Structural RNA alignments in vertebrate genomes

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 (1) are inside a human genomic region (hg38), (2) are closests (including overlapping) to a human gene identifier (as in the GENCODE 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'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.

Result page

[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