Is this something like you wanted...

use warnings;
use strict;

use autodie;

use Data::Dumper;

my %result;

my $lookup =<<'_LOOKUP';
CG32694-RD    NM_167211
CG32694-RC    NM_167210
CG32694-RA    NM_167209
CG32694-RB    NM_167212
CG33557-RA    NM_001014730
_LOOKUP

open LOOKUP, '<', \$lookup;
my %lookup = map {
    local @_ = split;
    $_[1] => $_[0];
} <LOOKUP>;
close LOOKUP;

while (<DATA>) {
    local @_ = split /[][#!@\s]+/;
    @{ $result{$_[2]}}{ qw/cg val/} = ($lookup{$_[2]}, $_[$#_]);
}

warn Dumper \%result;

__DATA__
385#19126!NM_167210@[1103;1104]    2
386#19127!NM_167211@[1103;1104]    2
387#19128!NM_167212@[1103;1104]    2
438#1781!NM_135492@[1337]    1
442#1794!NM_001042886@[1349]    1
[download]

$ perl tst.pl
$VAR1 = {
          'NM_167212' => {
                           'cg' => 'CG32694-RB',
                           'val' => '2'
                         },
          'NM_167210' => {
                           'cg' => 'CG32694-RC',
                           'val' => '2'
                         },
          'NM_167211' => {
                           'cg' => 'CG32694-RD',
                           'val' => '2'
                         },
          'NM_001042886' => {
                              'cg' => undef,
                              'val' => '1'
                            },
          'NM_135492' => {
                           'cg' => undef,
                           'val' => '1'
                         }
        };
[download]