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...conservation of mature sequence required for functional redundancy varies—some recent studies suggest that only the 5 0 so-called seed region of the sequence forms a tight duplex with the target mRNA =-=(16)-=-. Related hairpin precursor sequences may give rise to mature sequences with only marginal similarity and different miRNA numbers. The naming scheme is also complicated by instances where two differen...

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...ted in cellular roles as diverse as developmental timing in worms, cell death and fat metabolism in flies, haematopoiesis in mammals, and leaf development and floral patterning in plants [reviewed in =-=(4,5)-=-]. Recent reports have suggested that miRNAs may play roles in human cancers (6–8). The biogenesis of miRNA sequences has been largely elucidated [reviewed in (9)]. The mature miRNA (often designated ...

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...ty is therefore focused on predicting and validating miRNA gene targets. The miRBase database brings together the gene naming and sequence database roles previously fulfilled by the microRNA Registry =-=(11)-=-, with the first automated pipeline for predicting miRNA target genes in multiple animal genomes. These three functions are briefly discussed in turn. miRBase REGISTRY The rapid growth of the miRNA fi...

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... core algorithm assigns P-values to individual miRNA–target binding sites, multiple sites in a single UTR, and sites that appear to be conserved in multiple species based on robust statistical models =-=(22)-=-. The interface connects each miRNA to a list of predicted gene targets. The detailed target view page (Figure 2) illustrates individual binding sites for one or more miRNAs and their target in an ort...

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...l patterning in plants [reviewed in (4,5)]. Recent reports have suggested that miRNAs may play roles in human cancers (6–8). The biogenesis of miRNA sequences has been largely elucidated [reviewed in =-=(9)-=-]. The mature miRNA (often designated miR) is processed from a characteristic stem–loop sequence (called a pre-mir), which in turn may be excised from a longer primary transcript (or pri-mir). Only a ...

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...s of the genomic position of each miRNA sequence on the entry page (Figure 1) and also in GFF format on the FTP site. miRNA genes may be located within other genes, both protein-coding and non-coding =-=(17,18)-=-, and the context of the genomic location with respect to Ensembl genes is also annotated (Figure 1). 35% of mammalian miRNA loci overlap annotated genes—over 90% of these are located in introns. In c...

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...d fly miRNAs are intronic. Distributed annotation system (DAS) sources provide easy access to miRNA genomic locations, and the data are available for viewing within the Ensembl (19) and UCSC browsers =-=(20)-=-. miRBase TARGETS As focus shifts from miRNA gene identification to functional characterization, miRBase includes not only miRNA sequence data but also information about their genomic targets. The fun...

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...of gene names, and this function is continued by the miRBase Registry. Names are assigned by the Registry based on guidelines agreed by a number of prominent miRNA researchers and discussed elsewhere =-=(15)-=-. In order to minimize the gaps in the naming scheme and to take advantage of the peer review process to assess the validity of submitted miRNAs, names are assigned after a manuscript describing their...

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...parison, 14% of worm and fly miRNAs are intronic. Distributed annotation system (DAS) sources provide easy access to miRNA genomic locations, and the data are available for viewing within the Ensembl =-=(19)-=- and UCSC browsers (20). miRBase TARGETS As focus shifts from miRNA gene identification to functional characterization, miRBase includes not only miRNA sequence data but also information about their g...

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...s of the genomic position of each miRNA sequence on the entry page (Figure 1) and also in GFF format on the FTP site. miRNA genes may be located within other genes, both protein-coding and non-coding =-=(17,18)-=-, and the context of the genomic location with respect to Ensembl genes is also annotated (Figure 1). 35% of mammalian miRNA loci overlap annotated genes—over 90% of these are located in introns. In c...

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...ed by RNA polymerase II, and that the transcripts are capped and polyadenylated. Since the discovery of the founding members of the miRNA class, lin-4 and let-7 in Caenorhabditis elegans [reviewed in =-=(10)-=-], over 2000 miRNA sequences have been described in vertebrates, flies, worms and plants, and even in viruses. However, the functions of only a handful of these miRNAs have been experimentally determi...

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...ted in cellular roles as diverse as developmental timing in worms, cell death and fat metabolism in flies, haematopoiesis in mammals, and leaf development and floral patterning in plants [reviewed in =-=(4,5)-=-]. Recent reports have suggested that miRNAs may play roles in human cancers (6–8). The biogenesis of miRNA sequences has been largely elucidated [reviewed in (9)]. The mature miRNA (often designated ...