Description

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

• 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 are from snoRNABase, which is maintained at the Laboratoire de Biologie Moléculaire Eucaryote.

Display Conventions and Configuration

This track follows the general display conventions for gene prediction 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

Methods

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 hairpin structure.

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.

Credits

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.

References

When making use of these data, please cite the following articles and, if applicable, the primary sources of the RNA sequences:

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

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

Weber MJ. New human and mouse microRNA genes found by homology search. FEBS J. 2005 Jan;272(1):59-73. PMID: 15634332

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

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