Demo: Investigating genes with the Feature explorer app

The Feature explorer allows you to look at genomic feature details, such as genes, transcripts and variants. Follow this guide to learn how to use the app. NB: Some screenshots may still display the Feature explorer under its former app name, “Entity viewer.”

20 steps

Ensembl

Navigate to [beta.ensembl.org](https://beta.ensembl.org/)and open the [[Feature explorer]].

If this is your first time using the [[Feature Explorer]], it will open the search page. If you have multiple assemblies in your species list, select your assembly of interest first. We want to search for the gene in [[Human]].

Enter [[BRCA2]] into the text box and click [[Go]].

Click [[BRCA2]].

Select the [[Feature explorer]] from the pop-up menu.

On the Navigation bar on top, you can find the name and Ensembl stable ID of your gene of interest, its biotype, strandedness and exact coordinates.

*BRCA2* has 15 transcripts.

The [[Right-hand panel]] provides additional information about the gene. In the [[Overview]], you can find the gene name, description and its synonyms.

Click [[Europe PMC]] to find any publications associated with the gene.

[[External references]] lists links to associated entries in other databases, including: - GeneCards - Mendelian Inheritance in Men (MIM) - NCBI - UniProtKB

You can also find associated entries in external databases for each of the gene transcripts.

The [[Transcript]] tab lists all gene transcripts, including their IDs and structure. The top transcript is the representative transcript of the gene. In this case, it's the MANE Select transcript.

Click on the transcript structure to open its summary panel, which includes information about the transcript biotype, coordinates, and length.

Click [[More information]] to find relevant links to external resources, such as RefSeq and CCDS.

Click [[Download]] to export the gene sequence or specific transcript sequence.

The [[Gene function]] tab lists functional information for the gene, including: - Protein information (if applicable) - Variants found within the gene - Associated phenotypes - Gene expression across different tissues and cell-lines - Gene ontology - Biochemical pathways Greyed out are not currently available.

If the gene is protein-coding, the [[Proteins]] panel will list functional information, including protein domains and relevant links to protein-specific resources.

Click [[Gene relationships]] to view comparative genomics information related to the gene.

The [[Homology]] table lists gene homologues in other species, alignment statistics and the Ensembl gene ID of the homologue.

You can sort tables by clicking on the header you want to sort the table by.

If you are unsure what information a header is showing, use your mouse to hover over the blue question mark [[?]] for a description.

Demo: Investigating genes with the Feature explorer app

20 steps