DoChaP: The Domain Change Presenter

Abstract

Alternative RNA splicing results in multiple transcripts of the same gene, possibly encoding for different protein isoforms with different protein domains and functionalities. Whereas it is possible to manually determine the effect of a specific alternative splicing event on the domain composition of a particular encoded protein, the process requires the tedious integration of several data sources; it is therefore error prone and its implementation is not feasible for genome-wide characterization of domains affected by differential splicing. To fulfill the need for an automated solution, we developed the Domain Change Presenter (DoChaP), a web server for the visualization of the exon–domain association. DoChaP visualizes all transcripts of a given gene, the domains of the proteins that they encode, and the exons encoding each domain. The visualization enables a comparison between the transcripts and between the protein isoforms they encode for. The organization and visual presentation of the information makes the structural effect of each alternative splicing event on the protein structure easily identified. To enable a study of the conservation of the exon structure, alternative splicing, and the effect of alternative splicing on protein domains, DoChaP also facilitates an inter-species comparison of domain–exon associations. DoChaP thus provides a unique and easy-to-use visualization of the exon–domain association and its conservation between transcripts and orthologous genes and will facilitate the study of the functional effects of alternative splicing in health and disease.

Congenital myopathy as a new phenotype caused by two undescribed variants in ASCC1 gene

“…Both variants affect RNA‐ligase like domain. It was previously shown ASCC1 could work as a transcriptional coactivator and DNA repair protein, RNA‐ligase like domain plays a critical role in the protein's function (Gal‐Oz et al, 2021; Meunier et al, 2021). We suggested that p.Glu2_Met114del protein with a remaining domain could possibly be functional.…”

“…We suggested that Δ E × 2,3a transcript could produce a new truncated protein p.Glu2_Met114del. According to the domain structure of ASCC1 protein, the deletion led to shortened KH‐domain, but not the RNA‐ligase like domain (Figure 2) (Gal‐Oz et al, 2021).…”