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Our model recapitulates the previously reported 5′-to-3′ ramp of decreasing ribosome densities, although our analysis shows that this ramp is caused by rapid initiation of short genes rather than slow codons at the start of transcripts.
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Two of the three SNPs were located in or in close proximity to the P2Y12 gene: rs38211667 in the non-coding region of P2Y12 exon 2 and rs11922647 within 1000 bp of transcription start of transcript variant 2 of the P2Y12 gene.
Assay of the downstream start of transcript b involved incorporation of an extra base pair to prevent reporter expression from transcripts starting further upstream.
(coagulation factor VII; synonym: proconvertin): its promoter contains a biomedical SNP, namely, the -35A→C substitution relative to the start of transcript number 1 of this gene.
It is a -51T→C substitution relative to the start of transcript number 1 [ 102] that causes NOS2 overexpression according to clinical research [ 100- 102].
While the common exons of the three vab-3 transcripts lie in just over 2 kb of genomic DNA and the unique starts of transcripts b and c lie within the 1 kb upstream, the specific start of transcript a lies more than 10 kb away.
The gfp reporter was fused to the 2770 bp region upstream of the ceh-19a start codon, including the start of transcript b and the entire intergenic region, by Gateway recombinational cloning, creating pUL HF053.
Previously, we also studied this SNP in vitro by EMSA under both equilibrium [ 79] and nonequilibrium [ 80] conditions as well as in silico [ 83]. (apolipoprotein A-I) has the -35A→C substitution relative to the start of transcript number 3 of this gene.
(The start sites of transcripts on the reverse strand were taken as ENSEMBL's 'transcript end' position).
(A ) Schematic representation of the Pou3f3 locus showing start sites of transcripts in the region and positions of recognition sites of the BglII restriction endonuclease (small vertical bars) used for the 3C experiment.
We inspected 500 nt upstream of the 5' untranslated region (5'-UTR) start of each transcripts as annotated in FlyBase (Tweedie et al. 2009).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com