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RNA Splicing

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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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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Related Experiment Video

Updated: Mar 31, 2026

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

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

Published on: December 9, 2016

Two-pass alignment improves novel splice junction quantification.

Brendan A Veeneman¹, Sudhanshu Shukla², Saravana M Dhanasekaran²

¹Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology.

Bioinformatics (Oxford, England)

|November 1, 2015

Summary

This summary is machine-generated.

Two-pass alignment enhances the discovery and quantification of novel splice junctions in RNA sequencing data. This method improves read depth and accuracy for identifying new splicing events.

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Area of Science:

Transcriptomics
Bioinformatics
Computational Biology

Background:

Discovering novel splicing from RNA sequence data is crucial for transcriptomics.
Limited alignment power hinders accurate expression quantification of novel splice junctions.

Purpose of the Study:

To evaluate the performance of two-pass alignment for splice junction discovery and quantification.
To improve the identification and measurement of novel splicing events in RNA sequencing data.

Main Methods:

Two-pass alignment was implemented using sequential alignment, genome indexing, and re-alignment with STAR.
Performance was profiled across various transcriptome sequencing datasets.

Main Results:

Two-pass alignment improved quantification of over 94% of simulated novel splice junctions.
This method increased median read depth by up to 1.7-fold for novel splice junctions.
Alignment errors were found to be identifiable through simple classification.

Conclusions:

Two-pass alignment significantly advances the quantification and discovery of novel splicing events.
This approach offers improved accuracy and depth for analyzing splice variants.