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
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. The miRNA Registry 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
The miRNA annotation was contributed by Michel Weber of
Laboratoire de Biologie
Moléculaire Eucaryote, CNRS Université Paul Sabatier (UMR5099, Toulouse,
France) and Sam Griffiths-Jones of The Wellcome Trust Sanger Institute (Cambridge, UK).
The snoRNA annotations were contributed by Michel Weber and
Laurent Lestrade of the
Institut d'Exploration
Fonctionnelle des Génomes (IFR109, Toulouse, France).
Fan Hsu from the UCSC Genome Bioinformatics
Group created the combined annotation track.
References
When making use of these data, please cite:
Griffiths-Jones S.
The microRNA Registry.
Nucl. Acids Res. 2004 Jan 1;32(D):D109-11.
Weber MJ.
New human and mouse microRNA genes found by homology search.
Febs J. 2005 Jan;272(1):59-73.
You may also want to cite The Wellcome Trust Sanger Institute
miRNA Registry and The Laboratoire de Biologie Moleculaire
Eucaryote snoRNA
database.
The following publication provides guidelines on miRNA annotation:
Ambros V. et al.,
A uniform system for microRNA annotation.
RNA. 2003;9(3):277-9.
For more information on blat, see
Kent WJ.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002;12(4):656-664.
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