#! /usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

# May appear an attribute more than once in a record?
# Sorry this is not DRY, the attribute names are duplicated
# here and in the parser regex.
my %is_single = (
  'exon'          => 1,
  'gene_id'       => 1,
  'product_id'    => 1,
  'sno_rna'       => 1,
  'query_subject' => 0,
  'gene_name'     => 1,
  'link'          => 1,
  'other'         => 0,
);

# You can use split, just match the null string
# before the real match in a look-ahead.
my @records = split /^(?=\d+$)/m, do { local $/; <DATA> };

# An array of hash of something, one item / record.
my @parsed_records;
#my %sno_records;

for (@records) {
  my %record;
  # You probably want to eliminate those ugly trailing spaces first
  # and then leave out the '\s*' parts just before '$'.
  my $re = qr{
      (?:  ^           (?<exon>          \d+                 ) \s* $ )
    | (?:  ^ GI:\s*    (?<gene_id>       \d+                 ) \s* $ )
    | (?:  ^ NM_       (?<product_id>    \d+\.\d             ) \s* $ )
    | (?:  ^ snoRNA\s+ (?<sno_rna>       .+                  ) \s* $ )
    | (?s: ^           (?<query_subject> Query .*? Sbjct .*? ) \s* $ )
    | (?i: ^           (?<gene_name>     Homo \s sapiens .*  ) \s* $ )
    | (?:  ^           (?<link>          http://.*           ) \s* $ )
    | (?:  ^           (?<other>         .+                  ) \s* $ )
    # Order of branches matters, leave (?<other>) at the very end.
  }mx;

  while (m/$re/gc) {
    my ( $key ) = keys %+;
    my ( $val ) = values %+;
    # If a key can appear only once then simply store it.
    if ( $is_single{$key} ) {
      $record{$key} = $val;
    }
    # Else put it into an array.
    else {
      push @{ $record{$key} }, $val;
    }
  }

  # This @parsed_records is _not_ keyed by sno_rna, as it
  # seemed unnatural for me with the provided sample data.
  push @parsed_records, \%record;

  # But you can easily transform it to a data structure keyed by sno_rna
  # just uncomment the lines related to %sno_records.
  #push @{ $sno_records{ $record{sno_rna} } }, \%record;
  #delete $record{sno_rna};
}

print Dumper( \@parsed_records );
#print Dumper( \%sno_records );

__DATA__