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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...
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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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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Related Experiment Video

Updated: Jun 17, 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

Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments.

Hongchao Lu1, Lan Lin, Seiko Sato

  • 1Molecular Biology Institute, Center for Computational Biology, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA.

Plos Computational Biology
|December 19, 2009
PubMed
Summary
This summary is machine-generated.

A new bioinformatics method identifies functional alternative splicing (AS) events by measuring RNA selection pressure. This approach accurately predicts functional AS exons, offering a valuable dataset for researchers studying gene regulation.

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

  • Computational Biology
  • Genomics
  • Molecular Biology

Background:

  • High-throughput sequencing has identified numerous alternative splicing (AS) events, but determining their functional significance remains challenging.
  • Existing methods for identifying functional AS often lack sensitivity or struggle to differentiate RNA-specific selection pressure from protein-level constraints.

Purpose of the Study:

  • To develop and validate a sensitive bioinformatics approach for identifying functionally important alternative splicing events.
  • To predict exons under strong RNA selection pressure ratio (RSPR) across evolutionary families, indicating functional AS.

Main Methods:

  • Developed a bioinformatics approach to calculate RSPR, measuring evolutionary selection against mutations altering only mRNA sequence.
  • Applied the RSPR method to UCSC 28 vertebrate genome alignments to predict AS exons.
  • Validated predictions using experimental criteria including cross-species detection, reading frame preservation, and tissue-specific regulation.

Main Results:

  • The RSPR approach accurately predicted 50-75% of known NOVA splicing factor target AS exons.
  • Identified 345 strongly selected AS events in humans and 262 in mice.
  • High-RSPR exons showed significantly higher rates of tissue-specific regulation (75%) compared to low-RSPR exons (20%).

Conclusions:

  • RSPR is a powerful metric for identifying functionally important alternative splicing events.
  • The study provides a dataset of over 600 predicted functional AS events, including novel examples like EXOC7.
  • RSPR outperforms traditional sequence conservation and pairwise comparisons for predicting functional AS.