Genomic screen for structured RNAs in Drosophila melanogaster and related insects

Computational screens for conserved RNA structures (CRSs) have been performed in Drosophila melanogaster in the past using sliding window approaches on sequence-based whole genome alignments. However, these alignments can be prone to misalignments in regions with low sequence identity, as it is often observed for regions encoding non-coding RNAs and structured RNA elements. Here, we make use of the structural realignment approach provided by CMfinder, identifying ~30,000 CRSs in D. melanogaster and 26 related insects (UCSC 27-species insect tree). In addition, we observed differential expression of CRSs across the complete D. melanogaster development and in several cell lines.

Search for CRSs

You can search for CRSs

(1) inside a genomic region [Example],
Species:
[?]
Chromosome: [?]
Start: [?]
End: [?]
(2) overlapping or near a gene in Drosophila melanogaster [Example],
Gene symbol: [?]Exact match (otherwise partial pattern matching)
Maximal distance: [?]
(3) fullfilling specific structure/alignment features [Example],
Pscore: [?]
FDR: [?]
Sequence identity: [?]
GC content: [?]
Energy: [?]
Re-align: [?]

(4) by their identifier (this will ignore all other selections) [Example].
CRS or CRS region identifiers:[?]
   Show results in a new window      

Reference

Identification and characterization of novel conserved RNA structures in Drosophila
Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J BMC Genomics. 2018 Dec 11;19(1):899
[ PubMed | Paper | Dataresource ]


Release history

The current release is 2.0. For previous versions see below.
Data version Release date Comments
Version 2.0 2018-07-27 Searchable interface.
Version 1.0 2018-02-19 Predicted CRSs in dm6 and 27-species tree.