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. 2022 Jul 22;16:24. doi: 10.1186/s40246-022-00399-8

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Annotation of cap analysis of gene expression (CAGE) transcription start site (TSS) clusters. A. CAGE TSS clusters showed the classical distribution to “sharp” and “broad” classes. B. Distribution of distance from CAGE TSS clusters to TSSs annotated in Ensembl and RefSeq (most of our CAGE TSS clusters fall between ± 50 bp from annotated TSSs). C. Location of CAGE TSS clusters (ordered by priority) versus gene annotation. Additionally, putative alternative starts were verified using the coverage and exon–exon junction (RNA sequencing data) and annotated to corresponding genes. D. Number of CAGE TSS clusters annotated to different locations before (left panel) and after (right panel) elimination of low-abundance CAGE TSS clusters. E. Expression (median and interquartile range) of CAGE TSS clusters annotated to different locations. F. Overlap of CAGE TSS clusters from the FANTOM5 and refTSS projects with those in our study and 3764 first defined (probably muscle-specific) CAGE TSS clusters. G. Analysis of the coverage and exon–exon junctions for the first exon (RNA sequencing data; example for the NOS1 gene) allows the annotation, for the first time, of 290 CAGE TSS clusters belonging to 163 genes. CDS, coding sequence