Genomic Data Analyst About the Team The HAVANA team, part of Ensembl, produces reference-quality gene annotation for the human and mouse genomes as a core contributor to the GENCODE project, a Global Core Biodata Resource...

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

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

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
🧬 💻

GENCODE 2025: reference gene annotation for human and mouse Abstract. GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as n

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