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Protein and gene summary page

Just beneath the navigation, the full Refseq annotation for the currently viewed protein (left-hand side) and its corresponding gene (right-hand side) are displayed along with various identification information. Beside the protein and gene labels is the internal MiST2 identifier. To obtain either the protein/gene sequence click on the respective 'Sequence' link(s). Depending on which link was clicked, a bordered box will appear with either the amino acid or DNA sequence. Click either the 'Close' link or the 'Sequence' link to hide the box.

Domain architecture

The protein's full domain architecture is visualized below the Refseq annotation table and above this is an amino acid scale. Each predicted domain is labeled in a white, bordered box. Blue vertical boxes () represent transmembrane regions, red boxes () represent signal peptides, green boxes () represent coiled-coils regions, and pink boxes () represent low-complexity regions. Clicking the 'List domains' link will display a table of all the predicted domains for this protein sequence including those that are not visualized because they overlap with other domains. Links to the domain annotation are provided when available.

Another useful feature is the ability to quickly retrieve the subsequence corresponding to any visualized element of the domain architecture. Simply hover the mouse over a particular element and a bordered box will appear below that element with information about the region coordinates and clicking on the element will "freeze" the box in position and display its subsequence.

Genome neighborhood

The genome neighborhood section graphically portrays the genomic context of the currently viewed gene (shown as a red arrow) and provides a fluid, dynamic method for ascertaining the properties of neighboring genes (shown as gray arrows). Clicking on one of the gray arrows will dynamically update the page to display the information associated with the newly selected gene and encoded protein. In this manner it is possible to fluidly and rapidly navigate the genes encoded on the chromosome (or contig). It is also possible to pan the genome neighborhood window by clicking on the whitespace and dragging the mouse.

Upstream / downstream DNA retrieval

Because it is often desirable to retrieve the DNA sequence upstream and/or downstream of a given gene, we have introduced this feature in MiST2. Under the 'Neighboring DNA' section, simply select the direction relative to the current gene, the size of DNA sequence to fetch, and push the 'Submit' button. If Javascript is enabled, the corresponding DNA sequence will appear just beneath the form controls. Otherwise, a new page will open with the requested sequence data.

Additional cross-references

Any additional cross-references are displayed at the bottom of the page. The external databases that are indexed on a regular basis include: Uniprot, Uniprot/Swiss-Prot, NCBI non-redundant, and PDB.

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