Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence

Abstract

We identified 277 alternative splice forms in silkworm genes based on aligning expressed sequence tags with genomic sequences, using a transcript assembly program. A large fraction (74%) of these alternative splices are located in protein-coding regions and alter protein products, whereas only 26% are in untranslated regions. From the alternative splices located in protein-coding regions, some (43%) affect protein domains that bind various biological molecules. The vast majority of the detected alternative forms in this study appear to be novel, and potentially affect biologically meaningful control of function in silkworm genes. Our results indicate that alternative splicing in silkworm largely produces protein diversity and functional diversity, and is a widely used mechanism for regulating gene expression.

Environmental stresses induce the expression of putative glycine‐rich insect cuticular protein genes in adult Leptinotarsa decemlineata (Say)

“…The sequence analysis showed that Ld-GRP2v2 mRNA had two poly(A) adding sites leading to the formation of Ld-GRP2 and Ld-GRP2v2. The length of 3 ′ UTR is positively related to the stability of mRNA and thus to the amount of the gene product (Stamm et al ., 2005;Zha et al ., 2005). Such a positive correlation is found between the lengths of 3 ′ UTR of mKIAA cDNA and the relative expression in adult mouse brains (Okazaki et al ., 2005).…”

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

“…However, these are insufficient to provide a global view of alternative splicing and trans-splicing in the silkworm. Only 277 alternative splicing events were identified in a previous study based on the available EST sequences (Zha et al 2005). Recently, powerful high-throughput sequencing technology (RNA-seq) has been widely applied to transcriptome profiling and has been shown to be an effective and accurate method for the identification of novel transcripts and alternative splicing and trans-splicing events in many organisms, including D. melanogaster, C. elegans, rice, and human Zhang et al 2010;Daines et al 2011;Graveley et al 2011).…”

Common genomic structure for the Lepidoptera cadherin-like genes

“…The roles of introns in the 5′-UTR regions are diverse. A recent study has established that alternative splicing is a common phenomenon in the silkworm, and that the alternative translation initiation that occurs as a consequence of alternative splicing accounts for 25% of all the observed protein alterations (Zha et al, 2005). For this reason, alternative IRES have been sought in the three 5′-UTR gene sequences, albeit without success.…”