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 |
|---|---|---|---|---|---|---|---|---|
| 3038-YDR346C | YDR346C | SVF1 | SGI1 | Protein with a potential role in cell survival pathways; required for the diauxic growth shift; expression in mammalian cells increases survival under conditions inducing apoptosis; mutant has increased aneuploidy tolerance | Accessory | Ancestral | NA | NA |
| 3039-YDR347W | YDR347W | MRP1 | mitochondrial 37S ribosomal protein MRP1 | Mitochondrial ribosomal protein of the small subunit; MRP1 exhibits genetic interactions with PET122, encoding a COX3-specific translational activator, and with PET123, encoding a small subunit mitochondrial ribosomal protein | Accessory | Ancestral | NA | NA |
| 3040-YDR348C | YDR348C | PAL1 | NA | Protein of unknown function thought to be involved in endocytosis; physically interacts with Ede1p and is found at endocytic sites at cell periphery during early stages of endocytosis; green fluorescent protein (GFP)-fusion protein localizes to bud neck; potential Cdc28p substrate; similar to S. pombe Pal1 protein; relocalizes from bud neck to cytoplasm upon DNA replication stress; PAL1 has a paralog, YHR097C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 3041-YDR349C_NumOfGenes_2 | YDR349C | YPS7 | putative aspartic endopeptidase | Putative GPI-anchored aspartic protease; member of the yapsin family of proteases involved in cell wall growth and maintenance; located in the cytoplasm and endoplasmic reticulum | Core | NA | NA | NA |
| 3042-YDR350C | YDR350C | ATP22 | TCM10 | Specific translational activator for the mitochondrial ATP6 mRNA; Atp6p encodes a subunit of F1F0 ATP synthase; localized to the mitochondrial inner membrane | Core | NA | NA | NA |
| 3043-YDR351W | YDR351W | SBE2 | NA | Protein required for bud growth; involved in transport of cell wall components from the Golgi to the cell surface; SBE2 has a paralog, SBE22, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3044-YDR352W | YDR352W | YPQ2 | NA | Putative vacuolar membrane transporter for cationic amino acids; likely contributes to amino acid homeostasis by exporting cationic amino acids from the vacuole; member of the PQ-loop family, with seven transmembrane domains; mutant phenotype is functionally complemented by rat PQLC2 vacuolar transporter | Core | NA | NA | NA |
| 3045-YDR353W | YDR353W | TRR1 | thioredoxin-disulfide reductase TRR1 | Cytoplasmic thioredoxin reductase; key regulatory enzyme that determines the redox state of the thioredoxin system, which acts as a disulfide reductase system and protects cells against both oxidative and reductive stress; protein abundance increases in response to DNA replication stress; TRR1 has a paralog, TRR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3046-YDR354W_NumOfGenes_2 | YDR354W | TRP4 | anthranilate phosphoribosyltransferase | Anthranilate phosphoribosyl transferase; transferase of the tryptophan biosynthetic pathway; catalyzes the phosphoribosylation of anthranilate; subject to the general control system of amino acid biosynthesis | Core | NA | NA | NA |
| 3047-YDR356W_NumOfGenes_2 | YDR356W | SPC110 | NUF1|XCM1 | Inner plaque spindle pole body (SPB) component; ortholog of human kendrin; gamma-tubulin small complex (gamma-TuSC) receptor that interacts with Spc98p to recruit the complex to the nuclear side of the SPB, connecting nuclear microtubules to the SPB; promotes gamma-TuSC assembly and oligomerization to initiate microtubule nucleation; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner | Core | NA | NA | NA |
| 3048-YDR357C | YDR357C | CNL1 | BLC1 | Subunit of the BLOC-1 complex involved in endosomal maturation; interacts with Msb3p; null mutant is sensitive to drug inducing secretion of vacuolar cargo; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 3049-YDR358W | YDR358W | GGA1 | ubiquitin-binding protein | Golgi-localized protein with homology to gamma-adaptin; interacts with and regulates Arf1p and Arf2p in a GTP-dependent manner in order to facilitate traffic through the late Golgi; GGA1 has a paralog, GGA2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3050-YDR359C | YDR359C | EAF1 | VID21 | Component of the NuA4 histone acetyltransferase complex; acts as a platform for assembly of NuA4 subunits into the native complex; required for initiation of pre-meiotic DNA replication, likely due to its requirement for expression of IME1 | Core | NA | NA | NA |
| 3051-YDR360W | YDR360W | OPI7 | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps verified gene VID21/YDR359C | Accessory | Ancestral | NA | NA |
| 3052-YDR361C | YDR361C | BCP1 | protein-transporting protein BCP1 | Essential protein involved in nuclear export of Mss4p; Mss4p is a lipid kinase that generates phosphatidylinositol 4,5-biphosphate and plays a role in actin cytoskeleton organization and vesicular transport | Core | NA | NA | NA |