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 |
|---|---|---|---|---|---|---|---|---|
| 3608-YFR024C-A | YFR024C-A | LSB3 | YFR024C | Protein containing a C-terminal SH3 domain; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization; protein abundance increases in response to DNA replication stress; LSB3 has a paralog, YSC84, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3609-YFR025C | YFR025C | HIS2 | histidinol-phosphatase | Histidinolphosphatase; catalyzes the eighth step in histidine biosynthesis; mutations cause histidine auxotrophy and sensitivity to Cu, Co, and Ni salts; transcription is regulated by general amino acid control | Core | NA | NA | NA |
| 3610-YFR026C | YFR026C | ULI1 | NA | Protein of unknown function; involved in and induced by the endoplasmic reticulum unfolded protein response (UPR); SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum | Accessory | Unknown | NA | NA |
| 3611-YFR027W | YFR027W | ECO1 | CTF7 | Acetyltransferase; required for establishment of sister chromatid cohesion; acetylates Mps3p to regulate nuclear organization; modifies Smc3p at replication forks and Mcd1p in response to dsDNA breaks; phosphorylated by three kinases (Cdc28p, Cdc7p, Mck1p) to generate pair of phosphates spaced precisely for recognition by ubiquitin ligase SCF-Cdc4; mutations in human homolog ESCO2 cause Roberts syndrome; relative distribution to nucleus increases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 3612-YFR028C | YFR028C | CDC14 | phosphoprotein phosphatase CDC14|OAF3 | Protein phosphatase required for mitotic exit; required for rDNA segregation, cytokinesis, meiosis I spindle disassembly, environmental stress response; held in nucleolus by Cdc55p in early meiosis, liberated by FEAR and Mitotic Exit Network in anaphase, enabling it to effect a decrease in CDK/B-cyclin activity and mitotic exit; sequestered in metaphase II, released upon entry into anaphase II; human homolog CDC14A can complement thermosensitivity of yeast cdc14-1 mutant | Core | NA | NA | NA |
| 3613-YFR029W | YFR029W | PTR3 | RAA2|SSY3 | Component of the SPS plasma membrane amino acid sensor system; senses external amino acid concentration and transmits intracellular signals that result in regulation of expression of amino acid permease genes; other members are Ssy1p, Ptr3p, and Ssy5p | Core | NA | NA | NA |
| 3614-YFR030W | YFR030W | MET10 | sulfite reductase subunit alpha | Subunit alpha of assimilatory sulfite reductase; complex converts sulfite into sulfide | Core | NA | NA | NA |
| 3615-YFR031C | YFR031C | SMC2 | condensin subunit SMC2 | Subunit of the condensin complex; condensin reorganizes chromosomes during both mitosis and meiosis; essential SMC chromosomal ATPase family member that forms a subcomplex with Smc2p that has ATP-hydrolyzing and DNA-binding activity, but other condensin subunits are required for chromatin binding; required for clustering of tRNA genes at the nucleolus | Core | NA | NA | NA |
| 3616-YFR032C | YFR032C | RRT5 | NA | Putative protein of unknown function; non-essential gene identified in a screen for mutants with increased levels of rDNA transcription; expressed at high levels during sporulation | Core | NA | NA | NA |
| 3617-YFR032C-A | YFR032C-A | RPL29 | eL29|ribosomal 60S subunit protein L29|L29e|YL43|L29 | Ribosomal 60S subunit protein L29; not essential for translation, but required for proper joining of large and small ribosomal subunits and for normal translation rate; homologous to mammalian ribosomal protein L29, no bacterial homolog | Core | NA | NA | NA |
| 3618-YFR032C-B | YFR032C-B | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching | Core | NA | NA | NA |
| 3619-YFR033C | YFR033C | QCR6 | ubiquinol--cytochrome-c reductase subunit 6|UCR6|COR3 | Subunit 6 of the ubiquinol cytochrome-c reductase complex; the complex, also known as the cytochrome bc(1) complex or Complex III, is a component of the mitochondrial inner membrane electron transport chain; highly acidic protein; required for maturation of cytochrome c1; may be loosely associated with the complex since it is easily released into the intermembrane space | Core | NA | NA | NA |
| 3620-YFR034C | YFR034C | PHO4 | phosphate-sensing transcription factor PHO4|phoD | Basic helix-loop-helix (bHLH) transcription factor of the myc-family; activates transcription cooperatively with Pho2p in response to phosphate limitation; binding to 'CACGTG' motif is regulated by chromatin restriction, competitive binding of Cbf1p to the same DNA binding motif and cooperation with Pho2p; function is regulated by phosphorylation at multiple sites and by phosphate availability | Core | NA | NA | NA |
| 3621-YFR034W-A | YFR034W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps YFR035C; identified by gene-trapping, microarray expression analysis, and genome-wide homology searching | Accessory | Ancestral | NA | NA |
| 3622-YFR035C | YFR035C | NA | NA | Putative protein of unknown function; deletion mutant exhibits synthetic phenotype with alpha-synuclein | Accessory | Ancestral | NA | NA |