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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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TEDD: a comprehensive database for translation efficiency dynamics.

Wenyan Lei1,2,3, Cuidan Li1,2, Hengyu Zhou1,2,4

  • 1China National Center for Bioinformation, Beijing 100101, China.

Nucleic Acids Research
|November 11, 2025
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Summary
This summary is machine-generated.

We developed TEDD, a database for human translation efficiency (TE), translation ratio (TR), and elongation velocity index (EVI). It integrates multi-omics data to explore translational regulation by UTR features across various biological contexts.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Translation is crucial for gene expression and biological phenotypes.
  • Quantifying translation efficiency (TE), initiation (TR), and elongation (EVI) across contexts is limited.
  • UTR features significantly regulate translation in development and disease.

Purpose of the Study:

  • To create a comprehensive database (TEDD) for human TE, TR, and EVI.
  • To focus on the role of 5'/3' UTR features in translational regulation.
  • To provide a resource for exploring context-specific translational control.

Main Methods:

  • Integrated 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects.
  • Calculated TE, TR, and EVI metrics at gene and transcript levels.
  • Annotated regulatory 5'/3' UTR features for detailed analysis.

Main Results:

  • TEDD provides integrated data across 24 tissues/cell types, 74 cell lines, and 52 conditions.
  • Metrics are paired with detailed UTR annotations for fine-grained investigation.
  • The database enables multi-dimensional comparisons across genes, transcripts, and gene sets.

Conclusions:

  • TEDD is a valuable resource for studying translational control in humans.
  • It supports basic and translational research, including mRNA vaccine design and gene therapy.
  • The database facilitates exploration of translational regulation mechanisms and their applications.