RNA Splicer User Guide

Open a browser and navigate to: https://rddc.tsinghua-gd.org/zh/tool/rna-splicer to access the RNA Splicer homepage.

The tool supports 4 input modes, including: Paste, Mutation, Protein, and Transcript.

• Fill in the gene name: Enter "USH2A" in the "Gene Name" input box, and the system will automatically suggest recommended genes. Select the target gene.
• Select the transcript: The system loads the most commonly used transcript by default (e.g., NM_206933.4 for USH2A). If there are special requirements, users can also select other transcripts from the dropdown menu.

• Fill in the mutation site: Enter "c.8559-2A>G" in the "Standard Mutation Nomenclature" box, and the system will automatically parse the pre-mutation base (A) and the post-mutation base (G).
• Visualize mutation site: Click the【Unfold Diagram】button below the input box to visually inspect the mutation's position within the gene structure (e.g., intron, exon boundary).
• Add multiple mutations: If you need to analyze multiple mutation sites, click the【Add Mutation】button (to the left of the input box) and repeat the above steps to add new mutations.
• Submit and Await Results: After confirming that the information is correct, click the【Submit】button at the bottom of the page to start the AI model prediction. Wait for the prediction results. A progress bar will be displayed on the page after submission; the prediction time depends on the number of mutations and server load.

• Prediction Conclusion: Displays whether the mutation is likely to cause abnormal splicing, such as a conclusion of "deletion of 123bp, exon skipping".
• Splicing Pattern Diagram: Visually displays the changes in splicing sites between the wild-type (normal) and mutant types, annotating new or lost splice sites, exon skipping/retention, and other patterns.
• Numerical Score: Provides a quantitative score of the splicing impact (e.g., the higher the DanQ score, the higher the probability of abnormal splicing).
• Homologous Mutation Analysis in Multiple Species: To view the effects of homologous mutations in mice or rats, click the【Mouse】or【Rat】button in the upper right corner of the results page. The system will then display the mutation prediction results for the homologous gene.

• The page supports saving the results as a screenshot. You can click the question mark next to the prediction results to inquire about the calculation logic of the model parameters and view examples of result interpretation.

• Gene Name Standardization: Input standard gene symbols (e.g., "TP53" instead of "p53"). The correct name can be confirmed via NCBI Gene.
• Mutation Site Format: Follow HGVS nomenclature rules (e.g., "c.123A>T" for a coding region mutation, "g.456C>G" for a genomic mutation). Incorrect formats may lead to parsing failure.
• Transcript Selection: The tool selects the MANE transcript by default. Please ensure you select the correct transcript ID based on the source of the mutation, as an incorrect selection may lead to incorrect positioning.
• Multiple Mutation Analysis: A maximum of 5 mutation sites can be submitted at one time. Batch analysis requires separate submissions.

• Codon Chart: A Codon Chart is available on the page to help understand the impact of mutations on amino acid coding.
• Mutation Writing Rules: The question mark icon to the right of【Gene Name】provides a guide to mutation writing to help understand the correct format.
• Video Tutorial: Click the【Video Tutorial】link on the page to watch the official operational demonstration video.

• Research: Exploring the abnormal splicing effects caused by gene mutations in pathogenic mechanisms
• Clinical: Aiding in the interpretation and assessment of pathogenicity in gene mutation reports
• Education: Designing a visual teaching demonstration for splicing mechanisms and mutation effects