Whole database download

Basic annotations, variations, half-life, uncoupling, trans-factors and cis-elements data are contained, along with the table structure, in the MySQL database dump which you can download below.


A reduced form of the database, called AURAlight and including only regulatory sites for trans-factors and cis-elements on UTRs, with position, factor and UTR identity can be downloaded below.


DynaMIT annotation

Here you can download several files containing annotation that can be used right away with DynaMIT, the Dynamic Motif Integration Toolkit. These files include positional-weight matrices (PWMs) for human RBPs, obtained from CISBP-RNA and RBPDB and formatted for use with DynaMIT's MatrixSearcher; position-specific scoring matrices (PSSMs) derived from cis-elements included in AURA, such as AU-rich and TOP elements, to be used with DynaMIT's MatrixSearcher; also available is AURAlight for DynaMIT, i.e. the complete set of positional annotations concerning RBPs and cis-elements found in AURA, formatted for use in DynaMIT through the KnownSitesSearcher or the RegionsIntersectionSearcher.

AURAlight_DynaMIT.tar.gz CISBP-RNA_PWMs_DynaMIT.zip RBPDB_PWMs_DynaMIT.zip cis-elements_PSSMs_DynaMIT.zip

Sequence and phylogenetic conservation data

UTR sequences are obtained via a file that is external to the database and stored in the compressed 2bit format. Here you can download it along with its uncompressed FASTA-format counterpart. In order to extract sequences from or to compress a FASTA file to 2bit format you will need Jim Kent's tools and in particular the twoBitToFa and faToTwoBit programs.

UTR_hg19.2bit UTR_hg19.fasta
UTR_mm10.2bit UTR_mm10.fasta

Per-nucleotide UTR phylogenetic conservation scores are obtained via a pair of files that are external to the database and stored in the compressed Wiggle format. Here you can download these two. In order to extract conservation scores from or to compress a file to Wiggle format you will need Jim Kent's tools and in particular the wigEncode and hgWiggle programs.

UTR_hg19.wib UTR_hg19.wig
UTR_mm10.wib UTR_mm10.wig