What’s coming in Ensembl 92 and Ensembl Genomes 39

Both Ensembl release 92 and Ensembl Genomes release 39 are scheduled for April 2018.

Included are new genomes and genebuilds (Goat, Zebrafish, Marmoset, Stalk-eyed fly and Waterflea) and a command line version of our new Linkage Disequilibrium tool.

Here are the highlights you can look forward to:

Ensembl 92

New assemblies, gene sets and annotations

  • First annotation of the goat genome based on the ARS1 assembly
  • New genebuild for the latest zebrafish assembly GRCz11
  • New genebuild for the latest marmoset assembly ASM275486v1
  • Updated Ensembl-Havana human GENCODE gene set (release 28), including all CCDS genes and GRCH38.p12 patches
  • Import of the lastest human CCDS gene set (December 2017)
  • Annotation of lincRNAs for 13 primate species
  • Updated Ensembl-Havana mouse GENCODE gene set, including all CCDS genes
  • New/updated cDNA alignments for Zebrafish, Goat, Human and Mouse
  • Import of RefSeq gene sets for Zebrafish and Goat
  • New RNA-seq databases for Zebrafish, Goat and Marmoset

New tools

  • New command line tool for Linkage Disequilibrium calculations
  • Data Slicer and VCF to PED converter tool added to website

Other updates and highlights

  • New goat variation database (dbSNP build 143)
  • Update to our human variation databases with:
    • HGMD version 2017.4
    • COSMIC version 83
    • DGVa structural variants
    • Phenotypes from NHGRI-EBI GWAS, OMIM, ClinVar, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet
  • Update to animal variation databases with:
    • dbSNP build 151 for Horse and Dog
    • Phenotype data for Rat, Zebrafish and Mouse from the relevant databases
    • Genotype data for Sheep from the Sheep Genome Project – Run 1
    • Genotype data for Goat from the NextGen project
  • New/updated microarray probe mappings for Marmoset, Cat, Goat, Human, Mouse, Mouse 129S1/SvImJ, Mouse A/J, Mouse AKR/J, Mouse BALB/cJ, Mouse C3H/HeJ, Mouse C57BL/6NJ, Mouse CAST/EiJ, Mouse CBA/J, Mouse DBA/2J, Mouse FVB/NJ, Mouse LP/J, Mouse NOD/ShiLtJ, Mouse NZO/HlLtJ, Mouse PWK/PhJ, Mouse WSB/EiJ, Algerian mouse, C. elegans, Zebrafish, Ma’s night monkey, Capucin, Sooty mangabey, Gorilla, Crab-eating macaque, Pig-tailed macaque, Mouse lemur, Bonobo, Chimpanzee, Olive baboon, Black snub-nosed monkey, Golden snub-nosed monkey, Bolivian squirrel monkey, Upper Galilee mountains blind mole rat, Guinea pig
  • Updated comparative genomics analyses for all species


Ensembl Genomes 39


  • New genomes: Stalk-eyed fly (Teleopsis dalmanni) and Waterflea (Daphnia magna)
  • Updated protein features and BioMarts


  • Updated genomes: Ashbya gossypii, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus fumigatus A1163, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Aspergillus terreus, Blumeria graminis, Cryptococcus neoformans, Dothistroma septosporum, Gaeumannomyces graminis, Neosartorya fischeri, Pyrenophora tritici-repentis Pt-1C-BF
  • Updated protein features, BioMarts and comparative genomics analyses


  • Updated protein features and BioMarts


  • Updated names for Oryza sativa genes and homologues
  • Updated protein features and BioMarts


For more details on the declared intentions, please visit the Ensembl admin site (http://admin.ensembl.org/Changelog/Summary) and/or the Ensembl Genomes Release 39 Intentions (http://ensemblgenomes.org/info/release/39). Please note that these are intentions and are not guaranteed to make it into the releases.