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Related Concept Videos

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 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...
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...
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

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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

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SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Jie Wu1, Martin Akerman, Shuying Sun

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Bioinformatics (Oxford, England)
|September 8, 2011
PubMed
Summary
This summary is machine-generated.

SpliceTrap accurately quantifies exon inclusion levels from RNA-seq data, offering improved accuracy and reliability for studying alternative splicing regulation. This method provides a robust tool for transcriptomic mapping and understanding gene expression.

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Area of Science:

  • Genomics and Molecular Biology
  • Transcriptomics
  • Bioinformatics

Background:

  • Alternative splicing (AS) is a fundamental process in eukaryotes, generating diverse mRNA variants from a single gene.
  • Over 90% of human genes undergo alternative splicing, making its accurate quantification critical for transcriptomic studies.
  • Understanding exon inclusion levels is essential for mapping transcripts and investigating AS regulatory mechanisms.

Purpose of the Study:

  • To introduce SpliceTrap, a novel method for precise quantification of exon inclusion levels using paired-end RNA-seq data.
  • To provide a tool that estimates exon expression independently, differing from isoform-focused approaches.
  • To enable the identification of alternative splicing events without requiring background data for relative change estimation.

Main Methods:

  • SpliceTrap utilizes paired-end RNA-seq data for exon inclusion level quantification.
  • It employs a Bayesian inference approach for estimating the expression level of individual exons.
  • The method is designed to identify major alternative splicing event classes within a single cellular condition.

Main Results:

  • SpliceTrap demonstrated superior accuracy, robustness, and reliability in quantifying exon-inclusion ratios compared to existing state-of-the-art tools.
  • Validation through simulations and real data analysis confirmed the method's performance.
  • The tool effectively quantifies local exon-inclusion ratios from RNA-seq data.

Conclusions:

  • SpliceTrap is a valuable computational tool for advancing the study of alternative splicing regulation.
  • Its accuracy in quantifying exon inclusion levels makes it particularly useful for detailed transcriptomic analyses.
  • The method facilitates a deeper understanding of gene expression complexity driven by alternative splicing.