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 |
|---|---|---|---|---|---|---|---|---|
| 7358-YPL009C | YPL009C | RQC2 | TAE2 | Component of RQC, which mediates nascent chain degradation; RQC (ribosome quality control complex) is a ribosome-bound complex required for degradation of polypeptides arising from stalled translation; recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits; monitors translation stress and signals this to Hsf1p | Core | NA | NA | NA |
| 7359-YPL010W | YPL010W | RET3 | coatomer subunit zeta | Zeta subunit of the coatomer complex (COPI); COPI coats Golgi-derived transport vesicles; involved in retrograde transport between Golgi and ER | Core | NA | NA | NA |
| 7360-YPL011C | YPL011C | TAF3 | TafII47|TAF47 | TFIID subunit (47 kDa); involved in promoter binding and RNA polymerase II transcription initiation | Core | NA | NA | NA |
| 7361-YPL012W | YPL012W | RRP12 | mRNA-binding protein RRP12 | Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; has a role in nuclear import in association with Pse1p; also plays a role in the cell cycle and the DNA damage response; contains HEAT-repeats | Core | NA | NA | NA |
| 7362-YPL013C | YPL013C | MRPS16 | mitochondrial 37S ribosomal protein MRPS16 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 7363-YPL014W | YPL014W | CIP1 | NA | Cyclin-dependent kinase inhibitor; interacts with and inhibits the Cdc28p/Cln2p, G1/S phase cyclin-dependent kinase complex but not S-phase, or M-phase complexes; overexpression blocks cells in G1 phase and stabilizes the Cdc28p inhibitor Sic1p, while disruption accelerates the G1/S phase transition; phosphorylated during S phase in a Cdc28p-dependent manner; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus | Core | NA | NA | NA |
| 7364-YPL015C | YPL015C | HST2 | histone deacetylase HST2 | Cytoplasmic NAD(+)-dependent protein deacetylase; deacetylation targets are primarily cytoplasmic proteins; member of the silencing information regulator 2 (Sir2) family of NAD(+)-dependent protein deacetylases; modulates nucleolar (rDNA) and telomeric silencing; possesses NAD(+)-dependent histone deacetylase activity in vitro; contains a nuclear export signal (NES); function regulated by its nuclear export | Core | NA | NA | NA |
| 7365-YPL016W | YPL016W | SWI1 | [SWI(+)]|[SWI+]|LPA1|GAM3|ADR6 | Subunit of the SWI/SNF chromatin remodeling complex; regulates transcription by remodeling chromatin; required for transcription of many genes, including ADH1, ADH2, GAL1, HO, INO1 and SUC2; self-assembles to form [SWI+] prion and to alter expression pattern; human homolog ARID1A is a candidate tumor suppressor gene in breast cancer | Core | NA | NA | NA |
| 7366-YPL017C | YPL017C | IRC15 | NA | Microtubule associated protein; regulates microtubule dynamics; required for accurate meiotic chromosome segregation; null mutant displays large budded cells due to delayed mitotic progression, increased levels of spontaneous Rad52 foci; IRC15 has a paralog, LPD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7367-YPL018W | YPL018W | CTF19 | MCM18 | Outer kinetochore protein, needed for accurate chromosome segregation; component of kinetochore sub-complex COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) that functions as platform for kinetochore assembly; required for spindle assembly checkpoint; minimizes potentially deleterious centromere-proximal crossovers by preventing meiotic DNA break formation proximal to centromere; homolog of human centromere constitutive-associated network (CCAN) subunit CENP-P and fission yeast fta2 | Core | NA | NA | NA |
| 7368-YPL019C | YPL019C | VTC3 | vacuolar transporter chaperone|PHM2 | Regulatory subunit of the vacuolar transporter chaperone (VTC) complex; involved in membrane trafficking, vacuolar polyphosphate accumulation, microautophagy and non-autophagic vacuolar fusion; VTC3 has a paralog, VTC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7369-YPL020C | YPL020C | ULP1 | SUMO protease ULP1|NIB1 | Protease that specifically cleaves Smt3p protein conjugates; required for cell cycle progression; associates with nucleoporins and may interact with septin rings during telophase; sequestered to the nucleolus under stress conditions | Core | NA | NA | NA |
| 7370-YPL021W | YPL021W | ECM23 | SRD2 | Non-essential protein of unconfirmed function; affects pre-rRNA processing, may act as a negative regulator of the transcription of genes involved in pseudohyphal growth; homologous to Srd1p | Core | NA | NA | NA |
| 7371-YPL022W | YPL022W | RAD1 | RAD12|ssDNA endodeoxyribonuclease RAD1|LPB9 | Single-stranded DNA endonuclease (with Rad10p); cleaves single-stranded DNA during nucleotide excision repair and double-strand break repair; subunit of Nucleotide Excision Repair Factor 1 (NEF1); homolog of human XPF protein | Core | NA | NA | NA |
| 7372-YPL023C | YPL023C | MET12 | methylenetetrahydrofolate reductase (NAD(P)H) MET12 | Protein with MTHFR activity in vitro; null mutant has no phenotype and is prototrophic for methionine; MET13 encodes major isozyme of methylenetetrahydrofolate reductase (MTHFR) | Core | NA | NA | NA |