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 |
|---|---|---|---|---|---|---|---|---|
| 6083-YMR025W | YMR025W | CSI1 | NA | Subunit of the Cop9 signalosome; which is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone signaling; functional equivalent of canonical Csn6 subunit of the COP9 signalosome | Core | NA | NA | NA |
| 6084-YMR026C | YMR026C | PEX12 | ubiquitin-protein ligase peroxin 12|PAS11 | C3HC4-type RING-finger peroxin and E3 ubiquitin ligase; required for peroxisome biogenesis and peroxisomal matrix protein import; forms translocation subcomplex with Pex2p and Pex10p; mutations in human homolog cause peroxisomal disorder | Core | NA | NA | NA |
| 6085-YMR027W | YMR027W | NA | putative methyltransferase | A metal-dependent phosphatase, part of the DUF89 protein family; dephosphorylates fructose-1-phosphate; human ortholog, C6orf211 is involved in response to DNA damage; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; YMR027W is not an essential gene | Core | NA | NA | NA |
| 6086-YMR028W | YMR028W | TAP42 | NA | Essential protein involved in the TOR signaling pathway; physically associates with the protein phosphatase 2A and the SIT4 protein phosphatase catalytic subunits | Core | NA | NA | NA |
| 6087-YMR029C | YMR029C | FAR8 | NA | Protein involved in recovery from arrest in response to pheromone; acts in a cell cycle arrest recovery pathway independent from Far1p; interacts with Far3p, Far7p, Far9p, Far10p, and Far11p | Core | NA | NA | NA |
| 6088-YMR030W | YMR030W | RSF1 | NA | Protein required for respiratory growth; localized to both the nucleus and mitochondrion; may interact with transcription factors to mediate the transition to respiratory growth and activate transcription of nuclear and mitochondrial genes | Core | NA | NA | NA |
| 6089-YMR030W-A | YMR030W-A | NA | NA | Putative protein of unknown function; mCherry fusion protein localizes to the cytosol | Accessory | Ancestral | NA | NA |
| 6090-YMR031C | YMR031C | EIS1 | NA | Component of the eisosome required for proper eisosome assembly; similar to Uso1p; authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies; protein increases in abundance and relocalizes from plasma membrane to cytoplasm upon DNA replication stress; EIS1 has a paralog, YKL050C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6091-YMR031W-A | YMR031W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; null mutant displays shortened telomeres; partially overlaps the uncharacterized ORF YMR031C | Core | NA | NA | NA |
| 6092-YMR032W | YMR032W | HOF1 | formin-binding protein HOF1|CYK2 | Protein that regulates actin cytoskeleton organization; required for cytokinesis, actin cable organization, and secretory vesicle trafficking; localized to bud neck; phosphorylated by Dbf2p; regulates actomyosin ring dynamics and septin localization; contains an SH3 domain; N terminus controls cell size and levels of actin cables, while C terminus controls actin cable organization via direct regulation of the formin Bnr1p | Accessory | Ancestral | NA | NA |
| 6093-YMR033W | YMR033W | ARP9 | RSC12|SWP59 | Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation | Accessory | Ancestral | NA | NA |
| 6094-YMR034C | YMR034C | RCH1 | NA | Putative transporter; localizes to the plasma membrane in response to high levels of extracellular calcium; member of the SLC10 carrier family; identified in a transposon mutagenesis screen as a gene involved in azole resistance; YMR034C is not an essential gene | Accessory | Ancestral | NA | NA |
| 6095-YMR035W | YMR035W | IMP2 | endopeptidase catalytic subunit | Catalytic subunit of mitochondrial inner membrane peptidase complex; required for maturation of mitochondrial proteins of the intermembrane space; complex contains two catalytic subunits (Imp1p and Imp2p that differ in substrate specificity), and Som1p | Accessory | Ancestral | NA | NA |
| 6096-YMR036C | YMR036C | MIH1 | putative tyrosine protein phosphatase MIH1 | Protein tyrosine phosphatase involved in cell cycle control; regulates the phosphorylation state of Cdc28p; homolog of S. pombe cdc25 | Accessory | Ancestral | NA | NA |
| 6097-YMR037C | YMR037C | MSN2 | stress-responsive transcriptional activator MSN2 | Stress-responsive transcriptional activator; activated in stochastic pulses of nuclear localization in response to various stress conditions; binds DNA at stress response elements of responsive genes; relative distribution to nucleus increases upon DNA replication stress | Accessory | Ancestral | NA | NA |