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 |
|---|---|---|---|---|---|---|---|---|
| 5993-YML072C | YML072C | TCB3 | NA | Cortical ER protein involved in ER-plasma membrane tethering; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to the plasma membrane (PM) and regulate PM phosphatidylinositol-4-phosphate (PI4P) levels by controlling access of Sac1p phosphatase to its substrate PI4P in the PM; localized to the bud via specific mRNA transport; non-tagged protein detected in a phosphorylated state in mitochondria; C-termini of Tcb1p, Tcb2p and Tcb3p interact | Core | NA | NA | NA |
| 5994-YML073C | YML073C | RPL6A | eL6|ribosomal 60S subunit protein L6A|L6e|rp18|YL16|L6A|L17A|YL16A | Ribosomal 60S subunit protein L6A; N-terminally acetylated; binds 5.8S rRNA; homologous to mammalian ribosomal protein L6, no bacterial homolog; RPL6A has a paralog, RPL6B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5995-YML074C | YML074C | FPR3 | peptidylprolyl isomerase FPR3|NPI46 | Nucleolar peptidyl-prolyl cis-trans isomerase (PPIase); FK506 binding protein; affects expression of multiple genes via its role in nucleosome assembly; phosphorylated by casein kinase II (Cka1p-Cka2p-Ckb1p-Ckb2p) and dephosphorylated by Ptp1p; PPIase domain acts as a transcriptional repressor when tethered to DNA by lexA, and repressor activity is dependent on PPIase activity; FPR3 has a paralog, FPR4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5996-YML075C | YML075C | HMG1 | hydroxymethylglutaryl-CoA reductase (NADPH) HMG1 | HMG-CoA reductase; catalyzes conversion of HMG-CoA to mevalonate, which is a rate-limiting step in sterol biosynthesis; one of two isozymes; localizes to nuclear envelope; overproduction induces formation of karmellae; forms foci at nuclear periphery upon DNA replication stress; HMG1 has a paralog, HMG2, that arose from the whole genome duplication; human homolog HMGCR can complement yeast hmg1 mutant | Core | NA | NA | NA |
| 5997-YML076C | YML076C | WAR1 | NA | Homodimeric Zn2Cys6 zinc finger transcription factor; binds to a weak acid response element to induce transcription of PDR12 and FUN34, encoding an acid transporter and a putative ammonia transporter, respectively | Core | NA | NA | NA |
| 5998-YML077W | YML077W | BET5 | TRAPP subunit BET5 | Core component of transport protein particle (TRAPP) complexes I-III; TRAPP complexes are related multimeric guanine nucleotide-exchange factors for the GTPase Ypt1p, regulating ER-Golgi traffic (TRAPPI), intra-Golgi traffic (TRAPPII), endosome-Golgi traffic (TRAPPII and III) and autophagy (TRAPPIII); human homology TRAPPC1 complements yeast null mutant | Core | NA | NA | NA |
| 5999-YML078W | YML078W | CPR3 | peptidylprolyl isomerase CPR3|CYP3 | Mitochondrial peptidyl-prolyl cis-trans isomerase (cyclophilin); catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; involved in protein refolding after import into mitochondria | Core | NA | NA | NA |
| 6000-YML079W | YML079W | NA | NA | Non-essential protein of unknown function; has structural resemblance to plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) and to some enzymes (epimerase, germin); localizes to the nucleus and cytoplasm | Core | NA | NA | NA |
| 6001-YML080W | YML080W | DUS1 | tRNA dihydrouridine synthase | Dihydrouridine synthase; member of a widespread family of conserved proteins including Smm1p, Dus3p, and Dus4p; modifies pre-tRNA(Phe) at U17 | Core | NA | NA | NA |
| 6002-YML081C-A | YML081C-A | ATP18 | F1F0 ATP synthase subunit i | Subunit of the mitochondrial F1F0 ATP synthase; F1F0 ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; termed subunit I or subunit j; does not correspond to known ATP synthase subunits in other organisms | Accessory | Ancestral | NA | NA |
| 6003-YML081W | YML081W | TDA9 | AAF1 | Transcription factor that regulates acetate production; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; null mutant is sensitive to expression of the top1-T722A allele; not an essential gene; TDA9 has a paralog, RSF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6004-YML082W | YML082W | NA | putative cystathionine gamma-synthase | Putative protein predicted to have carbon-sulfur lyase activity; transcriptionally regulated by Upc2p via an upstream sterol response element; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and the cytoplasm; not an essential gene; YML082W has a paralog, STR2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6005-YML083C | YML083C | NA | NA | Protein of unknown function; transcriptionally regulated by Upc2p via an upstream sterol response element; strong increase in transcript abundance during anaerobic growth compared to aerobic growth; cells deleted for YML083C do not exhibit growth defects in anerobic or anaerobic conditions | Accessory | Ancestral | NA | NA |
| 6006-YML084W | YML084W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 6007-YML085C | YML085C | TUB1 | alpha-tubulin TUB1 | Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules; relative distribution to nuclear foci increases upon DNA replication stress; TUB1 has a paralog, TUB3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |