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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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Related Experiment Video

Updated: Oct 6, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Slinker: Visualising novel splicing events in RNA-Seq data.

Breon Schmidt^1,2, Marek Cmero^1,3,4, Paul Ekert^1,3,5,6,7

¹Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia.

|January 17, 2022

Summary

This summary is machine-generated.

Slinker visualizes RNA sequencing (RNA-Seq) data by assembling sample-specific superTranscripts, overcoming sparsity issues. This bioinformatics pipeline aids in identifying novel splicing and deletion events in rare diseases and cancer.

Keywords:

Novel Splicing Events RNA-Seq Visualisation bioinformatics superTranscripts

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Last Updated: Oct 6, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Published on: June 24, 2021

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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

Area of Science:

Genomics
Bioinformatics
Transcriptomics

Background:

RNA sequencing (RNA-Seq) data visualization faces sparsity due to reads mapping primarily to exons (under 3% of the human genome).
Exon-only references (superTranscripts) improve visualization by omitting introns but can lose information on novel splicing events.
Such variations in non-exonic regions may underlie pathogenic phenotypes, necessitating improved visualization methods.

Purpose of the Study:

To present Slinker, a bioinformatics pipeline for assembling sample-specific superTranscripts.
To enable data-driven visualization of RNA-Seq alignments across typically sparse genomic regions.
To identify novel splicing and deletion events potentially linked to disease.

Main Methods:

Slinker utilizes Stringtie2 for transcript assembly across any gene sequence.
Assembled transcripts are merged with reference transcripts and converted into superTranscripts.
Visualizations are generated using Plotly, incorporating annotation and coverage information.

Main Results:

Slinker was validated on five novel splicing events in rare disease samples (primary muscular disorders).
The pipeline effectively visualized deletion events in tumor samples within the IKZF1 gene.
Slinker provides succinct visualization of RNA-Seq alignments in sparse genomic regions.

Conclusions:

Slinker offers a novel approach to visualize RNA-Seq data, particularly in under-represented genomic regions.
The pipeline aids in the discovery and characterization of splicing and deletion events relevant to rare diseases and cancer.
Slinker is freely available on Github, promoting broader research accessibility.