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

You can search for CRSs

(1) inside a human genomic region (hg38) [Example],
Chromosome: [?]
Start: [?]
End: [?]
(2) overlapping or near a gene [Example],
Gene symbol: [?]
Maximal distance: [?]
(3) fullfilling specific structure/alignment features [Example],
Pscore: [?]
FDR: [?]
Sequence identity: [?]
Mutual information: [?]
GC content: [?]
Energy: [?]
Re-align: [?]

(4) by their identifier (this will ignore all other selections) [Example].
CRS or CRS region identifiers:[?]
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Reference

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, Gorodkin J Genome Research 2017, 27(8):1371-1383
[ PubMed | Paper | Dataresource | Supplement ]

Release history

The current release is 2.0. For previous versions see below.
Annotation version GENCODE release Release date Comments
Version 2.0 Release 25 2017-02-28 CRS annotation in hg38 and 100-species tree. Version of the Genome Res paper.
Version 1.0 Release 19 2015-09-08 CRS annotation in hg18 and 17-species tree.