.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-885658-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/8775aabfb3e092bfd3f19663003e74/.command.log
Size: 74.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-885658-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/eb712f6c1f03cf045aec3f0a6f6d90/fi_workdir/aih-tih-sc-885658-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/8775aabfb3e092bfd3f19663003e74/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/8775aabfb3e092bfd3f19663003e74/.command.run
==> STAGING COMPLETE (3 inputs)

Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 5071
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5071
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:5071
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


                           ------ Start checks ------                           
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------

------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------

-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
CAPN5--AC244258.1	HAVANA	gene	1033	18506	.	+	.	FI_gene_label "CAPN5^ENSG00000149260.18"  ; ID "CAPN5--AC244258.1^CAPN5^ENSG00000149260.18"  ; exon_id "ENSE00002449175.1"  ; exon_number 2 ; gene_id "CAPN5--AC244258.1^CAPN5^ENSG00000149260.18"  ; gene_name CAPN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165192.7"  ; havana_transcript "OTTHUMT00000382568.1"  ; hgnc_id "HGNC:1482"  ; level 1 ; orig_coord_info "chr11,77084887,77085051,+"  ; protein_id "ENSP00000409996.2"  ; tag basic exp_conf ; transcript_id "CAPN5--AC244258.1^ENST00000456580.6"  ; transcript_name "CAPN5-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CAPN5--AC244258.1	HAVANA	mRNA	1033	18506	.	+	.	FI_gene_label "CAPN5^ENSG00000149260.18"  ; ID "CAPN5--AC244258.1^ENST00000456580.6"  ; Parent "CAPN5--AC244258.1^CAPN5^ENSG00000149260.18"  ; exon_id "ENSE00002449175.1"  ; exon_number 2 ; gene_id "CAPN5--AC244258.1^CAPN5^ENSG00000149260.18"  ; gene_name CAPN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165192.7"  ; havana_transcript "OTTHUMT00000382568.1"  ; hgnc_id "HGNC:1482"  ; level 1 ; orig_coord_info "chr11,77084887,77085051,+"  ; protein_id "ENSP00000409996.2"  ; tag basic exp_conf ; transcript_id "CAPN5--AC244258.1^ENST00000456580.6"  ; transcript_name "CAPN5-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CST9--CST9L	HAVANA	gene	1001	3633	.	+	.	FI_gene_label "CST9^ENSG00000173335.5"  ; ID "CST9--CST9L^CST9^ENSG00000173335.5"  ; ccdsid "CCDS33450.1"  ; exon_id "ENSE00001472300.2"  ; exon_number 1 ; gene_id "CST9--CST9L^CST9^ENSG00000173335.5"  ; gene_name CST9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032076.1"  ; havana_transcript "OTTHUMT00000078341.1"  ; hgnc_id "HGNC:13261"  ; level 2 ; orig_coord_info "chr20,23605610,23605864,-"  ; protein_id "ENSP00000366170.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CST9--CST9L^ENST00000376971.4"  ; transcript_name "CST9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CST9--CST9L	HAVANA	mRNA	1001	3633	.	+	.	FI_gene_label "CST9^ENSG00000173335.5"  ; ID "CST9--CST9L^ENST00000376971.4"  ; Parent "CST9--CST9L^CST9^ENSG00000173335.5"  ; ccdsid "CCDS33450.1"  ; exon_id "ENSE00001472300.2"  ; exon_number 1 ; gene_id "CST9--CST9L^CST9^ENSG00000173335.5"  ; gene_name CST9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032076.1"  ; havana_transcript "OTTHUMT00000078341.1"  ; hgnc_id "HGNC:13261"  ; level 2 ; orig_coord_info "chr20,23605610,23605864,-"  ; protein_id "ENSP00000366170.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CST9--CST9L^ENST00000376971.4"  ; transcript_name "CST9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CST9--CST9L	HAVANA	gene	6634	9263	.	+	.	FI_gene_label "CST9L^ENSG00000101435.5"  ; ID "CST9--CST9L^CST9L^ENSG00000101435.5"  ; ccdsid "CCDS13157.1"  ; exon_id "ENSE00001472328.2"  ; exon_number 1 ; gene_id "CST9--CST9L^CST9L^ENSG00000101435.5"  ; gene_name CST9L ; gene_type protein_coding ; havana_gene "OTTHUMG00000032073.2"  ; havana_transcript "OTTHUMT00000078338.2"  ; hgnc_id "HGNC:16233"  ; level 2 ; orig_coord_info "chr20,23568211,23568450,-"  ; protein_id "ENSP00000366178.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CST9--CST9L^ENST00000376979.4"  ; transcript_name "CST9L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CST9--CST9L	HAVANA	mRNA	6634	9263	.	+	.	FI_gene_label "CST9L^ENSG00000101435.5"  ; ID "CST9--CST9L^ENST00000376979.4"  ; Parent "CST9--CST9L^CST9L^ENSG00000101435.5"  ; ccdsid "CCDS13157.1"  ; exon_id "ENSE00001472328.2"  ; exon_number 1 ; gene_id "CST9--CST9L^CST9L^ENSG00000101435.5"  ; gene_name CST9L ; gene_type protein_coding ; havana_gene "OTTHUMG00000032073.2"  ; havana_transcript "OTTHUMT00000078338.2"  ; hgnc_id "HGNC:16233"  ; level 2 ; orig_coord_info "chr20,23568211,23568450,-"  ; protein_id "ENSP00000366178.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CST9--CST9L^ENST00000376979.4"  ; transcript_name "CST9L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DCAF1--APPL1	HAVANA	gene	30651	55182	.	+	.	FI_gene_label "APPL1^ENSG00000157500.12"  ; ID "DCAF1--APPL1^APPL1^ENSG00000157500.12"  ; ccdsid "CCDS2882.1"  ; exon_id "ENSE00001277615.7"  ; exon_number 1 ; gene_id "DCAF1--APPL1^APPL1^ENSG00000157500.12"  ; gene_name APPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133756.14"  ; havana_transcript "OTTHUMT00000258196.3"  ; hgnc_id "HGNC:24035"  ; level 2 ; orig_coord_info "chr3,57227884,57227937,+"  ; protein_id "ENSP00000288266.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCAF1--APPL1^ENST00000288266.8"  ; transcript_name "APPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DCAF1--APPL1	HAVANA	mRNA	30651	55182	.	+	.	FI_gene_label "APPL1^ENSG00000157500.12"  ; ID "DCAF1--APPL1^ENST00000288266.8"  ; Parent "DCAF1--APPL1^APPL1^ENSG00000157500.12"  ; ccdsid "CCDS2882.1"  ; exon_id "ENSE00001277615.7"  ; exon_number 1 ; gene_id "DCAF1--APPL1^APPL1^ENSG00000157500.12"  ; gene_name APPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133756.14"  ; havana_transcript "OTTHUMT00000258196.3"  ; hgnc_id "HGNC:24035"  ; level 2 ; orig_coord_info "chr3,57227884,57227937,+"  ; protein_id "ENSP00000288266.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCAF1--APPL1^ENST00000288266.8"  ; transcript_name "APPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DCAF1--APPL1	ENSEMBL	gene	2131	25672	.	+	.	FI_gene_label "DCAF1^ENSG00000145041.15"  ; ID "DCAF1--APPL1^DCAF1^ENSG00000145041.15"  ; exon_id "ENSE00002274753.1"  ; exon_number 1 ; gene_id "DCAF1--APPL1^DCAF1^ENSG00000145041.15"  ; gene_name DCAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156895.4"  ; hgnc_id "HGNC:30911"  ; level 3 ; orig_coord_info "chr3,51483719,51483828,-"  ; protein_id "ENSP00000338857.5"  ; tag basic ; transcript_id "DCAF1--APPL1^ENST00000335891.5"  ; transcript_name "DCAF1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
DCAF1--APPL1	ENSEMBL	mRNA	2131	25672	.	+	.	FI_gene_label "DCAF1^ENSG00000145041.15"  ; ID "DCAF1--APPL1^ENST00000335891.5"  ; Parent "DCAF1--APPL1^DCAF1^ENSG00000145041.15"  ; exon_id "ENSE00002274753.1"  ; exon_number 1 ; gene_id "DCAF1--APPL1^DCAF1^ENSG00000145041.15"  ; gene_name DCAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156895.4"  ; hgnc_id "HGNC:30911"  ; level 3 ; orig_coord_info "chr3,51483719,51483828,-"  ; protein_id "ENSP00000338857.5"  ; tag basic ; transcript_id "DCAF1--APPL1^ENST00000335891.5"  ; transcript_name "DCAF1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
EPC1--AL158834.2	HAVANA	gene	3665	21440	.	+	.	FI_gene_label "EPC1^ENSG00000120616.16"  ; ID "EPC1--AL158834.2^EPC1^ENSG00000120616.16"  ; ccdsid "CCDS7172.1"  ; exon_id "ENSE00001817472.1"  ; exon_number 1 ; gene_id "EPC1--AL158834.2^EPC1^ENSG00000120616.16"  ; gene_name EPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017925.4"  ; havana_transcript "OTTHUMT00000047484.1"  ; hgnc_id "HGNC:19876"  ; level 2 ; orig_coord_info "chr10,32346763,32346915,-"  ; protein_id "ENSP00000263062.8"  ; tag basic CCDS ; transcript_id "EPC1--AL158834.2^ENST00000263062.8"  ; transcript_name "EPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EPC1--AL158834.2	HAVANA	mRNA	3665	21440	.	+	.	FI_gene_label "EPC1^ENSG00000120616.16"  ; ID "EPC1--AL158834.2^ENST00000263062.8"  ; Parent "EPC1--AL158834.2^EPC1^ENSG00000120616.16"  ; ccdsid "CCDS7172.1"  ; exon_id "ENSE00001817472.1"  ; exon_number 1 ; gene_id "EPC1--AL158834.2^EPC1^ENSG00000120616.16"  ; gene_name EPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017925.4"  ; havana_transcript "OTTHUMT00000047484.1"  ; hgnc_id "HGNC:19876"  ; level 2 ; orig_coord_info "chr10,32346763,32346915,-"  ; protein_id "ENSP00000263062.8"  ; tag basic CCDS ; transcript_id "EPC1--AL158834.2^ENST00000263062.8"  ; transcript_name "EPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EPC1--RPS24P13	HAVANA	gene	3665	21440	.	+	.	FI_gene_label "EPC1^ENSG00000120616.16"  ; ID "EPC1--RPS24P13^EPC1^ENSG00000120616.16"  ; ccdsid "CCDS7172.1"  ; exon_id "ENSE00001817472.1"  ; exon_number 1 ; gene_id "EPC1--RPS24P13^EPC1^ENSG00000120616.16"  ; gene_name EPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017925.4"  ; havana_transcript "OTTHUMT00000047484.1"  ; hgnc_id "HGNC:19876"  ; level 2 ; orig_coord_info "chr10,32346763,32346915,-"  ; protein_id "ENSP00000263062.8"  ; tag basic CCDS ; transcript_id "EPC1--RPS24P13^ENST00000263062.8"  ; transcript_name "EPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EPC1--RPS24P13	HAVANA	mRNA	3665	21440	.	+	.	FI_gene_label "EPC1^ENSG00000120616.16"  ; ID "EPC1--RPS24P13^ENST00000263062.8"  ; Parent "EPC1--RPS24P13^EPC1^ENSG00000120616.16"  ; ccdsid "CCDS7172.1"  ; exon_id "ENSE00001817472.1"  ; exon_number 1 ; gene_id "EPC1--RPS24P13^EPC1^ENSG00000120616.16"  ; gene_name EPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017925.4"  ; havana_transcript "OTTHUMT00000047484.1"  ; hgnc_id "HGNC:19876"  ; level 2 ; orig_coord_info "chr10,32346763,32346915,-"  ; protein_id "ENSP00000263062.8"  ; tag basic CCDS ; transcript_id "EPC1--RPS24P13^ENST00000263062.8"  ; transcript_name "EPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1	HAVANA	mRNA	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^ENST00000350221.4"  ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HOXC12--HOXC11	HAVANA	gene	8057	11095	.	+	.	FI_gene_label "HOXC11^ENSG00000123388.4"  ; ID "HOXC12--HOXC11^HOXC11^ENSG00000123388.4"  ; exon_id "ENSE00002374295.1"  ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC11^ENSG00000123388.4"  ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3"  ; havana_transcript "OTTHUMT00000407429.2"  ; hgnc_id "HGNC:5123"  ; level 1 ; orig_coord_info "chr12,53973242,53973927,+"  ; protein_id "ENSP00000243082.4"  ; tag basic exp_conf ; transcript_id "HOXC12--HOXC11^ENST00000243082.4"  ; transcript_name "HOXC11-201"  ; transcript_support_level 3 ; transcript_type protein_coding
HOXC12--HOXC11	HAVANA	mRNA	8057	11095	.	+	.	FI_gene_label "HOXC11^ENSG00000123388.4"  ; ID "HOXC12--HOXC11^ENST00000243082.4"  ; Parent "HOXC12--HOXC11^HOXC11^ENSG00000123388.4"  ; exon_id "ENSE00002374295.1"  ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC11^ENSG00000123388.4"  ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3"  ; havana_transcript "OTTHUMT00000407429.2"  ; hgnc_id "HGNC:5123"  ; level 1 ; orig_coord_info "chr12,53973242,53973927,+"  ; protein_id "ENSP00000243082.4"  ; tag basic exp_conf ; transcript_id "HOXC12--HOXC11^ENST00000243082.4"  ; transcript_name "HOXC11-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
HOXC12--HOXC11	HAVANA	gene	1001	5054	.	+	.	FI_gene_label "HOXC12^ENSG00000123407.4"  ; ID "HOXC12--HOXC11^HOXC12^ENSG00000123407.4"  ; ccdsid "CCDS8866.1"  ; exon_id "ENSE00001059266.3"  ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC12^ENSG00000123407.4"  ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3"  ; havana_transcript "OTTHUMT00000358868.3"  ; hgnc_id "HGNC:5124"  ; level 2 ; orig_coord_info "chr12,53954930,53955539,+"  ; protein_id "ENSP00000243103.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC11^ENST00000243103.4"  ; transcript_name "HOXC12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HOXC12--HOXC11	HAVANA	mRNA	1001	5054	.	+	.	FI_gene_label "HOXC12^ENSG00000123407.4"  ; ID "HOXC12--HOXC11^ENST00000243103.4"  ; Parent "HOXC12--HOXC11^HOXC12^ENSG00000123407.4"  ; ccdsid "CCDS8866.1"  ; exon_id "ENSE00001059266.3"  ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC12^ENSG00000123407.4"  ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3"  ; havana_transcript "OTTHUMT00000358868.3"  ; hgnc_id "HGNC:5124"  ; level 2 ; orig_coord_info "chr12,53954930,53955539,+"  ; protein_id "ENSP00000243103.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC11^ENST00000243103.4"  ; transcript_name "HOXC12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HOXC13--HOXC11	HAVANA	gene	1001	4357	.	+	.	FI_gene_label "HOXC13^ENSG00000123364.5"  ; ID "HOXC13--HOXC11^HOXC13^ENSG00000123364.5"  ; ccdsid "CCDS8865.1"  ; exon_id "ENSE00000838327.5"  ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC13^ENSG00000123364.5"  ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4"  ; havana_transcript "OTTHUMT00000358865.4"  ; hgnc_id "HGNC:5125"  ; level 2 ; orig_coord_info "chr12,53938907,53939642,+"  ; protein_id "ENSP00000243056.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC11^ENST00000243056.5"  ; transcript_name "HOXC13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HOXC13--HOXC11	HAVANA	mRNA	1001	4357	.	+	.	FI_gene_label "HOXC13^ENSG00000123364.5"  ; ID "HOXC13--HOXC11^ENST00000243056.5"  ; Parent "HOXC13--HOXC11^HOXC13^ENSG00000123364.5"  ; ccdsid "CCDS8865.1"  ; exon_id "ENSE00000838327.5"  ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC13^ENSG00000123364.5"  ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4"  ; havana_transcript "OTTHUMT00000358865.4"  ; hgnc_id "HGNC:5125"  ; level 2 ; orig_coord_info "chr12,53938907,53939642,+"  ; protein_id "ENSP00000243056.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC11^ENST00000243056.5"  ; transcript_name "HOXC13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HOXC13--HOXC11	HAVANA	gene	7360	10398	.	+	.	FI_gene_label "HOXC11^ENSG00000123388.4"  ; ID "HOXC13--HOXC11^HOXC11^ENSG00000123388.4"  ; exon_id "ENSE00002374295.1"  ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC11^ENSG00000123388.4"  ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3"  ; havana_transcript "OTTHUMT00000407429.2"  ; hgnc_id "HGNC:5123"  ; level 1 ; orig_coord_info "chr12,53973242,53973927,+"  ; protein_id "ENSP00000243082.4"  ; tag basic exp_conf ; transcript_id "HOXC13--HOXC11^ENST00000243082.4"  ; transcript_name "HOXC11-201"  ; transcript_support_level 3 ; transcript_type protein_coding
HOXC13--HOXC11	HAVANA	mRNA	7360	10398	.	+	.	FI_gene_label "HOXC11^ENSG00000123388.4"  ; ID "HOXC13--HOXC11^ENST00000243082.4"  ; Parent "HOXC13--HOXC11^HOXC11^ENSG00000123388.4"  ; exon_id "ENSE00002374295.1"  ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC11^ENSG00000123388.4"  ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3"  ; havana_transcript "OTTHUMT00000407429.2"  ; hgnc_id "HGNC:5123"  ; level 1 ; orig_coord_info "chr12,53973242,53973927,+"  ; protein_id "ENSP00000243082.4"  ; tag basic exp_conf ; transcript_id "HOXC13--HOXC11^ENST00000243082.4"  ; transcript_name "HOXC11-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
LHFPL5--CLPSL1	HAVANA	gene	3397	10913	.	+	.	FI_gene_label "LHFPL5^ENSG00000197753.11"  ; ID "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; ccdsid "CCDS4812.1"  ; exon_id "ENSE00003831190.2"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; gene_name LHFPL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014584.6"  ; havana_transcript "OTTHUMT00000040323.4"  ; hgnc_id "HGNC:21253"  ; level 2 ; orig_coord_info "chr6,35805671,35806082,+"  ; protein_id "ENSP00000353346.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000360215.3"  ; transcript_name "LHFPL5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LHFPL5--CLPSL1	HAVANA	mRNA	3397	10913	.	+	.	FI_gene_label "LHFPL5^ENSG00000197753.11"  ; ID "LHFPL5--CLPSL1^ENST00000360215.3"  ; Parent "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; ccdsid "CCDS4812.1"  ; exon_id "ENSE00003831190.2"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; gene_name LHFPL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014584.6"  ; havana_transcript "OTTHUMT00000040323.4"  ; hgnc_id "HGNC:21253"  ; level 2 ; orig_coord_info "chr6,35805671,35806082,+"  ; protein_id "ENSP00000353346.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000360215.3"  ; transcript_name "LHFPL5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LHFPL5--CLPSL1	HAVANA	gene	20636	22979	.	+	.	FI_gene_label "CLPSL1^ENSG00000204140.10"  ; ID "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; ccdsid "CCDS43456.1"  ; exon_id "ENSE00001569343.4"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; gene_name CLPSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014582.3"  ; havana_transcript "OTTHUMT00000040317.3"  ; hgnc_id "HGNC:21251"  ; level 2 ; orig_coord_info "chr6,35781111,35781209,+"  ; protein_id "ENSP00000362968.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000373861.6"  ; transcript_name "CLPSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LHFPL5--CLPSL1	HAVANA	mRNA	20636	22979	.	+	.	FI_gene_label "CLPSL1^ENSG00000204140.10"  ; ID "LHFPL5--CLPSL1^ENST00000373861.6"  ; Parent "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; ccdsid "CCDS43456.1"  ; exon_id "ENSE00001569343.4"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; gene_name CLPSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014582.3"  ; havana_transcript "OTTHUMT00000040317.3"  ; hgnc_id "HGNC:21251"  ; level 2 ; orig_coord_info "chr6,35781111,35781209,+"  ; protein_id "ENSP00000362968.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000373861.6"  ; transcript_name "CLPSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MYH9--NAP1L1	HAVANA	gene	1001	41543	.	+	.	FI_gene_label "MYH9^ENSG00000100345.22"  ; ID "MYH9--NAP1L1^MYH9^ENSG00000100345.22"  ; ccdsid "CCDS13927.1"  ; exon_id "ENSE00002732339.1"  ; exon_number 2 ; gene_id "MYH9--NAP1L1^MYH9^ENSG00000100345.22"  ; gene_name MYH9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030429.9"  ; havana_transcript "OTTHUMT00000259110.4"  ; hgnc_id "HGNC:7579"  ; level 1 ; orig_coord_info "chr22,36348904,36349236,-"  ; protein_id "ENSP00000216181.6"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MYH9--NAP1L1^ENST00000216181.11"  ; transcript_name "MYH9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MYH9--NAP1L1	HAVANA	mRNA	1001	41543	.	+	.	FI_gene_label "MYH9^ENSG00000100345.22"  ; ID "MYH9--NAP1L1^ENST00000216181.11"  ; Parent "MYH9--NAP1L1^MYH9^ENSG00000100345.22"  ; ccdsid "CCDS13927.1"  ; exon_id "ENSE00002732339.1"  ; exon_number 2 ; gene_id "MYH9--NAP1L1^MYH9^ENSG00000100345.22"  ; gene_name MYH9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030429.9"  ; havana_transcript "OTTHUMT00000259110.4"  ; hgnc_id "HGNC:7579"  ; level 1 ; orig_coord_info "chr22,36348904,36349236,-"  ; protein_id "ENSP00000216181.6"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MYH9--NAP1L1^ENST00000216181.11"  ; transcript_name "MYH9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MYH9--NAP1L1	HAVANA	gene	44613	62175	.	+	.	FI_gene_label "NAP1L1^ENSG00000187109.15"  ; ID "MYH9--NAP1L1^NAP1L1^ENSG00000187109.15"  ; ccdsid "CCDS9013.1"  ; exon_id "ENSE00003690648.1"  ; exon_number 2 ; gene_id "MYH9--NAP1L1^NAP1L1^ENSG00000187109.15"  ; gene_name NAP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169786.7"  ; havana_transcript "OTTHUMT00000405938.2"  ; hgnc_id "HGNC:7637"  ; level 2 ; orig_coord_info "chr12,76074203,76074219,-"  ; protein_id "ENSP00000376947.3"  ; tag alternative_3_UTR basic appris_principal_4 CCDS ; transcript_id "MYH9--NAP1L1^ENST00000393263.7"  ; transcript_name "NAP1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MYH9--NAP1L1	HAVANA	mRNA	44613	62175	.	+	.	FI_gene_label "NAP1L1^ENSG00000187109.15"  ; ID "MYH9--NAP1L1^ENST00000393263.7"  ; Parent "MYH9--NAP1L1^NAP1L1^ENSG00000187109.15"  ; ccdsid "CCDS9013.1"  ; exon_id "ENSE00003690648.1"  ; exon_number 2 ; gene_id "MYH9--NAP1L1^NAP1L1^ENSG00000187109.15"  ; gene_name NAP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169786.7"  ; havana_transcript "OTTHUMT00000405938.2"  ; hgnc_id "HGNC:7637"  ; level 2 ; orig_coord_info "chr12,76074203,76074219,-"  ; protein_id "ENSP00000376947.3"  ; tag alternative_3_UTR basic appris_principal_4 CCDS ; transcript_id "MYH9--NAP1L1^ENST00000393263.7"  ; transcript_name "NAP1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NADK2--RALYL	HAVANA	gene	1138	17664	.	+	.	FI_gene_label "NADK2^ENSG00000152620.13"  ; ID "NADK2--RALYL^NADK2^ENSG00000152620.13"  ; ccdsid "CCDS3917.1"  ; exon_id "ENSE00003688257.1"  ; exon_number 4 ; gene_id "NADK2--RALYL^NADK2^ENSG00000152620.13"  ; gene_name NADK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131105.6"  ; havana_transcript "OTTHUMT00000367600.2"  ; hgnc_id "HGNC:26404"  ; level 2 ; orig_coord_info "chr5,36225542,36225612,-"  ; protein_id "ENSP00000282512.3"  ; tag basic CCDS ; transcript_id "NADK2--RALYL^ENST00000282512.7"  ; transcript_name "NADK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NADK2--RALYL	HAVANA	mRNA	1138	17664	.	+	.	FI_gene_label "NADK2^ENSG00000152620.13"  ; ID "NADK2--RALYL^ENST00000282512.7"  ; Parent "NADK2--RALYL^NADK2^ENSG00000152620.13"  ; ccdsid "CCDS3917.1"  ; exon_id "ENSE00003688257.1"  ; exon_number 4 ; gene_id "NADK2--RALYL^NADK2^ENSG00000152620.13"  ; gene_name NADK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131105.6"  ; havana_transcript "OTTHUMT00000367600.2"  ; hgnc_id "HGNC:26404"  ; level 2 ; orig_coord_info "chr5,36225542,36225612,-"  ; protein_id "ENSP00000282512.3"  ; tag basic CCDS ; transcript_id "NADK2--RALYL^ENST00000282512.7"  ; transcript_name "NADK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NADK2--RALYL	HAVANA	gene	23877	37035	.	+	.	FI_gene_label "RALYL^ENSG00000184672.12"  ; ID "NADK2--RALYL^RALYL^ENSG00000184672.12"  ; ccdsid "CCDS55252.1"  ; exon_id "ENSE00002121177.1"  ; exon_number 1 ; gene_id "NADK2--RALYL^RALYL^ENSG00000184672.12"  ; gene_name RALYL ; gene_type protein_coding ; havana_gene "OTTHUMG00000164628.7"  ; havana_transcript "OTTHUMT00000379449.1"  ; hgnc_id "HGNC:27036"  ; level 2 ; orig_coord_info "chr8,84184999,84185014,+"  ; protein_id "ENSP00000430128.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NADK2--RALYL^ENST00000517638.5"  ; transcript_name "RALYL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NADK2--RALYL	HAVANA	mRNA	23877	37035	.	+	.	FI_gene_label "RALYL^ENSG00000184672.12"  ; ID "NADK2--RALYL^ENST00000517638.5"  ; Parent "NADK2--RALYL^RALYL^ENSG00000184672.12"  ; ccdsid "CCDS55252.1"  ; exon_id "ENSE00002121177.1"  ; exon_number 1 ; gene_id "NADK2--RALYL^RALYL^ENSG00000184672.12"  ; gene_name RALYL ; gene_type protein_coding ; havana_gene "OTTHUMG00000164628.7"  ; havana_transcript "OTTHUMT00000379449.1"  ; hgnc_id "HGNC:27036"  ; level 2 ; orig_coord_info "chr8,84184999,84185014,+"  ; protein_id "ENSP00000430128.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NADK2--RALYL^ENST00000517638.5"  ; transcript_name "RALYL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NAP1L1--MYH9	HAVANA	gene	32203	72745	.	+	.	FI_gene_label "MYH9^ENSG00000100345.22"  ; ID "NAP1L1--MYH9^MYH9^ENSG00000100345.22"  ; ccdsid "CCDS13927.1"  ; exon_id "ENSE00002732339.1"  ; exon_number 2 ; gene_id "NAP1L1--MYH9^MYH9^ENSG00000100345.22"  ; gene_name MYH9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030429.9"  ; havana_transcript "OTTHUMT00000259110.4"  ; hgnc_id "HGNC:7579"  ; level 1 ; orig_coord_info "chr22,36348904,36349236,-"  ; protein_id "ENSP00000216181.6"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "NAP1L1--MYH9^ENST00000216181.11"  ; transcript_name "MYH9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NAP1L1--MYH9	HAVANA	mRNA	32203	72745	.	+	.	FI_gene_label "MYH9^ENSG00000100345.22"  ; ID "NAP1L1--MYH9^ENST00000216181.11"  ; Parent "NAP1L1--MYH9^MYH9^ENSG00000100345.22"  ; ccdsid "CCDS13927.1"  ; exon_id "ENSE00002732339.1"  ; exon_number 2 ; gene_id "NAP1L1--MYH9^MYH9^ENSG00000100345.22"  ; gene_name MYH9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030429.9"  ; havana_transcript "OTTHUMT00000259110.4"  ; hgnc_id "HGNC:7579"  ; level 1 ; orig_coord_info "chr22,36348904,36349236,-"  ; protein_id "ENSP00000216181.6"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "NAP1L1--MYH9^ENST00000216181.11"  ; transcript_name "MYH9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NAP1L1--MYH9	HAVANA	gene	1070	18632	.	+	.	FI_gene_label "NAP1L1^ENSG00000187109.15"  ; ID "NAP1L1--MYH9^NAP1L1^ENSG00000187109.15"  ; ccdsid "CCDS9013.1"  ; exon_id "ENSE00003690648.1"  ; exon_number 2 ; gene_id "NAP1L1--MYH9^NAP1L1^ENSG00000187109.15"  ; gene_name NAP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169786.7"  ; havana_transcript "OTTHUMT00000405938.2"  ; hgnc_id "HGNC:7637"  ; level 2 ; orig_coord_info "chr12,76074203,76074219,-"  ; protein_id "ENSP00000376947.3"  ; tag alternative_3_UTR basic appris_principal_4 CCDS ; transcript_id "NAP1L1--MYH9^ENST00000393263.7"  ; transcript_name "NAP1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NAP1L1--MYH9	HAVANA	mRNA	1070	18632	.	+	.	FI_gene_label "NAP1L1^ENSG00000187109.15"  ; ID "NAP1L1--MYH9^ENST00000393263.7"  ; Parent "NAP1L1--MYH9^NAP1L1^ENSG00000187109.15"  ; ccdsid "CCDS9013.1"  ; exon_id "ENSE00003690648.1"  ; exon_number 2 ; gene_id "NAP1L1--MYH9^NAP1L1^ENSG00000187109.15"  ; gene_name NAP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169786.7"  ; havana_transcript "OTTHUMT00000405938.2"  ; hgnc_id "HGNC:7637"  ; level 2 ; orig_coord_info "chr12,76074203,76074219,-"  ; protein_id "ENSP00000376947.3"  ; tag alternative_3_UTR basic appris_principal_4 CCDS ; transcript_id "NAP1L1--MYH9^ENST00000393263.7"  ; transcript_name "NAP1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NSD3--UGT3A2	HAVANA	gene	42970	51311	.	+	.	FI_gene_label "UGT3A2^ENSG00000168671.10"  ; ID "NSD3--UGT3A2^UGT3A2^ENSG00000168671.10"  ; ccdsid "CCDS3914.1"  ; exon_id "ENSE00003618618.1"  ; exon_number 1 ; gene_id "NSD3--UGT3A2^UGT3A2^ENSG00000168671.10"  ; gene_name UGT3A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131108.4"  ; havana_transcript "OTTHUMT00000253771.3"  ; hgnc_id "HGNC:27266"  ; level 2 ; orig_coord_info "chr5,36066696,36066789,-"  ; protein_id "ENSP00000282507.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NSD3--UGT3A2^ENST00000282507.8"  ; transcript_name "UGT3A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NSD3--UGT3A2	HAVANA	mRNA	42970	51311	.	+	.	FI_gene_label "UGT3A2^ENSG00000168671.10"  ; ID "NSD3--UGT3A2^ENST00000282507.8"  ; Parent "NSD3--UGT3A2^UGT3A2^ENSG00000168671.10"  ; ccdsid "CCDS3914.1"  ; exon_id "ENSE00003618618.1"  ; exon_number 1 ; gene_id "NSD3--UGT3A2^UGT3A2^ENSG00000168671.10"  ; gene_name UGT3A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131108.4"  ; havana_transcript "OTTHUMT00000253771.3"  ; hgnc_id "HGNC:27266"  ; level 2 ; orig_coord_info "chr5,36066696,36066789,-"  ; protein_id "ENSP00000282507.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NSD3--UGT3A2^ENST00000282507.8"  ; transcript_name "UGT3A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NSD3--UGT3A2	HAVANA	gene	1001	17199	.	+	.	FI_gene_label "NSD3^ENSG00000147548.17"  ; ID "NSD3--UGT3A2^NSD3^ENSG00000147548.17"  ; ccdsid "CCDS6105.1"  ; exon_id "ENSE00002262898.1"  ; exon_number 2 ; gene_id "NSD3--UGT3A2^NSD3^ENSG00000147548.17"  ; gene_name NSD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165115.10"  ; havana_transcript "OTTHUMT00000381925.1"  ; hgnc_id "HGNC:12767"  ; level 2 ; orig_coord_info "chr8,38347497,38348171,-"  ; protein_id "ENSP00000313410.3"  ; tag basic CCDS ; transcript_id "NSD3--UGT3A2^ENST00000316985.7"  ; transcript_name "NSD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NSD3--UGT3A2	HAVANA	mRNA	1001	17199	.	+	.	FI_gene_label "NSD3^ENSG00000147548.17"  ; ID "NSD3--UGT3A2^ENST00000316985.7"  ; Parent "NSD3--UGT3A2^NSD3^ENSG00000147548.17"  ; ccdsid "CCDS6105.1"  ; exon_id "ENSE00002262898.1"  ; exon_number 2 ; gene_id "NSD3--UGT3A2^NSD3^ENSG00000147548.17"  ; gene_name NSD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165115.10"  ; havana_transcript "OTTHUMT00000381925.1"  ; hgnc_id "HGNC:12767"  ; level 2 ; orig_coord_info "chr8,38347497,38348171,-"  ; protein_id "ENSP00000313410.3"  ; tag basic CCDS ; transcript_id "NSD3--UGT3A2^ENST00000316985.7"  ; transcript_name "NSD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PRLR--AC090204.1	HAVANA	gene	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--AC090204.1^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--AC090204.1^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--AC090204.1^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRLR--AC090204.1	HAVANA	mRNA	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--AC090204.1^ENST00000231423.7"  ; Parent "PRLR--AC090204.1^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--AC090204.1^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--AC090204.1^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRLR--AC104027.1	HAVANA	gene	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--AC104027.1^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--AC104027.1^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--AC104027.1^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRLR--AC104027.1	HAVANA	mRNA	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--AC104027.1^ENST00000231423.7"  ; Parent "PRLR--AC104027.1^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--AC104027.1^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--AC104027.1^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRLR--NADK2	HAVANA	gene	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--NADK2^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--NADK2^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--NADK2^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRLR--NADK2	HAVANA	mRNA	8384	27807	.	+	.	FI_gene_label "PRLR^ENSG00000113494.17"  ; ID "PRLR--NADK2^ENST00000231423.7"  ; Parent "PRLR--NADK2^PRLR^ENSG00000113494.17"  ; ccdsid "CCDS56361.1"  ; exon_id "ENSE00003718358.1"  ; exon_number 1 ; gene_id "PRLR--NADK2^PRLR^ENSG00000113494.17"  ; gene_name PRLR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090789.7"  ; havana_transcript "OTTHUMT00000366863.1"  ; hgnc_id "HGNC:9446"  ; level 2 ; orig_coord_info "chr5,35089551,35089620,-"  ; protein_id "ENSP00000231423.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PRLR--NADK2^ENST00000231423.7"  ; transcript_name "PRLR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRLR--NADK2	HAVANA	gene	30945	47471	.	+	.	FI_gene_label "NADK2^ENSG00000152620.13"  ; ID "PRLR--NADK2^NADK2^ENSG00000152620.13"  ; ccdsid "CCDS3917.1"  ; exon_id "ENSE00003688257.1"  ; exon_number 4 ; gene_id "PRLR--NADK2^NADK2^ENSG00000152620.13"  ; gene_name NADK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131105.6"  ; havana_transcript "OTTHUMT00000367600.2"  ; hgnc_id "HGNC:26404"  ; level 2 ; orig_coord_info "chr5,36225542,36225612,-"  ; protein_id "ENSP00000282512.3"  ; tag basic CCDS ; transcript_id "PRLR--NADK2^ENST00000282512.7"  ; transcript_name "NADK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRLR--NADK2	HAVANA	mRNA	30945	47471	.	+	.	FI_gene_label "NADK2^ENSG00000152620.13"  ; ID "PRLR--NADK2^ENST00000282512.7"  ; Parent "PRLR--NADK2^NADK2^ENSG00000152620.13"  ; ccdsid "CCDS3917.1"  ; exon_id "ENSE00003688257.1"  ; exon_number 4 ; gene_id "PRLR--NADK2^NADK2^ENSG00000152620.13"  ; gene_name NADK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131105.6"  ; havana_transcript "OTTHUMT00000367600.2"  ; hgnc_id "HGNC:26404"  ; level 2 ; orig_coord_info "chr5,36225542,36225612,-"  ; protein_id "ENSP00000282512.3"  ; tag basic CCDS ; transcript_id "PRLR--NADK2^ENST00000282512.7"  ; transcript_name "NADK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNGTT--NCAM1	HAVANA	gene	23452	61725	.	+	.	FI_gene_label "NCAM1^ENSG00000149294.17"  ; ID "RNGTT--NCAM1^NCAM1^ENSG00000149294.17"  ; ccdsid "CCDS73385.1"  ; exon_id "ENSE00003906045.1"  ; exon_number 1 ; gene_id "RNGTT--NCAM1^NCAM1^ENSG00000149294.17"  ; gene_name NCAM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167196.8"  ; havana_transcript "OTTHUMT00000393677.3"  ; hgnc_id "HGNC:7656"  ; level 2 ; orig_coord_info "chr11,112961613,112961664,+"  ; protein_id "ENSP00000318472.8"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "RNGTT--NCAM1^ENST00000316851.12"  ; transcript_name "NCAM1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
RNGTT--NCAM1	HAVANA	mRNA	23452	61725	.	+	.	FI_gene_label "NCAM1^ENSG00000149294.17"  ; ID "RNGTT--NCAM1^ENST00000316851.12"  ; Parent "RNGTT--NCAM1^NCAM1^ENSG00000149294.17"  ; ccdsid "CCDS73385.1"  ; exon_id "ENSE00003906045.1"  ; exon_number 1 ; gene_id "RNGTT--NCAM1^NCAM1^ENSG00000149294.17"  ; gene_name NCAM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167196.8"  ; havana_transcript "OTTHUMT00000393677.3"  ; hgnc_id "HGNC:7656"  ; level 2 ; orig_coord_info "chr11,112961613,112961664,+"  ; protein_id "ENSP00000318472.8"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "RNGTT--NCAM1^ENST00000316851.12"  ; transcript_name "NCAM1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RNGTT--NCAM1	HAVANA	gene	1210	17456	.	+	.	FI_gene_label "RNGTT^ENSG00000111880.16"  ; ID "RNGTT--NCAM1^RNGTT^ENSG00000111880.16"  ; ccdsid "CCDS69153.1"  ; exon_id "ENSE00002223802.2"  ; exon_number 1 ; gene_id "RNGTT--NCAM1^RNGTT^ENSG00000111880.16"  ; gene_name RNGTT ; gene_type protein_coding ; havana_gene "OTTHUMG00000015190.5"  ; havana_transcript "OTTHUMT00000484165.2"  ; hgnc_id "HGNC:10073"  ; level 2 ; orig_coord_info "chr6,88963346,88963409,-"  ; protein_id "ENSP00000358487.4"  ; tag basic CCDS ; transcript_id "RNGTT--NCAM1^ENST00000369475.7"  ; transcript_name "RNGTT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RNGTT--NCAM1	HAVANA	mRNA	1210	17456	.	+	.	FI_gene_label "RNGTT^ENSG00000111880.16"  ; ID "RNGTT--NCAM1^ENST00000369475.7"  ; Parent "RNGTT--NCAM1^RNGTT^ENSG00000111880.16"  ; ccdsid "CCDS69153.1"  ; exon_id "ENSE00002223802.2"  ; exon_number 1 ; gene_id "RNGTT--NCAM1^RNGTT^ENSG00000111880.16"  ; gene_name RNGTT ; gene_type protein_coding ; havana_gene "OTTHUMG00000015190.5"  ; havana_transcript "OTTHUMT00000484165.2"  ; hgnc_id "HGNC:10073"  ; level 2 ; orig_coord_info "chr6,88963346,88963409,-"  ; protein_id "ENSP00000358487.4"  ; tag basic CCDS ; transcript_id "RNGTT--NCAM1^ENST00000369475.7"  ; transcript_name "RNGTT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CAPN5--AC244258.1	HAVANA	gene	23167	33479	.	+	.	FI_gene_label "AC244258.1^ENSG00000283453.2"  ; ID "CAPN5--AC244258.1^AC244258.1^ENSG00000283453.2"  ; exon_id "ENSE00003796339.1"  ; exon_number 1 ; gene_id "CAPN5--AC244258.1^AC244258.1^ENSG00000283453.2"  ; gene_name "AC244258.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191639.2"  ; havana_transcript "OTTHUMT00000488983.1"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr6,60281444,60281539,+"  ; tag pseudo_consens basic ; transcript_id "CAPN5--AC244258.1^ENST00000637553.1"  ; transcript_name "AC244258.1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
CAPN5--AC244258.1	HAVANA	RNA	23167	33479	.	+	.	FI_gene_label "AC244258.1^ENSG00000283453.2"  ; ID "CAPN5--AC244258.1^ENST00000637553.1"  ; Parent "CAPN5--AC244258.1^AC244258.1^ENSG00000283453.2"  ; exon_id "ENSE00003796339.1"  ; exon_number 1 ; gene_id "CAPN5--AC244258.1^AC244258.1^ENSG00000283453.2"  ; gene_name "AC244258.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191639.2"  ; havana_transcript "OTTHUMT00000488983.1"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr6,60281444,60281539,+"  ; tag pseudo_consens basic ; transcript_id "CAPN5--AC244258.1^ENST00000637553.1"  ; transcript_name "AC244258.1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
EPC1--AL158834.2	HAVANA	gene	25621	28289	.	+	.	FI_gene_label "AL158834.2^ENSG00000227253.3"  ; ID "EPC1--AL158834.2^AL158834.2^ENSG00000227253.3"  ; exon_id "ENSE00001696988.1"  ; exon_number 1 ; gene_id "EPC1--AL158834.2^AL158834.2^ENSG00000227253.3"  ; gene_name "AL158834.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017921.3"  ; havana_transcript "OTTHUMT00000047477.2"  ; level 2 ; orig_coord_info "chr10,32266289,32266410,+"  ; tag basic ; transcript_id "EPC1--AL158834.2^ENST00000415731.2"  ; transcript_name "AL158834.2-201"  ; transcript_support_level 2 ; transcript_type lncRNA
EPC1--AL158834.2	HAVANA	RNA	25621	28289	.	+	.	FI_gene_label "AL158834.2^ENSG00000227253.3"  ; ID "EPC1--AL158834.2^ENST00000415731.2"  ; Parent "EPC1--AL158834.2^AL158834.2^ENSG00000227253.3"  ; exon_id "ENSE00001696988.1"  ; exon_number 1 ; gene_id "EPC1--AL158834.2^AL158834.2^ENSG00000227253.3"  ; gene_name "AL158834.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017921.3"  ; havana_transcript "OTTHUMT00000047477.2"  ; level 2 ; orig_coord_info "chr10,32266289,32266410,+"  ; tag basic ; transcript_id "EPC1--AL158834.2^ENST00000415731.2"  ; transcript_name "AL158834.2-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
EPC1--RPS24P13	HAVANA	gene	25621	26017	.	+	.	FI_gene_label "RPS24P13^ENSG00000233190.1"  ; ID "EPC1--RPS24P13^RPS24P13^ENSG00000233190.1"  ; exon_id "ENSE00001769256.1"  ; exon_number 1 ; gene_id "EPC1--RPS24P13^RPS24P13^ENSG00000233190.1"  ; gene_name RPS24P13 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000017920.1"  ; havana_transcript "OTTHUMT00000047476.1"  ; hgnc_id "HGNC:36805"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,32231849,32232245,-"  ; tag pseudo_consens basic ; transcript_id "EPC1--RPS24P13^ENST00000442520.1"  ; transcript_name "RPS24P13-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
EPC1--RPS24P13	HAVANA	RNA	25621	26017	.	+	.	FI_gene_label "RPS24P13^ENSG00000233190.1"  ; ID "EPC1--RPS24P13^ENST00000442520.1"  ; Parent "EPC1--RPS24P13^RPS24P13^ENSG00000233190.1"  ; exon_id "ENSE00001769256.1"  ; exon_number 1 ; gene_id "EPC1--RPS24P13^RPS24P13^ENSG00000233190.1"  ; gene_name RPS24P13 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000017920.1"  ; havana_transcript "OTTHUMT00000047476.1"  ; hgnc_id "HGNC:36805"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,32231849,32232245,-"  ; tag pseudo_consens basic ; transcript_id "EPC1--RPS24P13^ENST00000442520.1"  ; transcript_name "RPS24P13-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1	HAVANA	RNA	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^ENST00000558209.1"  ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
LINC01138--SEC22B3P	HAVANA	gene	26085	30156	.	+	.	FI_gene_label "LINC01138^ENSG00000274020.4"  ; ID "LINC01138--SEC22B3P^LINC01138^ENSG00000274020.4"  ; exon_id "ENSE00001696836.1"  ; exon_number 1 ; gene_id "LINC01138--SEC22B3P^LINC01138^ENSG00000274020.4"  ; gene_name LINC01138 ; gene_type lncRNA ; havana_gene "OTTHUMG00000185296.8"  ; havana_transcript "OTTHUMT00000039545.2"  ; hgnc_id "HGNC:49454"  ; level 2 ; orig_coord_info "chr1,148297129,148297271,-"  ; transcript_id "LINC01138--SEC22B3P^ENST00000434245.3"  ; transcript_name "LINC01138-201"  ; transcript_support_level 5 ; transcript_type lncRNA
LINC01138--SEC22B3P	HAVANA	RNA	26085	30156	.	+	.	FI_gene_label "LINC01138^ENSG00000274020.4"  ; ID "LINC01138--SEC22B3P^ENST00000434245.3"  ; Parent "LINC01138--SEC22B3P^LINC01138^ENSG00000274020.4"  ; exon_id "ENSE00001696836.1"  ; exon_number 1 ; gene_id "LINC01138--SEC22B3P^LINC01138^ENSG00000274020.4"  ; gene_name LINC01138 ; gene_type lncRNA ; havana_gene "OTTHUMG00000185296.8"  ; havana_transcript "OTTHUMT00000039545.2"  ; hgnc_id "HGNC:49454"  ; level 2 ; orig_coord_info "chr1,148297129,148297271,-"  ; transcript_id "LINC01138--SEC22B3P^ENST00000434245.3"  ; transcript_name "LINC01138-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
LINC01138--SEC22B3P	HAVANA	gene	33158	36733	.	+	.	FI_gene_label "SEC22B3P^ENSG00000275140.1"  ; ID "LINC01138--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; exon_id "ENSE00003747856.1"  ; exon_number 1 ; gene_id "LINC01138--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1"  ; havana_transcript "OTTHUMT00000477871.1"  ; hgnc_id "HGNC:53891"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr1,148784482,148784594,-"  ; tag basic ; transcript_id "LINC01138--SEC22B3P^ENST00000616023.1"  ; transcript_name "SEC22B3P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
LINC01138--SEC22B3P	HAVANA	RNA	33158	36733	.	+	.	FI_gene_label "SEC22B3P^ENSG00000275140.1"  ; ID "LINC01138--SEC22B3P^ENST00000616023.1"  ; Parent "LINC01138--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; exon_id "ENSE00003747856.1"  ; exon_number 1 ; gene_id "LINC01138--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1"  ; havana_transcript "OTTHUMT00000477871.1"  ; hgnc_id "HGNC:53891"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr1,148784482,148784594,-"  ; tag basic ; transcript_id "LINC01138--SEC22B3P^ENST00000616023.1"  ; transcript_name "SEC22B3P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
PRLR--AC090204.1	HAVANA	gene	33337	36140	.	+	.	FI_gene_label "AC090204.1^ENSG00000247134.7"  ; ID "PRLR--AC090204.1^AC090204.1^ENSG00000247134.7"  ; exon_id "ENSE00001974977.2"  ; exon_number 1 ; gene_id "PRLR--AC090204.1^AC090204.1^ENSG00000247134.7"  ; gene_name "AC090204.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163952.14"  ; havana_transcript "OTTHUMT00000376538.1"  ; level 2 ; orig_coord_info "chr8,32996178,32996316,+"  ; transcript_id "PRLR--AC090204.1^ENST00000500843.2"  ; transcript_name "AC090204.1-202"  ; transcript_support_level 5 ; transcript_type lncRNA
PRLR--AC090204.1	HAVANA	RNA	33337	36140	.	+	.	FI_gene_label "AC090204.1^ENSG00000247134.7"  ; ID "PRLR--AC090204.1^ENST00000500843.2"  ; Parent "PRLR--AC090204.1^AC090204.1^ENSG00000247134.7"  ; exon_id "ENSE00001974977.2"  ; exon_number 1 ; gene_id "PRLR--AC090204.1^AC090204.1^ENSG00000247134.7"  ; gene_name "AC090204.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163952.14"  ; havana_transcript "OTTHUMT00000376538.1"  ; level 2 ; orig_coord_info "chr8,32996178,32996316,+"  ; transcript_id "PRLR--AC090204.1^ENST00000500843.2"  ; transcript_name "AC090204.1-202"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
PRLR--AC104027.1	HAVANA	gene	30808	31107	.	+	.	FI_gene_label "AC104027.1^ENSG00000253993.1"  ; ID "PRLR--AC104027.1^AC104027.1^ENSG00000253993.1"  ; exon_id "ENSE00002125170.1"  ; exon_number 1 ; gene_id "PRLR--AC104027.1^AC104027.1^ENSG00000253993.1"  ; gene_name "AC104027.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163953.1"  ; havana_transcript "OTTHUMT00000376539.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,33226848,33227147,-"  ; tag pseudo_consens basic ; transcript_id "PRLR--AC104027.1^ENST00000521887.1"  ; transcript_name "AC104027.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
PRLR--AC104027.1	HAVANA	RNA	30808	31107	.	+	.	FI_gene_label "AC104027.1^ENSG00000253993.1"  ; ID "PRLR--AC104027.1^ENST00000521887.1"  ; Parent "PRLR--AC104027.1^AC104027.1^ENSG00000253993.1"  ; exon_id "ENSE00002125170.1"  ; exon_number 1 ; gene_id "PRLR--AC104027.1^AC104027.1^ENSG00000253993.1"  ; gene_name "AC104027.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163953.1"  ; havana_transcript "OTTHUMT00000376539.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,33226848,33227147,-"  ; tag pseudo_consens basic ; transcript_id "PRLR--AC104027.1^ENST00000521887.1"  ; transcript_name "AC104027.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
405 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------

------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------

------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
754 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 35 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 0 second) ------                   


GFF3 file parsed