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This article will explain in detail what is the use of NONCODE 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.

NONCODE database is a comprehensive non-coding RNA database, which contains other types of non-coding RNA information except tRNA and rRNA, most of which are lncRNA.

Http://www.noncode.org/index.php

At present, the latest version is v5, which contains the non-coding RNA of 17 species. The species and the corresponding lncRNA are summarized as follows.

The database collects and organizes non-coding RNA information in two ways. The first is literature retrieval through pubmed, which is searched by ncrna, non-coding and other keywords, and then non-coding RNA; is extracted from articles. The second is through existing databases, such as RefSeq, GENCODE, lncRNAdb and so on.

All the non-coding RNA collected were recorded in gtf and bed formats, the same transcripts were merged by compare, the redundant transcripts and genes were assigned to NONCODE's ID;, and then CNCI was used to predict their protein coding potential, leaving only the transcripts with non-coding predicted by CNCI.

The above basic information of non-coding RNA can be obtained, in addition, it also provides annotation information such as expression profile in different tissues or cell lines, functional prediction, conservatism among different species, related diseases and so on. Human non-coding RNA expression profile is obtained from Human BodyMap2.0 project and GSE30554 project; mouse expression profile data is obtained from ERP000591, and the function prediction result of lncRNA is predicted by lnc-GFP software.

With Browse DB, you can view the information of each non-coding RNA in the database, as shown below

The transcript ID of the NONCODE database begins with NON, and the last three letters represent species, such as human corresponding to HSA, the next T represents the transcript, and the subsequent number is used to distinguish different transcripts; for each transcript, the information such as chromosome location, number of exons, length, CNCI score and so on are given.

Click on each transcript ID to view detailed information, including the following two types of information in addition to basic information such as sequences

1. Expression profile

two。 Secondary structure

Through the Function menu, you can retrieve the Go comments corresponding to lncRNA. The result is shown below.

The corresponding GO comments for lncRNA are obtained through ncFANS, an online website.

Through the Disease menu, you can retrieve information about diseases and mutations related to lncRNA, as shown below

The official website also provides an iLncRNA tool to predict lncRNA, as shown below

You only need to upload the GTF file or BED file corresponding to the transcript.

For lncRNA of all species, fasta and bed are available for download, and for common human, mouse, rat, files in gtf format are also provided.

This is the end of this article on "what is the use of NONCODE 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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