Abstract
ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.
Highlights
MicroRNAs are a class of non-coding RNAs that are transcribed from different loci in the genome and play a vital role in the regulation of gene expression at the transcriptional and post-transcriptional levels (Carthew and Sontheimer, 2009)
We present A rice miRNA (ARMOUR) database that consolidates extensive datasets of miRNA deep sequencing studies in different rice varieties under various experimental conditions
In ARMOUR the user experience (UX) is powered by Hypertext Preprocessor (PHP) and jQuery, while SQL queries were optimized for memory efficient data retrieval and specialized scripts were used for hassle free database updating
Summary
MicroRNAs are a class of non-coding RNAs that are transcribed from different loci in the genome and play a vital role in the regulation of gene expression at the transcriptional and post-transcriptional levels (Carthew and Sontheimer, 2009). A single miRNA may regulate the expression of many target transcripts and acts as a probable masterswitch in biological processes related to growth, development and response to environment (Djami-Tchatchou et al, 2017; Sharma et al, 2017). A miRNA gene is transcribed by RNA polymerase II into a primary miRNA transcript which is processed by DCL1 (DICER like 1) protein into a hairpin intermediate, called precursor miRNA (pre-miRNA). This is further acted upon by DCL1 to generate 20-24 nt long miRNA/miRNA∗ duplex in the nucleus. The duplex is transported to cytoplasm where it is incorporated into
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