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.

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 111, there are fifteen transcripts for the human BRCA2 gene. You can find more information about the transcripts in the ‘Biotype’ column. In our example, five transcripts in the table are protein coding (BRCA2-201, BRAC2-206, BRCA2-204, BRCA2-210 and BRCA2-214), six result in proteins that undergo nonsense mediated decay (BRCA2-202, BRCA2-203, BRCA2-207, BRCA2-208, BRCA2-209 and BRCA2-213), and four have the retained intron biotype (BRCA2-205, BRCA2-211, BRCA2-212 and BRCA2-215).

It’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.

See 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)