Piwi-interacting RNA databases | Non-coding transcript data analysis
For a long time, both the biogenesis of PIWI-interacting RNAs (piRNAs) as well as their mode of gene silencing has remained elusive. A recent body of work is shedding more light on both aspects and implicates PIWI in the establishment of transgenerational epigenetic states. In fact, the epigenetic states imposed by PIWI on targets may actually drive piRNA production itself. These findings start to couple small RNA biogenesis with small-RNA-mediated epigenetics.
A highly user-friendly resource which stores empirically known sequences and other related information on piRNAs reported in human, mouse and rat. piRNABank supports organism and chromosome-wise comprehensive search features including accession numbers, localization on chromosomes, gene name or symbol, sequence homology-based search, clusters and corresponding genes and repeat elements. It also displays each piRNA or piRNA cluster on a graphical genome-wide map.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.
Provides a resource focused on piRNA isoforms. IsopiRBank provides target analysis for piRNA isoforms, which is useful to prioritize them for further functional investigations. Users can retrieve three types of information: (i) a piRNA isoform sequence with advanced options to select the matching rules for input sequence, (ii) all piRNA isoforms of a given piRNA by using either piRNABank ID or piRBase ID, or (iii) a selection of piRNA isoforms expressed in a specific tissue.
Provides a curated resource of piRNAs, a class of small RNAs abundantly expressed in the animal germ line. piRBase is a database which focused on piRNA function analyses as well as piRNA annotation. The piRNAs assembled in this resource were obtained by four experimental methods: (i) small RNA sequencing, (ii) immunoprecipitation of Piwi or Piwi-associated proteins, (iii) Piwi protein crosslinking-immunoprecipitation and (iv) chromatography.
Provides predicted and experimentally identified piRNA targeting sites and to explore their regulatory function. piRTarbase is an integrative database of piRNA targeting sites in Caenorhabditis elegans. Users can input genes of interest and retrieve a list of piRNA targeting sites on the input genes. Alternatively, the user can also input a piRNA and retrieve a list of its mRNA targets.
Deals with human small non-coding RNAs (sncRNA) genes and mature sncRNA products. DASHR allows users to: (i) retrieves annotation; (ii) visualize expression data sncRNA loci, expression and annotation data as UCSC genome browser tracks; (iii) search for and compare both expression and processing information; Its annotation and expression data encompass the major classes of sncRNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), cytoplasmic or ribosomal RNAs (rRNAs).
Provides information on piRNAs and their genomic source loci. piRNA cluster database bundles small RNA sequence information obtained from different tissues and/or developmental stages which allows to get a complete picture of genomic loci that can produce piRNAs under certain conditions. It also facilitates the comparison of transcriptional activity for any piRNA producing locus in time and space. Finally, it supplies detailed information from standardized bioinformatic analysis pipelines for each incorporated sequence dataset and provides processed and pre-filtered sequence datasets which simplifies further comparative analyses of sequence data which is commonly not easily accessible as it is deposited as raw sequence data in NCBI's Sequence Read Archive.