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Related Concept Videos

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...
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...
Pre-mRNA Processing02:01

Pre-mRNA Processing

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 to it (7-Methyl guanosine). This 5’ cap helps the...

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Updated: Jun 15, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Computational siRNA design considering alternative splicing.

Young J Kim1

  • 1Department of Functional Genomics, University of Science & Technology (UST), Daejeon, Korea.

Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2010
PubMed
Summary
This summary is machine-generated.

AsiDesigner is a novel web tool for designing small interfering RNA (siRNA) to silence specific messenger RNA (mRNA) isoforms, even multiple ones simultaneously. This tool addresses alternative splicing challenges in eukaryotic gene silencing for functional genomics research.

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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

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Last Updated: Jun 15, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA interference (RNAi) using small interfering RNA (siRNA) is crucial for gene silencing in research.
  • Alternative splicing in eukaryotes generates diverse mRNA isoforms, complicating targeted gene silencing.
  • Studying individual protein functions requires silencing specific mRNA isoforms.

Purpose of the Study:

  • To develop a web-based siRNA design system, AsiDesigner, that accounts for alternative splicing.
  • To enable the design of siRNAs for silencing single or multiple mRNA isoforms from a target gene.
  • To provide advanced features for evaluating siRNA efficacy and specificity.

Main Methods:

  • Development of a novel algorithm to identify common target regions for siRNA design across multiple mRNA isoforms.
  • Implementation of AsiDesigner as a web-based software system.
  • Integration of scoring schemes, off-target searching (BLAST, FASTA), and secondary structure analysis.

Main Results:

  • AsiDesigner successfully designs siRNAs that account for alternative splicing.
  • The system can design common siRNAs to silence multiple mRNA isoforms simultaneously.
  • Validated effectiveness of the developed algorithm and AsiDesigner in gene silencing experiments.

Conclusions:

  • AsiDesigner is an effective tool for mRNA isoform-specific gene silencing.
  • The software facilitates functional genomics, drug discovery, and molecular biology research.
  • AsiDesigner is freely accessible online.