Transcript details panel

First of all, the transcript view allows access to transcript specific data like the protein and DNA sequence and colors the exons of the transcript on the sequences. Other transcripts of the gene can be visualized with respect to the current transcript and deletions, replacements and insertions that occur due to the splicing event are colour coded on the transcript sequence. Users can choose a protein structure that matches the transcript and this structure is then visualized and the correspondence of the gene structure (i.e. its exons) and the protein structure can interactively be explored. An exon or a group of exons can additionally be structurally classified in terms of different features like secondary structure content, solvent accessibility, structural contacts as well as domain classifications as defined by SCOP or PDP. Despite analyzing each exon individually, known splicing events, i.e. other known transcripts of the gene, can also be coloured on the structure level relative to the current transcript immediately showing deletions, insertions and replacements on the structure level.

Show transcript: By default this view is opened. It shows the amino acid sequence and the nucleic acid sequence of the transcript. In both sequences the exons are shown in alternating colors. If this view is not opened and you wish to see it click on the "Show transcript" button. Amino acids whose nucleotide triplet is provided by two neighboring exons (border amino acids) are coloured in green.

Show known alternatives:By clicking on this button you will view the alternative transcripts of this gene.(Alternative transcripts view)

Show structure information: Clicking on this button will lead you to an overview of the structure information that is available (Structure information view), the first model will be loaded immediatly. If no structure information is available this button is disabled.

Show all transcripts: When comparing different transcripts on the structure level it might be helpful to have the binary exon view at hand. Therefore you can open it in an additional window by clicking on this button.