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Although some of the findings of the initial multigene studies (8, 17) have since been corroborated with larger sequence (26 28) or transposable element (TE) insertion data sets (29), other proposed clades were not supported (27, 28).
We tested the ARED12 mutant line available in Nipponbare from the OryzaTagLine library (Larmande et al. 2008) which has an insertion in the NADH-GOGAT1 promoter but the expression of the gene was not affected by this insertion (data not shown).
Finally, for the data set with deletions, the length effect and heterozygosity was calculated only from deletions and, likewise, deletions were ignored for the insertion data.
Heme stain profiles of whole cell extracts separated by SDS-PAGE showed that expression of CymA and other Mtr proteins was not affected by the menC insertion (data not shown).
This band was absent from samples containing induced full-length OmpA without insertion and weakly detected in induced full-length OmpA with the SA-1 insertion (data not shown).
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Southern blotting showed that CHO PR328 cells did not contain any retroviral insertions (data not shown) indicating the presence of a spontaneous mutation in these cells.
Moreover, when larvae were grown under low-yeast conditions, ectopic expression of Cyclin D/Cdk4 led to reduced expression of these genes, again based on lacZ insertions (data not shown).
However, under the condition of triplet repeats transcription, we failed to see any significant expansion and contraction instabilities, except for repeats instability caused by IS1E insertions (data not shown).
TvMULE2, TvMULE3 and TvMULE4 are flanked by completely variable regions upstream and downstream of all insertions (data not shown).
Most of the clones from populations selected with MTX and GCV and failing to express GFP contained both correct and illegitimate insertions (data not shown).
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