diff --git a/lib/AGAT/OmniscientI.pm b/lib/AGAT/OmniscientI.pm
index 00aacc9f..3b81e951 100644
--- a/lib/AGAT/OmniscientI.pm
+++ b/lib/AGAT/OmniscientI.pm
@@ -1706,14 +1706,21 @@ sub _check_l2_linked_to_l3{
 	 			#L3 linked directly to L1
 				my $has_l1_feature = undef;
 				my $id_l2_to_replace = undef;
-	 			foreach my $tag_l1 (keys %{$hash_omniscient->{'level1'}}){ # primary_tag_key_level1 = gene or repeat etc...
+				
+				# ------------ Check for L1 features ------------
 
+				# Check if we have one l1 with that ID among all L1/tag tuples
+				foreach my $tag_l1 (keys %{$hash_omniscient->{'level1'}}){ 
 					if( exists_keys ($hash_omniscient, ('level1', $tag_l1, $id_l2))){
 						# case where it's linked by parent/ID attribute
 						$has_l1_feature = $hash_omniscient->{"level1"}{$tag_l1}{$id_l2};
+						last;
 					}
-					else{
+				}
 
+				# No l1_feature found yet, let's check if one L1 feature with the common tag
+				if (! $has_l1_feature){
+					foreach my $tag_l1 (sort {$a cmp $b} keys %{$hash_omniscient->{'level1'}}){ 
 						if(! $common_tag_in_l1 ){
 							$common_tag_in_l1 = _create_hash_common_tag_l1($hash_omniscient);
 						} # fill it (only once) because will be needed
@@ -1724,19 +1731,22 @@ sub _check_l2_linked_to_l3{
 							#check if we have the tag
 
 							foreach my $l3_feature (@{$hash_omniscient->{'level3'}{$tag_l3}{$id_l2}}){
+								print "fefe ".$l3_feature->gff_string()."\n";
 								if($l3_feature->has_tag($tag) ) {
-
+									print "has_tag $tag\n";
 									# case where it's linked by comon_tag attribute
 									if (exists_keys($common_tag_in_l1,( $tag, lc($l3_feature->_tag_value($tag)) ) ) ){
+										print "exists_keys\n";
 										if($#{$common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}} == 0){
 											my $id = $common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}[0]->{'id'};
 											my $ptag = $common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}[0]->{'ptag'};
 											$has_l1_feature = $hash_omniscient->{'level1'}{$ptag}{$id};
 											$id_l2_to_replace = $l3_feature->_tag_value('Parent');
+											print "goes into it !!!! $id_l2_to_replace \n";
 											last;
 										}
 										else{
-											dual_print($log, "\n\nSeveral potential L1 parent with comnon tag $tag with value ".lc($l3_feature->_tag_value($tag)).". We do not use any\n", 0);
+											dual_print($log, "\n\nSeveral potential L1 parent with comnon tag $tag with value ".lc($l3_feature->_tag_value($tag)).". We do not use any\n", $verbose);
 										}
 									}
 								}
@@ -1744,77 +1754,84 @@ sub _check_l2_linked_to_l3{
 							}
 						}
 					}
+				}
 
-					if ($has_l1_feature){
-
-						my $l1_ID = $has_l1_feature->_tag_value('ID');
-						my $has_gemoma_l2=undef;
-						foreach my $tag_l2 (keys %{$hash_omniscient->{'level2'}}){
-							if ( exists_keys($hash_omniscient,("level2", $tag_l2, lc($l1_ID))) ) {
-								# HERE we have seen there is a L2. We want to use it and modify it Only
-								# in case of GeMoMa issue #290
-								# to make the difference we check that no level3 feature is attached to the detected l2
-								$has_gemoma_l2=$tag_l2;
-								foreach	my $l2_feature ( @{$hash_omniscient->{'level2'}{$tag_l2}{lc($l1_ID)} } ){
-									foreach my $tag_l3 (sort {$a cmp $b} keys %{$hash_omniscient->{'level3'}}){
-										if ( exists_keys($hash_omniscient,("level3", $tag_l3, lc($l2_feature->_tag_value('ID')))) ) {
-											# Level3 features was attached to the L2, we cannot play the GeMoMa case
-											# otherwise interfer with other cases (level_missing.t tests testF, testB2 and gff_syntax.t 37_test.gff)
-											$has_gemoma_l2=undef;
-										}
+				# l1_feature found 
+				if ($has_l1_feature){
+
+					my $l1_ID = $has_l1_feature->_tag_value('ID');
+					my $has_gemoma_l2=undef;
+					foreach my $tag_l2 (keys %{$hash_omniscient->{'level2'}}){
+						if ( exists_keys($hash_omniscient,("level2", $tag_l2, lc($l1_ID))) ) {
+							# HERE we have seen there is a L2. We want to use it and modify it Only
+							# in case of GeMoMa issue #290
+							# to make the difference we check that no level3 feature is attached to the detected l2
+							$has_gemoma_l2=$tag_l2;
+							foreach	my $l2_feature ( @{$hash_omniscient->{'level2'}{$tag_l2}{lc($l1_ID)} } ){
+								foreach my $tag_l3 (sort {$a cmp $b} keys %{$hash_omniscient->{'level3'}}){
+									if ( exists_keys($hash_omniscient,("level3", $tag_l3, lc($l2_feature->_tag_value('ID')))) ) {
+										# Level3 features was attached to the L2, we cannot play the GeMoMa case
+										# otherwise interfer with other cases (level_missing.t tests testF, testB2 and gff_syntax.t 37_test.gff)
+										$has_gemoma_l2=undef;
 									}
 								}
 							}
 						}
+					}
 
-						my $l2_feature;
-						if (! $has_gemoma_l2) {
-							#create a copy of the first mRNA feature;
-							my $primary_tag_l2;
-							if (exists_keys($hash_omniscient,("level3",'cds', $id_l2) ) ){
-								 $primary_tag_l2 = 'mRNA'; 
-							} # guess mRNA
-							else{ $primary_tag_l2 = 'RNA' ;} #we cannot guess
-							$l2_feature = clean_clone( { omniscient => $hash_omniscient,
-													     feature => $has_l1_feature,
-														 new_primary_tag => $primary_tag_l2
-												   		} );
-
-						} else {
-							$l2_feature = @{$hash_omniscient->{"level2"}{$has_gemoma_l2}{lc($l1_ID)}}[0];
-							$id_l2_to_replace = $has_l1_feature->_tag_value('ID');
-							delete $mRNAGeneLink->{lc($l2_feature->_tag_value('ID'))}
-						}
+					my $l2_feature;
+					if (! $has_gemoma_l2) {
+						#create a copy of the first mRNA feature;
+						my $primary_tag_l2;
+						if (exists_keys($hash_omniscient,("level3",'cds', $id_l2) ) ){
+								$primary_tag_l2 = 'mRNA'; 
+						} # guess mRNA
+						else{ $primary_tag_l2 = 'RNA' ;} #we cannot guess
+
+						# Use a L3 feature as template (better as L1 see bug #441)
+						$l2_feature = clean_clone( { omniscient => $hash_omniscient,
+														feature => $hash_omniscient->{"level3"}{$tag_l3}{$id_l2}[0],
+														new_primary_tag => $primary_tag_l2,
+														new_id => $hash_omniscient->{"level3"}{$tag_l3}{$id_l2}[0]->_tag_value('Parent')
+													} );
+
+					} else {
+						$l2_feature = @{$hash_omniscient->{"level2"}{$has_gemoma_l2}{lc($l1_ID)}}[0];
+						$id_l2_to_replace = $has_l1_feature->_tag_value('ID');
+						delete $mRNAGeneLink->{lc($l2_feature->_tag_value('ID'))}
+					}
 
-						#Modify parent L2 (and L1 id if necessary)
-						create_or_replace_tag($l2_feature,'Parent', $l1_ID); #modify ID to replace by parent value
-						create_or_replace_tag($l2_feature,'ID', $id_l2_to_replace) if ($id_l2_to_replace); #modify ID to replace by parent value
-						check_level2_positions($hash_omniscient, $l2_feature);
-
-						if ( exists_keys ($hashID,('uid', lc($id_l2) ) ) ){ #the easiest is to modifiy the gene id
-
-							my $new_l1id = _check_uniq_id_feature($hash_omniscient, $hashID, $has_l1_feature); # to check if ID was already in used by level1 feature
-							create_or_replace_tag($l2_feature,'Parent', $new_l1id); #modify ID to replace by parent value
-							my $primary_tag_l1 =$has_l1_feature->primary_tag();
-							$hash_omniscient->{"level1"}{lc($primary_tag_l1)}{lc($new_l1id)} = delete $hash_omniscient->{"level1"}{lc($primary_tag_l1)}{lc($l1_ID)}; # now save it in omniscient
-							#fill the $mRNAGeneLink hash
-							$mRNAGeneLink->{ $id_l2 } = $new_l1id;
-							if ($has_gemoma_l2){
-								$hash_omniscient->{'level2'}{lc($l2_feature->primary_tag)}{lc($new_l1id)} = delete $hash_omniscient->{'level2'}{lc($l2_feature->primary_tag)}{lc($l1_ID)};
-							}
-							else {
-										push(@{$hash_omniscient->{"level2"}{lc($l2_feature->primary_tag)}{lc($new_l1id)}}, $l2_feature);
-							}
+					#Modify parent L2 (and L1 id if necessary)
+					create_or_replace_tag($l2_feature,'Parent', $l1_ID); #modify ID to replace by parent value
+					create_or_replace_tag($l2_feature,'ID', $id_l2_to_replace) if ($id_l2_to_replace); #modify ID to replace by parent value
+					check_level2_positions($hash_omniscient, $l2_feature);
+
+					if ( exists_keys ($hashID,('uid', lc($id_l2) ) ) ){ #the easiest is to modifiy the gene id
+
+						my $new_l1id = _check_uniq_id_feature($hash_omniscient, $hashID, $has_l1_feature); # to check if ID was already in used by level1 feature
+						create_or_replace_tag($l2_feature,'Parent', $new_l1id); #modify ID to replace by parent value
+						my $primary_tag_l1 =$has_l1_feature->primary_tag();
+						$hash_omniscient->{"level1"}{lc($primary_tag_l1)}{lc($new_l1id)} = delete $hash_omniscient->{"level1"}{lc($primary_tag_l1)}{lc($l1_ID)}; # now save it in omniscient
+						#fill the $mRNAGeneLink hash
+						$mRNAGeneLink->{ $id_l2 } = $new_l1id;
+						if ($has_gemoma_l2){
+							$hash_omniscient->{'level2'}{lc($l2_feature->primary_tag)}{lc($new_l1id)} = delete $hash_omniscient->{'level2'}{lc($l2_feature->primary_tag)}{lc($l1_ID)};
 						}
-						else{
-							#fill the $mRNAGeneLink hash
-							$mRNAGeneLink->{ $id_l2 } = $l1_ID; # Always need to keep track about l2->l1, else the method _check_l2_linked_to_l3 will recreate a l1 thinking this relationship is not fill
-							push(@{$hash_omniscient->{"level2"}{lc($l2_feature->primary_tag)}{lc($l1_ID)}}, $l2_feature);
+						else {
+									push(@{$hash_omniscient->{"level2"}{lc($l2_feature->primary_tag)}{lc($new_l1id)}}, $l2_feature);
 						}
-						dual_print($log, "L3 was directly linked to L1. Corrected by creating the intermediate L2 feature from L1 feature:\n".$l2_feature->gff_string()."\n", 0);
-						last
 					}
+					else{
+						#fill the $mRNAGeneLink hash
+						$mRNAGeneLink->{ $id_l2 } = $l1_ID; # Always need to keep track about l2->l1, else the method _check_l2_linked_to_l3 will recreate a l1 thinking this relationship is not fill
+						push(@{$hash_omniscient->{"level2"}{lc($l2_feature->primary_tag)}{lc($l1_ID)}}, $l2_feature);
+					}
+					dual_print($log, "L3 had a L1 feature but no L2 feature. Corrected by creating the intermediate L2 feature:\n".$l2_feature->gff_string()."\nUsing this feature template:\n".$hash_omniscient->{"level3"}{$tag_l3}{$id_l2}[0]->gff_string()."\n", $verbose);
+					last
 				}
+				
+
+				# ------------ No L1 features found ------------
         		# it was not previous case (L3 linked directly to L1)
 				if (! exists_keys($mRNAGeneLink,($id_l2 ) ) ) {
 	 				# ---- start fill L2 ----
diff --git a/lib/AGAT/OmniscientTool.pm b/lib/AGAT/OmniscientTool.pm
index c7cdb46a..aa2be4e2 100644
--- a/lib/AGAT/OmniscientTool.pm
+++ b/lib/AGAT/OmniscientTool.pm
@@ -1269,17 +1269,21 @@ sub clean_clone{
 	$cloned_feature->source_tag("AGAT");
 	# clean score
 	$cloned_feature->score(".");
+	# new primary tag
+	$cloned_feature->primary_tag($new_primary_tag) if $new_primary_tag;
 	# clean attributes
 	if ($clean_attributes){
 		my @tags = $cloned_feature->get_all_tags();
 		foreach my $tag (@tags){
-			if (lc($tag) ne "id" and lc($tag) ne "parent" and lc($tag) ne "gene_id" and lc($tag) ne "transcript_id"){
+			if ( lc($tag) ne "id" and lc($tag) ne "parent" and lc($tag) ne "gene_id" and lc($tag) ne "transcript_id" ){
+				$cloned_feature->remove_tag($tag);
+			}
+			if ( (lc($tag) eq "parent" or lc($tag) eq "transcript_id") and exists_keys($omniscient,("other","level","level1", lc($cloned_feature->primary_tag()) ) ) ){ # transcript_id and Parent attributes have to be removed for level1 feature anyway.
 				$cloned_feature->remove_tag($tag);
 			}
 		}
 	}
-	# new primary tag
-	$cloned_feature->primary_tag($new_primary_tag) if $new_primary_tag;
+
 	# remove Parent attribute if level1
 	if ($omniscient){
 		if ($cloned_feature->has_tag("Parent")){
diff --git a/t/gff_other.t b/t/gff_other.t
index 8a729202..63b8c230 100644
--- a/t/gff_other.t
+++ b/t/gff_other.t
@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-use Test::More tests => 5;
+use Test::More tests => 6;
 
 =head1 DESCRIPTION
 
@@ -80,4 +80,16 @@ system("$script --gff $input_folder/issue389.gff -o $pathtmp 2>&1 1>/dev/null");
 
 #run test
 ok( system("diff $pathtmp $correct_output") == 0, "issue389 check");
-unlink $pathtmp;
\ No newline at end of file
+unlink $pathtmp;
+
+# --------- Issue 441 transccipt_id used for GTF while L2 L1 created from L3 with isoforms ----
+$script = $script_prefix."bin/agat_convert_sp_gxf2gxf.pl";
+$correct_output = "$output_folder/issue441.gtf";
+
+system("$script_agat config --expose --output_format gtf 2>&1 1>/dev/null");
+system("$script --g $input_folder/issue441.gtf -o $pathtmp  2>&1 1>/dev/null");
+
+ok( system("diff $pathtmp $correct_output") == 0, "issue441 check");
+
+unlink $pathtmp;
+unlink $config;
\ No newline at end of file
diff --git a/t/gff_other/in/issue441.gtf b/t/gff_other/in/issue441.gtf
new file mode 100644
index 00000000..8ecedd0e
--- /dev/null
+++ b/t/gff_other/in/issue441.gtf
@@ -0,0 +1,16 @@
+Scaffold170	maker	exon	2883887	2884591	.	+	.	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2885735	2885878	.	+	.	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2885953	2886162	.	+	.	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2886451	2886531	.	+	.	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887224	2888594	.	+	.	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2884322	2884591	.	+	0	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2885735	2885878	.	+	0	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2885953	2886162	.	+	0	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2886451	2886531	.	+	0	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887224	2887376	.	+	0	transcript_id "GBI_15721-RE"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887524	2887566	.	+	.	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887651	2887775	.	+	.	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887917	2888009	.	+	.	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887524	2887566	.	+	0	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887651	2887775	.	+	2	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887917	2888009	.	+	0	transcript_id "GBI_15721-RF"; gene_id "GBI_15721"; gene_name "GBI_15721";
diff --git a/t/gff_other/out/issue441.gtf b/t/gff_other/out/issue441.gtf
new file mode 100644
index 00000000..0abfef70
--- /dev/null
+++ b/t/gff_other/out/issue441.gtf
@@ -0,0 +1,23 @@
+##gtf-version X
+# GFF-like GTF i.e. not checked against any GTF specification. Conversion based on GFF input, standardised by AGAT.
+Scaffold170	AGAT	gene	2883887	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	AGAT	mRNA	2883887	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "GBI_15721-RE"; Parent "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2883887	2884591	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-1"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2885735	2885878	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-2"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2885953	2886162	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-3"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2886451	2886531	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-4"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887224	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-5"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2884322	2884591	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-cds-1"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2885735	2885878	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-cds-2"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2885953	2886162	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-cds-3"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2886451	2886531	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-cds-4"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887224	2887376	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-cds-5"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	AGAT	five_prime_UTR	2883887	2884321	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-five_prime_utr-1"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	AGAT	three_prime_UTR	2887377	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-three_prime_utr-1"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
+Scaffold170	AGAT	mRNA	2887524	2888009	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "GBI_15721-RF"; Parent "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887524	2887566	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-exon-6"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887651	2887775	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-exon-7"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
+Scaffold170	maker	exon	2887917	2888009	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-exon-8"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887524	2887566	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-cds-6"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887651	2887775	.	+	2	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-cds-7"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
+Scaffold170	maker	CDS	2887917	2888009	.	+	0	gene_id "GBI_15721"; transcript_id "GBI_15721-RF"; ID "agat-cds-8"; Parent "GBI_15721-RF"; gene_name "GBI_15721";
diff --git a/t/gff_syntax/out/37_correct_output.gff b/t/gff_syntax/out/37_correct_output.gff
index da2c35f9..eec46277 100644
--- a/t/gff_syntax/out/37_correct_output.gff
+++ b/t/gff_syntax/out/37_correct_output.gff
@@ -7,12 +7,12 @@ xfSc0000000	protein_coding	CDS	8675	8697	.	-	2	ID=agat-cds-5;Parent=BL03703_cuf1
 xfSc0000000	protein_coding	CDS	9847	10147	.	-	0	ID=agat-cds-4;Parent=BL03703_cuf1;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
 xfSc0000000	AGAT	five_prime_UTR	10148	10149	.	-	.	ID=agat-five_prime_utr-1;Parent=BL03703_cuf1;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
 xfSc0000000	AGAT	three_prime_UTR	7096	8674	.	-	.	ID=agat-three_prime_utr-1;Parent=BL03703_cuf1;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
-xfSc0000000	AGAT	mRNA	12803	13319	.	-	.	ID=BL03703_evm0;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
+xfSc0000000	AGAT	mRNA	12803	13319	.	-	.	ID=BL03703_evm0;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
 xfSc0000000	protein_coding	exon	12803	13024	.	-	.	ID=agat-exon-3;Parent=BL03703_evm0;exon_number=2;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
 xfSc0000000	protein_coding	exon	13283	13319	.	-	.	ID=agat-exon-2;Parent=BL03703_evm0;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
 xfSc0000000	protein_coding	CDS	12803	13024	.	-	2	ID=agat-cds-3;Parent=BL03703_evm0;exon_number=2;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
 xfSc0000000	protein_coding	CDS	13283	13319	.	-	0	ID=agat-cds-2;Parent=BL03703_evm0;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
-xfSc0000000	AGAT	RNA	7096	9184	.	-	.	ID=BL03703_cuf0;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
+xfSc0000000	AGAT	RNA	7096	9184	.	-	.	ID=BL03703_cuf0;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149300;status=both;transcript_id=BL03703_cuf0
 xfSc0000000	protein_coding	exon	7096	9184	.	-	.	ID=agat-exon-4;Parent=BL03703_cuf0;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149300;status=both;transcript_id=BL03703_cuf0
 xfSc0000437	AGAT	gene	3712	3937	.	-	.	ID=BL03702;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
 xfSc0000437	AGAT	mRNA	3712	3937	.	-	.	ID=BL03702_evm3;Parent=BL03702;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
diff --git a/t/scripts_output/out/agat_sp_kraken_assess_liftover_1.gff b/t/scripts_output/out/agat_sp_kraken_assess_liftover_1.gff
index 569abf0d..b5aef8d9 100644
--- a/t/scripts_output/out/agat_sp_kraken_assess_liftover_1.gff
+++ b/t/scripts_output/out/agat_sp_kraken_assess_liftover_1.gff
@@ -1,6 +1,6 @@
 ##gff-version 3
 scaffold_823	AGAT	gene	105596	142103	.	+	.	ID=PP1S9_164V6;kraken_mapped=partial;gene_id=PP1S9_164V6;protein_id=PP1S9_164V6.1;transcript_id=PP1S9_164V6.1
-scaffold_823	AGAT	mRNA	105596	129298	.	+	.	ID=transcript:PP1S9_164V6.2;Parent=PP1S9_164V6;kraken_mapped=100.00%25;description=Mapped at 100.00%25;gene_id=PP1S9_164V6;protein_id=PP1S9_164V6.1;transcript_id=PP1S9_164V6.1
+scaffold_823	AGAT	mRNA	105596	129298	.	+	.	ID=transcript:PP1S9_164V6.2;Parent=PP1S9_164V6;kraken_mapped=100.00%25;description=Mapped at 100.00%25;gene_id=PP1S9_164V6;protein_id=PP1S9_164V6.2;transcript_id=PP1S9_164V6.2
 scaffold_823	jgi	exon	105596	105903	.	+	.	ID=PP1S9_164V6.2.exon1;Parent=transcript:PP1S9_164V6.2;kraken_mapped=TRUE;Name=PP1S9_164V6.2.exon1;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=PP1S9_164V6.2.exon1;gene_id=PP1S9_164V6;rank=1;transcript_id=PP1S9_164V6.2
 scaffold_823	jgi	exon	106102	106323	.	+	.	ID=PP1S9_164V6.2.exon2;Parent=transcript:PP1S9_164V6.2;kraken_mapped=TRUE;Name=PP1S9_164V6.2.exon2;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=PP1S9_164V6.2.exon2;gene_id=PP1S9_164V6;rank=2;transcript_id=PP1S9_164V6.2
 scaffold_823	jgi	exon	106856	107014	.	+	.	ID=PP1S9_164V6.2.exon3;Parent=transcript:PP1S9_164V6.2;kraken_mapped=TRUE;Name=PP1S9_164V6.2.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=PP1S9_164V6.2.exon3;gene_id=PP1S9_164V6;rank=3;transcript_id=PP1S9_164V6.2