Since your data set is fairly small, you might want to consider building the regex out of the pieces you're looking for:

#!/usr/bin/perl -w
use strict;

our ($Gene, $Target, $Input) = qw/gene.txt target.txt input.txt/;

open Gene or die "$Gene: $!\n";
open Target or die "$Target: $!\n";
open Input or die "$Input: $!\n";

my $gene = join "|", grep {chomp} <Gene>;
my $target = join "|", grep {chomp} <Target>;
chomp(my $input = <Input>);

close $_ for qw/Gene Target Input/;

my $verbs = 'localizes to|held|located in|localization|translocated to
+|targets|reaches|exported|export';

# Note corrected 'split' regex
for my $sentence (split /\. [A-Z]/, $input){
    my $found;
    for ($sentence =~ /($gene).*?($verbs).*?($target)/ig){
        print "$_\t";
        $found++;
    }
    print "\n" if $found;
}
[download]

Output:

PfAMA1  located in      micronemes
PfROM1  located in      Golgi
AMA1    held    micronemes
AMA1    held    micronemes
[download]