Fetching ENSEMBL Data in Jalview
Jalview Version 2.10 (October 2016) introduced support to retrieve annotated transcripts, peptides and genomic contigs from ENSEMBL.

Two types of ENSEMBL source are provided. ENSEMBL queries the main ENSEMBL warehouse containing data for higher eukaryotes, and EnsemblGenomes, which queries Ensembl Pathogens, and other warehouses.

General Use
If you have a set of Ensembl gene or transcript IDs, then you can retrieve them via the sequence fetcher dialog opened after selecting the most appropriate source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's Ensembl client has a couple of additional capabilities:

Retrieving aligned transcripts for a genomic ID

If a single genomic identifier is entered in the Ensembl fetcher, Jalview will return all transcripts and products for the locus, and display them in a split view - complete with sequence variant annotation.

Retrieving orthologs for a gene ID

If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl genomic identifiers for a predefined set of taxa (Mouse, Rat, Human, Yeast in Jalview 2.10).

Ensembl Sequence Features
Jalview 2.10 includes support for the visualisation and transfer genomic and transcriptomic sequence features onto protein product sequences. Retrieval of a genomic locus results in a set of transcripts that are annotated with nucleotide variant information and exonic regions. By default, intronic regions will be hidden.

Variant information on Protein Products
Jalview can translate genomic variant annotation into protein sequence variant codes for variants intersecting coding regions of a gene. To see this in action, use the Calculate→Show cross-references menu to view protein product sequences for the currently displayed (or selected) sequences. The same menu allows you to recover Ensembl exon, transcript and variant information when viewing UniProt sequences.

Viewing more information about variant annotation
Variants are highlighted as red sequence features on the protein sequence, with each one reporting all protein sequence variants observed at that position as a result of the genomic variants. Right-clicking a variant allows you to open the Ensembl Variants web page for each variant, via the Link submenu.

Work in Progress !
In the next few releases, we hope to improve and extend Jalview's support for working with Ensembl. If you have any problems, questions or suggestions then please get in contact with us via the Jalview discussion list.