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

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 sel...

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Main Authors:	Lestrade, Laurent, Weber, Michel J.
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347365/

id	pubmed-1347365
recordtype	oai_dc
spelling	pubmed-13473652006-01-25 snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs Lestrade, Laurent Weber, Michel J. Article 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 . It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track. Oxford University Press 2006-01-01 2005-12-28 /pmc/articles/PMC1347365/ /pubmed/16381836 http://dx.doi.org/10.1093/nar/gkj002 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lestrade, Laurent Weber, Michel J.
spellingShingle	Lestrade, Laurent Weber, Michel J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
author_facet	Lestrade, Laurent Weber, Michel J.
author_sort	Lestrade, Laurent
title	snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
title_short	snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
title_full	snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
title_fullStr	snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
title_full_unstemmed	snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
title_sort	snorna-lbme-db, a comprehensive database of human h/aca and c/d box snornas
description	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 . It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track.
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347365/
_version_	1611380319855837184

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

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