The liver-expression-specific nucleotide closest to the TSS is a C at the 3028th bp in the multiple alignment of 3447 bp of the putative promoters for the six UGT1A isoforms with hepatic expression and either a gap or a G for the three UGT1A isoforms not expressed in liver (see supplemental materials).
For most genes, the nucleosome enrichment began within 200 bp of the putative coding region.
They were designed using Primer3 [ 49] to obtain amplification of ca. 600 bp long fragment for the putative empty site.
The ExPEC adhesin I (yqi) 4,975 bp gene cluster coding for the putative subunit, chaperone, usher and adhesin was successfully cloned and over-expressed in an afimbriate strain E. coli AAEC189.
DNA fragments containing putative promoters of simD4 (P D4, 513 bp), simReg1 (P R1, 490 bp), simD3 (P D3, 300 bp), simX4 (P X4, 350 bp), simA7 (P A7, 300 bp), simEx2 (P Ex2, 550 bp), simB7 (P SR3, 319 bp), simX (P SEx1, 280 bp), simR (P SR2, 300 bp), and the putative promoter region between simX and simR genes (P R2Ex, 780 bp) (Figure 2) were used in EMSA.
The intergenic region varies between 1606 to 1680 bp for different clones, summing up to a total length of approx. 7900 bp (7827 to 7901 bp) for a putative full copy of LycEPRV.
Specifically, we use a "paired linear model" that assigns to each sequence a score that is the maximal weighted sum of two PWM match scores: one for the putative 9 bp ACS and the other for a candidate auxiliary motif.
Promoters were searched in regions comprising 200 bp upstream of the putative start codon of each ORF by screening for known promoter elements.
For the cell type restricting activity of the 134 bp NXNL1 region, the putative CRX binding site discussed above appears to be important.
This gene contains the putative promoter region (600 bp), 1,026-bp ORF, the putative terminator region (300 bp), and one putative intron (624 688) comprised of 64 nucleotides.
