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Related Concept Videos

RNA Splicing01:32

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...
RNA Splicing01:32

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 Splicing01:32

Pre-mRNA Processing: 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...
Alternative RNA Splicing02:18

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...
Alternative RNA Splicing02:18

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...
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

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...

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Updated: Jun 3, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Augmenting Transcriptome Annotations through the Lens of Splicing Evolution.

Xiaofei Carl Zang1, Ke Chen2, Irtesam Mahmud Khan2

  • 1Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.

Biorxiv : the Preprint Server for Biology
|November 22, 2024
PubMed
Summary
This summary is machine-generated.

TENNIS, an evolution-based model, predicts unannotated isoforms and refines transcriptome annotations. This method effectively identifies missing transcripts by analyzing alternative splicing evolution, enhancing annotation completeness.

Keywords:
alternative splicingisoform evolutiontranscript isoformtranscriptome annotation

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Using the E1A Minigene Tool to Study mRNA Splicing Changes
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Last Updated: Jun 3, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

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Using the E1A Minigene Tool to Study mRNA Splicing Changes
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Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Alternative splicing (AS) is a key eukaryotic process, with ~90% of human genes undergoing AS.
  • Current transcriptome annotations are incomplete, lacking evolutionary insights into AS.
  • Existing annotation methods rely heavily on experimental data like RNA-seq.

Purpose of the Study:

  • To address the gap in evolutionary understanding of transcriptomes.
  • To introduce TENNIS (Transcript EvolutioN for New Isoform Splicing), an evolution-based model.
  • To predict novel isoforms and refine existing transcriptome annotations without new experimental data.

Main Methods:

  • TENNIS models AS isoform evolution as sequential steps, each involving a single AS event.
  • The identification of missing transcripts is framed as an optimization problem to find minimal novel transcripts.
  • The model's premises are that AS isoforms evolve sequentially and each step involves one AS event.

Main Results:

  • Approximately 80% of multi-transcript groups from six annotations fit the TENNIS evolutionary model.
  • 40% of TENNIS-predicted isoforms were validated by deep long-read RNA-seq at high confidence.
  • TENNIS significantly outperformed baseline methods in precision (2.25-3x) and recall (3.5-3.9x) in simulated scenarios.

Conclusions:

  • TENNIS effectively identifies missing transcripts by adhering to evolutionary principles.
  • The model offers a powerful approach for transcriptome augmentation via alternative splicing evolution.
  • TENNIS provides a robust computational tool for advancing transcriptomic annotation accuracy.