diff --git a/bakta/features/cds.py b/bakta/features/cds.py
index 3c639811..19e555b1 100644
--- a/bakta/features/cds.py
+++ b/bakta/features/cds.py
@@ -214,12 +214,19 @@ def import_user_cdss(genome: dict, import_path: Path):
                     else:
                         contig_id, tool, feature_type, start, stop, score, strand, phase, attributes = line.split('\t')
                         if(feature_type.lower() == 'cds'):
+                            attributes = attributes.lower().split(';')
                             contig = contigs_by_id.get(contig_id, None)
                             if(contig is None):
                                 log.error('user-provided CDS: No contig found for id=%s', contig_id)
                                 raise Exception(f'user-provided CDS: No contig found for id={contig_id}')
                             user_cds = create_cds(contig, int(start), int(stop), strand, '', '')
                             user_cds['source'] = bc.CDS_SOURCE_USER
+                            if('pseudo=' in attributes  or  bc.INSDC_FEATURE_PSEUDOGENE in attributes):  # skip pseudo genes
+                                log.debug(
+                                    'skip user-provided CDS: reason=pseudogene contig=%s, start=%i, stop=%i, strand=%s',
+                                    user_cds['contig'], user_cds['start'], user_cds['stop'], user_cds['strand']
+                                )
+                                continue
                             try:
                                 nt = bu.extract_feature_sequence(user_cds, contig)
                                 user_cds['nt'] = nt
@@ -247,12 +254,30 @@ def import_user_cdss(genome: dict, import_path: Path):
             with xopen(str(import_path), threads=0) as fh_in:
                 for record in SeqIO.parse(fh_in, 'genbank'):
                     for feature in record.features:
-                        if(feature.type.lower() == 'cds'  and  'pseudo' not in feature.qualifiers and  bc.INSDC_FEATURE_PSEUDOGENE not in feature.qualifiers):
+                        if(feature.type.lower() == 'cds'):
                             contig = contigs_by_id.get(record.id, None)
                             if(contig is None):
                                 log.error('user-provided CDS: No contig found for id=%s', record.id)
                                 raise Exception(f'user-provided CDS: No contig found for id={record.id}')
                             strand = bc.STRAND_FORWARD if feature.location.strand == +1 else bc.STRAND_REVERSE
+                            if('<' in str(feature.location.start)  or  '>' in str(feature.location.end)):
+                                log.debug(
+                                    'skip user-provided CDS: reason=partial, contig=%s, start=%s, stop=%s, strand=%s',
+                                    contig['id'], feature.location.start, feature.location.end, strand
+                                )
+                                continue
+                            elif('pseudo' in feature.qualifiers  or  bc.INSDC_FEATURE_PSEUDOGENE in feature.qualifiers):
+                                log.debug(
+                                    'skip user-provided CDS: reason=pseudo, contig=%s, start=%i, stop=%i, strand=%s',
+                                    contig['id'], feature.location.start, feature.location.end, strand
+                                )
+                                continue
+                            elif('ribosomal_slippage' in feature.qualifiers):
+                                log.debug(
+                                    'skip user-provided CDS: reason=ribosomal slippage, contig=%s, start=%i, stop=%i, strand=%s',
+                                    contig['id'], feature.location.start, feature.location.end, strand
+                                )
+                                continue
                             user_cds = create_cds(contig, feature.location.start + 1, feature.location.end, strand, '', '')
                             user_cds['source'] = bc.CDS_SOURCE_USER
                             try: