diff --git a/seqann/sequence_annotation.py b/seqann/sequence_annotation.py
index 6d6a7e7..82cdeff 100644
--- a/seqann/sequence_annotation.py
+++ b/seqann/sequence_annotation.py
@@ -772,6 +772,7 @@ def ref_align(self, found_seqs, sequence: Seq=None,
                                     ##Make sure order of alignment make sense
                                     if an.features[f].location.start == 0 \
                                             and f != "five_prime_UTR" \
+                                            and annotation.annotation \
                                             and 'three_prime_UTR' in annotation.annotation:
                                         del an.features[f]
                                         continue