UTRome.org - Tour

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Tour of the UTRome website.

Search the database.

A productive search in the database returns a comprehensive list of genes and UTRs matching the query. For each gene in the result list, we provide general information extracted from WormBase, such as the Cosmid ID, Locus name, Chromosome, and a brief description (accessible by mousing over any Gene or 3'UTR).

The first column indicates whether the corresponding gene is targeted by our pipeline (blue if in the UTRome pipeline, empty otherwise). If the 3'UTR has been previously annotated in WormBase, we indicate its length in base pairs. For 3'UTRs in our cloning pipeline, we assign a color-coded flag (green, orange or red circles) as an indicator of confidence as to whether a given UST is a bona fide 3'UTR for the targeted gene.

Explaining the genome graph.

The graphical display shows the transcript model(s) for the given gene and, if available, previously mapped ESTs and mRNAs (from WormBase), predicted miRNA binding sites (from both PicTar and miRanda), and sequence conservation with the C. briggsae genome.

Providing feedback.

A web form near the bottom of the page allows users to submit (anonymously, if desired) comments, suggestions, or requests (e.g. for inclusion of additional data) to the database administrator.

Gel picture.

The "Gel" page shows an agarose gel image containing the PCR bands for a set of 96 cloned USTs, with the UST of interest highlighted for easy reference. This raw data can provide information about 3'UTR heterogeneity since additional bands could indicate the presence of multiple, previously undocumented, isoforms in the original mini-pool.

ABI trace file viewer.

The ABI trace file page present in the "Trace" page allows the user either to view the chromatogram produced by the ABI sequencer corresponding to the given UST, or to download it in SCF format. The chromatogram is rendered graphically using a Java applet, which enables the user to browse the entire sequence trace from 5' to 3', to extract the sequence in FASTA format, and view comments produced by the ABI sequencer.

This page enables interactive access to the raw sequence data and its inspection at a great level of detail.

Seconday structure prediction.

In the "FOLD" links to a webpage we display the predicted secondary structure for the 3'UTR region of the corresponding transcript, calculated using the MFOLD algorithm. Secondary structures in RNA molecules may influence the accessibility of sequence-specific recognition motifs by factors such as miRNAs and can also serve as structural features recognized by some RNA-binding proteins.

Although MFOLD predictions are not experimentally validated, they represent a valuable starting point to model the interaction of the given 3'UTR with RNA binding factors.