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 |
|---|---|---|---|---|---|---|---|---|
| 2708-YDR018C | YDR018C | NA | putative acyltransferase | Probable membrane protein with three predicted transmembrane domains; similar to C. elegans F55A11.5 and maize 1-acyl-glycerol-3-phosphate acyltransferase; YDR018C has a paralog, CST26, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2709-YDR019C | YDR019C | GCV1 | glycine decarboxylase subunit T|GSD1 | T subunit of the mitochondrial glycine decarboxylase complex; glycine decarboxylase is required for the catabolism of glycine to 5,10-methylene-THF; expression is regulated by levels of levels of 5,10-methylene-THF in the cytoplasm | Core | NA | NA | NA |
| 2710-YDR020C | YDR020C | DAS2 | putative uridine kinase DAS2|RRT3 | Putative protein of unknown function; non-essential gene identified in a screen for mutants with increased levels of rDNA transcription; weak similarity with uridine kinases and with phosphoribokinases | Core | NA | NA | NA |
| 2711-YDR021W | YDR021W | FAL1 | ATP-dependent RNA helicase FAL1 | Nucleolar protein required for maturation of 18S rRNA; member of the eIF4A subfamily of DEAD-box ATP-dependent RNA helicases; 18S rRNA biogenesis defect of the null mutant is functionally complemented by human EIF4A3 | Core | NA | NA | NA |
| 2712-YDR022C | YDR022C | ATG31 | CIS1 | Autophagy-specific protein required for autophagosome formation; forms a complex with Atg17p and Atg29p that localizes other proteins to the pre-autophagosomal structure; constitutively phosphorylated, and phosphorylation of residue S174 is required for function; high-copy suppressor of CIK1 deletion | Core | NA | NA | NA |
| 2713-YDR023W | YDR023W | SES1 | serine--tRNA ligase SES1|SerRS | Cytosolic seryl-tRNA synthetase; class II aminoacyl-tRNA synthetase that aminoacylates tRNA(Ser), displays tRNA-dependent amino acid recognition which enhances discrimination of the serine substrate, interacts with peroxin Pex21p | Core | NA | NA | NA |
| 2714-YDR024W | YDR024W | FYV1 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; mutation decreases survival upon exposure to K1 killer toxin | Core | NA | NA | NA |
| 2715-YDR025W | YDR025W | RPS11A | uS17|ribosomal 40S subunit protein S11A|S17|rp41A|YS12|S18A|S11A | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S11 and bacterial S17; N-terminally propionylated in vivo; RPS11A has a paralog, RPS11B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2716-YDR026C | YDR026C | NSI1 | YTT1 | RNA polymerase I termination factor; binds to rDNA terminator element, required for efficient Pol I termination; required for rDNA silencing at NTS1; facilities association of Sir2p with NTS1, contributes to rDNA stability and cell longevity; interacts physically with Fob1p and RENT subunits, Sir2p and Net1p; may interact with ribosomes, based on co-purification experiments; Myb-like DNA-binding protein; NSI1 has a paralog, REB1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2717-YDR027C | YDR027C | VPS54 | TCS3|CGP1|LUV1 | Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; potentially phosphorylated by Cdc28p; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p | Core | NA | NA | NA |
| 2718-YDR028C | YDR028C | REG1 | protein phosphatase regulator REG1|SRN1|SPP43|PZF240|HEX2 | Regulatory subunit of type 1 protein phosphatase Glc7p; involved in negative regulation of glucose-repressible genes; involved in regulation of the nucleocytoplasmic shuttling of Hxk2p; REG1 has a paralog, REG2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2719-YDR029W | YDR029W | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YDR029W is not an essential gene | Core | NA | NA | NA |
| 2720-YDR030C | YDR030C | RAD28 | NA | Protein involved in DNA repair; related to the human CSA protein that is involved in transcription-coupled repair nucleotide excision repair | Core | NA | NA | NA |
| 2721-YDR031W | YDR031W | MIX14 | MIC14 | Mitochondrial intermembrane space protein of unknown function; required for normal oxygen consumption; contains twin cysteine-x9-cysteine motifs; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2722-YDR032C | YDR032C | PST2 | flavodoxin-like fold family protein | Protein with similarity to a family of flavodoxin-like proteins; induced by oxidative stress in a Yap1p dependent manner; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; protein abundance increases in response to DNA replication stress; PST2 has a paralog, RFS1, that arose from the whole genome duplication | Core | NA | NA | NA |