Alignment of human and mouse APP 5′UTRs with human PrP 5′UTR sequences relative to the L- and H-ferritin Iron-responsive elements (IREs).
Panel A: The human and mouse APP 5′UTR specific IRE-like RNA stem loops, the human PrP 5′UTR, and the human and mouse SNCA specific IRE –like stem loops each aligned adjacent to the ferritin L- and H IRE RNA stem loops. Shown, the L- and H-mRNAs encode canonical IRE RNA stem loops whereas the APP IRE in non canonical although fully iron responsive . The α-synuclein IRE (SNCA IRE) represents a non canonical IRE traversing the central splice junction of exon-1 and exon-2 (the CAGUGN loop/splice site sequences) of SNCA mRNA . Typical IRE stem loops fold to exhibit an apical AGU pseudotriloop which is depicted in red lettering at the apex of the H-ferritin and SNCA IREs  relative to an analogous AGA from the IRE–like stem loop encoded by APP mRNA . Panel B: Maps of the 5′UTRs encoding by the human and mouse APP mRNAs, PrP mRNA, SNCA mRNA, and the mRNAs for L- and H-ferritin (IRE stem loops are displayed as lollipops). Panel C: Relative alignment of the sequences that encode the 5′UTR specific IRE-like stem loops in human APP mRNA, PrP mRNA, SNCA mRNA, and the L- and H-ferritin mRNAs. Panel D: Screen and counter-screening Constructs : The human APP 5′UTR cassette was subcloned in front of the luciferase reporter gene in the dicistronic pCD(APP) reporter construct. The same-sized and related PrP 5′UTR was subcloned in an identical format into the pCD(PrP) reporter construct for the purpose of counter-screening, as described in the materials and methods section.