Abstract
It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
Highlights
CircRNAs dataset identified from the Gliomas RNA-Seq dataset by our research group[17]
The primary data may have false positives and redundancy, so we filtered the dataset according to gene annotation GTF file, and obtained a total of 32,914 human exonic circRNAs
Its detailed genomic information are listed in the database, including its best matched transcript and the corresponding exon splicing information, genome sequences, in addition to all the possible isoforms and the corresponding exon splicing information
Summary
CircRNAs dataset identified from the Gliomas RNA-Seq dataset by our research group[17]. CircRNA is classified as a non-coding RNA, researchers have reported that eukaryotic ribosome can initiate translation on circRNA, but only when the RNA contains internal ribosome entry site (or IRES) elements[18]. In 1995, Chen and colleagues showed that a synthetic circRNA containing IRES elements could recruit the ribosome to initiate translation, whereas those circRNAs without IRES did not[18]. In this work we annotated the internal ribosome entry site and open reading frame (ORF) for the circRNA with protein-coding potential. Their protein expression evidences by mass spectrometry were provided. Human circRNA data sets, along with its genomic features, protein coding potential and protein features were integrated into circRNADb
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