Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs - PubMed (original) (raw)

. 2007 Jan;35(Database issue):D183-7.

doi: 10.1093/nar/gkl873. Epub 2006 Nov 11.

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Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs

Jun Xie et al. Nucleic Acids Res. 2007 Jan.

Abstract

Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

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Figures

Figure 1

Figure 1

The schematic illustration of the sno/scaRNAbase.

Figure 2

Figure 2

The sno/scaRNAbase browse page. a. Browsing result ordered by organism. b. Sorting buttons. c. Browsing selection I: browsing sno/scaRNAs by organism. d. A collapsing or expanding button. e. Browsing selection II: browsing sno/scaRNAs by three categories. f. Buttons for viewing previous or next pages.

Figure 3

Figure 3

An example of a sno/scaRNA record page. a. Links to home/main pages, the previous/next sno/scaRNA record page, and the help page. b. A selected sno/scaRNA name. c. Possible homologues found in the sno/scaRNAbase. d. A link to the predicted secondary structure.

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