Structural RNA alignments in vertebrate genomes

We computationally screened for conserved RNA structures (CRSs) in vertebrate genomes using structural alignments predicted with CMfinder. Around 520k human genomic regions were predicted to host CRSs.
The manuscript to the study has been submitted to Genome Research under the title Structural RNA alignments in vertebrate genomes and CaptureSeq reveal novel expressed RNAs and associate conserved RNA structures to transcribed regulatory regions. Supplementary data files to the revised manuscript are available here.

Search the data collection

This is the outdated search engine for CRS annotation in hg18 and 17-species tree.
Switch to database for hg38 and 100-species tree.

You can search for CRSs (1) inside a human genomic region, (2) closests (including overlapping) to a human gene identifier, and (3) with specific structure features, or (4) directly by their identifier:

Human assembly:
Chromosome:
Start:
End: [Example]
Gene identifier: [Example]
Maximal distance: [Example]
Pscore: [Example]
FDR: [Example]
Sequence identity: [Example]
GC content: [Example]
Energy: [Example]
Re-align: [Example]

Identifier of CRS or CRS region: [Example CRS][Example CRS region]

Database version: rth_data_collection_2015-09-08_14:12:49_9206 (based on Gencode v19).