Exon-derived circular RNAs (circRNAs) have been identified from thousands of genomic loci in mammals through back-spliced exon circularization.Recent research into circRNA biogenesis has shown that exon back-splicing is enhanced by cis-complementary sequences in flanking introns.Strikingly,a single gent 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 computational pipeline-CIRCexplorer2,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 altemative splicing.Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket altemative back-splice sites.Unexpectedly,thousands of previously unarmotated 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 (http://www.picb.ac.cn/momics/circpedia).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.b.