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

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

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Data version: Release 13.0 (March 2009)
Data last updated: 2009-06-11

Description

The miRNA track shows microRNAs from miRBase.

Display Conventions and Configuration

The precursor forms of microRNAs (mirs) 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. For this track, a score of 960 signifies that the miRNA is on the + strand and a score of 480 signifies that it is on the - strand.

Methods

Precursor miRNA genomic locations from miRBase were calculated using wublastn for sequence alignment with the requirement of 100% identity. 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

Genome coordinates for this track were obtained from the miRBase sequences FTP site.

References

When making use of these data, please cite the folowing articles in addition to the primary sources of the miRNA sequences:

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan 1;36(Database issue):D154-8.

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.

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

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

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.