diff --git a/src/long_read_profiles.py b/src/long_read_profiles.py
index 73a0efe6..71347077 100644
--- a/src/long_read_profiles.py
+++ b/src/long_read_profiles.py
@@ -139,7 +139,8 @@ def construct_profile_for_features(self, read_features, mapped_region=(0, 0), po
                 matched_features[read_pos].append(gene_pos)
                 gene_pos += 1
             elif overlaps(read_feature, isoform_feature):
-                intron_profile[gene_pos] = -1
+                if self.absence_condition(mapped_region, isoform_feature):
+                    intron_profile[gene_pos] = -1
                 gene_pos += 1
 
         # eliminating non unique features
diff --git a/tests/test_long_read_profile.py b/tests/test_long_read_profile.py
index 8be455dc..49cba9d5 100644
--- a/tests/test_long_read_profile.py
+++ b/tests/test_long_read_profile.py
@@ -72,7 +72,9 @@ def test_intron_profile(self, known_features, gene_region, read_exons, polya_pos
                               ([(20, 60), (90, 110), (180, 200)], (20, 200), [(20, 60), (90, 110)],
                                -1, -1, 3, [1, 1, 0], [1, 1]),
                               ([(20, 60), (90, 110), (180, 200)], (20, 200), [(90, 110), (180, 200)],
-                               -1, -1, 3, [0, 1, 1], [1, 1])
+                               -1, -1, 3, [0, 1, 1], [1, 1]),
+                              ([(20, 60), (90, 110), (180, 200)], (20, 200), [(20, 60), (90, 100)],
+                               -1, -1, 3, [1, 0, 0], [1, -1]),
                               ])
     def test_exon_profile(self, known_features, gene_region, read_exons, polya_pos, polyt_pos, delta, expected_gene, expected_read):
         exon_profile_constructor = \