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 |
|---|---|---|---|---|---|---|---|---|
| 3863-YGL224C | YGL224C | SDT1 | nucleotidase|SSM1 | Pyrimidine nucleotidase; responsible for production of nicotinamide riboside and nicotinic acid riboside; overexpression suppresses the 6-AU sensitivity of transcription elongation factor S-II, as well as resistance to other pyrimidine derivatives; SDT1 has a paralog, PHM8, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3864-YGL225W | YGL225W | VRG4 | GDP-mannose transporter|VIG4|LDB3|GOG5|VAN2 | Golgi GDP-mannose transporter; regulates Golgi function and glycosylation in Golgi; VRG4 has a paralog, HVG1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3865-YGL226C-A | YGL226C-A | OST5 | dolichyl-diphosphooligosaccharide--protein glycotransferase subunit | Zeta subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes asparagine-linked glycosylation of newly synthesized proteins | Core | NA | NA | NA |
| 3866-YGL226W | YGL226W | MTC3 | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the mitochondrion; mtc3 is synthetically sick with cdc13-1 | Core | NA | NA | NA |
| 3867-YGL227W | YGL227W | VID30 | glucose-induced degradation complex subunit VID30|GID1 | Central component of GID Complex, involved in FBPase degradation; interacts strongly with Gid8p to serve as a scaffold for other GID Complex subunits; contains SPRY domain and 3 domains that are also found in Gid8p - LisH, CTLH, and CRA; required for association of Vid vesicles and actin patches in vacuole import and degradation pathway; shifts the balance of nitrogen metabolism toward glutamate production; localizes to the nucleus and the cytoplasm | Core | NA | NA | NA |
| 3868-YGL228W | YGL228W | SHE10 | NA | Protein involved in outer spore wall assembly; likely involved directly in dityrosine layer assembly; putative GPI-anchored protein; overexpression causes growth arrest;; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the endoplasmic reticulum; SHE10 has a paralog, OSW7/YFR039C, that arose from the whole genome duplication; paralogs are redundant for spore wall dityrosine assembly | Core | NA | NA | NA |
| 3869-YGL229C | YGL229C | SAP4 | NA | Protein required for function of the Sit4p protein phosphatase; member of a family of similar proteins that form complexes with Sit4p, including Sap155p, Sap185p, and Sap190p; SAP4 has a paralog, SAP155, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3870-YGL230C | YGL230C | NA | NA | Putative protein of unknown function; non-essential gene | Core | NA | NA | NA |
| 3871-YGL231C | YGL231C | EMC4 | chaperone EMC4 | Member of conserved ER transmembrane complex; required for efficient folding of proteins in the ER; null mutant displays induction of the unfolded protein response; homologous to worm ZK616.6/EMC-4 and fly CG11137; mutation is functionally complemented by human EMC4 | Core | NA | NA | NA |
| 3872-YGL232W | YGL232W | TAN1 | putative tRNA acetyltransferase | Putative tRNA acetyltransferase; RNA-binding protein required for the formation of the modified nucleoside N(4)-acetylcytidine in serine and leucine tRNAs but not required for the same modification in 18S rRNA; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3873-YGL233W | YGL233W | SEC15 | Rab GTPase-binding exocyst subunit SEC15 | Essential 113 kDa subunit of the exocyst complex; the exocyst mediates polarized targeting and tethering of post-Golgi secretory vesicles to active sites of exocytosis prior to SNARE-mediated fusion; interacts with and functions as a downstream effector of active, GTP-bound Sec4p, a Rab family GTPase | Core | NA | NA | NA |
| 3874-YGL234W | YGL234W | ADE5,7 | bifunctional aminoimidazole ribotide synthase/glycinamide ribotide synthase | Enzyme of the 'de novo' purine nucleotide biosynthetic pathway; contains aminoimidazole ribotide synthetase and glycinamide ribotide synthetase activities | Core | NA | NA | NA |
| 3875-YGL236C_NumOfGenes_2 | YGL236C | MTO1 | tRNA modification protein MTO1|IPS1 | Mitochondrial protein; forms heterodimer complex with Mss1p that performs 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs; required for respiration in paromomycin-resistant 15S rRNA mutants; human homolog MTO1 can complement yeast null mutant | Accessory | Ancestral | NA | NA |
| 3876-YGL237C | YGL237C | HAP2 | NA | Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex; complex is heme-activated and glucose-repressed; complex is a transcriptional activator and global regulator of respiratory gene expression; contains sequences sufficient for both complex assembly and DNA binding; respiratory defect of the null mutant is functionally complemented by human NFYA | Accessory | Ancestral | NA | NA |
| 3877-YGL238W | YGL238W | CSE1 | importin-alpha export receptor|KAP109 | Nuclear envelope protein that acts as a recycling factor; mediates the nuclear export of Srp1p (importin alpha) back to the cytoplasm after its import substrates have been released into the nucleoplasm, thereby allowing the participation of Srp1p in multiple rounds of nuclear import; required for accurate chromosome segregation; homolog of metazoan CAS and human CSE1L, overexpression of which is implicated in cancer progression | Core | NA | NA | NA |