Ensembl 86 has been released!

What’s New in e86:

Mouse strain genomes

In Ensembl 86, you will now be able to view the annotated genome assemblies, variation data and comparative analyses of 16 different mouse strains, produced by the Mouse Genomes Project. While the GRCm38 assembly (produced from Mus musculus strain C57BL/6J) remains the reference assembly, variants and comparative analyses for the other strains can be viewed through the Gene tab and the Location tab. You can find the gene trees and orthologue/paralogue predictions for the mouse strains through the Strains option in the menu in the Gene tab. The mouse strain gene tree depicts the evolutionary history of genes (left) and protein alignment (right) for the individual mouse strains and rat. mouse strain treemouse strain orthologues You can find the variants between these mouse strains through the Strain table option in the menu in the Location tab. The strain table displays the alleles identified at variant positions across the 16 mouse strains. strain variant table

Updated assemblies, gene sets and annotations

In Ensembl 86, there will also be a number of updates to the assemblies and gene sets for a number of different species:

  • Human: updated cDNA alignments and RefSeq import
  • Mouse: updated cDNA alignments and RefSeq import
  • Zebrafish: updated gene set and RefSeq import
  • Chicken: updated to the Galgal_5.0 assembly
  • Mouse lemur: updated to the Mmur_2.0 assembly
  • Macaque:  updated to the Mmul_8.0.1 assembly

New lincRNA data

New Mobile Site Views

As of release 86, you can now view transcripts on the mobile version of Ensembl. You can also view exon sequence, cDNA sequence and protein sequence by clicking on the lefthand arrow.

mobile site- transcript[1]mobile site- transcript[2]

The gene sequence is also now available to view on mobile devices. Just go to any gene page and click on the left hand arrow and then choose sequence.


Other News

  • Variation and phenotype databases updated
  • You can now select ‘Manhattan plot’ as an option when configuring bigWig files

A complete list of the changes can be found on the Ensembl website

Find out more about the new release and ask the team questions, in our free webinar: Tuesday 11th October, 4pm BST. Register here.

12 thoughts on “Ensembl 86 has been released!

  1. Well done! Is there any way to download the DNA and gene sets of the different mouse strains from Ensembl?

    • Hi Trevor,

      Thanks, we hope you find the new data in Ensembl 86 useful. The data you need should be available for download via the FTP. For example, the following link will take you to the GFF3 files for all Ensembl 86 species, including the mouse strains:


      Please let me know if you have any further questions.

      Best wishes


      • Hi Ben,

        Thank you! That helps immensely. If I may, I have another stupid question: in addition to the “mus_musculus” folder, there is a “mus_musculus_c57bl6nj” folder. If C57BL/6J is already the reference, what is this other folder? It seems like its file sizes are different than the reference as well.

        Thanks again,

          • Thank you Ben! Last question (and I promise I’ll stop bothering you): are the whole-genome alignments between strains by chance available? It’d just be nice to take locally called SNPs from one mouse strain, and to have them translated into another strain’s coordinates. I was poking around Compara’s resources but it doesn’t look like it has the new strains.

          • No problem, Trevor. Unfortunately, the whole genome alignments are not currently available, but this is something that we are working on. We hope to include these alignments in an Ensembl release in the near future.

            Best wishes

            Ensembl Helpdesk

  2. Hello,
    I guess I discovered a bug. If I want to export data of a gene in EMBL format, it is generating fasta as output.

    On grCh37 everything works normal.

    fin swimmer

    • Hi Fin,

      Thank you for reporting this problem. We are aware of this bug in the data export function, and are working to resolve it as quickly as possible.

      Sorry for any inconvenience caused.

      Best wishes

      Ensembl Helpdesk

      • Hi Fin,

        We believe this bug has now been fixed. Please let us know if you are still experiencing the same problems.

        Best wishes

        Ensembl Helpdesk

  3. Hello dears Ensembl;

    I have Problem in BLAST function in horse Genome.
    it is not working !!!!

    please help !!

    • Dear Saria,

      We’re sorry to hear you are having problems with the BLAST tool. Could you please send a message to helpdesk@ensembl.org describing your BLAST query and any error messages that you encounter. It will help us diagnose the problem and resolve it as quickly as possible.

      Best wishes

      Ensembl Helpdesk