Description

This track shows predicted microRNA target sites in GENCODE transcripts, for medium-conserved microRNA families. Predictions include atypical regions such as 5'UTRs and CDS. The GENCODE annotation includes >10,000 long non-coding RNA (lncRNA) genes, as well as known coding genes. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is evaluated based on the 46 vertebrates multiZ alignment. More information can be found on the miRcode page.

Display Conventions and Configuration

Darker shading indicates stronger site conservation. Displayed sites indicate the 5' end of the microRNA.

It is recommended that this track is displayed in conjunction with GENCODE or ENSEMBL gene annotation tracks.

Methods

Briefly, all GENCODE transcripts were screened for complementary matches to known microRNA seed families. Site predictions were done on individual transcripts, and later aggregated into non-redundant sets for individual genes. Currently, miRcode is based on GENCODE version 11. Please see paper below, or the miRcode page, for further details.

Credits

This track was produced by the Larsson Lab at the Sahlgrenska Academy, University of Gothenburg, Sweden (contact: Erik Larsson).

We thank the Swedish Research Council for support.

References

Ashwini J, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 1;28(15):2062-3.