CIRCpedia Edit

Citations: 78

z-index: 26

Basic information
Short name CIRCpedia
Full name A database of circular RNAs
Description CIRCpedia v2 is an updated comprehensive database containing circRNA annotations from over 180 RNA-seq datasets across six different species.
Year founded 2015-10-12
Last update & version 2018-07-07 2.0
Availability Free to academic users only
Contact information
University/Institution hosted CAS-MPG Partner Institute for Computational Biology
Address 320 Yue Yang Road, Shanghai 200031, P.R.China
City Shanghai
Country/Region China
Contact name (PI/Team) Li Yang
Contact email (PI/Helpdesk)
Data information
Data object
Data type
Database category
Major organism
  • CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison. [PMID: 30172046]
    Rui Dong, Xu-Kai Ma, Guo-Wei Li, Li Yang

    Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at

    Genomics Proteomics Bioinformatics 2018:16(4)

    1 Citations (from Europe PMC, 2019-04-13)

  • Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. [PMID: 27365365]
    Xiao-Ou Zhang, Rui Dong, Yang Zhang, Jia-Lin Zhang, Zheng Luo, Jun Zhang, Ling-Ling Chen, Li Yang

    Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines. Compared with their linear cognate RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket alternative back-splice sites. In addition, all four basic types of alternative splicing that have been identified in the (linear) mRNA process were found within circRNAs, and many exons were predominantly spliced in circRNAs. Unexpectedly, thousands of previously unannotated exons were detected in circRNAs from the examined cell lines. Although these novel exons had similar splice site strength, they were much less conserved than known exons in sequences. Finally, both alternative back-splicing and circRNA-predominant alternative splicing were highly diverse among the examined cell lines. All of the identified alternative back-splicing and alternative splicing in circRNAs are available in the CIRCpedia database ( Collectively, the annotation of alternative back-splicing and alternative splicing in circRNAs provides a valuable resource for depicting the complexity of circRNA biogenesis and for studying the potential functions of circRNAs in different cells.

    Genome Res 2016:26(9)

    77 Citations (from Europe PMC, 2019-04-13)


  • Ranking in all databases: No. 263
  • Ranking in category/categories:
    • Expression: No. 30
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of CIRCpedia.

Word cloud

Related Database

Record metadata

  • Created on: 2018-09-21
    • ***ang@*** [2018-12-02]
    • ***d@*** [2018-09-21]
    • ***mengyu@*** [2018-09-21]

Community reviews 0 stars (0 reviews)

quality & quantity
organization & presentation
accessibility & reliability
Reviewed by