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Alternative-Splicing Analysis

Alternative-Splicing Analysis

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RNA alternative splicing (AS) is a post-transcriptional step in the regulation of eukaryotic gene expression that relies on the fine synergy of multifactorial and cis-acting elements. Its abnormalities are very common in diseases, especially in cancer. However, the identification of novel alternative splicing requires the support of relevant databases and bioinformatic analysis.

Our in-house RNA sequencing data analysis platform is dedicated to unraveling the complex mechanisms of gene regulation and solving complex biological problems.

What is alternative-splicing?

Alternative splicing is the process of generating different mRNA splice isoforms from one mRNA precursor by different splicing methods (choosing different combinations of splice sites), so that the final protein products will exhibit different or mutually antagonistic functional and structural properties, or will be expressed at different levels in the same cell, resulting in different phenotypes.

During alternative splicing events, exons can be selectively included or eliminated, while introns can be selectively retained or sheared. Alternative splicing is an important part of the regulation of gene expression in eukaryotes, and it plays an important role in cell differentiation, growth, and signal transduction.

Splicing of mRNA precursors (pre-mRNAs) allows a single gene to generate multiple transcripts and is a major contributor to maintaining proteome diversity. There is growing evidence that aberrant splicing is associated with multiple human cancers and contributes to tumorigenesis and tumor progression by producing aberrant proteins and genetic isoforms. Therefore, the discovery of new tumor-associated AS and the exploration of detailed mechanisms of dysregulated splicing will provide effective strategies for treating tumors by correcting alternative RNA splicing.

Main types of alternative splicing eventsMain types of alternative splicing events (Rosenkranz R R E et al., 2022)

Alternative splicing analysis pipelineAlternative splicing analysis pipeline (Albert Lahat B.Sc. et al. 2016)

We can help you with:

  • Flexible analysis services: Depending on customer needs and data characteristics, we can provide quantification of expression levels of known, previously annotated splice isoforms, or detection of new splicing events.
  • Gene function research: The production of different alternative splicing isoforms of the same gene often has important effects on gene function, such as the ability to make a gene function differently in different cell types or at different developmental stages.
  • Disease mechanisms research: The occurrence and regulation of alternative splicing in some diseases have also been widely studied, for example, abnormal alternative splicing may lead to the development of some neurodegenerative diseases.
  • Develop new therapeutic approaches: Understanding the regulatory mechanisms of variable shear can provide new ideas for the development of new drugs, for example, by interfering with the occurrence of certain alternative splicing events to achieve therapeutic goals.
  • Establish new bioinformatics tools: The analysis of AS requires a large number of bioinformatics tools and methods, and the development and optimization of these tools and methods is also an important direction for alternative splicing research.

Workflow of Our Alternative-Splicing Analysis

  • Read Mapping
  • Read Assembly
  • Isoform Quantification
  • Visualising Alternative Splicing

Table 1 Partial software and database list

Software or database Principle Differential Analysis AS Type
rMATS event-based yes 5
MAJIQ event-based yes 5
LeafCutter intron excision yes Unkown
SUPPA2 event-based yes 7
SplAdder event-based yes 5
Whippet event-based yes 9

How It Works

Initial Consultation

Initial Consultation

  • Meet with technical experts to understand the client's research goals and objectives
  • Discuss project design and scope of work
  • Determine sample preparation and sequencing requirements
  • Provide an estimated schedule and budget

Project Confirmation

Project Confirmation

  • If you don't have data yet, we can also provide omics sequencing services
  • Project confirmation process

Data Analysis

Data Analysis

  • Perform quality control and data filtering
  • Align the reads to the reference genome
  • Identify and annotate genetic variants or gene expression levels
  • Perform downstream analysis such as functional annotation, pathway analysis, or gene network analysis


Results Delivery

  • Provide the client with a detailed report summarizing the analysis results
  • Include visualizations of the data, such as heat maps, scatter plots, or volcano plots
  • Provide recommendations for future research directions


  1. Rosenkranz R R E, Ullrich S, Löchli K, et al. Relevance and regulation of alternative splicing in plant heat stress response: current understanding and future directions[J]. Frontiers in Plant Science, 2022, 13.
  2. Field guidelines for genetic experimental designs in high-throughput sequencing[M]. Springer, 2016.
* For Research Use Only. Not for use in diagnostic procedures.
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