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In the present work, we selected five main splicing patterns for further study (see Materials and Methods for details).
Moreover, in order to investigate the relationships between exons' splicing frequency and genes' splicing pattern, we have selected five main splicing patterns (cassette exons, mutually exclusively exons, retained intron, alternative acceptor site and alternative donor site) of alternatively spliced human and orthologous mouse genes from the ASTRA database (http://alterna.cbrc.jp/index.php).
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Saudemont, B. et al. The fitness cost of mis-splicing is the main determinant of alternative splicing patterns.
Interestingly, three of the main milk proteins showed structural differences, with allelic variation and some flexibility in splicing patterns of primary transcripts arising from the corresponding genes.
Alternative splicings can occur together, causing complicated splicing patterns.
On the other hand, the main focus of our study was the detection of changes in splicing patterns associated with cis-sQTL, and it may explain the discrepancy between our results.
Heterogeneous splicing patterns in response to knockdown of conserved splicing factors.
Changes in splicing patterns have been described in disease states.
Among 5 basic splicing patterns, alternative 5′ and 3′ splicing, and intron retention were detected.
Detailed functional analysis of the top candidate splicing factor, Ptbp1, revealed that it is a critical barrier for the acquisition of cardiomyocyte-specific splicing patterns in fibroblasts.
Splicing patterns of SRSF1 splicing targets were altered in a dose dependent manner (Supplementary Fig. 7D) and without any effect on SRSF1 protein levels (Supplementary Fig. 7E).
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