The new Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.
This feature requires an up-to-date web browser.
Gene View for gene HBA1 : Hemoglobin alpha protein representative chains 2W72.A and 1C7C.A (blue) mapped to exons of HBA1 gene (orange)
The graphical view is built on top of the BioDalliance genome browser. Users can use the mouse to move through the region around a human gene as shown in the Gene View.
Gene View displays information in several horizontal rows called tracks, which can be reordered by dragging the title box. The view can be zoomed in or out.
- The Genome track displays the position of the region of the genome and the nucleotide (when zoomed out as a letter code, when zoomed in as a color-coded region (Guanine: black, Adenine: green, Cytosine: blue, Thymine: red).
- The PDB track shows the region of the gene with available PDB protein chains. Clicking on the region displays more information about the mapped protein.
- The Genes track displays the annotated gene, as provided by the Gencode project. White boxes represent UTRs (untranslated regions) and orange boxes represent protein coding regions. Black lines connecting boxes represent introns (regions that get removed during mRNA splicing).
- The Repeats track shows regions that have been annotated to contain various repeats. Data provided by UCSC Genome Browser.
- The Conservation track shows PhastCons conservation scores derived from multiple alignments of 45 vertebrate genomes to the human genome. Data provided by UCSC Genome Browser.
Gene View can be launched from a Structure Summary page for a human protein under "Molecular Description":
Molecular description section from the 2W72 Structure Summary page with links to Gene View for genes HBA1 and HBA2
The Gene View is also accessible from the top bar search box by selecting a matched gene symbol from the autocomplete suggestions:
Link to Gene View for gene HBA1 using the autocomplete search suggestions (Note: Protein Feature View is also accessible using the gene symbol: see next section).