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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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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Updated: Sep 3, 2025

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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BaseScope™ Approach to Visualize Alternative Splice Variants in Tissue.

Alexandra Bunda1, Arturo Andrade2,3

  • 1Department of Biological Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 27, 2022
PubMed
Summary

BaseScope™ technology identified a rare splice variant, e37a-Cacna1b, in the presynaptic calcium channel CaV2.2. This variant is specifically found in excitatory neurons of the brain and motor neurons in the spinal cord.

Keywords:
Alternative splicingBaseScope™CaV2.2Cacna1bIn situ hybridizationN-type

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Area of Science:

  • Neuroscience
  • Molecular Biology
  • Genetics

Background:

  • Understanding cell-specific alternative splicing is crucial for functional insights in complex tissues.
  • Deep sequencing and genetic strategies have advanced the study of cell-specific exon usage, particularly in the nervous system.
  • BaseScope™ offers a sensitive alternative to in situ hybridization for determining exon composition with spatial context.

Purpose of the Study:

  • To detail the utilization of BaseScope™ for detecting the e37a-Cacna1b splice variant of the CaV2.2 (N-type) presynaptic calcium channel.
  • To investigate the expression pattern of the underrepresented e37a-Cacna1b splice variant.

Main Methods:

  • Utilized BaseScope™ technology for highly sensitive detection of splice variants.
  • Focused on the mutually exclusive exons e37a and e37b within the Cacna1b gene.
  • Analyzed exon composition in tissue with spatial and morphological context.

Main Results:

  • Successfully detected the e37a-Cacna1b splice variant using BaseScope™.
  • Confirmed that e37a-Cacna1b is significantly underrepresented compared to the e37b-Cacna1b variant.
  • Discovered that e37a-Cacna1b is specifically expressed in excitatory pyramidal neurons (hippocampus and cortex) and spinal cord motor neurons.

Conclusions:

  • BaseScope™ is effective for identifying rare splice variants in specific neuronal populations.
  • The e37a-Cacna1b splice variant has a distinct expression pattern in the central nervous system.
  • This finding contributes to the understanding of cell-specific alternative splicing in neuronal function.