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 |
|---|---|---|---|---|---|---|---|---|
| 4718-YJL020C_NumOfGenes_2 | YJL020C | BBC1 | YJL021C|MTI1 | Protein possibly involved in assembly of actin patches; interacts with an actin assembly factor Las17p and with the SH3 domains of Type I myosins Myo3p and Myo5p; localized predominantly to cortical actin patches | Accessory | Unknown | S. paradoxus | NA |
| 4719-YJL023C_NumOfGenes_3 | YJL023C | PET130 | NA | Protein required for respiratory growth; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 4720-YJL024C | YJL024C | APS3 | YKS7 | Small subunit of the clathrin-associated adaptor complex AP-3; involved in vacuolar protein sorting; related to the sigma subunit of the mammalian clathrin AP-3 complex; suppressor of loss of casein kinase 1 function; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4721-YJL025W | YJL025W | RRN7 | NA | Component of the core factor (CF) rDNA transcription factor complex; CF is required for transcription of 35S rRNA genes by RNA polymerase I and is composed of Rrn6p, Rrn7p, and Rrn11p | Core | NA | NA | NA |
| 4722-YJL026W_NumOfGenes_2 | YJL026W | RNR2 | ribonucleotide-diphosphate reductase subunit RNR2|CRT6 | Ribonucleotide-diphosphate reductase (RNR), small subunit; the RNR complex catalyzes the rate-limiting step in dNTP synthesis and is regulated by DNA replication and DNA damage checkpoint pathways via localization of the small subunits; RNR2 has a paralog, RNR4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4723-YJL027C | YJL027C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 4724-YJL028W | YJL028W | NA | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments | Core | NA | NA | NA |
| 4725-YJL029C | YJL029C | VPS53 | NA | 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; required for vacuolar protein sorting; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p; human ortholog is implicated in progressive cerebello-cerebral atrophy type 2 (PCCA2) | Core | NA | NA | NA |
| 4726-YJL030W | YJL030W | MAD2 | spindle checkpoint protein MAD2 | Component of the spindle-assembly checkpoint complex; delays onset of anaphase in cells with defects in mitotic spindle assembly; forms a complex with Mad1p; regulates APC/C activity during prometaphase and metaphase of meiosis I; gene dosage imbalance between MAD1 and MAD2 leads to chromosome instability | Core | NA | NA | NA |
| 4727-YJL031C_NumOfGenes_2 | YJL031C | BET4 | Rab geranylgeranyltransferase BET4 | Alpha subunit of Type II geranylgeranyltransferase; required for vesicular transport between the endoplasmic reticulum and the Golgi; provides a membrane attachment moiety to Rab-like proteins Ypt1p and Sec4p | Core | NA | NA | NA |
| 4728-YJL033W | YJL033W | HCA4 | RNA-dependent ATPase HCA4|ECM24|DBP4 | DEAD box RNA helicase; component of the SSU; interacts with Bfr2p and Enp2p; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis | Core | NA | NA | NA |
| 4729-YJL034W | YJL034W | KAR2 | Hsp70 family ATPase KAR2|BIP|GRP78 | ATPase involved in protein import into the ER; also acts as a chaperone to mediate protein folding in the ER and may play a role in ER export of soluble proteins; regulates the unfolded protein response via interaction with Ire1p | Core | NA | NA | NA |
| 4730-YJL035C | YJL035C | TAD2 | tRNA(adenine34) deaminase | Subunit of tRNA-specific adenosine-34 deaminase; forms a heterodimer with Tad3p that converts adenosine to inosine at the wobble position of several tRNAs | Core | NA | NA | NA |
| 4731-YJL036W | YJL036W | SNX4 | ATG24|CVT13 | Sorting nexin; involved in retrieval of late-Golgi SNAREs from post-Golgi endosomes to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX phosphoinositide-binding domain; forms complexes with Snx41p and with Atg20p | Core | NA | NA | NA |
| 4732-YJL037W | YJL037W | IRC18 | OSW6 | Protein involved in outer spore wall assembly; possible role in assembly of the dityrosine layer; similar to adjacent ORF, LOH1; irc18 loh1 double mutant exhibits reduced dityrosine fluorescence relative to single mutants; SWAT-GFP fusion protein localizes to the ER and vacuole, while mCherry fusion localizes to the vacuole; expression induced in respiratory-deficient cells and carbon-limited chemostat culture; null mutant displays increased levels of spontaneous Rad52p foci | Core | NA | NA | NA |