Investigating a gene

 

When you search the browser with a gene name, you can click on the results to go the gene tab. This tab contains all the information associated at the gene level; for example, the genomic sequence for the BRCA2 gene. 

Figure 10. The gene tab top section provides an overview of the splice variants for one specific gene (in this example, BRCA2 transcripts).

 

Gene IDs. Ensembl gene IDs begin with ENS for Ensembl, and then a G for gene. In this case, ENSG00000139618 is the Ensembl gene ID for BRCA2. The number is unique, and should not change, even if the gene is updated. A three-letter code is inserted into the identifier, in the case of species other than human. For example, ENSMUSG00000041147 would indicate the BRCA2 gene in mouse (Mus musculus).

Synonyms. Alternative gene symbols that have been used in the literature to describe this gene.

Location. The genomic location and strand where this gene is found.

Transcript table. At the top of the gene summary, the number of transcripts, or splice isoforms, are shown in a table. In our example, for Ensembl release 89, there are seven transcripts for the human BRCA2 gene. You can find more information about the transcripts in the 'Biotype' column. In our example, two transcripts in the table are protein coding (BRCA2-201 and BRAC2-206), two result in proteins that undergo nonsense mediated decay (BRCA2-202 and BRCA2-203), and three not translated (BRCA2-204, BRCA2-205 and BRCA2-207).

InformationIt’s a good idea to write down the gene identifier of any gene you work with, and the date. This allows you to go back to that specific gene model in Ensembl, even if an update has occurred.
HelpSee the Ensembl documentation for extensive information about genome annotation.

 

We will use the menu on the left-hand-side to explore:

  • Gene sequence (introns and exons)
  • Homologues
  • Sequence variations
  • GO terms (gene function)