Conserved RNA Structures (CRSs) in the vertebrate genome

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This is the outdated search engine for CRSs. Switch to the latest version 2.1.

You can search for CRSs in one of three ways

(1) inside a human genomic region (hg38) [Example],
Chromosome: Start: End: [?]
(2) overlapping or near a gene [Example],
Gene symbol: Maximal distance: [?]
(3) by their identifier (this will ignore all other selections) [Example].
CRS or CRS region identifiers:[?]

The search for CRS may be further restricted by requiring certain structure or alignment features. The restriction of the search can be used alone without entering information above, or it can be used in combination with region searches (1). It cannot be combined with searching near a gene or when searching for a specific CRS (2 and 3).

Structure/alignment features [Example],
Pscore: [?]
FDR: [?]
Sequence identity: [?]
Mutual information: [?]
GC content: [?]
Energy: [?]
Re-align: [?]

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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, Gorodkin J Genome Res. 2017 Aug;27(8):1371-1383. Epub 2017 May 9
[ PubMed | Paper | Dataresource | Supplement ]

Release history

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