RNA Sequence Viewer¶

Overview¶

The RNA Sequence Viewer provides detailed nucleotide-level visualization of RNA sequences with comprehensive annotations and multiple rendering modes. This plugin enables researchers to examine mRNA and CDS sequences with full structural annotations including UTRs, exons, codons, and their corresponding amino acid translations. Additionally, it displays complementary base-pairing information for each nucleotide, facilitating the design of antisense oligonucleotides (ASOs) and primers. When integrated with the ASO Design plugin, it becomes a powerful toolkit. With flexible color-coding schemes for nucleotide composition analysis (GC content, purine/pyrimidine distribution) and synchronized multi-window comparison capabilities, it serves as an essential tool for sequence analysis, oligonucleotide design, motif identification, and functional element characterization.

Cross-window Real-time Rendering¶

The multi-window feature allows you to compare different sequence representations and annotations simultaneously, providing comprehensive views of your transcript of interest.

How to use multi-window mode:

Open a new window: Click the button in the plugin interface to create an additional RNA Sequence Viewer window.
Compare rendering modes: Use different windows to display various sequence rendering modes simultaneously. For example:
Window 1: View nucleotide sequence in standard color mode
Window 2: Display GC content distribution
Compare sequence modes: Open multiple windows with different sequence modes (mRNA vs. CDS) to compare:
Full mRNA sequence including UTRs and regulatory elements
CDS-only view focusing on protein-coding regions
Identify differences in annotation between sequence representations
Synchronized navigation: All open windows automatically synchronize to the same transcript ID when you search for or select a transcript in the search box. This ensures that all windows display the same gene for direct comparison.

Cross-plugin synchronization:

The RNA Sequence Viewer integrates seamlessly with other RBrowser plugins, enabling multi-dimensional analysis of the same transcript region:

Synchronized selection: When you select a region in any plugin window, all other plugin windows (including RNA 2D Structure, RNA 3D Structure, and RNA Sequence) will highlight the same region.
Multi-scale analysis: Examine your region of interest across different representations:Linear view, 2D structure, 3D structure, Single-nucleotide resolution.

This synchronized, multi-plugin approach allows you to comprehensively investigate transcript features from sequence to structure, providing insights that would be difficult to obtain from any single view alone.

Render Mode¶

The RNA Sequence Viewer offers multiple color-coding schemes to highlight different aspects of nucleotide composition, helping you identify sequence patterns and functional elements relevant to your research question.

Available render modes:

Nucleotide Mode¶

The standard nucleotide rendering uses conventional color-coding to display the RNA sequence:

A (Adenine)
U (Uracil)
G (Guanine)
C (Cytosine)

This mode is ideal for:

General sequence examination and reading
Identifying specific nucleotide patterns or motifs
Visual comparison of sequence regions
Locating mutation or variant positions

GC Content Mode¶

Highlights guanine (G) and cytosine (C) nucleotides with distinct coloring to emphasize GC-rich regions:

G and C nucleotides
A and U nucleotides

This mode is particularly useful for:

Identifying GC-rich regions that may form stable secondary structures
Analyzing promoter regions and CpG islands
Detecting regions with biased nucleotide composition
Examining thermodynamic stability patterns (GC pairs are more stable than AU pairs)
Identifying potential miRNA binding sites (often have specific GC content requirements)

Purine vs. Pyrimidine Mode¶

Differentiates between purine bases (A, G) and pyrimidine bases (U, C):

Purines (A, G): Larger, two-ring bases
Pyrimidines (U, C): Smaller, single-ring bases

This mode is valuable for:

Identifying purine-rich or pyrimidine-rich regions (RY-rich tracts)
Analyzing RNA editing sites (often involve purine-to-purine or pyrimidine-to-pyrimidine changes)
Detecting sequence bias in regulatory elements
Examining splice sites (which often have purine/pyrimidine composition patterns)
Investigating RNA-binding protein recognition motifs (many RBPs have purine or pyrimidine preferences)

Switching between render modes:

Click on the render mode selector in the toolbar to cycle through different visualization schemes. The sequence updates in real-time, allowing you to quickly identify regions of interest based on nucleotide composition.

Sequence Mode¶

The RNA Sequence Viewer provides two complementary sequence display modes to accommodate different research focuses, from studying regulatory elements to analyzing protein-coding sequences.

mRNA Mode¶

The mRNA mode displays the complete messenger RNA transcript with comprehensive structural and functional annotations:

Annotated features:

5' UTR (Untranslated Region): The regulatory region upstream of the start codon, important for translation initiation, mRNA localization, and stability
Start Codon (AUG): The translation initiation site, clearly marked for easy identification
Exons: All exonic sequences including both coding and non-coding exons, helping you understand the gene structure
Stop Codon (UAA, UAG, or UGA): The translation termination site, marking the end of the protein-coding sequence
3' UTR: The regulatory region downstream of the stop codon, containing elements for mRNA stability, localization, and post-transcriptional regulation
Codon triplets: Three-nucleotide groups with their corresponding amino acid translations displayed
Splice junctions: Boundaries between exons (when viewing genomic context)

Use cases for mRNA mode:

Analyze regulatory elements in UTRs (e.g., upstream ORFs, IRESs, miRNA binding sites)
Examine the complete transcript structure and isoform differences
Study post-transcriptional regulatory motifs
Investigate RNA modifications in non-coding regions
Analyze mRNA stability determinants

CDS Mode¶

The CDS (Coding Sequence) mode focuses exclusively on the protein-coding region, providing a streamlined view optimized for translation analysis:

Annotated features:

CDS (Coding Sequence): The complete protein-coding sequence from start to stop codon
Reading frame: Maintained throughout the sequence for accurate translation
Amino acid sequence: One-letter or three-letter amino acid codes displayed below codons

Use cases for CDS mode:

Analyze codon usage bias and optimization
Identify synonymous vs. non-synonymous mutations
Study protein domains at the sequence level
Examine translation efficiency signals
Investigate rare codons that may affect expression
Map protein variants and their genomic positions

Amino Acid Translation¶

A key feature available in both sequence modes is the automatic display of amino acid translations for codon triplets. This translation is maintained when switching between mRNA and CDS modes, facilitating:

Mutation impact analysis: Immediately see whether nucleotide changes result in synonymous or non-synonymous substitutions
Frameshift detection: Identify regions where insertions/deletions disrupt the reading frame
Protein domain mapping: Correlate nucleotide sequences with known protein functional domains
Stop codon identification: Quickly locate premature termination codons
Codon optimization: Compare native codons with optimal codons for expression systems

Switching between sequence modes:

Use the sequence mode selector in the toolbar to toggle between mRNA and CDS views. The transition is instantaneous, allowing you to quickly compare the same region in different contexts. This is particularly useful when used with the multi-window feature, where you can keep both modes visible simultaneously.

Download¶

This plugin allows you to download the currently adjusted image (PNG, JPEG) as well as the sequence (FASTA) file. Simply click the button to start the download.

Best Practices¶

To maximize your productivity with the RNA Sequence Viewer:

Use multi-window mode strategically: Open multiple windows with different render modes and sequence modes to gain complementary insights simultaneously.
Combine with structure plugins: Take advantage of cross-plugin synchronization by using RNA Sequence Viewer alongside RNA 2D Structure and RNA 3D Structure plugins for comprehensive analysis.
Choose the appropriate render mode:
Use GC Content mode when investigating RNA stability or secondary structure potential
Use Purine vs. Pyrimidine mode when examining RBP binding sites or RNA editing patterns
Use standard Nucleotide mode for general sequence reading and motif identification
Select the right sequence mode:
Use mRNA mode for regulatory element analysis and full transcript structure investigation
Use CDS mode for codon optimization, mutation analysis, and protein-focused studies
Leverage amino acid translations: Always check the amino acid sequence when analyzing variants or mutations to understand their functional impact.

Troubleshooting¶

Issue: The sequence appears truncated or incomplete. Solution: Check that you've selected the correct transcript isoform. Some isoforms may be incomplete or lack certain regions.

Issue: Annotations (UTRs, exons) are not visible. Solution: Verify that the transcript has complete annotations in the database. Zoom in if necessary, as some annotations may not be visible at low zoom levels.

Issue: Different windows show different sequences. Solution: Ensure that all windows are synchronized. Search for the same transcript ID in each window to synchronize them.

For additional support, please visit the Contact page.