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The Ensembl Genome Browser

Gene Recorder

Screen shot of Ensembl gene recorder

On this page:

  • Use the tabs at the top to navigate between the gene view and the location view 
    • As you click on more features (transcripts), more tabs will open at the top
  • Use the menu at the left to access different types of data for your gene 
    • When you click options on the left menu, the content in the main section of the page will change according to your selection
  • At the top of the page will be general information about the gene, with links to other features

In the transcript table:

  • Links to transcript ID, protein transcript records, coding sequences (external), UniProt record (external), NCBI RefSeq IDs (external) and evidence flags.
  • In the Biotype column, gold transcripts for protein coding isoforms indicate agreement between Ensembl andVEGA/Havana gene records (although you will occasionally see gold transcripts that are processed but not listed as protein coding), red transcripts indicate that the isoform is also protein coding, but the data are from eitherEnsembl or VEGA/Havana. Blue, pink/purple or grey transcripts are non-protein coding
  • Use the transcript support flags to determine the level of support for each transcript

Scroll down the page to see a brief summary of your gene with some more external links. Below this is the genome browser view.

 

Screen shot of browser view

  • If you want zooming capability, use the link above the browser view to go to the Region in Detail
  • In the browser, click on the labels on the left to configure or turn off the default tracks
  • Transcripts are (usually) arranged with the isoforms that begin closest to the 5' end of the forward strand first, but transcripts may be clustered on lines to save space 
    • For full-length transcripts, the primary isoform (according to APPRIS notation and RefSeq) is usually shown first, with others below it
  • Click on any transcript (or other feature) to open a descriptive dialog box with links to records for that feature 
    • You can zoom to that feature, mark it, see the info about the length of the transcript, coding strand and open new links
    • When you click on a link in a feature pop-up box, a new tab opens at the top of the page with a specific record for that page
  • Genes will be shown with forward strand above the contig view, and reverse strand below the contigs
  • To add tracks to the browser, use the Configure this Page link in the main left menu or the small configuration menu in the upper left corner of the browser frame