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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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: Jun 21, 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

Resolving deconvolution ambiguity in gene alternative splicing.

Yiyuan She1, Earl Hubbell, Hui Wang

  • 1Affymetrix Inc, Santa Clara, CA 95051, USA. yshe@stat.fsu.edu

BMC Bioinformatics
|August 6, 2009
PubMed
Summary
This summary is machine-generated.

Resolving splice variant abundances is challenging due to data ambiguity. This study provides mathematical conditions and a Bayesian framework to accurately estimate transcript abundances, even with uncertain constraints.

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

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Splice variant deconvolution from intensity data is often ambiguous, termed the "degeneracy problem".
  • This ambiguity arises from ill-posed problems requiring additional information for unique solutions.

Purpose of the Study:

  • To mathematically define conditions for resolving splice variant ambiguity.
  • To develop a robust method for estimating transcript abundances using uncertain constraints.

Main Methods:

  • Rigorous mathematical analysis of matrix models for splice variants.
  • Development of a Bayesian framework incorporating probe sequence model uncertainty.
  • Incorporation of micro-model prediction uncertainty into macro-model of probe intensities.

Main Results:

  • Identified necessary and sufficient conditions for resolving splice variant ambiguity.
  • Demonstrated that probe sequence information can provide constraints, but models have prediction inaccuracies.
  • Presented a Bayesian framework to estimate variant abundances with uncertain constraints.

Conclusions:

  • Matrix analysis aids in identifying situations needing additional constraints for splice variant resolution.
  • The Bayesian framework offers a general solution for unique transcript abundance estimation with uncertain real-world constraints.
  • The method's efficacy is validated through simulations and biological data analysis.