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This suggested that the deleted element had a positive function on the transactivation of this promoter in basal conditions.
In agreement with previous findings, a complete MITE was followed by a partial one (including a direct repeat of the second half of the element) in the Lpx- B1.1a allele, and there was a partially deleted element in the Lpx-B1.1b allele, while in the Lpx-B1.2 and Lpx-B1.3 genes the MITE was completely absent.
The RNA levels in cells with the internally deleted element were measured as somewhat lower than those of cells with the wild-type element, but this slight reduction is unlikely to account for the complete absence of retrotransposition in these cells.
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Given the book's sizable length, Zaillian deleted elements to match Fincher's desired running time.
By blasting the putative full length element to the Vitis whole genome shotgun database we could also find non-autonomous or deleted elements of the same family which have lost the TPase gene.
The deleted elements (ISE2, ISAR, and so on) or RNA structure may also be involved in the ESRPs-dependent promotion of exon 8 recognition, although more clarification is required.
This scenario is supported by the observation that in other internally deleted elements (that have not amplified), the size distribution does not exhibit any strong bias (not shown).
Indeed, most of the MITE lineages corresponded to internally deleted elements; for example, Dromar5eug contains 112 MITE copies of 526 bp and 63 full-length copies.
It has long been a puzzle as to how these deleted elements are able to amplify to a much higher copy number than their parents.
However, unlike autonomous elements, MITEs have no coding capacity, and unlike other deleted elements, MITEs amplify to high copy number and copies are homogeneous in size (usually <500 bp) (Feschotte et al. 2002).
Elements that were deleted from this reference should then be detected as insertions in the resequencing data of the reference strain Col-0, and the positions of the deleted elements have been used to benchmark the predictions of Jitterbug and RetroSeq.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com