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A large set of cis-regulatory elements retrieved from the OsEUL promoter sequences can be classified in the WRKY, basic leucine-zipper (bZIP) and NAC transcription factor families, known to be associated with abiotic stress responses (Banerjee and Roychoudhury 2017; Fang et al. 2008; Nijhawan et al. 2008).
We analyzed the promoter sequences of the 1,501 potentially active mouse L1 elements retrieved from the GenBank and L1Xplore databases and evaluated their transcription factors binding sites and CpG content.
To explore this hypothesis, we performed comparative analyses of the 5'UTR sequences of mouse elements, particularly focusing on all active mouse L1 elements retrieved from the GenBank and L1Xplore databases, and analyzed the transcription factor binding sites and CpG dinucleotides within the 5'-UTR sequences.
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Vegard's law behavior is found for the lattice parameter in systems without oxygen vacancies, and the Shannon crystal radii for the doping elements are retrieved from the lattice expansions.
This is used by learners and in this module the elements are retrieved from the database and presented to the learner at the specified time intervals (or time points) during video execution.
Sequences and annotation data for mouse L1 elements were retrieved from the L1Base (UCSC mm5, Ensembl version 24.33) database (http://l1base.molgen.mpg.de/).molgen.mpg.de/
Sequence intervals for Bm Lep1 elements were retrieved from the assembled B. mori scaffold for chromosome 1 (Z chromosome) using a custom PERL script, reverse complements generated using the Sequence Manipulation Suite (SMS) at http://www.bioinformatics.org/sms2/rev_comp.html, and FASTA formatted text imported into MEGA 5.0.
The regions (2,500 nt long) flanking the Ty elements detected were retrieved from the assemblies of the strains investigated.
Thirty elements each were retrieved from the Macaca mulatta (MMU) and Nomascus leucogenys (NLE) genomes by BLAT [ 35, 36] using the SVA2 3' unique sequence as query.
The cDNA sequences of these elements were initially retrieved from the Arabidopsis database (www.arabidopsis.org), and further blasted on the apple geneset (Additional file 2: Figure S2).
Yet, the frequency distribution of all elements, including those retrieved from the database, shows an overabundance of rare inserts in Florida.
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