With the advent of high-throughput sequencing technologies and relevant computational methods, a large number of circular RNAs produced from back-spliced exons (circRNAs) have been recently identified from fly and worm to mouse and human. Although the function of most circRNAs is awaiting to be uncovered, some circRNAs have been reported to play important roles in gene regulation. Recent progress of circRNA biogenesis has been shown that back-splicing is catalyzed by canonical spliceosomal machinery, and multiple circRNAs can be produced from single gene loci through alternative back-splice site selection and/or alternative splice site selection. However, the detailed landscape of alternative (back-)splicing in circRNAs and their dynamics were still lacking.
CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. Through employing an upgraded circRNA characterization pipeline (CIRCexplorer2), thousands of alternative back-splicing and alternative splicing events in circRNAs were identified. All these identified alternative back-splicing and alternative splicing in circRNAs, together with novel exons, are formatted and classified for being easily searched, browsed and downloaded from CIRCpedia.
Currently, the database contains circRNA back-splicing and alternative splicing from 31 human, 26 mouse, 30 fly and 12 worm samples, and information on a wider spectrum of cell-line, tissue and species samples will be constructed when additional high-quality RNA-seq datasets are available.
Notes: To identifying alternative back-splicing of circular RNAs, p(A)– (w/o RNase R) or Ribo– (w/o RNase R) samples are recommended. Meanwhile, p(A)+ and p(A)– (w/o RNase R) are needed for alternative splicing analysis in circRNAs, p(A)–/RNase R samples are highly recommended for alternative splicing analysis.
Summary of human samples
Summary of mouse samples
Summary of fly samples
Summary of worm samples
12/15/16 Another 8 human samples, 6 mouse samples, 30 fly samples and 12 worm samples have been added into CIRCpedia.
09/26/16 CIRCexplorer2 releases version 2.2.6 on github
08/16/16 Hs68 has been added into CIRCpedia.
07/26/16 Another 25 samples are added into CIRCpedia.
07/22/16 CIRCexplorer2 releases version 2.1.2 on github
04/05/16 CIRCexplorer2 releases version 2.0.0 on github
12/10/15 CIRCpedia is offically online and in beta version.