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2025-01-18 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >
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This article will explain in detail what is the use of miRcode 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.
TargetScan is a software for predicting miRNA binding sites, which is very effective for predicting miRNA binding sites in mammals. In order to facilitate the study of miRNA, for human miRNA, the developers of miRcode predicted the interaction between miRNA and various types of RNA, such as mRNA, lncRNA, etc., and compiled the results into a database to facilitate everyone's use and learning.
Http://www.mircode.org/index.php
Based on the hg19 version of the genome, the transcript annotation comes from the Gencode v11 version, and the transcript is divided into different categories, as shown below
Intergenic lncRNA indicates that there is no overlap between lncRNA and protein coding gene, while Overlapping indicates that lncRNA;other with overlap between protein coding gene and protein coding gene represents tRNA,snoRNA and other types of RNA.
When predicting miRNA binding sites, miRNA family defined by TargetScan V6 is used. MiRNA under the same family has the same binding site type, as shown below.
Relevant comments are also provided for the predicted region of miRNA binding sites. firstly, according to the comparative genomic results of 46 vertebrates, the conservatism of binding sites among different species is defined and divided into different categories. Secondly, the distribution information of binding sites in transcripts is provided, which is divided into 3'UTR, CDS, 5'UTR and other regions. Finally, according to whether there are repetitive elements near the binding site, repeat-related annotations are provided.
The information in the database can be easily retrieved through the retrieval function, and the search box is as follows
The results can be filtered and screened according to the gene category, the conservatism of the binding site and the distribution on the transcript. The search results are as follows
With the continuous updating of Gencode, targetscan and other databases, it seems that the contents of the database are too old, but the ideas of its analysis are still worth using for reference.
This is the end of this article on "what is the use of miRcode 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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