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 |
|---|---|---|---|---|---|---|---|---|
| 2663-YDL218W | YDL218W | NA | NA | Putative protein of unknown function; YDL218W transcription is regulated by Azf1p and induced by starvation and aerobic conditions; expression also induced in cells treated with the mycotoxin patulin | Core | NA | NA | NA |
| 2664-YDL219W | YDL219W | DTD1 | D-tyrosyl-tRNA(Tyr) deacylase | D-Tyr-tRNA(Tyr) deacylase; functions in protein translation, may affect nonsense suppression via alteration of the protein synthesis machinery; ubiquitous among eukaryotes | Core | NA | NA | NA |
| 2665-YDL220C | YDL220C | CDC13 | telomere-binding protein CDC13|EST4 | Single stranded DNA-binding protein found at TG1-3 telomere G-tails; key roles in regulation of telomerase, telomere end protection, conventional telomere replication; regulates telomere replication through recruitment of specific sub-complexes, essential function is telomere capping; forms homodimer via N-terminus; disruption of dimerization leads to short telomeres; autophagy and proteasome are involved in Cdc13p degradation; differentially phosphorylated through cell cycle | Core | NA | NA | NA |
| 2666-YDL221W | YDL221W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the 3' end of essential gene CDC13 | Accessory | Ancestral | NA | NA |
| 2667-YDL222C | YDL222C | FMP45 | NA | Integral membrane protein localized to mitochondria; required for sporulation and maintaining sphingolipid content; similar to SUR7; FMP45 has a paralog, YNL194C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2668-YDL223C | YDL223C | HBT1 | NA | Shmoo tip protein, substrate of Hub1p ubiquitin-like protein; mutants are defective for mating projection formation, thereby implicating Hbt1p in polarized cell morphogenesis; HBT1 has a paralog, YNL195C, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2669-YDL224C | YDL224C | WHI4 | NA | Putative RNA binding protein; regulates the cell size requirement for passage through Start and commitment to cell division; WHI4 has a paralog, WHI3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2670-YDL225W | YDL225W | SHS1 | septin SHS1|SEP7 | Component of the septin ring that is required for cytokinesis; present at the ends of rod-like septin hetero-oligomers; C-terminal extension is important for recruitment of Bni5p to the mother-bud neck, which in turn is required for Myo1p recruitment and cytokinesis; undergoes sumoylation and phosphorylation during mitosis; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2671-YDL226C | YDL226C | GCS1 | NA | ADP-ribosylation factor GTPase activating protein (ARF GAP); involved in ER-Golgi transport; required for prospore membrane formation; regulates phospholipase Spo14p; shares functional similarity with Glo3p; GCS1 has a paralog, SPS18, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 2672-YDL227C | YDL227C | HO | NA | Site-specific endonuclease; required for gene conversion at the MAT locus (homothallic switching) through the generation of a ds DNA break; expression restricted to mother cells in late G1 as controlled by Swi4p-Swi6p, Swi5p, and Ash1p | Accessory | Ancestral | NA | NA |
| 2673-YDL229W_NumOfGenes_3 | YDL229W | SSB1 | Hsp70 family ATPase SSB1|YG101 | Cytoplasmic ATPase that is a ribosome-associated molecular chaperone; functions with J-protein partner Zuo1p; may be involved in folding of newly-made polypeptide chains; member of the HSP70 family; interacts with phosphatase subunit Reg1p; SSB1 has a paralog, SSB2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2674-YDL230W_NumOfGenes_2 | YDL230W | PTP1 | tyrosine protein phosphatase PTP1 | Phosphotyrosine-specific protein phosphatase; dephosphorylates a broad range of substrates in vivo, including Fpr3p; localized to the cytoplasm and the mitochondria; proposed to be a negative regulator of filamentation | Core | NA | NA | NA |
| 2675-YDL231C_NumOfGenes_3 | YDL231C | BRE4 | NA | Zinc finger protein containing five transmembrane domains; null mutant exhibits strongly fragmented vacuoles and sensitivity to brefeldin A, a drug which is known to affect intracellular transport | Core | NA | NA | NA |
| 2676-YDL232W | YDL232W | OST4 | olichyl-diphosphooligosaccharide--protein glycotransferase OST4 | Subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes protein asparagine-linked glycosylation; type I membrane protein required for incorporation of Ost3p or Ost6p into the OST complex | Core | NA | NA | NA |
| 2677-YDL233W_NumOfGenes_2 | YDL233W | MFG1 | NA | Regulator of filamentous growth; interacts with FLO11 promoter and regulates FLO11 expression; binds to transcription factors Flo8p and Mss11p; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YDL233W is not an essential gene | Core | NA | NA | NA |