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 |
|---|---|---|---|---|---|---|---|---|
| 3653-YGL007C-A | YGL007C-A | NA | NA | Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; deletion exhibits slow-growth phenotype; computationally predicted to have a role in cell budding | Accessory | Ancestral | NA | NA |
| 3654-YGL007W | YGL007W | BRP1 | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; located in the upstream region of PMA1; deletion leads to polyamine resistance due to downregulation of PMA1 | Core | NA | NA | NA |
| 3655-YGL008C | YGL008C | PMA1 | H(+)-exporting P2-type ATPase PMA1|KTI10 | Plasma membrane P2-type H+-ATPase; pumps protons out of cell; major regulator of cytoplasmic pH and plasma membrane potential; long-lived protein asymmetrically distributed at plasma membrane between mother cells and buds; accumulates at high levels in mother cells during aging, buds emerge with very low levels of Pma1p, newborn cells have low levels of Pma1p; Hsp30p plays a role in Pma1p regulation; interactions with Std1p appear to propagate [GAR+] | Core | NA | NA | NA |
| 3656-YGL009C | YGL009C | LEU1 | 3-isopropylmalate dehydratase LEU1 | Isopropylmalate isomerase; catalyzes the second step in the leucine biosynthesis pathway | Core | NA | NA | NA |
| 3657-YGL010W | YGL010W | MPO1 | NA | Protein involved in metabolism of phytosphingosine; not an essential gene | Core | NA | NA | NA |
| 3658-YGL011C | YGL011C | SCL1 | proteasome core particle subunit alpha 1|PRC2 | Alpha 1 subunit of the 20S proteasome; involved in the degradation of ubiquitinated substrates; 20S proteasome is the core complex of the 26S proteasome; essential for growth; detected in the mitochondria | Core | NA | NA | NA |
| 3659-YGL012W | YGL012W | ERG4 | delta(24(24(1)))-sterol reductase | C-24(28) sterol reductase; catalyzes the final step in ergosterol biosynthesis; mutants are viable, but lack ergosterol | Core | NA | NA | NA |
| 3660-YGL013C | YGL013C | PDR1 | drug-responsive transcription factor PDR1|TPE3|TPE1|TIL1|SMR2|NRA2|CYH3|BOR2|ANT1|AMY1 | Transcription factor that regulates the pleiotropic drug response; zinc cluster protein that is a master regulator involved in recruiting other zinc cluster proteins to pleiotropic drug response elements (PDREs) to fine tune the regulation of multidrug resistance genes; relocalizes to the cytosol in response to hypoxia; PDR1 has a paralog, PDR3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3661-YGL014W_NumOfGenes_2 | YGL014W | PUF4 | YGL023 | Member of the PUF protein family; PUF family is defined by the presence of Pumilio homology domains that confer RNA binding activity; preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors | Core | NA | NA | NA |
| 3662-YGL015C | YGL015C | NA | NA | Putative protein of unknown function; null mutants accumulate cargo in the Golgi | Core | NA | NA | NA |
| 3663-YGL016W_NumOfGenes_2 | YGL016W | KAP122 | PDR6 | Karyopherin beta; responsible for import of the Toa1p-Toa2p complex into the nucleus; binds to nucleoporins Nup1p and Nup2p; may play a role in regulation of pleiotropic drug resistance | Core | NA | NA | NA |
| 3664-YGL017W_NumOfGenes_2 | YGL017W | ATE1 | arginyltransferase | Arginyl-tRNA-protein transferase; catalyzes post-translational conjugation of arginine to the amino termini of acceptor proteins which are then subject to degradation via the N-end rule pathway | Core | NA | NA | NA |
| 3665-YGL018C_NumOfGenes_2 | YGL018C | JAC1 | J-type chaperone JAC1 | Specialized J-protein that functions in Fe-S cluster biogenesis; functions with Hsp70 in Fe-S cluster biogenesis in mitochondria; involved in iron metabolism; contains a J domain typical to J-type chaperones; localizes to the mitochondrial matrix | Core | NA | NA | NA |
| 3666-YGL019W_NumOfGenes_2 | YGL019W | CKB1 | casein kinase 2 regulatory subunit CKB1 | Beta regulatory subunit of casein kinase 2 (CK2); a Ser/Thr protein kinase with roles in cell growth and proliferation; CK2, comprised of CKA1, CKA2, CKB1 and CKB2, has many substrates including transcription factors and all RNA polymerases | Accessory | Ancestral | NA | NA |
| 3667-YGL020C_NumOfGenes_2 | YGL020C | GET1 | GET complex subunit GET1|MDM39 | Subunit of the GET complex; involved in insertion of proteins into the ER membrane; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance | Accessory | Ancestral | NA | NA |