Structural RNA alignments in vertebrate genomes

We computationally screened the genomes in the UCSC 100-species vertebrate tree for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~520k human genomic regions containing CRSs.

The CRSs and CaptureSeq expression can be viewed in the UCSC genome browser using the project's UCSC track hub.

Search for CRSs

This is the search engine for CRS annotation in hg38 and 100-species tree.
Database version: rth_data_collection_2017-02-28_18:19:19_4115 (based on Gencode v25).
Switch to previous database: hg18 and 17-species tree.

You can search for CRSs that (1) are inside a human genomic region (hg38), (2) are closests (including overlapping) to a human gene identifier, and (3) have specific structure/alignment features.
End: [Example]
Closest gene:
Maximal distance: [Example]
Sequence identity:
Mutual information:
GC content:
Re-align: [Example]

You can also directly search one or many (separated by ',') CRSs or CRS regions by their identifier (this will ignore all other selections).
CRS/CRS region identifiers:[Example]
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The identification and functional annotation of RNA structures conserved in vertebrates
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL and Gorodkin J Genome Res. 2017, Advance May 9, 2017, doi: 10.1101/gr.208652.116
Supplemental Data files are available here.