miRNA Track Settings
MicroRNAs from miRBase   (All Genes and Gene Predictions tracks)

Display mode:      Duplicate track

Show only items with score at or above:   (range: 0 to 1000)

Data schema/format description and download
Data last updated at UCSC: 2006-04-11


The miRNA track shows microRNAs from miRBase.

Display Conventions and Configuration

Mature miRNAs (miRs) are represented by thick blocks. The predicted stem-loop portions of the primary transcripts are indicated by thinner blocks. miRNAs in the sense orientation are shown in black; those in the reverse orientation are colored grey. When a single precursor produces two mature miRs from its 5' and 3' parts, it is displayed twice with the two different positions of the mature miR.

To display only those items that exceed a specific unnormalized score, enter a minimum score between 0 and 1000 in the text box at the top of the track description page.


Mature and precursor miRNAs from the miRNA Registry were aligned against the genome using blat. The extents of the precursor sequences were not generally known, and were predicted based on base-paired hairpin structure. miRBase is described in Griffiths-Jones, S. et al. (2006). The miRNA Registry is described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the References section below.


This track was created by Michel Weber of Laboratoire de Biologie Moléculaire Eucaryote, CNRS Université Paul Sabatier (Toulouse, France), Yves Quentin of Laboratoire de Microbiologie et Génétique Moléculaires (Toulouse, France) and Sam Griffiths-Jones of The Wellcome Trust Sanger Institute (Cambridge, UK).


When making use of these data, please cite:

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4. PMID: 16381832; PMC: PMC1347474

Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. PMID: 14681370; PMC: PMC308757

Weber MJ. New human and mouse microRNA genes found by homology search. FEBS J. 2005 Jan;272(1):59-73. PMID: 15634332

The following publication provides guidelines on miRNA annotation:
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al. A uniform system for microRNA annotation. RNA. 2003 Mar;9(3):277-9. PMID: 12592000; PMC: PMC1370393

For more information on blat, see Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518