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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...
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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.
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Ribosome Profiling

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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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Related Experiment Video

Updated: May 14, 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

Estimation of data-specific constitutive exons with RNA-Seq data.

Ellis Patrick1, Michael Buckley, Yee Hwa Yang

  • 1School of Mathematics and Statistics, University of Sydney, Sydney NSW 2006, Australia.

BMC Bioinformatics
|January 31, 2013
PubMed
Summary

We developed exClust, a novel method to identify constitutive exons for accurate gene transcription measurement. This approach offers unbiased estimation of gene expression by focusing on consistently spliced exons.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA sequencing (RNA-Seq) is a powerful tool for studying cellular processes.
  • Accurately estimating overall gene transcription is challenging due to variations in exon usage.
  • Constitutive exons, consistently present in spliced transcripts, offer a reliable measure of gene transcription.

Purpose of the Study:

  • To develop a robust method for identifying constitutive exons from RNA-Seq data.
  • To provide an unbiased estimation of overall gene transcription.
  • To improve the accuracy of gene expression analysis.

Main Methods:

  • A clustering-based approach named exClust was developed.
  • The method integrates gene annotation and experimental RNA-Seq data.
  • exClust is implemented as an R package called sydSeq.

Main Results:

  • exClust effectively identifies constitutive exons within RNA-Seq datasets.
  • The method incorporates information from both annotations and the specific dataset.
  • The sydSeq R package provides an open-source implementation.

Conclusions:

  • exClust significantly increases the number of reads used for analysis compared to standard methods.
  • The method demonstrates improved concordance with quantitative reverse transcription PCR (qRT-PCR) data.
  • exClust provides robust and reliable estimates of overall gene transcription.