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This article will explain in detail what is the use of circinteractome database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

RNA binding protein, called RNA binding protein for short, is a class of proteins that regulate the metabolism of RNA, which mainly mediates the maturation, transport, localization and translation of RNA. MiRNA is a kind of small RNA about the length of 21bp, which can bind to the target RNA, inhibit its translation or degrade it, and play a post-transcriptional regulatory role. These two substances play a very important role in RNA regulation.

With the development of high-throughput sequencing and biological information, the number of circular RNA identified is increasing, but the biological function of most circular RNA is still unknown. In order to explore the function of circular RNA, some scholars have sorted out the regulation information between annular RNA and RBP,miRNA, and constructed a circinteractome database at the following URL

Https://circinteractome.nia.nih.gov/index.html

The process of building the database is as follows

The genomic location information of circular RNA was obtained from circbase, and the sequence of circular RNA was extracted by UCSC, and the junction reads formed by head-to-tail connection of circular RNA was used to query the results of CLIP analysis. The binding information of circular RNA and RBP protein was obtained, and the PCR primers for verifying circular RNA were designed to query siRNA sites. The full-length RNA sequence was used to query RBP binding sites, miRNA binding sites, and IRES sites.

Through this database, you can achieve the following functions

1. CircRNA

Query the basic information of circular RNA, including circular RNA ID, chromosome location, source gene, RBP binding and so on. The results are as follows

2. RBP on CircRNA

Query the RNA protein binding site on the circular RNA, and the results are as follows

3. MiRNA target Sites

Query the miRNA binding sites on annular RNA and predict them by targetscan software. The results are as follows

4. Divergent Primers

When the circular RNA sequence is amplified by PCR, the direction of PCR primers is different from that of conventional linear RNA, as shown below.

In practice, 50 to 100bp sequences from each side of the circular RNA junction are taken to design PCR primers. The results given in the database are as follows.

5. SiRNA design

SiRNA, called small interference RNA, is a double-stranded RNA with a length of 20-25bp, which is similar to miRNA. It can bind to the target RNA and has the function of regulating gene expression. Through this database, we can query the possible siRNA binding sequences of annular RNA, thus helping us to design siRNA. The results are shown below.

The database not only provides the regulatory network of circular RNA and RBP,miRNA, but also helps us to design PCR primers to verify circular RNA, or to design siRNA to interfere with the expression of circular RNA.

This is the end of this article on "what is the use of circinteractome database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

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