What’s coming in Ensembl release 88

Ensembl 88 is scheduled for release in March 2017. Read on for more information:


Ensembl 88 is scheduled for release in March 2017. Highlights include:

Updated assemblies, gene sets and annotations:

  • Human: the human gene set will be updated to Ensembl-Havana GENCODE release 26 and will include all CCDS genes. In addition, there will be updates to cDNA alignments and RefSeq mappings.
  • Mouse: the mouse Ensembl-Havana gene set will be updated and will include all CCDS genes.There will also be updates to cDNA alignments and RefSeq mappings.
  • Rat: the rat gene set will be updated to include the latest manual annotations from Havana.
  • Pika: the name of the pika assembly will be altered to OchPri2.0-Ens to reflect differences between the Ensembl-annotated version and OchPri2.0.

New and updated REST endpoints:

  • Variation: a new REST endpoint will be developed to return phenotype associations overlapping a defined region.
  • Regulation: data from GTEx v6 will be available from the eQTL rest endpoint.
  • Comparative genomics: new family and phylogenetic tree REST endpoints will be available.

Masthead redesign:

  • The masthead of most Ensembl browser pages will change to indicate whether a species’ genome was annotated in-house or by an external project.

New variation and phenotype data:

  • dbSNP: dbSNP data will be updated to the latest version (149) for human, rat, platypus and opossum.
  • Structural variation: new data will be imported from DGVa, and existing data will be updated, for human, pig and sheep.
  • COSMIC: COSMIC data will be updated to version 79 for human.
  • HapMap: a VCF file containing HapMap genotype data (by population) will be available on the Ensembl site.
  • PolyPhen: new pathogenicity predictions will be available for human, from PolyPhen 2.2.2r405c.

New regulation data:

  • Microarray probes will be remapped for 17 species in total, including those with updated assemblies.The full list of species is as follows: Bos taurus, Caenorhabditis elegans, Canis familiaris, Ciona intestinalis, Danio rerio, Drosophila melanogaster, Gallus gallus, Homo sapiens, Macaca mulatta, Mus musculus, Ornithorhynchus anatinus, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Saccharomyces cerevisiae, Sus scrofa, Xenopus tropicalis.
  • Microarray probes will also be mapped independently to mouse strain genomic sequence (following the import of sequence data for 16 mouse strains into Ensembl version 86).
  • The Funcgen Perl API will be updated to enable retrieval of probe sequences and probe-to-transcript mappings.

New comparative genomics analyses:

  • Protein families: HMM-based protein family predictions will be updated for all species. For human, transcript isoforms encoded by non-reference haplotype sequence will also be included.
  • Phylogenetic trees: Protein and ncRNA trees will be updated for all species, followed by updates to homology predictions.


  • lincRNA models will be included for mouse lemur.
  • BioMart Genes, Variation, Regulation, Vega and Mouse Genes databases will be updated; BioMart Genes, Variation, Regulation and Vega databases will be updated on the Ensembl GRCh37 site.

For more details on the intentions declared, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to appear in the release.