Interacting with the UCSC Genome Browser

• Open the UCSC genome informatics page.

• The horizontal blue menu provides access to the tools.

• Particularly useful links are Genomes, Genome Browser, Tools and My Data.

• Clicking on the Genomes link will lead to a page that allows selection of organism and genome assembly.

1. Position or search term queries - examples of how to query the database.

2. Assembly details - General assembly information

3. Summary Statistics - Detailed statistics of the active assembly

• Proceed to the genome assembly by clicking "Go"

• Search for the gene Protocadherin 10 by pasting that name into the "position or search term" box and clicking "submit".

The Genome Browser

• The genome browser is the central visualization tool of the UCSC Genome Informatics Group.

• Most everything is hyperlinked and adjustable

• Restore the visualization to default by clicking the "default tracks" button under the image. Note that settings from previous sessions with the browser may be retained by your browser.

Positional and scale controls are located above and below the browser image (red boxes)

• Zoom and movement buttons

• Coordinate window

• Coordinate bar in view - click re-centers and zooms in 3x

• Dragging across the upper track is a zoom to selection function.

• Move start and end functions

• Clicking in window and dragging re-positions the view

• Clicking the chromosome ideogram re-positions the window to selected part of the chromosome

Data organization and track controls (blue boxes)

• Like the search results, the information displayed in the browser window is organized into groups and tracks of data. The kinds of tracks being displayed and the ways they are presented can be controlled.

• NOTE: This human assembly is mature, heavily annotated and extensively analyzed. The genomes of other organisms with less mature assemblies have less associated information and therefore fewer tracks.

• The buttons "default tracks" and "hide all" will do as their name suggests.

• The "configure" button displays a list of the available data with display options.

• The bottom of the page consists of a series of pull-down menus. Each is associated with a type of data and the options control display mode.

• IMPORTANT: Useful details about each track can be obtained by clicking the hyperlinked track name.

• Navigate to chr4:133,101,179-133,262,320 using the position window.

• In the "Genes and Gene Predictions Tracks" section, use the pull-down menu to set the "GENCODEv24" track to full.

• Click the "refresh" button. Toggle the GENCODEv24 track between dense and full using the pull-down menu and refresh button.

• For reference, the effects of these different options are described HERE

Note:After changes are made to the pull-down menus, refresh is required for them to take effect.

• The visual cues that you see in the "Full" display of known genes are:

  • Arrowheads indicate the strand of the gene.

  • Thin lines are introns, medium lines are non-coding portions of the mRNA, thick lines are coding region.

• Zoom in to display the region around the 5' end of the PCDH10 gene using coordinates chr4:133,148,483-133,162,403