The HAVANA team at EMBL-EBI has multiple open positions to support the GENCODE and PARADIGM projects. We're recruiting gene annotators (bit.ly/4qG28g5), an annotation project lead (bit.ly/4qv05v6), and bioinformaticians (bit.ly/4qevYIY). Please apply via the links. We’d love to hear from you!
New Webinar: This Wednesday, join speakers Jorge Barista da Rocha, PhD, and Jane Loveland, PhD, as they explore the @ensembl.org genome browser and provide practical skills beyond the traditional reference genome. Register here: bit.ly/432kP4b #ASHG #HumanGenetics @gencodegenes.bsky.social
These new transcripts all have a CDS that is based upon the MANE_Select transcript for the gene, but have unique splicing either within their UTRs or between internal coding exons. Each of these unique splice sites has passed our stringent QC filters to ensure their accuracy.
This release sees the addition of >121000 new full-length human protein-coding transcripts based on long-read RNA-seq data that have been integrated into GENCODE using the TAGENE annotation pipeline.
The latest human GENCODE releases for Human (49) and Mouse (M38), have just been released. They're available via gencodegenes.org and visible in @ensembl genome browser as part of Ensembl 115 ensembl.org
The GENCODE Primary dataset is now displayed by default for human and mouse in @ensembl.bsky.social. More information about how this set is created is available here: www.gencodegenes.org/pages/gencod... and details on how to change the default display settings here: www.ensembl.info/2025/04/29/d...
The latest human GENCODE releases for Human (48) and Mouse (M37), have just been released. They're available via gencodegenes.org and visible in @ensembl.bsky.social genome browser as part of Ensembl 114 ensembl.org
Can also confirm that intron in 3' UTR does not exclude from MANE consideration - see e.g. BSN (www.ensembl.org/Homo_sapiens...) but for such cases we require evidence of NMD avoidance/functional product in the event of NMD. 2/2
@nickywhiffin.bsky.social - HAVANA group here - sorry no reference comes immediately to mind. But we'll do some digging as its a good question! As @iansudbery.bsky.social says, assumption has been that introns in UTR are no different to introns in CDS. 1/2
Do you want to go further with your proteomics? Looking for something new in cancer?
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
We're pleased to share our GENCODE 2025 NAR database paper: tinyurl.com/3etnfw4j Thanks to all our collaborators, friends and users. This is now the main citation for our resource, and hopefully also a good explanation of how and why we do what we do.
The GENCODE manual annotation team, part of the Ensembl group at the EMBL-EBI. See our website for our latest gene annotations: www.gencodegenes.org
