In a few cases of ambiguous alignments of upstream regions, we were unable to tell with confidence which octanucleotide in one species was orthologous to TATA box in another.
For alignment of the upstream sequences the DIALIGN program [ 47] from Genomatix was used.
The P. luminescens ompN mRNA 5' UTR was deduced from alignment of sequences upstream of the ATG coding start site with 5'UTR sequences of Yersinia species.
There was very little alignment of the upstream region sequences and many gaps caused by the presence of numerous insertion elements.
The average percent identity for alignment of the upstream exon, as well as flanking introns, was calculated, and so was the downstream exon.
F 1 3 sites in P. luminescens were deduced by the alignment of sequences upstream of the ATG translational start site of ompN and of ompF from the four enteric bacteria shown.
An alignment of the 5' upstream regions (promoter) of PINK1 in mouse and human indicate a high degree of conservation, implying that PINK1 transcriptional regulation may be similar across these species.
The putative P. luminescens ompA mRNA 5' UTR sequence was deduced from an alignment of sequences upstream of the P. luminescens ompA ATG start with E.coli and Y. pestis ompA mRNA 5' UTR sequences.
(A ) Alignment of the upstream and downstream regions of gD located within the HSV-1 BamHI J fragment encoded in VD60 cells and within the genome of Δ gD −/− using LALIGN (ExPASy) (Myers and Miller, 1988 ).
