Conserved RNA Structures (CRSs) in the vertebrate genome
You would like to explore the universe of Conserved RNA Structures (CRSs) existent in the human genome but don't know how to get started? Then read further!
Help
Search for CRSs
The data source can be searched for CRSs that
- are inside a human genomic region (hg38),
- are near (including overlapping) to a human gene (allows partial matches to gene symbols in the GENCODE annotation), and
- 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's or CRS region's 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] links to get started. Hover over the '[?]' behind the different query fields with the mouse cursor to get more information!
Result page
Hint: Additional information to many of the annotation tracks is available by hover over the annotation titles with the mouse cursor!
[UCSC Genome browser]
Link to the UCSC genome browser to the hg38 location of the respective CRS. The link also adds the project's track hub with the Hub Name
CMfinder vert screen for Assembly
hg38 consisting of the tracks
CaptureSeq (CRS targeting CaptureSeq) with subtracks
42deg (annealing temperature of 42 degrees) and
70deg (annealing temperature of 70 degrees),
CMfinder CRSs (CMfinder predicted CRSs (pscore>50)) and
probes (60nt long CaptureSeq probes).
+ Summary
General features of the conserved RNA structure (CRS)
+ Annotation
Gene annotation in human
+ Evolutionary selection
Several tests for purifying selection of CRSs
+ Chromatin signatures
DNase hypersensitive sites and chromatin modifications in human
+ Protein binding sites
ChIP and CLIP-seq in human
+ Expression
Poly-A selected RNA-seq, total RNA-seq and targeted total RNA-seq in human (our CaptureSeq experiment in human fetal brain targeting CRSs with 60 nt probes)
+ Transcript boundaries and stability
Closest upstream 5' site (CAGE) and downstream poly-A site (3'-end sequencing), and exosome sensitivity (CAGE) in human
+ Consensus structure
CMfinder predicted structure with color coding from 17-species alignment and sequence from human
+ Alignment
Alignments based on the CMfinder predicted covariance model