 5'-phosphate synthase | Protein of unknown function; predicted to encode a pyridoxal 5'-phosphate synthase based on sequence similarity but purified protein does not possess this activity, nor does it bind flavin mononucleotide (FMN); null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2; YLR456W has a paralog, YPR172W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5915-YLR457C_NumOfGenes_2 | YLR457C | NBP1 | NA | Spindle pole body (SPB) component; required for the insertion of the duplication plaque into the nuclear membrane during SPB duplication; essential for bipolar spindle formation; component of the Mps2p-Bbp1p complex; NBP1 has a paralog, YPR174C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 5916-YLR459W | YLR459W | GAB1 | GPI-anchor transamidase subunit GAB1|CDC91 | GPI transamidase subunit; involved in attachment of glycosylphosphatidylinositol (GPI) anchors to proteins; may have a role in recognition of the attachment signal or of the lipid portion of GPI | Accessory | Ancestral | NA | NA |
| 5917-YLR460C_NumOfGenes_2 | YLR460C | NA | NA | Member of the quinone oxidoreductase family; up-regulated in response to the fungicide mancozeb; possibly up-regulated by iodine | Accessory | Ancestral | NA | NA |