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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Jun 14, 2025

Identification of Circular RNAs using RNA Sequencing
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A Representation Learning Approach for Predicting circRNA Back-Splicing Event via Sequence-Interaction-Aware Dual

Chengxin He, Lei Duan, Huiru Zheng

    IEEE Transactions on Nanobioscience
    |September 3, 2024
    PubMed
    Summary

    This study introduces SIDE, a novel computational method for identifying circular RNAs (circRNAs). SIDE effectively predicts circRNA formation by analyzing RNA sequences, improving upon existing methods for disease research.

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Molecular Biology

    Background:

    • Circular RNAs (circRNAs) are vital in gene regulation and disease due to their stable, looped structure.
    • Current computational methods for circRNA identification often overlook crucial back-splicing event features.
    • Predicting circRNA formation is essential for understanding their biological roles and disease associations.

    Purpose of the Study:

    • To develop a novel computational approach for predicting circRNA back-splicing events using only raw RNA sequences.
    • To improve the accuracy of circRNA identification by leveraging sequence characteristics.
    • To provide a more effective tool for circRNA research in genomics and disease studies.

    Main Methods:

    • Proposed a new method named SIDE (Sequence-based Identification of circRNA Events).
    • Employed a dual encoder architecture to capture global and interactive RNA sequence features.
    • Utilized contrastive learning in the decoder to fuse discriminative features for enhanced prediction.

    Main Results:

    • Demonstrated the effectiveness of SIDE on three independent real-world datasets.
    • SIDE accurately predicts circRNA back-splicing events, outperforming existing approaches.
    • Further analyses confirmed the robustness and efficacy of the proposed method.

    Conclusions:

    • SIDE offers a powerful, sequence-based approach for identifying circRNA formation.
    • The method effectively utilizes sequence characteristics, including positional and interaction features.
    • SIDE advancements contribute to a deeper understanding of circRNA functions and their links to diseases.