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lncRNA stands for long non-coding RNA, which refers to non-coding RNA with a length of more than 200nt. lncRNA plays an important role in cell cycle regulation, cell differentiation regulation, disease occurrence and development, and is one of the research hotspots.

Unlike miRNA, which started very early, lncRNA gradually emerged in the last ten years. The current situation is that there are many databases, and the naming methods of lncRNA in different databases are not uniform. This chaotic naming pattern increases the difficulty of research.

LNWikipedia is a comprehensive database of human lncRNA, integrating lncRNA records from multiple databases and articles, and giving them a unified ID, the URL is as follows

https://lncipedia.org/

lncRNA information in this database comes from the following databases

LncRNAdb

Broad Institute

Ensembl

Gencode

Refseq

NONCODE

FANTOM

It also contains lncRNA information found in Nielsen, Hangauer and other literatures.

For lncRNAs from multiple sources, a uniform ID is assigned after redundancy is removed. For lncRNAs that already have a gene symbol, the gene symbol is still used. If there is no gene symbol, they are named according to the nearest protein-coding gene, such as lnc-MYCN-1, which represents an lncRNA near the MYCN gene. If multiple lncRNAs use the same reference protein-coding gene, a numerical suffix is used to distinguish different lncRNA genes.

lncRNA is classified according to the following principles:

lncRNAs that overlap the same strand as the protein-coding gene are classified as intronic if they do not overlap all exons, otherwise they are classified as sense overlapping.

lncRNAs that overlap with the reverse complementary region of the protein-coding gene are classified as antisense;

lncRNAs that do not intersect with any protein-coding gene are classified as bidirectional if there is a transcription start site for the white-coding gene within 1000bp upstream of the transcription start site, otherwise they are classified as intergenic;

Different software was also used to assess the protein coding potential. The software list is as follows

CPC

HMMER

PRIDE

PhyloCSF

CPAT

Ribosome-profiling

We can download the fasta,gtf, bed file corresponding to lncRNA directly from the website, providing hg19 and hg38 versions, as follows

Search can be done by clicking Search button on the homepage. Take LINC01725:47 as an example. The results are as follows.

1. basic information

The results include lncRNA gene ID, transcript iD, chromosome location, type, length, etc., as shown below

2. sequence information

3. protein coding potential

The results of protein coding potential predicted by different software are given as follows

4. lncRNA conservation

The conservation of lncRNA was analyzed by the conservation of protein-coding genes adjacent to lncRNA among different species. If the reference protein-coding gene of an lncRNA has homology in other species, it is considered that the corresponding lncRNA should also exist in other species. The results are shown as follows

The website also provides API service, which obtains corresponding information through gene id or transcript id, as shown below.

https://lncipedia.org/api/transcript/HOTAIR:1https://lncipedia.org/api/gene/HOTAIR

Through this comprehensive database, the inconvenience caused by different naming methods in different databases can be avoided.

How to understand the human lncRNA database LNWikipedia is shared here. I hope the above content can improve everyone. If you want to learn more, please pay more attention to the updates of Xiaobian. Thank you for your attention to the website!

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