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Primers were designed to amplify a 500-bp fragment 892 to 1,392 bases upstream of the bovine PRL gene.
There appeared to be few or no genes with sites closer than 100 bases upstream, or sites farther than 450 bases upstream that had the expected expression pattern.
This model requires a Cbf1 site to be 9 to 68 bases upstream of a Met31 site with either orientation, and for the Met31 site to be no more than 450 bases upstream of the translational initiation codon.
For both Cbf1 and Met31, we only considered binding sites within 1000 bases upstream of the closest gene start.
The distinctions in this region arise mainly from bases upstream of −53 pairing with downstream sequences in fhlA220.
PRNP htSNP 4136 is located in the promoter region exactly 14 bases upstream from exon 1 (GenBank file DQ457195).
Interestingly, the consensus RBS was six bases upstream of the start codon less often than either five or seven bases.
Basehoar et al. found an enrichment of TATAs between 50 and 200 bases upstream of the translational start [33].
Regulatory DNA was defined to be 250 bases upstream of the +1 start site of an operon or single transcription unit.
A total of 1912 bases upstream of the putative 5' end of the gene were sequenced producing a contiguous assembly of 10,125 bases.
Introns were scanned for branch point consensus matches within a region 21 to 34 bases upstream of the 3' intron end according to Gao et al. [48].
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