miRNA genome coordinates
We have precalculated the locations of all animal miRNAs in the database on the latest genome assemblies -- (we intend to add the plant locations soon!). These positions are available from a number of locations both on the miRBase pages, and in external genome annotation databases:
1. All calculated data are available in GFF format from the miRBase FTP site. The genome assembly version is encoded in the file name and in the header of the GFF file. Click here to see a list of the genome assembly versions used.
2. Positions of human and mouse miRNAs are viewable in the EnsEMBL genome browser.
- Goto a contigview page of your region of interest.
- In the "detailed region", click the "DAS sources menu"
- Choose "Manage sources", and then click "Attach DAS".
- Type "das.sanger.ac.uk" in the URL box and "show sources".
- Scroll down and click your choice of miRNA annotation. At the time of writing the two choices are "mirna_mouse_ncbi32" and "mirna_human_ncbi34".
- Scroll to the bottom of the list and click "Attach DAS".
- Click "Reload" or "Refresh" in your browser to view the miRNA annotation track.
3. miRNA positions are also available for several organisms in the UCSC genome browser. In the genome browser view, make sure that the "miRNA" track (in the "Genes and Gene Prediction Tracks" section) is selected. The Table browser also allows you to ask for things like "give me the sequences of all miRNAs on human chromosome 1, including 1kb of flanking sequence".