UCbase & miRfunc: a database of ultraconserved sequences and microRNA function - PubMed (original) (raw)

. 2009 Jan;37(Database issue):D41-8.

doi: 10.1093/nar/gkn702. Epub 2008 Oct 22.

Enrica Fabbri, Rosa Visone, Stefano Volinia, George A Calin, Louise Y Fong, Roberto Gambari, Arianna Bottoni, Mario Acunzo, John Hagan, Marilena V Iorio, Claudia Piovan, Giulia Romano, Carlo Maria Croce

Affiliations

UCbase & miRfunc: a database of ultraconserved sequences and microRNA function

Cristian Taccioli et al. Nucleic Acids Res. 2009 Jan.

Abstract

Four hundred and eighty-one ultraconserved sequences (UCRs) longer than 200 bases were discovered in the genomes of human, mouse and rat. These are DNA sequences showing 100% identity among the three species. UCRs are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs (miRNAs). Here we present UCbase & miRfunc, the first database which provides ultraconserved sequences data and shows miRNA function. Also, it links UCRs and miRNAs with the related human disorders and genomic properties. The current release contains over 2000 sequences from three species (human, mouse and rat). As a web application, UCbase & miRfunc is platform independent and it is accessible at http://microrna.osu.edu/.UCbase4.

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Figures

Figure 1.

Figure 1.

Multi-queries text box (red square). Multiple queries can be performed typing the names of selected miRNAs or UCRs and obtaining as output the band, the gene name, the coordinates, the human diseases related to the band and the secondary structure up to 500 bp up/downstream.

Figure 2.

Figure 2.

Search Page. miRNA and UCRs information can be retrieved searching for band, human Mendelian inheritance disorders related to that band or just typing the name of a gene (red highlighted boxes). The use of an interactive map of biological systems and diseases allows to link miRNAs and ultraconserved sequences to the related disorders (blue arrow).

Figure 3.

Figure 3.

Function page. It provides tables showing ultraconserved elements properties (enhancer activity, alternative splicing, splicing NMD regulation and transcription evidence) and miRNA ‘experimentally proved’ function.

Figure 4.

Figure 4.

Sequence comparison page. This page allows the researchers to match selected sequences against miRNAs and ultraconserved elements (exact/500/1000/2000/5000/10 000 bp up/downstream). Checking the parsing option it is possible to turn the output into a single-line summary (blue arrow).

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