Description

The ENCODE4 long-read RNA-seq collection annotates trancripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This method reveals how promoter selection, splice pattern, and 3’ processing are deployed across human tissues.

Display Conventions

Transcript names include a triplet annotation that represents transcript start site, exon junction chain, and transcript end site. For example, if transcript A has the label [1,2,3] and transcript B is labeled [1,1,3], then those transcripts share start and end sites but have a different combination of exons.
GENCODE V29 and V40 were used as reference data; any transcript not present in either of these is colored blue.
Mouseover on transcripts shows their ENCODE gene ID and the tissue or cell line where it’s most highly expressed, and its TPM in that sample.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API.
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Methods

Data were retrieved from https://zenodo.org/records/15116042. The transcript gtf was converted to Bed format, and expression and CDS data added from the relevant files using a custom script.

Credits

Thanks to Fairlie Reese for providing data access and for helpful feedback.

References

Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y et al. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv. 2023 May 16;. PMID: 37292896; PMC: PMC10245583