What’s coming in Ensembl release 104 / Ensembl Genomes 51?

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Ensembl 104 and Ensembl Genomes 51 are expected in April. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the final release.

Human

  • Update of the human gene set to GENCODE 38
  • MANE Select will be used as the canonical transcripts for protein coding genes where available
  • The Ensembl Canonical selection algorithm will be updated for protein coding genes without MANE Select transcripts and all other gene biotypes

GRCh37

  • Updated regulatory build
  • Updated variation data including the latest data from dbSNP build 154, ClinVar and COSMIC

Mouse

  • Update of mouse genes to GENCODE M27

New genomes

Plants

  • Persian walnut (Juglans regia)
  • Sesame (Sesamum indicum)
  • TRITEX barley (Hordeum vulgare) assembly
  • Diploid potato (Solanum tuberosum) cultivar rh8903916

New Assemblies and/or Annotation

Vertebrates

New assemblies:

  • Anole lizard (Anolis carolinensis)
  • Turkey (Meleagris gallopavo)
  • Flycatcher (Ficedula albicollis)
  • Turbot (Scophthalmus maximus)

New species with variation:

  • Nile tilapia (Oreochromis niloticus)
  • Mink (Neovison vison)
  • Great tit (Parus major)
  • Rabbit (Oryctolagus cuniculus)

Plants

New assemblies and annotation:

  • Maize (Zea mays)
  • Banana (Musa acuminata)

Metazoa

  • Updated protein features for all species using InterProScan with version 83 of InterPro
  • Updates derived from the VectorBase release 49 of VEuPathDB incorporating community based annotations for 43 species, plus recalculated variant effects for all species with variation data:
    • Aedes aegypti (LVP_AGWG)
    • Aedes albopictus
    • Anopheles albimanus
    • Anopheles arabiensis
    • Anopheles atroparvus
    • Anopheles christyi
    • Anopheles coluzzii
    • Anopheles coluzzii (Ngousso)
    • Anopheles culicifacies
    • Anopheles darlingi
    • Anopheles dirus
    • Anopheles epiroticus
    • Anopheles farauti
    • Anopheles funestus
    • Anopheles gambiae
    • Anopheles maculatus
    • Anopheles melas
    • Anopheles merus
    • Anopheles minimus
    • Anopheles quadriannulatus
    • Anopheles sinensis (China)
    • Anopheles sinensis
    • Anopheles stephensi
    • Anopheles stephensi (Indian)
    • Biomphalaria glabrata
    • Cimex lectularius
    • Culex quinquefasciatus
    • Glossina austeni
    • Glossina brevipalpis
    • Glossina fuscipes
    • Glossina morsitans
    • Glossina pallidipes
    • Glossina palpalis
    • Ixodes scapularis
    • Ixodes scapularis (ISE6)
    • Leptotrombidium deliense
    • Lutzomyia longipalpis
    • Musca domestica
    • Pediculus humanus
    • Phlebotomus papatasi
    • Rhodnius prolixus
    • Sarcoptes scabiei
    • Stomoxys calcitrans

Other Updates and Highlights

  • Gene names derived from BAC clones will be replaced by Ensembl stable IDs for human, mouse, rat and zebrafish. More details here.
  • The VEP REST response has been updated for SpliceAI and DisGeNET to improve clarity. This is not backwards compatible
  • Physcomitrella patens will be renamed Physcomitrium patens
  • Updated cross-references for Arabidopsis thaliana
  • Retirement of Ensembl 84 archive site