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Genes and regulation

Example view

A top panel shows information specific to the variant. Read more about the top panel in this help page.

Genes and regulatory features which overlap the structural variation are listed.

Tables

Two tables are shown.

The Gene and Transcript consequences table shows the position and effect of the variation on specific genes and transcripts.

Columns in the table are as follows:

  • Gene - The Ensembl Gene ID. Click for more information about the gene. The HGNC ID is also listed.
  • Transcript (strand) - The Ensembl Transcript ID. Click on the ID for more information about the transcript. The biotype is also listed.
  • Allele type -
  • Consequence types - The consequence type. Note this is transcript dependent (the variation consequence may vary between transcripts). For variation types, see this article.
  • Position in transcript - Nucleotide position in the transcript, counting from the transcript start.
  • Position in CDS - Nucleotide position in the CoDing Sequence (CDS), counting from the start of the coding sequence (ATG).
  • Position in protein - Amino acid position in the protein sequence.
  • Exons - The exons of the transcript that are affected by the variation.
  • Transcript coverage - The proportion of the transcript that is affected by the variation. This is shown in bp, as a percentage and as a graphic.

The Regulatory consequences table shows Ensembl regulatory features and motifs at the variant position that may be involved in gene regulation from the Regulatory Build.

Columns in the table are as follows:

  • Feature - The Ensembl stable ID is shown for regulatory features (ENSR#). An ID from the relevant source (e.g. JASPAR) is shown for motifs, specifically binding motifs or Position Weight Matrices. The Ensembl ID associated with the motif is shown under the motif name.
  • Feature type - This is either an Ensembl regulatory feature, or a motif.
  • Allele type -
  • Consequence types - The consequence type of the variant ('regulatory region' is the most generic value here).
  • Feature coverage - The proportion of the feature that is affected by the variation. This is shown in bp, as a percentage and as a graphic.

Note: Use the Show/hide columns button to turn unwanted columns off (or on). Expore the table using the 'CSV' button at the top right of each table. The Filter box provides a search.