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Nucleic Acids Research 2006 34(Database Issue):D158-D162; doi:10.1093/nar/gkj002
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Nucleic Acids Research, 2006, Vol. 34, Database issue D158-D162
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

Laurent Lestrade and Michel J. Weber1,*

Institut d'Exploration Fonctionnelle des Génomes IFR109, CNRS/Université Paul Sabatier 118 route de Narbonne 31062 Toulouse Cedex, France 1Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS/Université Paul Sabatier 118 route de Narbonne 31062 Toulouse Cedex, France

*To whom correspondence should be addressed. Tel: +33 56133 5956; Fax: +33 56133 5886; Email: weber{at}ibcg.biotoul.fr

Received June 15, 2005. Revised July 13, 2005. Accepted July 28, 2005.

The snoRNA-LBME-db is a dedicated database containing human C/D box and H/ACA box small nucleolar RNAs (snoRNAs), and small Cajal body-specific RNAs (scaRNAs). C/D box and H/ACA box snoRNAs are part of ribonucleoparticles that guide 2'-O-ribose methylation and pseudouridilation, respectively, of selected residues of 28S, 18S or 5.8S rRNAs or of the spliceosomal U6 RNA. Similarly, scaRNAs guide modifications of the spliceosomal RNAs transcribed by RNA polymerase II (U1, U2, U4, U5 and U12) and are often composed of both C/D box and H/ACA box domains. However, some snoRNAs do not function as modification guide RNAs, but rather as RNA chaperones during the maturation of pre-rRNA. The database was built by a compilation of the literature, and comprises human sno/scaRNAs that were experimentally verified, as well as the human orthologs of snoRNAs that were cloned in other vertebrate species, and some snoRNAs that are predicted by bioinformatics search in loci submitted to genomic imprinting, but have not all been experimentally verified. For each entry, the database identifies the modified nucleotide(s) in the target RNA(s), indicates the corresponding predicted base pairing, gives a few pertinent references and provides a link to the position of the sno/scaRNA on the UCSC Genome Browser. The ‘Find guide RNA’ function allows one to find the sno/scaRNAs predicted to guide the modification of a particular nucleotide in the rRNA and spliceosomal RNA sequences. The ‘Browse’ function allows one to download the sequences of selected sno/scaRNAs in the FASTA format. The database is available online at http://www-snorna.biotoul.fr/. It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track.


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