Ensembl 87 has been released!

What’s New in e87:

Updated assemblies, gene sets and annotations

In Ensembl 87, there are a number of updates to the assemblies and gene sets for several species:

  • Human: updated cDNA alignments and RefSeq import
  • Mouse: updated gene set and assembly, see below
  • Zebrafish: updated gene set
  • Chicken: updated gene set

Updated gene models for mouse olfactory receptors

e87 includes an updated Ensembl-Havana mouse gene set, a merge of complete Ensembl gene models and the latest Havana gene annotation. All CCDS genes are included in this gene set.

This latest Havana gene annotation includes improved gene models for the mouse olfactory receptors. Over 2Mbp of additional sequence has been added to the mouse olfactory genes to create several hundred multi-exonic models. These new models are based on RNA-seq data from Ibarra-Soria X et. al.

The mouse assembly has been updated to GRCm38.p5. The patches for GRCm38.p5 were annotated using a combination of manual annotation, annotation projected from the primary assembly and annotation derived from cDNA and protein alignment evidence.

New lincRNA data

New regulation summary activity table

Due to the high number of epigenomes now available in the Human Regulatory Build, we can no longer show them all by default on the Regulation Summary image, in the Regulation Tab. We have therefore added a table listing the cell types by their regulatory feature activity.

Regulation Cell Type Activity table

Other News

  • DGVa structural variant study updates for Human, Cow and Macaque
  • dbSNP updates for Sheep
  • Cosmic version 78 imported for human
  • Phenotype data updates for several species

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: Wednesday 14th December, 4pm GMT. Register here.

3 thoughts on “Ensembl 87 has been released!

  1. Dear ENSEMBL curator(s),

    Just a brief message to mention that, in release 87, GTF files for mouse strains are named identical to release 86. Two examples:

    Mus_musculus_wsbeij.WSB_EiJ_v1.86.gtf.gz
    Mus_musculus_pwkphj.PWK_PhJ_v1.86.gtf.gz

    We assume that the reason is these files did not changed. However, we are wondering if it is a feature or a bug.

    –We are developers of Breaking-Cas, a CRISPR/Cas tool that uses these files (downloaded) for showing annotations in minibrowsers–

    Many thanks!

    Juan Carlos

    • Dear Juan,

      You are exactly right- the file names did not change (i.e still contain ‘.86.’) because the files have not changed between Ensembl releases 86 and 87. This is a special case with the mouse strains. The GTF files normally correlate with the release number for the other species in Ensembl, even if the gene model has not changed between releases.

      I hope this answers your question, but please do get back in touch if you have any further questions.

      Best wishes

      Ben
      Ensembl Helpdesk