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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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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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Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
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The actual hypothesis testing begins by considering two hypotheses. They are termed  the null hypothesis and the alternative hypothesis. These hypotheses contain opposing viewpoints.
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Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
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Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter.

Zheng Kuang1, Stefan Canzar2

  • 1Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 7, 2018
PubMed
Summary
This summary is machine-generated.

SpliceHunter is a new tool that analyzes long-read sequencing data to identify and understand alternative splicing events. This helps researchers interpret complex transcriptomes and discover new protein-coding genes.

Keywords:
Alternative splicingLong-read sequencingPacBio sequencingRNA sequencingSpliceHunterTime course analysisTranscript isoform

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Alternative splicing significantly expands the functional capacity of genomes by producing diverse transcript isoforms from single genes.
  • Short-read sequencing technologies detect many splicing events but struggle with complete transcript reconstruction, limiting functional interpretation.
  • Long-read sequencing offers a more comprehensive view of full-length transcripts, crucial for understanding splicing complexity.

Purpose of the Study:

  • To introduce SpliceHunter, a computational tool designed for the analysis of long-read sequencing data.
  • To enable the precise definition, tracking, and interpretation of alternative splicing isoforms and novel transcription units.
  • To facilitate the comparison of observed splicing patterns with existing genomic annotations and predict potential protein products.

Main Methods:

  • Utilizing long-read sequencing data (e.g., from Pacific Biosciences).
  • Developing SpliceHunter for computational analysis of transcript sequences.
  • Implementing functions to define, track isoforms, and identify novel transcription units across different time points.
  • Comparing identified splicing patterns against reference annotations and translating transcripts into protein sequences.

Main Results:

  • SpliceHunter successfully processes long-read data to provide a detailed view of transcript isoforms.
  • The tool enables the identification and characterization of novel transcription units.
  • Comparative analysis with reference annotations aids in understanding splicing variations and their functional implications.

Conclusions:

  • SpliceHunter enhances the functional interpretation of complex transcriptomes generated by long-read sequencing.
  • This tool is valuable for researchers studying alternative splicing, transcript variation, and protein diversity.
  • It bridges the gap between raw sequencing data and biological understanding of gene expression complexity.