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 |
|---|---|---|---|---|---|---|---|---|
| 5933-YML012W | YML012W | ERV25 | NA | Member of the p24 family involved in ER to Golgi transport; role in misfolded protein quality control; forms a heterotrimeric complex with Erp1, Erp2p, and Emp24, | Core | NA | NA | NA |
| 5934-YML013W_NumOfGenes_2 | YML013W | UBX2 | SEL1 | Bridging factor involved in ER-associated protein degradation (ERAD); bridges the cytosolic Cdc48p-Npl1p-Ufd1p ATPase complex and the membrane associated Ssm4p and Hrd1p ubiquitin ligase complexes; contains a UBX (ubiquitin regulatory X) domain and a ubiquitin-associated (UBA) domain; redistributes from the ER to lipid droplets during the diauxic shift and stationary phase; required for the maintenance of lipid homeostasis | Core | NA | NA | NA |
| 5935-YML014W | YML014W | TRM9 | tRNA (carboxymethyluridine(34)-5-O)-methyltransferase|KTI1 | tRNA methyltransferase; catalyzes modification of wobble bases in tRNA anticodons to 2, 5-methoxycarbonylmethyluridine and 5-methoxycarbonylmethyl-2-thiouridine; may act as part of a complex with Trm112p; deletion mutation increases translational infidelity, including amino acid misincorporation and -1 frameshifting, and also confers resistance to zymocin; null mutant displays activation of stress responses | Core | NA | NA | NA |
| 5936-YML015C | YML015C | TAF11 | TafII40|TAF40 | TFIID subunit (40 kDa); involved in RNA polymerase II transcription initiation, similar to histone H3 with atypical histone fold motif of Spt3-like transcription factors | Core | NA | NA | NA |
| 5937-YML016C | YML016C | PPZ1 | salt homeostasis regulator | Serine/threonine protein phosphatase Z, isoform of Ppz2p; involved in regulation of potassium transport, which affects osmotic stability, cell cycle progression, and halotolerance | Core | NA | NA | NA |
| 5938-YML017W | YML017W | PSP2 | MRS15 | Asn rich cytoplasmic protein that contains RGG motifs; high-copy suppressor of group II intron-splicing defects of a mutation in MRS2 and of a conditional mutation in POL1 (DNA polymerase alpha); possible role in mitochondrial mRNA splicing | Core | NA | NA | NA |
| 5939-YML018C | YML018C | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of the vacuole; physical interaction with Atg27p suggests a possible role in autophagy; YML018C is not an essential gene; relative distribution to the vacuolar membrane decreases upon DNA replication stress; YML018C has a paralog, THI74, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5940-YML019W | YML019W | OST6 | dolichyl-diphosphooligosaccharide--protein glycotransferase | Subunit of the oligosaccharyltransferase complex of the ER lumen; complex catalyzes asparagine-linked glycosylation of newly synthesized proteins; similar to and partially functionally redundant with Ost3p | Core | NA | NA | NA |
| 5941-YML020W | YML020W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5942-YML021C | YML021C | UNG1 | uracil-DNA glycosylase | Uracil-DNA glycosylase; required for repair of uracil in DNA formed by spontaneous cytosine deamination; efficiently excises uracil from single-stranded DNA in vivo; not required for strand-specific mismatch repair; cell-cycle regulated, expressed in late G1; localizes to mitochondria and nucleus | Core | NA | NA | NA |
| 5943-YML022W | YML022W | APT1 | adenine phosphoribosyltransferase APT1 | Adenine phosphoribosyltransferase; catalyzes the formation of AMP from adenine and 5-phosphoribosylpyrophosphate; involved in the salvage pathway of purine nucleotide biosynthesis; APT1 has a paralog, APT2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5944-YML023C | YML023C | NSE5 | Smc5-Smc6 complex subunit NSE5 | Component of the SMC5-SMC6 complex; this complex plays a key role in the removal of X-shaped DNA structures that arise between sister chromatids during DNA replication and repair | Core | NA | NA | NA |
| 5945-YML024W | YML024W | RPS17A | eS17|ribosomal 40S subunit protein S17A|S17e|rp51A|S17A|RPL51A|RP51A | Ribosomal protein 51 (rp51) of the small (40s) subunit; homologous to mammalian ribosomal protein S17, no bacterial homolog; RPS17A has a paralog, RPS17B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5946-YML025C | YML025C | YML6 | mitochondrial 54S ribosomal protein YmL6 | Mitochondrial ribosomal protein of the large subunit; has similarity to E. coli L4 ribosomal protein and human mitoribosomal MRP-L4 protein; essential for viability, unlike most other mitoribosomal proteins | Core | NA | NA | NA |
| 5947-YML026C | YML026C | RPS18B | uS13|ribosomal 40S subunit protein S18B|S18B|S13 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S18 and bacterial S13; RPS18B has a paralog, RPS18A, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |