Non-coding RNA sno/miRNA Track Settings
 
C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase

Track collection: RNA sequences that do not code for a protein

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+  All tracks in this collection (4)

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Data version: miRBase Release 22 (March 2018) and snoRNABase Version 3 (lifted from hg19)
Data last updated: 2018-05-26

Description

This track displays positions of four different types of RNA in the human genome:

C/D box and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation, respectively, of rRNAs and snRNAs, although many of them have no documented target RNA. The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase II, and often contain both C/D and H/ACA domains.

Display Conventions and Configuration

This track follows the general display conventions for gene prediction tracks.

The miRNA precursor forms (pre-miRNA) are represented by red blocks.

C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs are represented by blue, green and magenta blocks, respectively. At a zoomed-in resolution, arrows superimposed on the blocks indicate the sense orientation of the snoRNAs.

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. (2004) and Weber, M.J. (2005) in the References section below.

The snoRNAs and scaRNAs from the snoRNABase were aligned against the human genome using blat.

Credits

Genome coordinates for this track were obtained from the miRBase sequences FTP site and from snoRNABase coordinates download page.

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.

You may also want to cite The Wellcome Trust Sanger Institute miRBase and The Laboratoire de Biologie Moleculaire Eucaryote snoRNABase.

The following publication provides guidelines on miRNA annotation: Ambros V. et al., A uniform system for microRNA annotation. RNA. 2003;9(3):277-9.