Shulou(Shulou.com)06/01 Report--

This article is to share with you about the use of REDIportal databases. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

REDIportal database contains human A-to-I type RNA editing site information, a total of more than 4 million sites, can be called the largest RNA editing site database, the database is completely free and open, and the website is as follows

Http://srv00.recas.ba.infn.it/atlas/index.html

These RNA editing sites come from samples of different parts and different tissue types, and the samples of each tissue type are shown below.

Since August 2018, the database has also begun to include RNA editing site information from other species. Through the search function of the official website, you can easily retrieve the database, and the search page is as follows

At present, it only supports the search of hg19, which can be searched according to chromosome location and gene name.

Through location, the results are defined according to the repeated sequence information of the RNA editing site, including Alu, REP, and NOREP3 species.

Genic Regoin defines the results according to the region of the genome, including 5'UTR, 3'UTR, Exonic, Intronic and Intergenic5 species regions.

AA change limited the results according to whether the RNA editing site caused changes in amino acids, including synonymous, Nonsynonymous and Stop Loss,Unknown4 species, while Tissue and Body Site limited the results according to tissue type and sampling site, respectively.

The search results are as follows

Similar to other databases, it provides chromosome information, repetitive sequence annotation, gene annotation and other information of RNA editing sites. In addition to these basic information, it also provides link with other databases. U in the first column represents UCSC genome browser, dbSNP represents NCBI SNP database, if there is corresponding SNP information at the site, it is expressed in green, if not, it is expressed in red. KnownIn represents other RNA to edit the link to the site database, R for RADAR, and A for DARNED.

Click the blue arrow in the first column of each RNA edit site to view the detailed information, as shown below

For RNA editing sites detected simultaneously in multiple tissues, two visualization methods, heatmap and boxplot, are provided to explore their tissue specificity. The above picture shows the presentation form of heatmap, and the presentation form of boxplot is as follows

Click the menu in the upper right corner to export the corresponding picture. Alternative Annotations provides two kinds of gene annotation information, Refseq and UCSC, as shown below

Editing Details can view the number of samples, tissue type and other information corresponding to the RNA editing site, as shown below

Click the blue button below to see the specific data set, as shown below

Compared with RADAR and DAREND database, REDIportal database not only contains more numbers, but also provides more detailed annotation information.

Thank you for reading! This is the end of this article on "what's the use of REDIportal 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, you can share it for more people to see!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.