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
Assembly: Mouse Feb. 2006 (NCBI36/mm8)
Data last updated at UCSC: 2007-05-31

Description

The miRNA track shows microRNAs from miRBase.

Display Conventions and Configuration

The precursor forms of microRNAs (mirs) are represented by thin blocks. miRNAs in the sense orientation are shown in black; those in the reverse orientation are colored grey.

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.

Methods

Precursor miRNAs from miRBase 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.

Credits

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).

References

When making use of these data, please cite:

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

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

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