Hi, what is the syntax error according to the error message?

The code you posted produces:

Global symbol "$element" requires explicit package name (did you forge
+t to declare "my $element"?) at 1203983.pl line 14.
Global symbol "@element" requires explicit package name (did you forge
+t to declare "my @element"?) at 1203983.pl line 16.
Global symbol "@element" requires explicit package name (did you forge
+t to declare "my @element"?) at 1203983.pl line 17.
Missing right curly or square bracket at 1203983.pl line 21, at end of
+ line
syntax error at 1203983.pl line 21, at EOF
Execution of 1203983.pl aborted due to compilation errors.
[download]

Note that the last line of the message tells you exactly where one of the errors is.

I assume you also didn't have the undeclared variable error in your real code, but it was a typing error here. See:

• How do I post a question effectively?
• SSCCE

You have a number of unneeded loops and variables in your script. Meanwhile the main error is in your attempt to match one of a list of values against a string. Please see perlrequick for a beginner's intro to regular expressions. You might have to go on to perlretut for character classes, which is what's used below.

Here's a version that does what you want, with sample data and a Test::More test to verify that the code is working correctly.

use strict; use warnings; use feature 'say';
use Test::More tests => 1;

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

my @transcript_ids;

while ( my $line = <$fh> ) {
    my @columns = split / /, $line;
    if ( $columns[16] =~ /^[uxis]$/ ) {
        push @transcript_ids, $columns[10];
    }
}

is_deeply(
    \@transcript_ids, [qw/ bb cc dd ee /],
    'the right lines were matched'
);

__DATA__
1: 01 02 03 04 05 06 07 08 09 aa 11 12 13 14 15 a
2: 01 02 03 04 05 06 07 08 09 bb 11 12 13 14 15 u
3: 01 02 03 04 05 06 07 08 09 cc 11 12 13 14 15 x
4: 01 02 03 04 05 06 07 08 09 dd 11 12 13 14 15 i
5: 01 02 03 04 05 06 07 08 09 ee 11 12 13 14 15 s
6: 01 02 03 04 05 06 07 08 09 ff 11 12 13 14 15 z
[download]

Note that I am using the _DATA_ section but you can read from a file just as well.

Update: While I was updating this node to show some helpful links and an example, Brother Athanasius composed his excellent reply (although note that he and I came to different conclusions about what your actual problem spec is).

Hope this helps!