Conserved RNA Structures (CRSs) in the vertebrate genome

CRS logo 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 G+C content, we predict 520k human genomic regions containing CRSs. Consult Help for more details.

The CRSs can be viewed in the UCSC genome browser using the UCSC track hub.

Search for CRSs

The 3 options are exclusive (you can only choose one of them). Expert structure/alignment features only apply for option 1 and 2.

(1) Inside a genomic region [Example]
Species:
[?]
Position: [?]

(2) Overlapping or near a gene annotated in human [Example Gene name]
Gene symbol: [?]
Maximal distance: [?]

+ Expert structure/alignment features

Pscore: [?]
FDR: [?]
Sequence identity: [?]
Mutual information: [?]
GC content: [?]
Energy: [?]
Re-align: [?]

(3) CRS identifier [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 Res. 2017 Aug;27(8):1371-1383. Epub 2017 May 9
[ PubMed | Paper | Dataresource | Supplement ]

Release history

The current release is 2.1. For previous versions see below.
Version GENCODE Release date Comments
2.1 Release 25 2020-08-12 Link to RNAcentral . Non-redundant CRSs. R-scape. Selection ratio. Fixed human coordinates. Layout update incl interactive structure and alignment.
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.