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Related Concept Videos

Alternative RNA Splicing02:18

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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.
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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data.

Naima Ahmed Fahmi1,2, Heba Nassereddeen2,3, Jaewoong Chang4

  • 1Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.

International Journal of Molecular Sciences
|April 30, 2021
PubMed
Summary
This summary is machine-generated.

AS-Quant is a new bioinformatics tool that efficiently detects and visualizes alternative splicing events from RNA-sequencing data. It outperforms existing methods and aids in understanding gene expression complexity.

Keywords:
RNA-seqRT-PCRalternative splicingtranscriptomevisualization

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • The central dogma's simplicity doesn't explain the genome-proteome complexity.
  • Alternative splicing is a key post-transcriptional mechanism driving proteome diversity.
  • RNA-sequencing (RNA-seq) is vital for transcriptome analysis but lacks user-friendly tools for alternative splicing detection.

Purpose of the Study:

  • To introduce AS-Quant, a robust bioinformatics program for genome-wide alternative splicing event identification and visualization.
  • To provide a user-friendly tool for analyzing alternative splicing from RNA-seq data.
  • To enhance the understanding of gene expression regulation through alternative splicing.

Main Methods:

  • AS-Quant calculates exon and gene read coverage from RNA-seq data.
  • It categorizes splicing events, assesses their significance between conditions, and generates visualization plots.
  • The tool was evaluated using simulated and real RNA-seq datasets against existing methods.

Main Results:

  • AS-Quant demonstrates superior performance in detecting alternative splicing events compared to SUPPA2, rMATS, and diffSplice.
  • The tool successfully visualizes splicing events with short-read coverage plots and gene annotations.
  • Key alternative splicing events identified by AS-Quant were validated using RT-PCR.

Conclusions:

  • AS-Quant is an effective and user-friendly tool for alternative splicing analysis.
  • The program aids in the genome-wide detection and visualization of alternative splicing events.
  • AS-Quant contributes to a deeper understanding of gene expression regulation and proteome complexity.