Genomic screen for structured RNAs in Drosophila melanogaster and related insects


Search for Conserved RNA Structures (CRSs)

The data source can be searched for CRSs that
  1. are inside a genomic region of any of the insect genomes of UCSC's 27-species insect tree,
  2. are near (including overlapping) to a Drosophila melanogaster gene (allows partial or exact matches to gene symbols or gene identifiers in the FlyBase annotation), and
  3. have specific structure/alignment features.
The list of CRSs matching the query will be listed in a sortable table of their genomic locations, FDR and any additional queried features. By default the table is sorted by genomic coordinates.

In case you know the CRS or CRS region identifier you can also directly search for it (this will ignore all other selections). If you want to look into more than one CRS or CRS region identifier then list them all separated by ','.

Use the [Example] queries to get started. Hover over the '[?]' behind the different query fields with the mouse cursor to get more information.

Result page - CRS

Hint: Additional information to the annotation tracks is available by hovering over the annotation titles with the mouse cursor.

[UCSC Genome Browser]

Link to the D. melanogaster (dm6) location of the respective CRS in the UCSC genome browser. The link also adds the project's track hub with the Hub Name CMfinder insect screen for Assembly dm6 consisting of the tracks CMfinder CRSs (CMfinder predicted CRSs (pscore > 80, repeat-filtered, FDR <= 10%)) and tiling (Genome-wide modENCODE tiling array transcript regions [Graveley et al., Nature, 2011]).

+ Summary

General features of the CRS

+ Annotation

Gene annotation in D. melanogaster (FlyBase). On each strand, all overlapping annotation elements are listed together with the size of the overlap. In case there is no overlap (the genomic context on this strand is then intergenic), the closest annotated element is given instead, together with the distance. A negative distance means that the closest gene annotation is upstream of the CRS, regardless of strands.

+ Consensus structure

CMfinder predicted structure with color coding from 27-species alignment and sequence from D. melanogaster

+ Alignment

Alignment based on the CMfinder predicted covariance model

+ Species

Genomic coordinates of all sequences in the CRS alignment

Result page - CRS region

+ Summary

General features of the CRS region

+ Expression

List of all modENCODE genome-wide tiling array experiments [Graveley et al., Nature, 2011] in which the CRS region is expressed (CRS region overlaps an expressed tiling region by at least 50% of its size)

+ Contained CRSs

List of individual CRSs that have been merged into the CRS region