This track displays positions of four different types of RNA in the human
- precursor forms of microRNAs (pre-miRNAs)
- C/D box small nucleolar RNAs (C/D box snoRNAs)
- H/ACA box snoRNAs
- small Cajal body-specific RNAs (scaRNAs)
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.
The pre-miRNA data are from the
miRBase Sequence Database at the Wellcome Trust Sanger Institute. The snoRNA and scaRNA data
snoRNABase, which is
maintained at the Laboratoire de Biologie Moléculaire Eucaryote.
Display Conventions and Configuration
This track follows the general display conventions for
tracks. At a zoomed-in resolution, arrows superimposed on the blocks
indicate the sense orientation of the RNAs. The RNA types are represented by
blocks of the following colors:
- red = pre-miRNA
- blue = C/D box snoRNA
- green = H/ACA box snoRNA
- magenta = scaRNA
Pre-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
The snoRNAs and scaRNAs genomic locations from snoRNABase were aligned to the hg18 human genome assembly
using BLAT and were then lifted to the hg19 assembly.
In a few cases, no exact match was found for the published sequences; these
likely correspond to sequencing errors. In these cases, the best BLAT hit (which
differed from the published sno/scaRNA sequence by 1-3 nucleotides) was adopted.
The genome coordinates for the pre-miRNAs were obtained from the
miRBase Sequence Database FTP site, and the genome
coordinates for the snoRNA and scaRNA were obtained from the
snoRNABase coordinates download page.
When making use of these data, please cite the following articles and, if
applicable, the primary sources of the RNA sequences:
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
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
miRBase: tools for microRNA genomics.
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8.
PMID: 17991681; PMC: PMC2238936
Lestrade L, Weber MJ.
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D158-62.
PMID: 16381836; PMC: PMC1347365
New human and mouse microRNA genes found by homology search.
FEBS J. 2005 Jan;272(1):59-73.
For more information on BLAT, see
BLAT--the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518
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