Figure 7

Signatures of true 3' flank transduction. The source locus in the main genome consists of an L1 element with TSDs (blue arrows) which moves to the target or current locus along with a part of the 3' flank (brown bold line) forming new TSDs (black arrows). In contrast, no flank transduction takes place in the current locus in the comparative genome. As indicated, the query consists of one copy of the original TSD (blue line), the transduced flank (brown bold line) and the second poly A tail (dotted brown line). When blasted on the main genome, at least two hits are obtained - one complete match at the current locus and one almost complete match (barring the poly A tail) at the source locus. In the comparative genome, no match is found at the orthologous current locus (since no transposition event has taken place for lack of L1 element at the source locus as shown here, or otherwise). The match at the source locus in the comparative genome is similar to the match at the source locus in the main genome and on corresponding chromosomal homologue. RISCI has an inbuilt module for 3' flank transduction confirmation which enlists the putative transduced sequence, the number of blast hits obtained in the main and comparative genomes and the most probable source locus in the two genomes in case multiple hits are obtained. From left to right - Pink line - 5' flank at the source locus, blue arrows - TSDs at the source locus, green line - repeat, dotted line - poly A tail, brown and orange lines - 3' flank at the source locus, purple line - 5' flank at the current locus, black arrows - TSDs at the current locus, grey line - 3' flank at the current locus.