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 |
|---|---|---|---|---|---|---|---|---|
| 7523-YPL175W | YPL175W | SPT14 | phosphatidylinositol N-acetylglucosaminyltransferase SPT14|GPI3|CWH6 | UDP-glycosyltransferase subunit of the GPI-GnT complex; UDP-GlcNAc-binding and catalytic subunit of the enzyme that mediates the first step in glycosylphosphatidylinositol (GPI) biosynthesis, mutations cause defects in transcription and in biogenesis of cell wall proteins | Core | NA | NA | NA |
| 7524-YPL176C | YPL176C | TRE1 | NA | Transferrin receptor-like protein; plasma membrane protein that binds Bsd2p and regulates ubiquitination and vacuolar degradation of the metal transporter Smf1p; functionally redundant with Tre2p; TRE1 has a paralog, TRE2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7525-YPL177C | YPL177C | CUP9 | NA | Homeodomain-containing transcriptional repressor; regulates expression of PTR2, which encodes a major peptide transporter; imported peptides activate ubiquitin-dependent proteolysis, resulting in degradation of Cup9p and de-repression of PTR2 transcription; CUP9 has a paralog, TOS8, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7526-YPL178W | YPL178W | CBC2 | CBP20|SAE1|MUD13 | Small subunit of the heterodimeric cap binding complex with Sto1p; interacts with Npl3p, possibly to package mRNA for export from the nucleus; may have a role in telomere maintenance; contains an RNA-binding motif | Core | NA | NA | NA |
| 7527-YPL179W | YPL179W | PPQ1 | SAL6 | Protein phosphatase that regulates the mating response; negatively regulates the MAP kinase signaling cascade during mating; member of the serine/threonine phosphatase PP1 family | Core | NA | NA | NA |
| 7528-YPL180W | YPL180W | TCO89 | NA | Subunit of TORC1 (Tor1p or Tor2p-Kog1p-Lst8p-Tco89p); regulates global H3K56ac; TORC1 complex regulates growth in response to nutrient availability; cooperates with Ssd1p in the maintenance of cellular integrity; deletion strains are hypersensitive to rapamycin | Core | NA | NA | NA |
| 7529-YPL181W | YPL181W | CTI6 | RXT1 | Component of the Rpd3L histone deacetylase complex; relieves transcriptional repression by binding to the Cyc8p-Tup1p corepressor and recruiting the SAGA complex to the repressed promoter; contains a PHD finger domain | Core | NA | NA | NA |
| 7530-YPL182C | YPL182C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CTI6/YPL181W | Accessory | Ancestral | NA | NA |
| 7531-YPL183C | YPL183C | RTT10 | TRM734|ERE2 | WD40 domain-containing protein involved in endosomal recycling; forms a complex with Rrt2p that functions in the retromer-mediated pathway for recycling internalized cell-surface proteins; interacts with Trm7p for 2'-O-methylation of N34 of substrate tRNAs; has a role in regulation of Ty1 transposition; human ortholog is WDR6 | Core | NA | NA | NA |
| 7532-YPL183W-A | YPL183W-A | RTC6 | putative mitochondrial 54S ribosomal protein RTC6|TAE4|GON5 | Protein involved in translation; mutants have defects in biogenesis of nuclear ribosomes; sequence similar to prokaryotic ribosomal protein L36, may be a mitochondrial ribosomal protein; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 7533-YPL184C | YPL184C | MRN1 | PTR69 | RNA-binding protein that may be involved in translational regulation; binds specific categories of mRNAs, including those that contain upstream open reading frames (uORFs) and internal ribosome entry sites (IRES); interacts genetically with chromatin remodelers and splicing factors, linking chromatin state, splicing and as a result mRNA maturation | Core | NA | NA | NA |
| 7534-YPL185W | YPL185W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified gene UIP4/YPL186C | Core | NA | NA | NA |
| 7535-YPL186C | YPL186C | UIP4 | NA | Protein that interacts with Ulp1p; a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates; detected in a phosphorylated state in the mitochondrial outer membrane; also detected in ER and nuclear envelope | Core | NA | NA | NA |
| 7536-YPL187W | YPL187W | MF(ALPHA)1 | NA | Mating pheromone alpha-factor, made by alpha cells; interacts with mating type a cells to induce cell cycle arrest and other responses leading to mating; also encoded by MF(ALPHA)2, although MF(ALPHA)1 produces most alpha-factor; binds copper(II) ions | Core | NA | NA | NA |
| 7537-YPL188W | YPL188W | POS5 | NADH kinase | Mitochondrial NADH kinase; phosphorylates NADH; also phosphorylates NAD(+) with lower specificity; required for the response to oxidative stress | Core | NA | NA | NA |