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 |
|---|---|---|---|---|---|---|---|---|
| 3848-YGL206C | YGL206C | CHC1 | clathrin heavy chain|SWA5 | Clathrin heavy chain; subunit of the major coat protein involved in intracellular protein transport and endocytosis; the clathrin triskelion is a trimeric molecule composed of three heavy chains that radiate from a vertex and three light chains which bind noncovalently near the vertex of the triskelion; the light chain (CLC1) is thought to regulate function | Core | NA | NA | NA |
| 3849-YGL207W | YGL207W | SPT16 | chromatin-remodeling protein SPT16|SSF1|CDC68 | Subunit of the heterodimeric FACT complex (Spt16p-Pob3p); FACT associates with chromatin via interaction with Nhp6Ap and Nhp6Bp, and reorganizes nucleosomes to facilitate access to DNA by RNA and DNA polymerases; specifically required for diauxic shift-induced H2B deposition onto rDNA genes; mutations cause reduced nucleosome occupancy over highly transcribed regions; coregulates transcription with Mot1p through preinitiation complex assembly and nucleosome organization | Core | NA | NA | NA |
| 3850-YGL208W | YGL208W | SIP2 | SPM2 | One of three beta subunits of the Snf1 kinase complex; involved in the response to glucose starvation; null mutants exhibit accelerated aging; N-myristoylprotein localized to the cytoplasm and the plasma membrane; SIP2 has a paralog, GAL83, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3851-YGL209W | YGL209W | MIG2 | MLZ1 | Zinc finger transcriptional repressor; cooperates with Mig1p in glucose-induced gene repression; under low glucose conditions relocalizes to mitochondrion, where it interacts with Ups1p, antagonizes mitochondrial fission factor Dnm1p, indicative of a role in mitochondrial fusion or regulating morphology; regulates filamentous growth in response to glucose depletion; activated in stochastic pulses of nuclear localization in response to low glucose | Core | NA | NA | NA |
| 3852-YGL210W | YGL210W | YPT32 | Rab family GTPase YPT32 | Rab family GTPase involved in the exocytic pathway; mediates intra-Golgi traffic or the budding of post-Golgi vesicles from the trans-Golgi; protein abundance increases in response to DNA replication stress; YPT32 has a paralog, YPT31, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3853-YGL211W | YGL211W | NCS6 | TUC1|YGL210W-A | Protein required for uridine thiolation of Gln, Lys, and Glu tRNAs; required for the thiolation of uridine at the wobble position of Gln, Lys, and Glu tRNAs; has a role in urmylation and in invasive and pseudohyphal growth; inhibits replication of Brome mosaic virus in S. cerevisiae | Core | NA | NA | NA |
| 3854-YGL212W | YGL212W | VAM7 | VPL24|VPS43 | Vacuolar SNARE protein; functions with Vam3p in vacuolar protein trafficking; has an N-terminal PX domain (phosphoinositide-binding module) that binds PtdIns-3-P and mediates membrane binding; SNAP-25 homolog; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3855-YGL213C_NumOfGenes_2 | YGL213C | SKI8 | SKI complex subunit WD repeat protein SKI8|REC103 | Ski complex component and WD-repeat protein; mediates 3'-5' RNA degradation by the cytoplasmic exosome; also required for meiotic double-strand break recombination; null mutants have superkiller phenotype | Core | NA | NA | NA |
| 3856-YGL215W | YGL215W | CLG1 | NA | Cyclin-like protein that interacts with Pho85p; has sequence similarity to G1 cyclins PCL1 and PCL2 | Core | NA | NA | NA |
| 3857-YGL216W_NumOfGenes_2 | YGL216W | KIP3 | tubulin-dependent ATPase KIP3 | Kinesin-related antiparallel sliding motor protein; involved in mitotic spindle positioning; sliding activity promotes bipolar spindle assembly and maintenance of genome stability; inhibits spindle elongation, destabilizing late anaphase spindle microtubules that polymerize beyond the midzone | Core | NA | NA | NA |
| 3858-YGL219C_NumOfGenes_2 | YGL219C | MDM34 | ERMES complex subunit MDM34|MMM2 | Mitochondrial component of the ERMES complex; links the ER to mitochondria and may promote inter-organellar calcium and phospholipid exchange as well as coordinating mitochondrial DNA replication and growth; required for mitophagy; ERMES complex is often co-localized with peroxisomes and with concentrated areas of pyruvate dehydrogenase | Core | NA | NA | NA |
| 3859-YGL220W | YGL220W | BOL2 | FRA2|AIM15 | Cytosolic protein involved in repression of iron regulon transcription; forms an iron-independent complex with Fra1p, Grx3p, and Grx4p; null mutant fails to repress the iron regulon and is sensitive to nickel; sequence similarity to human BOLA family member, BOLA2 | Core | NA | NA | NA |
| 3860-YGL221C | YGL221C | NIF3 | hypothetical protein | Protein of unknown function; similar to Listeria monocytogenes major sigma factor (rpoD gene product); the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 3861-YGL222C | YGL222C | EDC1 | NA | RNA-binding protein that activates mRNA decapping directly; binds to mRNA substrate and enhances activity of decapping proteins Dcp1p and Dcp2p; has a role in translation during heat stress; protein becomes more abundant and forms cytoplasmic foci in response to DNA replication stress; EDC1 has a paralog, EDC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3862-YGL223C | YGL223C | COG1 | Golgi transport complex subunit COG1|SEC36|LDB11|COD3 | Essential component of the conserved oligomeric Golgi complex; a cytosolic tethering complex (Cog1p through Cog8p) that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments | Core | NA | NA | NA |