[ensembl-dev] predicted RNA structures

Ben Moore bmoore at ebi.ac.uk
Thu Feb 25 11:40:43 GMT 2021

Hi Bogdan,

Ensembl displays RNA secondary structures through the ’Secondary Structure’ page within the gene tab for your gene of interest. E.g:
http://www.ensembl.org/Homo_sapiens/Gene/SecondaryStructure?db=core;g=ENSG00000277995;r=CHR_HSCHR5_2_CTG1:29079384-29079498;t=ENST00000611262 <http://www.ensembl.org/Homo_sapiens/Gene/SecondaryStructure?db=core;g=ENSG00000277995;r=CHR_HSCHR5_2_CTG1:29079384-29079498;t=ENST00000611262>

The displayed structural information comes primarily from the covariance models provided by RFAM and used for each ncRNA gene family in Ensembl. If the genes could not be found in the RFAM database, we use RNAFold to predict their structure. The 2D plots are generated using the r2r package.

Best wishes


> On 23 Feb 2021, at 21:57, Bogdan Tanasa <tanasa at gmail.com> wrote:
> Dear all, 
> please would you let me know, is there any track available for predicted RNA SECONDARY STRUCTURES for human or mouse genomes ?
> thanks a lot, 
> bogdan
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Dr. Ben Moore (he/him)
Ensembl Outreach Manager

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
CB10 1SD

bmoore at ebi.ac.uk
+44 (0)1223 494265

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