Circbank: a comprehensive database for circRNA with standard nomenclature

Abstract

Circular RNAs (circRNAs) represent a new type of regulatory RNA which forms a covalently closed continuous loop from back-splicing events, a process in which the downstream 5' splice site and the 3' splice site are covalently linked. Emerging evidence indicates that circRNAs exert a new layer of transcriptional and post-transcriptional regulation of gene expression. However, there is no standard nomenclature of circRNA, although the study of circRNAs has exploded in the past few years. Here we present circbank ( www.circbank.cn ), a comprehensive database for human circRNAs, where a novel naming system of circRNAs based on the host genes of circRNAs was implemented. In addition to the new naming system, circbank collected other five features of circRNAs including the miRNA binding site, conservation of circRNAs, m⁶A modification of circRNAs, mutation of circRNAs and protein-coding potential of circRNAs. Circbank is publicly available and allows users to query, browse and download circRNAs with all six features we provided, based on different search criteria. The database may serve as a resource to facilitate the research of function and regulation of circRNAs.

Keywords: CircRNAs; circbank; database; nomenclature.

Figure 1.

Nomenclature of circRNA at circbank. (a) schematic diagram for nomenclature of circRNAs (b) an example of circRNAs from EGFR gene (c) UCSC genome visualization of 15 circRNAs from EGFR gene.

Figure 2.

The summary of binding sites of circRNA-miRNA pairs.

Figure 3.

Overview of web interface in circbank. (a) ‘circRNA’ search panel web page information; (b) ‘miRNA’ search panel web page information; (c, d) detailed information page of hsa_circHIPK3_004.

Figure 4.

The UCSC genome visualization of 15 circRNAs from EGFR gene.