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Fig. 2 | Cancer Cell International

Fig. 2

From: DMD transcripts in CRL-2061 rhabdomyosarcoma cells show high levels of intron retention by intron-specific PCR amplification

Fig. 2

Electropherograms of PCR-amplified products of parts of the DMD transcript. MK molecular size marker. a Exons 67–72. A single amplified product was obtained from muscle (M), whereas two products obtained from CRL-2061 cells (CRL). The upper band in the latter was the normally spliced product, whereas the smaller sized product lacked exon 71 completely. The exon structure of the two products is shown schematically on the right. Boxes and numbers in the boxes represent exons and exon numbers, respectively. Partial nucleotide sequences at the junctions between exons 70 and 72 are shown under the boxes. b Exons 58–66. A single amplified product was obtained from muscle (M), whereas three products were obtained from CRL-2061 cells (CRL). The major band was the normally spliced product. Sequencing showed that the smallest-sized bane was a non-specific product, whereas the largest band contained full-length intron 58 between exons 58 and 59. The exon structure of the two products is shown schematically on the right. Boxes and numbers in the boxes represent exons and exon numbers, respectively. Bar indicates intron 58. Partial nucleotide sequences at the junctions between exon 58 and intron 58, and between intron 58 and exon 59 are shown under the boxes. The third codon in intron 58 is a TGA stop codon (box). c Exons 36–41. A single amplified product was obtained from muscle (M), whereas four bands, two dense and 2 weak, were obtained from CRL-2061 cells (CRL). The upper dense band was the normally spliced product and the lower dense band lacked exon 38. Sequencing showed that the largest sized product was non-specific, whereas the other large product contained exon 41e between exons 40 and 41. The exon structure of the two products is shown schematically on the right. Boxes and numbers in the boxes represent exons and exon numbers, respectively. Bar indicates intron 40. Partial nucleotide sequences under the boxes show the junctions between exons 38 and 39, exon 40 and intron 40, and intron 40 and exon 41. d Exons 70–79. A single amplified product was obtained from muscle (M), whereas several bands were obtained from CRL-2061 cells (CRL). The CRL sample lacked the band observed in M, but contained a single smaller, but broader band as its major product. Subcloning and sequencing showed that the larger sized products were non-specific. The smallest band represented an amplified product with deletions of exons 71–74 and 78. The major broad bands consisted of five products. Six clones showed deletion of exon 78, four showed deletion of exon 71, and three showed deletion of both. One clone showed deletion of exon 73 alone and one showed deletions of exons 73 and 78. The exon structures of these products are shown schematically on the right, with numbers to the left of these structures indicating the number of sequenced clones. Boxes and numbers in the boxes represent exons and exon numbers, respectively

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