CIRCpedia v2 is an updated comprehensive database containing circRNA annotations from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse and download circRNAs with expression characteristics/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 for the comparison of circRNA expression between samples. The updated database is accessible at http://www.picb.ac.cn/rnomics/circpedia. Otherwise, alternative splicing analysis needs additional related p(A)+ samples and the alternative splicing information can be found in CIRCpedia v1.