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Transcription01:10

Transcription

154.7K
Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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Transcription01:17

Transcription

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Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
32.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

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Improving Translational Accuracy02:07

Improving Translational Accuracy

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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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Transfer RNA Synthesis02:35

Transfer RNA Synthesis

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Transfer RNA Synthesis02:36

Transfer RNA Synthesis

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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
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Related Experiment Video

Updated: Dec 31, 2025

IR-TEx: An Open Source Data Integration Tool for Big Data Transcriptomics Designed for the Malaria Vector Anopheles gambiae
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Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R.

Warren D Anderson1, Fabiana M Duarte2, Mete Civelek1,3

  • 1Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.

Bioinformatics (Oxford, England)
|January 10, 2020
PubMed
Summary
This summary is machine-generated.

Accurate primary transcript annotations are essential for interpreting genomic run-on sequencing data. The new primaryTranscriptAnnotation R package infers transcript start and termination sites, improving analysis of transcriptional regulation.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nascent transcript measurements from run-on sequencing are vital for studying transcriptional mechanisms.
  • Existing mRNA gene annotations often do not align with primary transcript boundaries, hindering accurate data interpretation.
  • There is a need for precise primary transcript annotations to effectively analyze genomic run-on data.

Purpose of the Study:

  • To develop a computational tool for inferring primary transcript start and termination sites.
  • To create novel, data-driven primary transcript annotations for genomic run-on data analysis.
  • To integrate these annotations with de novo identified transcriptional units.

Main Methods:

  • Development of the primaryTranscriptAnnotation R package.
  • Inference of transcriptional start and termination sites using genomic run-on data.
  • Annotation of transcriptional units based on inferred primary transcript coordinates.

Main Results:

  • The primaryTranscriptAnnotation R package enables data-driven primary transcript annotation.
  • This approach allows for unbiased identification of transcriptional units.
  • The methodology enhances the detection of differentially expressed transcripts.
  • More accurate quantification of RNA polymerase pause indices is achieved.

Conclusions:

  • Accurate primary transcript coordinates are crucial for interpreting genomic run-on sequencing data.
  • The primaryTranscriptAnnotation R package offers a novel solution for precise transcript annotation.
  • This tool improves the analysis of transcriptional regulation and RNA polymerase dynamics.