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Reposted by APPRIS database

FlyBase @flybase.bsky.social · 20/08/2026

Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...

nature.com

Treat biological databases as infrastructure, not projects

Letter to the Editor

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APPRIS database @appris.bsky.social · 17/08/2026

At the same time, researchers should disregard MANE Select transcripts that are annotated as Minor:M.

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APPRIS database @appris.bsky.social · 17/08/2026

Transcripts that are annotated as Minor:M have little or no supporting evidence. Manual annotation concentrates on genes where APPRIS principal and MANE Select transcripts do not agree. Genes with MANE Select transcripts tagged as Alternative:M have at least two possible principal transcripts.

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APPRIS database @appris.bsky.social · 17/08/2026

We tag transcripts as Principal:M based on experimental information. Principal:M transcripts supersede all other principal transcripts. Manual annotation either replaces principal transcripts or fixes them. Transcripts annotated as Alternative:M have substantial supporting evidence.

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APPRIS database @appris.bsky.social · 17/08/2026

Somewhat behind schedule (technical reasons) we have uploaded principal isoforms for @gencodegenes.bsky.social G49 (human) and M38 (mouse) versions, corresponding to @ensembl.org 115. 239 human genes have at least one manual APPRIS annotation and 133 are annotated with Principal:M transcripts.

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APPRIS database @appris.bsky.social · 19/06/2026

You can still use APPRIS. Some browsers (some versions of Firefox, Vivaldi, Safari) will allow you to visit the "unsafe" site.

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APPRIS database @appris.bsky.social · 18/06/2026

APPRIS currently has an expired certificate. Unfortunately, the IT department is particularly short-staffed (for reasons beyond our control) and we cannot estimate when the problem will be fixed.

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Reposted by APPRIS database

bioRxiv Genomics @biorxiv-genomic.bsky.social · 29/05/2026

More than 100 dual coding regions have evidence for selection constraints in both reading frames www.biorxiv.org/content/10.64898/20…

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Reposted by APPRIS database

EMBL-EBI Training @training.ebi.embl.org · 12/05/2026

Explore genomic #StructuralVariants and #GenomeAlignments in our upcoming #webinar on the new Alignments viewer in the Ensembl Data Platform. It includes a live demo comparing human reference and alternative assemblies. Registration free but essential www.ebi.ac.uk/training/eve... @ensembl.org

Graphics image showing webinar at EMBL-EBI about The new Ensembl Alignments viewer tool for exploring genomic structural variation. The webinar will run on 21 May 2026 at 14:30 UK time. The speakers are Sarah Hunt and Thomas Walsh. Image credit: Rebecca Nicholl, EMBL-EBI

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APPRIS database @appris.bsky.social · 15/12/2025

Unless you use APPRIS principal isoforms, of course, where this can't happen.

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Reposted by APPRIS database

Michael Tress @michaeltress.bsky.social · 15/12/2025

... OK, I plucked that 17% out of thin air. With @appris.bsky.social principal isoforms as the main representative of each gene, 14.7% of Ensembl reference genes have signal peptides, as do 13.8% of the 14,888 genes we had detected in our proteomics experiments. Exported proteins are in the cell.

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Reposted by APPRIS database

Ensembl @ensembl.org · 02/12/2025

Attention developers and researchers working with Ensembl programmatically! Upcoming Ensembl API and data access changes are live on our blog. Read more about the new platform, new services, and migration timelines here: www.ensembl.info/2025/12/02/...

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APPRIS database @appris.bsky.social · 03/12/2025

Has APPRIS selected the wrong principal isoform? Send us an email via the adresses on the website and we will investigate.

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APPRIS database @appris.bsky.social · 15/10/2025

We have recalculated APPRIS principal isoforms for GENCODE v48 / Ensembl 114 human. GENCODE added loss of function genes to this version and we discovered that this caused the TRIFID scores to change, affecting some of the PRINCIPAL:2 -> PRINCIPAL:5 isoforms. Our fault, we asked for the change!

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Reposted by APPRIS database

Saccharomyces Genome Database @yeastgenome.bsky.social · 09/06/2025

FlyBase needs your help! Because of recent changes to government funding, the NIH grant that supported FlyBase has been "terminated." flybase.org

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APPRIS database @appris.bsky.social · 12/06/2025

We have updated APPRIS to @gencodegenes.bsky.social v48/ @ensembl.bsky.social v114. New principal isoforms for human, mouse, rat, cow and fruit fly ( @flybase.bsky.social ). Principal isoforms for a total of 73 human genes have been updated manually.

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APPRIS database @appris.bsky.social · 25/02/2025

One example is ACOT2 where APPRIS has the correct biological isoform. The MANE Select ACOT2 isoform is almost certainly produced by an inefficient translation initiation process, would lose the mitochondrial signal sequence and will end up in the wrong compartment. academic.oup.com/nar/article/...

academic.oup.com

Evidence for widespread translation of 5′ untranslated regions

Abstract. Ribosome profiling experiments support the translation of a range of novel human open reading frames. By contrast, most peptides from large-scale

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APPRIS database @appris.bsky.social · 24/02/2025

Many of the novel Principal:M isoforms correspond to MANE Select transcripts because we are preferentially annotating those 1,000+ genes where MANE and APPRIS do not agree. However, we do occasionally choose a 3rd isoform and most principal isoforms are unchanged after manual curation.

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APPRIS database @appris.bsky.social · 24/02/2025

Changes to Principal:M isoforms are based on known protein structure and funcional domains, and cross-species conservation, as well as RNA-Seq and proteomics evidence. Principal isoforms changed by manual curation are now targged as "Alternative:M".

Old and new principal isoforms in gene RAPH1

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APPRIS database @appris.bsky.social · 24/02/2025

For DCD, the Principal:2 isoform was the isoform with the intact Pfam domain. Unfortunately, the Pfam domain was based on erroneous transcript predictions in primates. Structure and function is known for the 110 aa protein (Principal:M), while the 121 aa protein (Alternative:M) is uninteresting.

The PDB structure (2YMK) for the hexamer of dermcidin (DCD)

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APPRIS database @appris.bsky.social · 24/02/2025

Users of APPRIS may have noticed that there is a new category of principal isoforms, Principal:M. These principal isoforms are exclusive to the human gene set and are principal isoforms that have been manually corrected. In GENCODE v47 there were 45 genes with Principal:M isoforms. Here is DCD:

APPRIS web page screenshot showing the new Principal:M annotation for the gene DCD

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APPRIS database @appris.bsky.social · 27/01/2025

Nice try, Luka. But even in a sham election with the real opposition candidates in jail, that is still some way short. of the 99.86% of supported ClinVar pathogenic mutations that map to APPRIS principal isoforms ...

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APPRIS database @appris.bsky.social · 22/01/2025

APPRIS has updated to GENCODE v47 and mouse M36. Danio rerio has also been updated to Ensembl 113. in this release 80.7% of human coding genes have a PRINCIPAL:1 isoform. Also, we have begun the manual curation of principal isoforms. More soon. @gencodegenes.bsky.social @ensembl.bsky.social

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APPRIS database @appris.bsky.social · 03/07/2024

APPRIS has new annotations for GENCODE human v46 and mouse M35. The human reference set now has 16,483 genes with Principal:P1 isoforms and mouse has 18,782 genes. Agreement with MANE Select transcripts in human (no MANE Select in mouse) has risen slightly to 17,661 genes. appris.bioinfo.cnio.es#/

appris.bioinfo.cnio.es

{APPRIS} - Annotating principal splice isoforms

Explore and download data on alternative splicing annotations and principal isoforms with the APPRIS Database, WebServer and WebServices.

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APPRIS database @appris.bsky.social · 26/03/2024

APPRIS has annotated principal and alternative isoforms and TRIFID functional isoform scores for Ensembl Bos taurus version e111: appris.bioinfo.cnio.es#/

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