If your file size is small then you can use this simple approach.

open(INPUT1, "file1");

my ($havar1, $havar2i, $Genename);

while (<INPUT1>) {
        my $startvar;
        if ($_ =~ /([^-]+)-(.*)/) {
                $Genename = $1;
                my @sparr = split('_', $2);
                open(INPUT2, "file2");
                while(<INPUT2>) {
                        if ($_ =~ /([^-]+)-(.*)/) {
                                my @sparr1 = split('_', $2);
                                if (($Genename eq $1) && ($sparr[0] < 
+$sparr1[0]) && ($sparr[1] > $sparr1[0])) {
                                        print "$Genename\t$sparr[0]\t$
+sparr[1]\t$1\t$sparr1[0]\t$sparr1[1]\n";
                                }
                        }
                }
                close(INPUT2);
        }
}
close(INPUT1);
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----Otherwise hash will be the better option -------

my ($havar1, $havar2);
open(INPUT1, "file1");
open(INPUT2, "file2");

while (<INPUT1>) {
        map{push(@{$havar1->{$1}}, $_)} split('_',$2) if ($_ =~ /([^-]
++)-(.*)/);
}
while (<INPUT2>) {
        map{push(@{$havar2->{$1}}, $_)} split('_',$2) if ($_ =~ /([^-]
++)-(.*)/);
}
close(INPUT1);
close(INPUT2);

foreach my $key (keys %{$havar1}) {
        if (exists $havar2->{$key}) {
                my $cnt = @{$havar1->{$key}};
                my $cnt1 =  @{$havar2->{$key}};
                for(my $i=0; $i < $cnt; $i=$i+2) {
                        for (my $j=0; $j < $cnt1; $j=$j+2) {
                                if (($havar1->{$key}->[$i] < $havar2->
+{$key}->[$j]) && ($havar1->{$key}->[$i+1] > $havar2->{$key}->[$j])) {
                                        print "$key\t$havar1->{$key}->
+[$i]\t$havar1->{$key}->[$i+1]\t$key\t$havar2->{$key}->[$j]\t$havar2->
+{$key}->[$j+1]\n";
                                }
                        }
                }
        }
}
[download]