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Related Concept Videos

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...
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...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: 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...

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Related Experiment Video

Updated: May 21, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and

Timothy J Robinson1, Eleonora Forte, Raul E Salinas

  • 1Molecular Cancer Biology Program, Duke University Medical Center, Durham, North Carolina 27710, USA.

RNA (New York, N.Y.)
|June 28, 2012
PubMed
Summary

SplicerEX is a new algorithm that detects changes in messenger RNA (mRNA) isoforms from microarray data. It accurately identifies alternative splicing events and corrects for technical artifacts, aiding biological research.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Related Experiment Videos

Last Updated: May 21, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

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

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • The central dogma of molecular biology, "one gene, one protein," has been challenged by the discovery of alternative mRNA processing.
  • Alternative splicing allows a single gene to produce multiple messenger RNA (mRNA) transcripts, leading to diverse protein isoforms.

Purpose of the Study:

  • To introduce SplicerEX, a novel algorithm for detecting and categorizing changes in mRNA isoforms from microarray data.
  • To address and mitigate technological artifacts inherent in exon array-based alternative splicing detection.
  • To compare the performance of SplicerEX with existing methods and validate its findings.

Main Methods:

  • Development and application of the SplicerEX algorithm.
  • Analysis of both conventional and splice-sensitive microarray data, including Affymetrix GeneChips and Human Exon Arrays.
  • Experimental validation using Reverse Transcription Polymerase Chain Reaction (RT-PCR).
  • Comparison with the MiDAS analysis tool using publicly available microarray datasets.

Main Results:

  • SplicerEX effectively detects widespread changes in mRNA isoforms and categorizes underlying processing mechanisms.
  • The algorithm successfully mitigates artifacts associated with exon array detection, such as signal attenuation and saturation.
  • SplicerEX demonstrated superior detection of 3'-located mRNA processing changes compared to the Human Exon Array.
  • Novel Epstein-Barr virus (EBV)-regulated mRNA isoform changes in caspases 6, 7, and 8 were identified.
  • SplicerEX provided more efficient categorization of mRNA isoform changes than MiDAS, with a higher proportion of validated events.

Conclusions:

  • SplicerEX is a valuable tool for biologists studying mRNA isoform usage from various microarray platforms.
  • The algorithm enhances the analysis of alternative splicing, particularly from archival microarray data.
  • SplicerEX facilitates a deeper understanding of gene expression regulation through alternative mRNA processing.