Nucleic Acids Research, 31 December, 2025, DOI：https://doi.org/10.1093/nar/gkaf1280

CircTarget: a comprehensive database of circRNA–target RNA interactions across multiple cell types

Hongmei Zhang, Yuyang Zhang, Peng Li, Zhen Yuan, Wanglong Liu, Jinyue Zhang, Ruitian Li, Chen Lu, Ping Zhu, Yuanchao Xue

Abstract

Circular RNAs (circRNAs) are stable, widespread regulatory molecules produced primarily by back-splicing of pre-mRNAs, with critical roles in gene regulation and disease pathogenesis. While significant progress has been made in circRNA identification, their targets remain largely unexplored. To address this, we present CircTarget, the first comprehensive database of experimentally supported circRNA–target RNA interactions mapped at single-nucleotide resolution. By analyzing RNA–RNA interactome data from multiple crosslinking methods across 13 cell lines and hippocampal tissues from human and mouse, we identified 132 517 high-confidence circRNA–target RNA interactions. Each entry in CircTarget is richly annotated, including circRNA basic information, disease associations, interaction regions, supporting chimeric read counts, predicted hybrid duplex structures, and disease-linked variants from GWAS Catalog, ClinVar, and ICGC databases. CircTarget provides a valuable resource for deciphering circRNA functions and is freely accessible at https://circtarget.cn.

Article link：https://academic.oup.com/nar/article/54/D1/D89/8383825