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The transcription unit is made up of 7665 bp, and the transcription start site located at –197 bp from the initial ATG of the ORF.
The 156,662 small scaffolds (<1000 bp) from the initial CLC assembly that were excluded from the final scaffolding and gap-filling manipulations encompassed 69,241,306 bp (Supplementary Table 2).
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It may be that it has recruited a new promoter (e.g. a fragment of the transposon Galileo located 3-bp from the initial codon; see Figure 5) and acquired a new function or it is on the way to becoming a pseudogene.
36 bp reads from the initial library as well as the round 3 sub-library were aligned to the HBV genome (3.2 kb) using ELAND (see Materials and Methods) [21].
Albeit untested experimentally, the modulation caused by the +190 G/C polymorphism, which is just 26 bp upstream the initial codon, may arise from altered stem-loop structure of the 5'UTR of HSPA1A mRNA, thus confer different efficiency of HSPA1A mRNA translation.
We then made a 400 500 bp nested PCR product from the initial PCR product.
After removing adaptor sequences, 15 35 bp sequences were retrieved from the initial data set for further analysis.
Primer deletion and GBLOCKS 5' and 3' trimming resulted in 235 bp of the initial 330 bp (71%).
A total of 4790 bp of the VvDXS locus, from the initial ATG start codon to the TAG stop codon, was resequenced corresponding to base pair numbers 3759954-3764743 of NC_012011.
In a recent study, we found that this progressive effect of salt on BP appeared to be distinct from the initial acute response to salt loading in Dahl-S rats [ 13].
Initial assembled scaffolds over 1000 bp from the CLC assembly were scaffolded using SSPACE, and remaining gaps were filled using GAPFILLER.
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