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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

24.7K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Detection of Alternative Splicing During Epithelial-Mesenchymal Transition11:48

Detection of Alternative Splicing During Epithelial-Mesenchymal Transition

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Alternative splicing regulation has been shown to contribute to the epithelial-mesenchymal transition (EMT), an essential cellular program in various physiological and pathological processes. Here we describe a method utilizing an inducible EMT model for the detection of alternative splicing during...
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Alternative splicing (AS) and alternative polyadenylation (APA) expand the diversity of transcript isoforms and their products. Here, we describe bioinformatic protocols to analyze bulk RNA-seq and 3' end sequencing assays to detect and visualize AS and APA varying across experimental...
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Dissection of the Transversus Abdominis Muscle for Whole-mount Neuromuscular Junction Analysis06:12

Dissection of the Transversus Abdominis Muscle for Whole-mount Neuromuscular Junction Analysis

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In this video we demonstrate a protocol for dissection of the transversus abdominis muscle of the mouse and use immunofluorescence and microscopy to visualize neuromuscular...
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Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay11:22

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

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An in situ hybridization (ISH) protocol that uses short antisense oligonucleotides to detect alternative pre-mRNA splicing patterns in mouse brain sections is...
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Related Experiment Video

Updated: Jan 20, 2026

Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
11:48

Detection of Alternative Splicing During Epithelial-Mesenchymal Transition

Published on: October 9, 2014

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ASJA: A Program for Assembling Splice Junctions Analysis.

Jingjing Zhao1,2, Qin Li1,2, Yuchen Li1,2

  • 1Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Computational and Structural Biotechnology Journal
|August 30, 2019
PubMed
Summary
This summary is machine-generated.

Assembling Splice Junctions Analysis (ASJA) is a new software tool that identifies and characterizes all RNA splice junctions from RNA sequencing data. This tool aids in the discovery of novel splice junctions and provides their expression levels.

Keywords:
Circular RNARNA splicingRNA-seqSplice junctions

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Related Experiment Videos

Last Updated: Jan 20, 2026

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Alternative RNA Splicing: Regulated Splicing of Exons and Introns
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RNA Splicing, Lariat and the Spliceososme
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA splicing generates diverse splice junctions, including linear, back-splice, and fusion types.
  • Existing software for splice junction detection and quantification is limited.

Purpose of the Study:

  • To introduce Assembling Splice Junctions Analysis (ASJA), a novel software package for comprehensive splice junction identification and characterization.
  • To enable the analysis of all splice junction types from high-throughput RNA sequencing data.

Main Methods:

  • ASJA processes assembled transcripts and chimeric alignments generated by STAR aligner and StringTie assembler.
  • The software identifies unique junction positions and provides normalized expression levels.
  • Integrative analysis with annotations allows for additional filtering and identification of novel junctions.

Main Results:

  • ASJA successfully identifies and characterizes a comprehensive set of splice junctions, including linear, back-splice, and fusion types.
  • The software provides unique positional information and normalized expression levels for each detected junction.
  • ASJA facilitates the discovery of novel splice junctions through annotation and integrative analysis.

Conclusions:

  • ASJA is a valuable bioinformatics tool for the comprehensive analysis of splice junctions in RNA sequencing data.
  • The software enhances the ability to detect and quantify diverse splice junction types, including novel ones.
  • ASJA supports further research in RNA splicing mechanisms and gene expression analysis.