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The Ensembl Genome Browser

Splice Variants

The splice variants option in the left menu provides a great deal of information on exons in each transcript for your gene of interest.

Click on the Splice Variants option in the left menu.
Note: if your gene has a lot of splice variants, it may take a while to load this page. Sometimes you will retrieve an error message. Just be patient and try reloading the page by clicking on the Splice Variants option again.

 

Screen shot of splice variant view

 

  • Each exon will be represented vertically across all transcripts that contain that exon
  • For protein-coding isoforms, domains from various protein databases will be shown in purple below the transcript  
    • Click on any of the features in the transcript's graphic to see the number of amino acids in the feature and links to the database of source for the information
  • This is a great way to get an overall picture of known or predicted sites in the protein encoded by your gene of interest

Transcript Comparison

Click on Transcript Comparison in the left menu

You will be asked to Select transcripts from a new option that will appear in the left menu at the bottom. Click that Select transcripts button. 

In the window that opens, you can click on individual transcripts "+" sign to add them to your comparison. Or you can use the drop-down menu on the left to select by type (none, protein coding, all, etc.). In this example I'll use the menu to select all protein coding transcripts.

When you're done making your selections, click the checkmark in the upper right corner of the selection window. The view will refresh with your selections shown.

 

Screen shot of transcription comparison view

  • It may take a while to load if you have selected a number of transcripts and your gene is a long one. Be patient.
  • The results are displayed as a multiple sequence alignment, with the consensus gene sequence displayed in dark red bold letters and all your selected transcripts below it.
  • Sequence is colored by translation status, and variants are highlighted by colored blocks surrounding the altered bases.
  • Again, this is a good way to get an overview of the transcripts' differences
  • You can BLAST this sequence or download it in FASTA or RTF format (suitable for displaying or editing in Word)

 

 

There are other ways to get individual transcript features. Toward the top of this page, if the transcript table is hidden, click the Show transcript table button.

Now select a transcript by clicking on its Transcript ID in the table. This example will use the APP-201 (ENST00000346798.7) transcipt.

You now have a linear diagram of just one transcript, and a new tab has opened at the top of the page (so you can still go back to the Gene or Location views). The menu on the left has also changed.

Transcript-based display menu

  • Summary
  • Sequence features
  • Protein information
  • Genetic variation
  • External references (general identifiers and oligo probes for this transcript)
  • ID history

If you want to see the length of each exon, intron and UTR ends, click on the Exons link in the left menu.

Screen shot of transcript-displays option bar.

 

You will now see the start and stop coordinates and length of each exon, intron UTR and flanking sequence. Again, sites of variation are shown with color-coded highlighting

  • Do you need to see the full intronic sequence for each intron? Select Configure this page from the left menu and click the checkbox to show full intronic sequence (plus other formatting options).
  • You can download the sequence as FASTA or RTF. If you choose FASTA, you have to option to omit certain sequence features from the FASTA file.
  • Each variation is a clickable link that will open a menu describing the genomic location, alleles, amino acid consequences, and links to get more information or see the variant in other transcript locations.

There are more efficient ways to explore variants by gene, transcript and protein.