#!/usr/bin/perl
use warnings;
use strict;

my %seen;
my $header;
my $gn;
while (<>) {
    if (/^>.* GN=([^ ]+)/) {
        $gn = $1;
        $header = exists $seen{$gn} ? undef : $_;
    } elsif ($header) {
        undef $seen{$gn};
        print $header, $_;
    }
}