A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max

Additional file 1:

Alignment of Tgm1 subterminal direct repeats. The repeated sequences have been organized in this figure starting from the 3'end of the transposon right border. Each direct repeat was read from the 3'-end to the 5'-end. A consensus sequence motif was deduced and is shown boxed.

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Additional file 2:

Alignment of Tgm-Express1 subterminal direct repeats. The repeated sequences have been organized in this figure starting from the 3'end of the transposon right border. Each sequence repeat was read from the 3'-end to the 5'-end. A consensus sequence motif was deduced and is shown boxed.

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Additional file 3:

Alignment of Tgmw4m subterminal direct repeats. The repeated sequences have been organized in this figure starting from the 3'end of the transposon right border. Each repeat has been read from the 3'-end to the 5'-end. A consensus sequence motif was deduced and is shown boxed.

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Additional file 4:

Tgmt* and En-1 amino acid sequence alignment. The transposase amino acid sequences predicted with Softberry- FGeneSH and aligned with the MultAlin program (Corpet, 1988) have 258 aa identities (33%) in the 780 aa at the 5'-end. These regions of both transposases contain the tnp2 domains that map at the same location (highlighted in yellow). Beyond the 780 aa stretch the two proteins diverge considerably with only 141 aa identities (10%), two different conserved domains TNP1 in Tgmt* (highlighted in green) and ptta in En-1 (highlighted in blue) that map in different locations, and many gaps that reflect their differences in length.

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Additional file 5:

Alignment of cDNA sequences of clones 43–53 to Tgmt* genomic sequence. The sequences from RT-PCR derived cDNA clones (43, 44, 45, 47 and 53) were aligned to Tgmt* genomic sequence with MultAlin program (Corpet, 1988) to reveal the exon-intron junctions and the canonical GT-AG splice boundaries. The exon sequences appear in red and blue depending on the number of clones bearing the exon.

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Additional file 6:

Alignment of Mosaic-cDNA sequences to Tgmt* genomic sequence. The sequences from RT-PCR derived cDNA clones amplified with primers 1 and 7 (Figure 8) (No.:37, 38, 39, 42 and 56) were aligned to Tgmt* genomic sequence with MultAlin program (Corpet, 1988). It revealed the splicing site (marked with an asterisk) that does not conform to the canonical GT-AG intron-exon splice boundaries (GA, following the 346 bp of Exon-1 and AT, prior to the 23 bp of Intron-10). The 23 bp of Intron-10 have been highlighted in yellow. The exon sequences appear in red and blue depending on the number of clones bearing the exon.

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Additional file 7:

Tgmt* Gene-1 precursor transcripts sequence. The sequence of a precursor transcript (7,554 bp) expressed by Gene-1 was composed with all 24 exon sequences present in the cDNA clones analyzed (Figure 8 and see Additional file 5: Alignment of cDNA sequences of clones 43–53 to Tgmt* genomic sequence).

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Additional file 8:

Tgmt* Mosaic-transcript sequence. The sequence of the largest (2,572 bp) cDNA clone, No. 37, amplified with primers -1 and -7 contains all 14 exons of the Gene-1 3'-end and the 346 bp (1/9) portion of Exon-1. Purple letters represent Exon-1 bases, highlighted yellow are Intron-10 bases and orange letters are Exons 11–24 bases. Highlighted pink and green are primer 1 and 7 sequences respectively.

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Additional file 9:

Tgmt* genomic sequence (20,544 bp). The reverse complement of Tgmt* genomic sequence (20,544 bp) is shown. Exons are in orange letters. Purple letters are the portion of Exon-1 that splices with Intron-10 to form the mosaic-transcripts. The 23 bases of Intron-10 that are part of Mosaic transcripts are shown in yellow. Also in yellow are the bases of Intron-19 and -20 that are not spliced out in cDNA clone 47. The direct and reverse subterminal repeats are highlighted in yellow and green respectively. The 13 bp CACTA terminal inverted repeats are highlighted in blue. Sequences of Primers 1, 3 and 5 are highlighted in pink and those of primers 2, 4, 6 and 7 are highlighted in green.

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Additional file 10:

Alignment of sequences of 3 contigs from 71B1 BAC clone in the 7× draft sequence assembly (JGI).

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