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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RNA Splicing01:32

RNA Splicing

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...
RNA Splicing01:32

RNA Splicing

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...
Alternative RNA Splicing02:18

Alternative RNA Splicing

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...
Alternative RNA Splicing02:18

Alternative RNA Splicing

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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Related Experiment Video

Updated: May 16, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Identifying differentially spliced genes from two groups of RNA-seq samples.

Weichen Wang1, Zhiyi Qin, Zhixing Feng

  • 1MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China. weichenw@princeton.edu

Gene
|December 12, 2012
PubMed
Summary

This study introduces a new exon-based method using a negative binomial (NB) statistic to identify differentially spliced genes from RNA-sequencing data. The approach efficiently detects splicing variations without needing isoform information, highlighting key exons involved.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing generates multiple transcript isoforms from a single gene, impacting biological functions.
  • Differential splicing analysis is crucial for understanding transcriptomes using next-generation sequencing (NGS).
  • Existing methods often rely on isoform composition or expression estimation.

Purpose of the Study:

  • To develop a novel exon-based statistical method for detecting differentially spliced genes between two RNA-sequencing sample groups.
  • To provide an alternative to isoform-based approaches that require complex isoform information.
  • To identify specific exons contributing to differential splicing events.

Main Methods:

  • Utilized the negative binomial (NB) distribution to model RNA-sequencing reads on exons.
  • Proposed an NB-statistic for comparing exon read counts between sample groups.
  • Developed the DSGseq software tool for implementing the NB-statistic method.

Main Results:

  • The NB-statistic method demonstrated good performance and applicability on simulated and real RNA-seq data (human kidney and liver).
  • The method successfully identified differentially spliced genes without prior annotation of alternative splicing.
  • It can highlight specific exons that are most likely differentially spliced.

Conclusions:

  • The NB-statistic offers an effective exon-based approach for differential splicing detection in RNA-seq studies.
  • The method simplifies analysis by not requiring isoform structure inference or expression estimation.
  • DSGseq provides a valuable tool for researchers comparing two groups of RNA-seq samples and identifying key splicing events.