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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.
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...
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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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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Related Experiment Video

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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AStrap: identification of alternative splicing from transcript sequences without a reference genome.

Guoli Ji1, Wenbin Ye1, Yaru Su2

  • 1Department of Automation, Xiamen University, Xiamen, China.

Bioinformatics (Oxford, England)
|December 12, 2018
PubMed
Summary
This summary is machine-generated.

A new tool, AStrap, enables the detection and classification of alternative splicing (AS) events without a reference genome. This method enhances transcriptome diversity analysis in non-model organisms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing (AS) increases transcriptome and proteome diversity.
  • Detecting AS and its types is challenging in organisms lacking reference genomes.

Purpose of the Study:

  • To develop a de novo approach (AStrap) for AS analysis without a reference genome.
  • To identify and predict AS types in non-model organisms.

Main Methods:

  • AStrap uses pairwise transcript alignments to identify AS events.
  • A machine-learning model with over 500 features predicts AS types.
  • Evaluated on rice, human, and Amborella trichopoda data.

Main Results:

  • AStrap identifies more AS events with high accuracy compared to existing methods.
  • AS type prediction achieved an accuracy of approximately 0.87 across species.
  • Demonstrated robustness and flexibility across various parameters and datasets.

Conclusions:

  • AStrap is a valuable tool for studying AS in non-model organisms with limited genomic resources.
  • Facilitates deeper understanding of transcriptome diversity in diverse species.