CIRCpedia v3

CIRCpedia v3 integrates NGS and TGS datasets to annotate circRNAs from back-splicing of exons and ciRNAs from intron lariats, enabling quantitative comparison of circular/linear isoform dynamics, functional predictions, and prioritization of context-specific circular RNA candidates in biological or disease conditions.

Key Features:

• Community-recommended nomenclature: Enables quantitative comparison of circular/linear isoform dynamics with enhanced molecular profiling.
• Interactive platform: Supports real-time comparative analyses of circRNAs and visualizations.
• Base-editable site identification: Identifies base-editable sites in circular RNAs.
• Subcellular localization prediction: Predicts circRNA subcellular localization.
• Degradation signal detection: Detects circRNA degradation signals for stability optimization.
• m6A modification prediction: Predicts m6A modification sites in circular RNAs.
• Coding potential assessment: Assesses circRNA coding potential.
• Primer and siRNA design: Designs divergent polymerase chain reaction primers and small interfering RNAs (siRNAs).
• Cross-species integration: Integrates insights from cross-species expression, molecular characterization, and functional predictions across 20 species.

Scientific Applications:

• Circular RNA annotation: Annotates both circRNAs from back-splicing of exons and ciRNAs from intron lariats across 2413 sequencing datasets and 20 species.
• Isoform dynamics analysis: Enables quantitative comparison of circular/linear isoform dynamics.
• Functional prioritization: Empowers researchers to prioritize context-specific circular RNA candidates in biological or disease conditions.
• Mechanistic discovery: Accelerates mechanistic discovery of circular RNA functions.
• Therapeutic development: Supports therapeutic development targeting circular RNAs.

Methodology:

CIRCpedia v3 profiles 2413 sequencing datasets across 20 species using NGS and TGS datasets, identifying over 2 million circular RNAs.