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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...
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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Related Experiment Video

Updated: May 16, 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

Intron-centric estimation of alternative splicing from RNA-seq data.

Dmitri D Pervouchine1, David G Knowles, Roderic Guigó

  • 1Centre de Regulació Genòmica, 08003 Barcelona, Spain. dp@crg.eu

Bioinformatics (Oxford, England)
|November 23, 2012
PubMed
Summary

This study introduces a new framework to analyze complex RNA splicing events beyond simple exon skipping. The bam2ssj tool quantifies splicing rates at intron ends, offering a standardized method for RNA-seq data analysis.

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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

Related Experiment Videos

Last Updated: May 16, 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:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput sequencing generates vast amounts of data, posing challenges for analysis.
  • The standard percent-spliced-in (PSI) metric is limited to simple exon-skipping events.
  • Most human splicing events are more complex than single exon skipping.

Purpose of the Study:

  • To generalize RNA splicing event quantification beyond single exon skipping.
  • To introduce a novel intron-centric framework for analyzing splicing.
  • To provide a standardized protocol for splice junction quantification from RNA-seq data.

Main Methods:

  • Developed a framework that generalizes the PSI metric to arbitrary splicing events.
  • Introduced two indices, and , to measure splicing rates at the 5' and 3' ends of introns.
  • Implemented the framework as bam2ssj, a BAM-file-processing pipeline for strand-specific read counting.

Main Results:

  • The new framework deconvolutes distinct elementary acts of the splicing reaction.
  • The completeness of splicing index is decomposed similarly.
  • bam2ssj provides a consistent protocol for quantifying splice junctions from RNA-seq data.

Conclusions:

  • The proposed framework and bam2ssj tool enable comprehensive analysis of complex splicing events.
  • This offers a standardized approach for RNA-seq data analysis, addressing current limitations.
  • The open-source C code is available for broader research community adoption.