by ·Comments Off on Ensembl 116 and Ensembl Genomes 63 have been released!

Ensembl 116 and Ensembl Genomes 63 are here! Highlights include new pig & cattle assemblies, 26 oat genomes, updated alignments and new Ensembl VEP plugins.

Special Notice – Ensembl Transition

Ensembl 116 and Ensembl Genomes 63 are the final releases on the current Ensembl site and platforms. 

All new data from this point will only be available through the new Ensembl site. In the next few months, the ensembl.org site will bring you to the site hosted on beta.ensembl.org. 

You will continue to have access to current Ensembl versions via Ensembl Archives, with the latest archives having extended tool support. The Ensembl USEast and Asia mirrors of the current main site will be retired over the transition period this summer.

Continue reading

by ·Comments Off on New visualisation of genomic variants in the context of genomic alignments 

We have developed a novel visualisation to enable the investigation of structural variants (SVs) in the context of functional elements, pairwise alignments and segmental duplications. Developed in collaboration with the Human Genomic Structural Variation Consortium (HGSVC), with genomic alignment data provided by the Human Pangenome Reference Consortium (HPRC), the new Alignments viewer makes it easier to explore haplotype-specific variation.

Continue reading

by ·Comments Off on Expanded transcript set available in the latest human GRCh38 partial release on the new Ensembl site

In the current Ensembl release (Ensembl 115), the GRCh38 human Ensembl/GENCODE reference annotation was updated to include approximately 121,000 new protein-coding transcripts. This expanded set is based on long-read RNA-seq data processed by the manually supervised automated pipeline TAGENE, which is presented as the source in both browser and files.

The latest partial release for GRCh38 on the new Ensembl (partial release 2026-01-26) includes this new geneset. Some genes and genomic features in this set have several hundred transcripts, such as ZBTB20 (ENSG00000181722) which has 360 transcripts.

Continue reading

by ·Comments Off on What’s coming in Ensembl release 116 / Ensembl Genomes 63?

Ensembl 116 and Ensembl Genomes 63 are expected in April 2026. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the release. 

Special Notice

Ensembl 116 and Ensembl Genomes 63 will be the final releases on the current Ensembl site and platforms.

From the summer of 2026, all new data will only be available through the new Ensembl site. The site, ensembl.org, will redirect to the site currently hosted on beta.ensembl.org. 

Continue reading

by ·Comments Off on Large plant protein clusters accessible via gene families view

In Ensembl release 116 (Ensembl Genomes 63), two large protein clusters in Plants have incomplete or missing homology data due to production constraints. To address this, we set about making these clusters accessible via the gene families view. Please read on if you’d like to know more about these clusters, both associated with the Panther subfamily ‘PTHR11439_SF127’.

Continue reading

by ·Comments Off on Service notice – server issues affecting the Ensembl mirror sites

We are working on server issues affecting the Ensembl mirror sites. A workaround is to use the Ensembl main site via the following link – https://ensembl.org?redirect=no or a recent archive such as https://may2025.archive.ensembl.org/. You can also try the new Ensembl site at https://beta.ensembl.org and let us know about the features you would like to see there.

by ·Comments Off on Updates to programmatic access to Ensembl and transitioning to the new Ensembl Platform

Ensembl is currently undergoing a major transformation to provide faster, more flexible, and more scalable access to genome data. As outlined in our Ensembl 2026 publication, work on the new platform is well underway and can already be explored at beta.ensembl.org. In this blog, we are sharing important information about upcoming changes to Ensembl data access, including timelines, new services, and what you need to do to prepare.

Continue reading