In your lines 15-18 you only read the first line of text.

open (IF, "/home/stanley/Desktop/18048320.txt");
my $text = <IF>;
my @splittext = split (/[.] [A-Z]/, $text);
close (IF);
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Better something like this:

open my $if, '<', '/path/to/file' or die "/path/to/file: $!";
# complete file content in one scalar
my $text = do { local $/; <$if> }
close $if;
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Then, instead using for to iterate over a filehandle, use while:

#for my $gene ( <HANDLE> ) {
while ( my $gene = <HANDLE> ) {
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