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Updated: May 25, 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

Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing.

Kian Huat Lim¹, William Guy Fairbrother

¹Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903, USA.

Bioinformatics (Oxford, England)

|February 14, 2012

Summary

This summary is machine-generated.

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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 Splicing

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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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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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pre-mRNA Processing

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...

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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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Splicing elements depend on their location. A new tool, Spliceman, analyzes DNA sequences to predict how mutations near splice sites affect pre-messenger RNA splicing across 11 genomes.

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Splicing elements exhibit positional dependence, meaning their location influences their function.
Understanding this relationship is crucial for predicting the impact of genetic variations on gene expression.

Purpose of the Study:

To develop a computational tool, Spliceman, for predicting the functional impact of mutations on pre-mRNA splicing.
To leverage the positional distribution patterns of splicing elements to assess mutation effects.

Main Methods:

Comparative analysis of positional distributions of 4096 hexamers around human splice sites.
Development of a distance measure to quantify the disruption of splicing by point mutations.
Implementation of Spliceman as an online tool analyzing DNA sequences with mutations.

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Using the E1A Minigene Tool to Study mRNA Splicing Changes

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

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Last Updated: May 25, 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

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

Main Results:

Point mutations causing larger positional distance changes were found to disrupt splicing.
Mutations with smaller distance changes generally had no significant effect on splicing.
Spliceman successfully predicts the likelihood of mutations disrupting splicing based on positional distributions.

Conclusions:

Functional splicing elements possess characteristic positional distributions around constitutively spliced exons.
Spliceman provides a valuable resource for predicting mutation effects on splicing across multiple species.
The tool analyzes 11 genomes, including human, mouse, and zebrafish, enhancing its broad applicability.