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