Additional file 2.

Sequence similarity of CRM1TR consensus sequences with CRM1. Multiple sequence alignment of consensus sequences derived from CRM1TR locus I monomers (LI_S-IR-EB) and locus II monomers (LII_S-IRx3-EB and LII_S IRx3-EA) with the two CRM1 elements with three IRs (CRM1_B_ID1 and CRM1_B_ID2) and the consensus CRM1A (CRM1_A) and CRM1B (CRM1_B) sequences. Sequence similarities to CRM1A and CRM1B are indicated by green and yellow highlights, respectively. The horizontal arrows above the alignment indicate the CRM1TR subsequences S (red), IR (shades of gray), and EA/EB (blue). Vertical black lines delineate the internal IR variants. Each IR sequence terminates in an A-rich region that is longer in monomers from locus I than those from locus II. LII_S-IRx3-EA appears to be a recombinant with higher sequence similarity to CRM1A than CRM1B both in the A-rich region near, as well as downstream of, the IR-EA junction. The recombination breakpoint is predicted to be on either end of CRM1A homologous region in CRM1TR_LII-IRx3-EA, where CRM1A and CRM1B sequences are indistinguishable (boxed with green highlight). Blue and red/orange stars on top of alignment indicate the position of SNPs in the S and IR regions respectively.

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Sharma et al. BMC Genomics 2013 14:142   doi:10.1186/1471-2164-14-142