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 |
|---|---|---|---|---|---|---|---|---|
| 4538-YIL053W | YIL053W | GPP1 | RHR2|glycerol-1-phosphatase RHR2 | Constitutively expressed DL-glycerol-3-phosphate phosphatase; also known as glycerol-1-phosphatase; involved in glycerol biosynthesis, induced in response to both anaerobic and osmotic stress; GPP1 has a paralog, GPP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4539-YIL054W | YIL054W | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels | Core | NA | NA | NA |
| 4540-YIL055C | YIL055C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 4541-YIL056W | YIL056W | VHR1 | NA | Transcriptional activator; required for the vitamin H-responsive element (VHRE) mediated induction of VHT1 (Vitamin H transporter) and BIO5 (biotin biosynthesis intermediate transporter) in response to low biotin concentrations; VHR1 has a paralog, VHR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4542-YIL057C | YIL057C | RGI2 | NA | Protein of unknown function; involved in energy metabolism under respiratory conditions; expression induced under carbon limitation and repressed under high glucose; RGI2 has a paralog, RGI1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4543-YIL058W | YIL058W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | NA | NA |
| 4544-YIL061C | YIL061C | SNP1 | U1 snRNP complex subunit SNP1|U1-70K | Component of U1 snRNP required for mRNA splicing via spliceosome; substrate of the arginine methyltransferase Hmt1p; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4545-YIL062C | YIL062C | ARC15 | NA | Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches; has mRNA binding activity | Core | NA | NA | NA |
| 4546-YIL063C | YIL063C | YRB2 | NA | Protein of unknown function; involved in nuclear processes of the Ran-GTPase cycle; involved in nuclear protein export; contains Ran Binding Domain and FxFG repeats; interacts with Srm1p, GTP-Gsp1p, Rna1p and Crm1p; relocalizes to the cytosol in response to hypoxia; not essential for viability | Core | NA | NA | NA |
| 4547-YIL064W | YIL064W | EFM4 | SEE1 | Lysine methyltransferase; involved in the dimethylation of eEF1A (Tef1p/Tef2p) at lysine 316; sequence similarity to S-adenosylmethionine-dependent methyltransferases of the seven beta-strand family; role in vesicular transport | Core | NA | NA | NA |
| 4548-YIL065C | YIL065C | FIS1 | MDV2 | Protein involved in mitochondrial fission and peroxisome abundance; may have a distinct role in tethering protein aggregates to mitochondria in order to retain them in the mother cell; required for localization of Dnm1p and Mdv1p during mitochondrial division; mediates ethanol-induced apoptosis and ethanol-induced mitochondrial fragmentation | Core | NA | NA | NA |
| 4549-YIL066C | YIL066C | RNR3 | ribonucleotide-diphosphate reductase subunit RNR3|RIR3|DIN1 | Minor isoform of large subunit of ribonucleotide-diphosphate reductase; the RNR complex catalyzes rate-limiting step in dNTP synthesis, regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits; RNR3 has a paralog, RNR1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4550-YIL067C_NumOfGenes_2 | YIL067C | NA | NA | Uncharacterized protein of unknown function | Core | NA | NA | NA |
| 4551-YIL068C_NumOfGenes_2 | YIL068C | SEC6 | SNARE-binding exocyst subunit SEC6 | Essential 88kDa subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis at the plasma membrane prior to SNARE-mediated fusion; anchors the assembled complex to sites of secretion; interacts with SM-like protein and SNARE regulator Sec1p and may recruit it to sites of secretion; binds to SNARE complexes binteracting with Sec9p | Core | NA | NA | NA |
| 4552-YIL069C | YIL069C | RPS24B | eS24|ribosomal 40S subunit protein S24B|S24e|S24B|RPS24EB | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S24, no bacterial homolog; RPS24B has a paralog, RPS24A, that arose from the whole genome duplication | Core | NA | NA | NA |