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 |
|---|---|---|---|---|---|---|---|---|
| 5858-YLR401C_NumOfGenes_2 | YLR401C | DUS3 | tRNA dihydrouridine synthase DUS3 | Dihydrouridine synthase; member of a widespread family of conserved proteins including Smm1p, Dus1p, and Dus4p; contains a consensus oleate response element (ORE) in its promoter region; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |
| 5859-YLR402W | YLR402W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 5860-YLR403W_NumOfGenes_2 | YLR403W | SFP1 | zinc-coordinating transcription factor SFP1|[ISP+]|[ISP(+)] | Regulates transcription of ribosomal protein and biogenesis genes; regulates response to nutrients and stress, G2/M transitions during mitotic cell cycle and DNA-damage response, and modulates cell size; regulated by TORC1 and Mrs6p; sequence of zinc finger, ChIP localization data, and protein-binding microarray (PBM) data, and computational analyses suggest it binds DNA directly at highly active RP genes and indirectly through Rap1p at others; can form the [ISP+] prion | Core | NA | NA | NA |
| 5861-YLR404W_NumOfGenes_2 | YLR404W | SEI1 | seipin|FLD1 | Seipin involved in lipid droplet (LD) assembly; controls lipid particle morphology, number, and size; promotes initiation of LD formation on the ER; ensures that LDs bud from the ER towards the cytosolic side of the membrane; forms a complex with Ldb16p at ER-LD contact sites, stabilizing these sites; null mutants have localized accumulation of phosphatidic acid (PA) marker proteins; BSCL2, human homolog implicated in congenital lipodystrophy, complements yeast null mutant | Core | NA | NA | NA |
| 5862-YLR405W_NumOfGenes_2 | YLR405W | DUS4 | tRNA dihydrouridine synthase | Dihydrouridine synthase; member of a widespread family of conserved proteins including Smm1p, Dus1p, and Dus3p | Core | NA | NA | NA |
| 5863-YLR406C_NumOfGenes_2 | YLR406C | RPL31B | eL31|ribosomal 60S subunit protein L31B|L31e|YL28|L34B|L31B | Ribosomal 60S subunit protein L31B; associates with karyopherin Sxm1p; loss of both Rpl31p and Rpl39p confers lethality; homologous to mammalian ribosomal protein L31, no bacterial homolog; RPL31B has a paralog, RPL31A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5864-YLR406C-A | YLR406C-A | NA | NA | Putative protein of unknown function; SWAT-GFP fusion protein localizes to the endoplasmic reticulum and vacuole, while mCherry fusion localizes to just the vacuole | Accessory | Unknown | NA | NA |
| 5865-YLR407W_NumOfGenes_2 | YLR407W | NA | NA | Putative protein of unknown function; null mutant displays elongated buds and a large fraction of budded cells have only one nucleus | Core | NA | NA | NA |
| 5866-YLR408C_NumOfGenes_2 | YLR408C | BLS1 | BLB1 | Subunit of the BLOC-1 complex involved in endosomal maturation; green fluorescent protein (GFP)-fusion protein localizes to the endosome; YLR408C is not an essential gene | Core | NA | NA | NA |
| 5867-YLR409C_NumOfGenes_2 | YLR409C | UTP21 | rRNA-processing protein UTP21 | Subunit of U3-containing 90S preribosome and SSU processome complexes; involved in production of 18S rRNA and assembly of small ribosomal subunit; synthetic defect with STI1 Hsp90 cochaperone; human homolog linked to glaucoma; Small Subunit processome is also known as SSU processome | Core | NA | NA | NA |
| 5868-YLR410W_NumOfGenes_2 | YLR410W | VIP1 | inositol polyphosphate kinase VIP1 | Inositol hexakisphosphate and inositol heptakisphosphate kinase; inositol heptakisphosphate (IP7) production is important for phosphate signaling; involved in cortical actin cytoskeleton function, and invasive pseudohyphal growth analogous to S. pombe asp1; inositol hexakisphosphate is also known as IP6 | Core | NA | NA | NA |
| 5869-YLR411W_NumOfGenes_2 | YLR411W | CTR3 | high-affinity Cu transporter CTR3 | High-affinity copper transporter of the plasma membrane; acts as a trimer; gene is disrupted by a Ty2 transposon insertion in many laboratory strains of S. cerevisiae | Core | NA | NA | NA |
| 5870-YLR412C-A | YLR412C-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5871-YLR412W_NumOfGenes_2 | YLR412W | BER1 | NA | Protein involved in microtubule-related processes; GFP-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS; YLR412W is not an essential gene; similar to Arabidopsis SRR1 gene | Core | NA | NA | NA |
| 5872-YLR413W_NumOfGenes_2 | YLR413W | INA1 | NA | Protein of unknown function; not an essential gene; YLR413W has a paralog, FAT3, that arose from the whole genome duplication | Core | NA | NA | NA |