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Alternative RNA Splicing

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 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...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

Chromatin Structure and RNA Splicing

Chromatin Structure and RNA Splicing

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

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Related Experiment Video

Updated: May 12, 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

rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud.

Jenea I Adams^1,2, Eric Kutschera², Qiang Hu³

¹Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.

Genomics, Proteomics & Bioinformatics

|May 9, 2025

Summary

This summary is machine-generated.

rMATS-cloud offers a portable solution for alternative splicing analysis from RNA sequencing (RNA-seq) data in any cloud environment. This tool efficiently processes large datasets, making it ideal for cloud-based bioinformatics research.

Keywords:

Alternative splicing Bioinformatics Cloud computing RNA-seq Transcriptomics

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Cloud-based bioinformatics tools are increasingly common for gene expression analysis.
However, accessible cloud solutions for alternative splicing analysis are limited.
rMATS has been a maintained, fast, and versatile tool for quantifying alternative splicing since 2014.

Purpose of the Study:

To present rMATS-cloud, a portable version of the rMATS workflow.
To enable rMATS analysis in diverse cloud environments for biomedical research.
To evaluate the performance of rMATS-cloud across different cloud platforms.

Main Methods:

Developed rMATS-cloud as a portable workflow.
Tested rMATS-cloud on two RNA-sequencing (RNA-seq) datasets.
Compared performance across three cloud platforms: Cavatica, Terra, and Seqera.

Main Results:

rMATS-cloud demonstrated efficient processing of RNA-seq datasets.
The workflow successfully handled datasets with thousands of samples.
Performance was consistent across tested cloud platforms, indicating broad applicability.

Conclusions:

rMATS-cloud is a versatile and portable tool for alternative splicing analysis.
It is well-suited for large-scale RNA-seq data processing in cloud environments.
rMATS-cloud enhances accessibility for cloud-based alternative splicing research.