Use some default value. How about zero or the empty string or 'N/A'? You're the only one who knows what these values mean, so you'll have to figure out what an appropriate default value might be.

You might use a default() routine:

sub default {
    return 0 unless( @_ && length $_[0] );
    return $_[0];
}
$$ref_entry{$1} = default( $2 ) if /^(\w +?)\s+:.(\d+)/;
$$ref_entry{$1} = default( $2 ) if /^(\w +?)\s+:.'(.*)'/;
$$ref_entry{$1} = default( $2 ) if /^(\w +?)\s+:.>(.*)</
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TTTATCGGTCGTTATATAGATGTTTGCA