A region in detail

Understanding the location tab - the main view

The location tab's main display is the 'region in detail', which shows a region of the genome up to 1Mb long in a highly customisable view (Figure 24). The 'Region in detail' display supports data visualisation from numerous sources.  

Understanding the location tab

Figure 24. The region in detail display for BRCA2.

 

NotesChromosome. The chromosome is shown at the top [A], with the position of the region of interest marked by a red box. You can use this image to zoom in and out of the chromosome.

Region in detail.

  • 1 MB region.An overview of all genes in a 1Mb region, centred on the gene of interest (in this case, BRCA2), is shown [B]. Each gene is clickable, and following links to gene or transcript IDs opens the gene or transcript tab, respectively. The genome is divided into light and dark blue bars, reflecting individual contigs. Information such as markers can be added to the top panel by turning on data types in 'configure this page'.
  • Main panel. The section in the lower part of the region in detail panel [C] is highly customisable, and can be zoomed in (down to 1 bp) or out (up to 1 Mb). To change the zoom you can use the zoom slide, type in a new location or gene, or click and drag a box around a region with your mouse. Turning on data tracks using 'configure this page' will draw new data tracks along the genome. (The data tracks shown in [C] are Chromosome bands, Species specific RefSeq mRNA/cDNA, non-mammal UniProt, mammal UniProt, and the CCDS set.) Find out more information about any track by clicking on the name.

 

InformationA quick way to zoom is to drag a box around a region with your mouse, and then 'jump to region'.

 

Information

Data tracks can be turned on using the 'Configure this page' tool at the left of the page.