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RNA-seq

RNA-seq

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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Updated: Jan 14, 2026

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration.

Si-Nan Zhai^1,2, Yu-Yao Zhang¹, Mo-Han Chen¹

¹Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Nucleic Acids Research

|October 22, 2025

Summary

This summary is machine-generated.

CIRCpedia v3 is an expanded repository for circular RNAs (circRNAs) and circular RNAs from intron lariats (ciRNAs). It offers new tools for molecular profiling, comparative analysis, and functional prediction to advance circRNA research.

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Last Updated: Jan 14, 2026

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Circular RNAs (circRNAs) and circular RNAs from intron lariats (ciRNAs) play diverse biological roles, but their molecular characteristics and functions require further elucidation.
Systematic characterization of circRNAs is crucial for understanding their involvement in biological processes and diseases.

Purpose of the Study:

To introduce CIRCpedia v3, an enhanced repository for annotating circRNAs and ciRNAs across multiple species.
To provide advanced tools for circRNA research, including nomenclature, comparative analysis, and functional prediction.

Main Methods:

Profiling of 2413 sequencing datasets across 20 species to identify and annotate circRNAs and ciRNAs.
Development of an interactive platform for real-time comparative analyses and visualizations.
Integration of toolkits for base-editable site identification, subcellular localization prediction, degradation signal detection, m6A site prediction, coding potential assessment, and primer/siRNA design.

Main Results:

>2 million circular RNAs identified and annotated in CIRCpedia v3.
Introduction of community-recommended nomenclature for quantitative comparison of circular/linear isoform dynamics.
Development of integrated toolkits enabling comprehensive molecular profiling and functional prediction of circRNAs.

Conclusions:

CIRCpedia v3 significantly expands the annotation of circRNAs and ciRNAs, facilitating cross-species expression and molecular characterization.
The integrated toolkits empower researchers to prioritize circRNA candidates and accelerate mechanistic discovery and therapeutic development.
CIRCpedia v3 serves as a valuable resource for advancing circRNA research in biological and disease contexts.