The UCSC Genome Browser

Depending on your search terms, you may have to select a specific transcript product from an intermediate page of results grouped by gene source (UCSC, RefSeq, etc).  If you have searched for a unique enough term or have used the suggestions from the search term box, you will be taken directly to the browser view.

At the top of the browser view are a number of choices you can use to change your display.

You can

• move up and downstream

• choose from zoom options, including the choice to zoom immediately to the sequence view by selecting the base button.  

• add coordinates to the view in the text box to widen your view

• view the location of your view by the red marker on the chromosome graphic

Below the chromosome graphic is the browser map with default tracks displayed.  The top section is general gene information, scale, chromosomal coordinates, genes in graphic view.

• Small arrows show the direction the gene is transcribed on the strand
• You will notice that your selected gene's name may be highlighted in black
• Color key for GENCODE Comprehensive Transcript Set (this section used to be called "UCSC Genes") 
  • Black - feature has a corresponding protein entry in PDB
  • Dark blue - the transcript has been reviewed or validated by  either RefSeq, SwissProt or CCDS
  • Medium blue - other known RefSeq transcripts
  • Light blue - non-RefSeq transcripts
• Don't be concerned if you don't see multiple color options for the transcripts: they are updated and annotated regularly, so some transcripts may change color as they are verified and others may be removed.
• Click the vertical bars on the left of any displayed track to see all the information available about that track's display features and legend
• Click on a transcript line to open the gene's complete information page