use strict;
use warnings;

my $filename = 'gff.annotated.gtf';
open(my $fh, '<:encoding(UTF-8)', $filename) or die "Can't open $filename: $!";

my @transcript_id = ();

my @lines = <$fh>;

foreach my $lines (@lines)
{
    my @column= split /\t/, $lines;

    foreach $element (@column)
    {
        if ($element[16] eq '"u"' || '"x"' || '"i"' || '"s"')
        {
            push @transcript_id, $element[10];
        }

}

print @transcript_id; 

##</code><code>##

foreach my $element (@column)
#       ^^

##</code><code>##

if ($element eq 'u' ||
    $element eq 'x' ||
    $element eq 'i' ||
    $element eq 's')
{
    push @transcript_id, $column[10];
}

##</code><code>##

foreach $element (@column)
{
    if ($element eq 'u' ||
        $element eq 'x' ||
        $element eq 'i' ||
        $element eq 's')
    {
        push @transcript_id, $column[10];
        last;
    }
}