Research design workflow
This is a hypothesis-generating tool. In mammalian capped mRNAs, translation initiation usually involves cap-dependent scanning and Kozak/start-context recognition—not a bacterial Shine–Dalgarno ribosome-binding site. No 5′ UTR can be declared universally “maximum ribosome binding” from sequence heuristics alone.
1. Coding sequence design
Supply a complete protein-coding sequence (start AUG and terminal stop) or a protein beginning with M. All synonymous candidates are independently reverse-translated and verified against the same amino-acid sequence.
No human/HEK293/A549 codon-use reference is bundled; absent weights have neutral preference. Partial weight files are not validated host profiles.
2. 5′ and 3′ UTR design
Start from UTRs you have obtained or selected independently. The tool creates simple, labeled sequence comparisons—it does not supply proprietary, experimentally validated UTRs.
5′ UTR ends just before the CDS start AUG. A −3 purine and the CDS +4 base are reviewed together.
Motif checks are not transcript half-life predictions. Cap, chemical modifications, and poly(A) are not added in export.
Synthetic sequences only; not a commercial or biologically validated design.
3. Generate and compare candidate designs
CDS optimization considers GC targets, short repeated tracts, and any user-provided codon weights. UTR alternatives include limited start-context and motif variants; all require subsequent laboratory validation.
—Amino acids (excluding stop)
—CDS length (nt)
—Assembled transcript (nt)
| CDS candidate | Observed GC | GC target | Synonymous codons changed | AA preserved |
|---|
Select coding variant
5′ UTR candidates
3′ UTR candidates
The 3′ UTR motif variants may remove real regulatory functions or create new ones. Treat them as experimental comparators, not “stabilized UTRs.”
Review flags and assumptions
4. Assembled mRNA transcript hypothesis
5′ UTR + selected ORF + 3′ UTR. Exports contain sequence only, not an in vitro transcribed, capped, modified or polyadenylated RNA product.
Generate a candidate to view the assembly and enable exports.
5′ UTR
AUG → coding ORF → stop
3′ UTR
Independent verification: ViennaRNA RNAfold ↗ for thermodynamic RNA structure; NCBI ORFfinder ↗ for ORF review. Translation/stability and tissue-specific expression must be measured in appropriate biological systems.