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 |
|---|---|---|---|---|---|---|---|---|
| 6533-YNL142W | YNL142W | MEP2 | ammonium permease MEP2 | Ammonium permease involved in regulation of pseudohyphal growth; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation | Accessory | Ancestral | NA | NA |
| 6534-YNL143C | YNL143C | NA | NA | Protein of unknown function; expressed at both mRNA and protein levels | Core | NA | NA | NA |
| 6535-YNL144C_NumOfGenes_2 | YNL144C | NA | NA | Putative protein of unknown function; non-tagged protein is detected in highly purified mitochondria in high-throughput studies; contains a PH domain and binds phosphatidylinositols and phosphatidylethanolamine in a large-scale study; YNL144C has a paralog, YHR131C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6536-YNL145W | YNL145W | MFA2 | mating pheromone a | Mating pheromone a-factor; made by a cells; interacts with alpha cells to induce cell cycle arrest and other responses leading to mating; biogenesis involves C-terminal modification, N-terminal proteolysis, and export; also encoded by MFA1 | Core | NA | NA | NA |
| 6537-YNL146C-A | YNL146C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6538-YNL146W | YNL146W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YNL146W is not an essential gene | Core | NA | NA | NA |
| 6539-YNL147W | YNL147W | LSM7 | Sm-like protein LSM7 | Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA; protein abundance increases and forms cytoplasmic foci in response to DNA replication stress | Core | NA | NA | NA |
| 6540-YNL148C | YNL148C | ALF1 | NA | Alpha-tubulin folding protein; similar to mammalian cofactor B; Alf1p-GFP localizes to cytoplasmic microtubules; required for the folding of alpha-tubulin and may play an additional role in microtubule maintenance | Core | NA | NA | NA |
| 6541-YNL149C | YNL149C | PGA2 | NA | Essential protein required for maturation of Gas1p and Pho8p; involved in protein trafficking; GFP-fusion protein localizes to the ER and YFP-fusion protein to the nuclear envelope-ER network; null mutants have a cell separation defect | Accessory | Ancestral | NA | NA |
| 6542-YNL150W | YNL150W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; extensive overlap with PGA2/YNL149C, an uncharacterized gene with a proposed role in protein trafficking | Accessory | Ancestral | NA | NA |
| 6543-YNL151C | YNL151C | RPC31 | DNA-directed RNA polymerase III subunit C31|C31|RPC8|ACP2 | RNA polymerase III subunit C31 | Core | NA | NA | NA |
| 6544-YNL152W | YNL152W | INN1 | NA | Essential protein that associates with contractile actomyosin ring; required for ingression of the plasma membrane into the bud neck during cytokinesis; C2 domain, a membrane targeting module, is required for function; activates chitin synthase activity of Chs2p during cytokinesis | Core | NA | NA | NA |
| 6545-YNL153C | YNL153C | GIM3 | tubulin-binding prefolding complex subunit GIM3|PFD4 | Subunit of the heterohexameric cochaperone prefoldin complex; prefoldin binds specifically to cytosolic chaperonin and transfers target proteins to it; prefoldin complex also localizes to chromatin of actively transcribed genes in the nucleus and facilitates transcriptional elongation | Core | NA | NA | NA |
| 6546-YNL154C | YNL154C | YCK2 | serine/threonine protein kinase YCK2 | Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking, and glucose sensing; stabilized by Sod1p binding in the presence of glucose and oxygen, causing glucose repression of respiratory metabolism; involved in the phosphorylation and regulation of glucose sensor Rgt2p; YCK2 has a paralog, YCK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6547-YNL155W | YNL155W | CUZ1 | NA | Protein with a role in the ubiquitin-proteasome pathway; interacts with ubiquitinated protein, Cdc48p and the proteasomal regulatory particle; may protect cells from trivalent metalloid induced proteotoxicity; contains a PACE promoter element and is co-regulated with proteasome subunit genes; AN1-type zinc finger protein, with DHHC and ubiquitin-like domains (UBL); ortholog of ZFAND1, a human gene linked to cancer; protein abundance increases under DNA replication stress | Core | NA | NA | NA |