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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 Regulates pre-mRNA Processing

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

Chromatin Structure and RNA Splicing

Chromatin Structure and RNA Splicing

Pre-mRNA Processing: Modification of pre-mRNA Ends

Pre-mRNA Processing: Modification of pre-mRNA Ends

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 (7-methyl guanosine). This 5' cap helps...

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Related Experiment Video

Updated: Aug 28, 2025

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

APPRIS principal isoforms and MANE Select transcripts define reference splice variants.

Fernando Pozo¹, José Manuel Rodriguez², Laura Martínez Gómez¹

¹Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.

Bioinformatics (Oxford, England)

|September 20, 2022

Summary

This summary is machine-generated.

Selecting the best splice variant is key for genetic analysis. MANE Select and APPRIS principal isoforms are superior to using the longest variant or expression data for identifying main cellular isoforms.

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Last Updated: Aug 28, 2025

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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

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Accurate selection of representative splice variants is critical for gene function studies and clinical variant mapping.
Most coding genes express a single dominant protein isoform, yet selecting this representative variant can be challenging.

Purpose of the Study:

To compare different methods for selecting biologically important reference splice variants for large-scale analyses.
To determine the most effective strategy for identifying the main cellular isoform of a coding gene.

Main Methods:

Comparison of longest splice isoforms, MANE Select transcripts, APPRIS principal isoforms, and gene expression data.
Analysis of selective pressure on exons unique to different splice variants.
Validation against proteomics data for main cellular isoforms.

Main Results:

APPRIS principal isoforms and MANE Select transcripts effectively identify main cellular isoforms, unlike using the longest splice variant or expression data.
Exons unique to the longest splice isoforms lack selective pressure and are likely non-functional.
MANE and APPRIS provide representatives for nearly 95% of genes, aligning with proteomics data over 98.2% when they agree.

Conclusions:

MANE Select and APPRIS principal isoforms are the preferred methods for selecting representative splice variants in large-scale genomic analyses.
The longest splice variant is an unreliable proxy for the main cellular isoform.
These curated isoform sets are crucial for accurate genetic variation interpretation and functional genomics.