.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/933dbd25d9f0333fdc30a77955ed43/.command.out
Size: 55.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt
Content

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

 ------------------------------------------------------------------------------
|   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: 2580
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2580
=> 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:2580
  => 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 1 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: 
AL669831.1--SEPTIN14	HAVANA	gene	24499	38046	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.1--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AL669831.1--SEPTIN14	HAVANA	mRNA	24499	38046	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.1--SEPTIN14^ENST00000388975.4"  ; Parent "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.1--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AL669831.4--SEPTIN14	HAVANA	mRNA	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^ENST00000388975.4"  ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
BFAR--APC2	ENSEMBL	gene	16498	35959	.	+	.	FI_gene_label "APC2^ENSG00000115266.12"  ; ID "BFAR--APC2^APC2^ENSG00000115266.12"  ; ccdsid "CCDS12068.1"  ; exon_id "ENSE00003508879.1"  ; exon_number 2 ; gene_id "BFAR--APC2^APC2^ENSG00000115266.12"  ; gene_name APC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180059.11"  ; hgnc_id "HGNC:24036"  ; level 3 ; orig_coord_info "chr19,1453002,1453142,+"  ; protein_id "ENSP00000233607.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000233607.6"  ; transcript_name "APC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BFAR--APC2	ENSEMBL	mRNA	16498	35959	.	+	.	FI_gene_label "APC2^ENSG00000115266.12"  ; ID "BFAR--APC2^ENST00000233607.6"  ; Parent "BFAR--APC2^APC2^ENSG00000115266.12"  ; ccdsid "CCDS12068.1"  ; exon_id "ENSE00003508879.1"  ; exon_number 2 ; gene_id "BFAR--APC2^APC2^ENSG00000115266.12"  ; gene_name APC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180059.11"  ; hgnc_id "HGNC:24036"  ; level 3 ; orig_coord_info "chr19,1453002,1453142,+"  ; protein_id "ENSP00000233607.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000233607.6"  ; transcript_name "APC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BFAR--APC2	HAVANA	gene	1021	12429	.	+	.	FI_gene_label "BFAR^ENSG00000103429.11"  ; ID "BFAR--APC2^BFAR^ENSG00000103429.11"  ; ccdsid "CCDS10554.1"  ; exon_id "ENSE00003646355.1"  ; exon_number 2 ; gene_id "BFAR--APC2^BFAR^ENSG00000103429.11"  ; gene_name BFAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000129848.5"  ; havana_transcript "OTTHUMT00000252088.2"  ; hgnc_id "HGNC:17613"  ; level 2 ; orig_coord_info "chr16,14644347,14644609,+"  ; protein_id "ENSP00000261658.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000261658.7"  ; transcript_name "BFAR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BFAR--APC2	HAVANA	mRNA	1021	12429	.	+	.	FI_gene_label "BFAR^ENSG00000103429.11"  ; ID "BFAR--APC2^ENST00000261658.7"  ; Parent "BFAR--APC2^BFAR^ENSG00000103429.11"  ; ccdsid "CCDS10554.1"  ; exon_id "ENSE00003646355.1"  ; exon_number 2 ; gene_id "BFAR--APC2^BFAR^ENSG00000103429.11"  ; gene_name BFAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000129848.5"  ; havana_transcript "OTTHUMT00000252088.2"  ; hgnc_id "HGNC:17613"  ; level 2 ; orig_coord_info "chr16,14644347,14644609,+"  ; protein_id "ENSP00000261658.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000261658.7"  ; transcript_name "BFAR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC6--PDE1C	ENSEMBL	gene	3274	27911	.	+	.	FI_gene_label "DNAJC6^ENSG00000116675.16"  ; ID "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16"  ; ccdsid "CCDS58005.1"  ; exon_id "ENSE00003684627.1"  ; exon_number 3 ; gene_id "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16"  ; gene_name DNAJC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009066.4"  ; hgnc_id "HGNC:15469"  ; level 3 ; orig_coord_info "chr1,65364652,65364785,+"  ; protein_id "ENSP00000263441.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000263441.11"  ; transcript_name "DNAJC6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DNAJC6--PDE1C	ENSEMBL	mRNA	3274	27911	.	+	.	FI_gene_label "DNAJC6^ENSG00000116675.16"  ; ID "DNAJC6--PDE1C^ENST00000263441.11"  ; Parent "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16"  ; ccdsid "CCDS58005.1"  ; exon_id "ENSE00003684627.1"  ; exon_number 3 ; gene_id "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16"  ; gene_name DNAJC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009066.4"  ; hgnc_id "HGNC:15469"  ; level 3 ; orig_coord_info "chr1,65364652,65364785,+"  ; protein_id "ENSP00000263441.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000263441.11"  ; transcript_name "DNAJC6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC6--PDE1C	HAVANA	gene	37267	68688	.	+	.	FI_gene_label "PDE1C^ENSG00000154678.18"  ; ID "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18"  ; ccdsid "CCDS55099.1"  ; exon_id "ENSE00001281920.2"  ; exon_number 2 ; gene_id "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18"  ; gene_name PDE1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000023836.10"  ; havana_transcript "OTTHUMT00000215076.2"  ; hgnc_id "HGNC:8776"  ; level 2 ; orig_coord_info "chr7,32070293,32070393,-"  ; protein_id "ENSP00000318105.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000321453.12"  ; transcript_name "PDE1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DNAJC6--PDE1C	HAVANA	mRNA	37267	68688	.	+	.	FI_gene_label "PDE1C^ENSG00000154678.18"  ; ID "DNAJC6--PDE1C^ENST00000321453.12"  ; Parent "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18"  ; ccdsid "CCDS55099.1"  ; exon_id "ENSE00001281920.2"  ; exon_number 2 ; gene_id "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18"  ; gene_name PDE1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000023836.10"  ; havana_transcript "OTTHUMT00000215076.2"  ; hgnc_id "HGNC:8776"  ; level 2 ; orig_coord_info "chr7,32070293,32070393,-"  ; protein_id "ENSP00000318105.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000321453.12"  ; transcript_name "PDE1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GTF2A1L--STON1-GTF2A1L	HAVANA	gene	1059	10137	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTF2A1L--STON1-GTF2A1L	HAVANA	mRNA	1059	10137	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8"  ; Parent "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ME1--UBE3D	HAVANA	gene	20339	39653	.	+	.	FI_gene_label "UBE3D^ENSG00000118420.17"  ; ID "ME1--UBE3D^UBE3D^ENSG00000118420.17"  ; exon_id "ENSE00002062478.1"  ; exon_number 1 ; gene_id "ME1--UBE3D^UBE3D^ENSG00000118420.17"  ; gene_name UBE3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000015108.8"  ; havana_transcript "OTTHUMT00000366290.1"  ; hgnc_id "HGNC:21381"  ; level 2 ; orig_coord_info "chr6,83065680,83065718,-"  ; protein_id "ENSP00000237186.6"  ; transcript_id "ME1--UBE3D^ENST00000237186.10"  ; transcript_name "UBE3D-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ME1--UBE3D	HAVANA	mRNA	20339	39653	.	+	.	FI_gene_label "UBE3D^ENSG00000118420.17"  ; ID "ME1--UBE3D^ENST00000237186.10"  ; Parent "ME1--UBE3D^UBE3D^ENSG00000118420.17"  ; exon_id "ENSE00002062478.1"  ; exon_number 1 ; gene_id "ME1--UBE3D^UBE3D^ENSG00000118420.17"  ; gene_name UBE3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000015108.8"  ; havana_transcript "OTTHUMT00000366290.1"  ; hgnc_id "HGNC:21381"  ; level 2 ; orig_coord_info "chr6,83065680,83065718,-"  ; protein_id "ENSP00000237186.6"  ; transcript_id "ME1--UBE3D^ENST00000237186.10"  ; transcript_name "UBE3D-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ME1--UBE3D	HAVANA	gene	1001	17338	.	+	.	FI_gene_label "ME1^ENSG00000065833.9"  ; ID "ME1--UBE3D^ME1^ENSG00000065833.9"  ; ccdsid "CCDS34492.1"  ; exon_id "ENSE00000760044.5"  ; exon_number 1 ; gene_id "ME1--UBE3D^ME1^ENSG00000065833.9"  ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3"  ; havana_transcript "OTTHUMT00000041350.3"  ; hgnc_id "HGNC:6983"  ; level 2 ; orig_coord_info "chr6,83430877,83430954,-"  ; protein_id "ENSP00000358719.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--UBE3D^ENST00000369705.4"  ; transcript_name "ME1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ME1--UBE3D	HAVANA	mRNA	1001	17338	.	+	.	FI_gene_label "ME1^ENSG00000065833.9"  ; ID "ME1--UBE3D^ENST00000369705.4"  ; Parent "ME1--UBE3D^ME1^ENSG00000065833.9"  ; ccdsid "CCDS34492.1"  ; exon_id "ENSE00000760044.5"  ; exon_number 1 ; gene_id "ME1--UBE3D^ME1^ENSG00000065833.9"  ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3"  ; havana_transcript "OTTHUMT00000041350.3"  ; hgnc_id "HGNC:6983"  ; level 2 ; orig_coord_info "chr6,83430877,83430954,-"  ; protein_id "ENSP00000358719.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--UBE3D^ENST00000369705.4"  ; transcript_name "ME1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MYO18A--KRT18P55	HAVANA	gene	1001	48046	.	+	.	FI_gene_label "MYO18A^ENSG00000196535.17"  ; ID "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17"  ; ccdsid "CCDS45642.1"  ; exon_id "ENSE00002189252.1"  ; exon_number 2 ; gene_id "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17"  ; gene_name MYO18A ; gene_type protein_coding ; havana_gene "OTTHUMG00000166360.11"  ; havana_transcript "OTTHUMT00000389396.2"  ; hgnc_id "HGNC:31104"  ; level 2 ; orig_coord_info "chr17,29165942,29166940,-"  ; protein_id "ENSP00000437073.1"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18A--KRT18P55^ENST00000527372.7"  ; transcript_name "MYO18A-202"  ; transcript_support_level 1 ; transcript_type protein_coding
MYO18A--KRT18P55	HAVANA	mRNA	1001	48046	.	+	.	FI_gene_label "MYO18A^ENSG00000196535.17"  ; ID "MYO18A--KRT18P55^ENST00000527372.7"  ; Parent "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17"  ; ccdsid "CCDS45642.1"  ; exon_id "ENSE00002189252.1"  ; exon_number 2 ; gene_id "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17"  ; gene_name MYO18A ; gene_type protein_coding ; havana_gene "OTTHUMG00000166360.11"  ; havana_transcript "OTTHUMT00000389396.2"  ; hgnc_id "HGNC:31104"  ; level 2 ; orig_coord_info "chr17,29165942,29166940,-"  ; protein_id "ENSP00000437073.1"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18A--KRT18P55^ENST00000527372.7"  ; transcript_name "MYO18A-202"  ; 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: 
PLEKHG1--MTHFD1L	HAVANA	gene	11157	31558	.	+	.	FI_gene_label "PLEKHG1^ENSG00000120278.16"  ; ID "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16"  ; ccdsid "CCDS34552.1"  ; exon_id "ENSE00001444243.1"  ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16"  ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7"  ; havana_transcript "OTTHUMT00000042691.3"  ; hgnc_id "HGNC:20884"  ; level 2 ; orig_coord_info "chr6,150733682,150734092,+"  ; protein_id "ENSP00000351318.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6"  ; transcript_name "PLEKHG1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PLEKHG1--MTHFD1L	HAVANA	mRNA	11157	31558	.	+	.	FI_gene_label "PLEKHG1^ENSG00000120278.16"  ; ID "PLEKHG1--MTHFD1L^ENST00000358517.6"  ; Parent "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16"  ; ccdsid "CCDS34552.1"  ; exon_id "ENSE00001444243.1"  ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16"  ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7"  ; havana_transcript "OTTHUMT00000042691.3"  ; hgnc_id "HGNC:20884"  ; level 2 ; orig_coord_info "chr6,150733682,150734092,+"  ; protein_id "ENSP00000351318.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6"  ; transcript_name "PLEKHG1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PLEKHG1--MTHFD1L	HAVANA	gene	34596	42321	.	+	.	FI_gene_label "MTHFD1L^ENSG00000120254.16"  ; ID "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16"  ; ccdsid "CCDS56457.1"  ; exon_id "ENSE00003713432.1"  ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16"  ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4"  ; havana_transcript "OTTHUMT00000474291.1"  ; hgnc_id "HGNC:21055"  ; level 2 ; orig_coord_info "chr6,150865823,150866049,+"  ; protein_id "ENSP00000356276.4"  ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8"  ; transcript_name "MTHFD1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLEKHG1--MTHFD1L	HAVANA	mRNA	34596	42321	.	+	.	FI_gene_label "MTHFD1L^ENSG00000120254.16"  ; ID "PLEKHG1--MTHFD1L^ENST00000367307.8"  ; Parent "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16"  ; ccdsid "CCDS56457.1"  ; exon_id "ENSE00003713432.1"  ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16"  ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4"  ; havana_transcript "OTTHUMT00000474291.1"  ; hgnc_id "HGNC:21055"  ; level 2 ; orig_coord_info "chr6,150865823,150866049,+"  ; protein_id "ENSP00000356276.4"  ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8"  ; transcript_name "MTHFD1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNF135--AC005552.1	HAVANA	gene	1040	8369	.	+	.	FI_gene_label "RNF135^ENSG00000181481.14"  ; ID "RNF135--AC005552.1^RNF135^ENSG00000181481.14"  ; ccdsid "CCDS11263.1"  ; exon_id "ENSE00001315229.5"  ; exon_number 1 ; gene_id "RNF135--AC005552.1^RNF135^ENSG00000181481.14"  ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7"  ; havana_transcript "OTTHUMT00000256344.2"  ; hgnc_id "HGNC:21158"  ; level 2 ; orig_coord_info "chr17,30971074,30971445,+"  ; protein_id "ENSP00000323693.4"  ; tag basic CCDS ; transcript_id "RNF135--AC005552.1^ENST00000324689.8"  ; transcript_name "RNF135-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RNF135--AC005552.1	HAVANA	mRNA	1040	8369	.	+	.	FI_gene_label "RNF135^ENSG00000181481.14"  ; ID "RNF135--AC005552.1^ENST00000324689.8"  ; Parent "RNF135--AC005552.1^RNF135^ENSG00000181481.14"  ; ccdsid "CCDS11263.1"  ; exon_id "ENSE00001315229.5"  ; exon_number 1 ; gene_id "RNF135--AC005552.1^RNF135^ENSG00000181481.14"  ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7"  ; havana_transcript "OTTHUMT00000256344.2"  ; hgnc_id "HGNC:21158"  ; level 2 ; orig_coord_info "chr17,30971074,30971445,+"  ; protein_id "ENSP00000323693.4"  ; tag basic CCDS ; transcript_id "RNF135--AC005552.1^ENST00000324689.8"  ; transcript_name "RNF135-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNF135--TMEM132E	HAVANA	gene	11372	24274	.	+	.	FI_gene_label "TMEM132E^ENSG00000181291.8"  ; ID "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8"  ; exon_id "ENSE00001405658.4"  ; exon_number 1 ; gene_id "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8"  ; gene_name TMEM132E ; gene_type protein_coding ; havana_gene "OTTHUMG00000132927.4"  ; havana_transcript "OTTHUMT00000256440.3"  ; hgnc_id "HGNC:26991"  ; level 2 ; orig_coord_info "chr17,34581077,34581143,+"  ; protein_id "ENSP00000316532.5"  ; tag basic appris_alternative_2 ; transcript_id "RNF135--TMEM132E^ENST00000321639.7"  ; transcript_name "TMEM132E-201"  ; transcript_support_level 5 ; transcript_type protein_coding
RNF135--TMEM132E	HAVANA	mRNA	11372	24274	.	+	.	FI_gene_label "TMEM132E^ENSG00000181291.8"  ; ID "RNF135--TMEM132E^ENST00000321639.7"  ; Parent "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8"  ; exon_id "ENSE00001405658.4"  ; exon_number 1 ; gene_id "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8"  ; gene_name TMEM132E ; gene_type protein_coding ; havana_gene "OTTHUMG00000132927.4"  ; havana_transcript "OTTHUMT00000256440.3"  ; hgnc_id "HGNC:26991"  ; level 2 ; orig_coord_info "chr17,34581077,34581143,+"  ; protein_id "ENSP00000316532.5"  ; tag basic appris_alternative_2 ; transcript_id "RNF135--TMEM132E^ENST00000321639.7"  ; transcript_name "TMEM132E-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RNF135--TMEM132E	HAVANA	gene	1040	8369	.	+	.	FI_gene_label "RNF135^ENSG00000181481.14"  ; ID "RNF135--TMEM132E^RNF135^ENSG00000181481.14"  ; ccdsid "CCDS11263.1"  ; exon_id "ENSE00001315229.5"  ; exon_number 1 ; gene_id "RNF135--TMEM132E^RNF135^ENSG00000181481.14"  ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7"  ; havana_transcript "OTTHUMT00000256344.2"  ; hgnc_id "HGNC:21158"  ; level 2 ; orig_coord_info "chr17,30971074,30971445,+"  ; protein_id "ENSP00000323693.4"  ; tag basic CCDS ; transcript_id "RNF135--TMEM132E^ENST00000324689.8"  ; transcript_name "RNF135-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RNF135--TMEM132E	HAVANA	mRNA	1040	8369	.	+	.	FI_gene_label "RNF135^ENSG00000181481.14"  ; ID "RNF135--TMEM132E^ENST00000324689.8"  ; Parent "RNF135--TMEM132E^RNF135^ENSG00000181481.14"  ; ccdsid "CCDS11263.1"  ; exon_id "ENSE00001315229.5"  ; exon_number 1 ; gene_id "RNF135--TMEM132E^RNF135^ENSG00000181481.14"  ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7"  ; havana_transcript "OTTHUMT00000256344.2"  ; hgnc_id "HGNC:21158"  ; level 2 ; orig_coord_info "chr17,30971074,30971445,+"  ; protein_id "ENSP00000323693.4"  ; tag basic CCDS ; transcript_id "RNF135--TMEM132E^ENST00000324689.8"  ; transcript_name "RNF135-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^ENST00000403751.8"  ; Parent "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^ENST00000404752.6"  ; Parent "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; 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: 
TRAF4--AC011840.1	HAVANA	gene	1007	7728	.	+	.	FI_gene_label "TRAF4^ENSG00000076604.15"  ; ID "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15"  ; ccdsid "CCDS11243.1"  ; exon_id "ENSE00002729975.2"  ; exon_number 1 ; gene_id "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15"  ; gene_name TRAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132677.8"  ; havana_transcript "OTTHUMT00000255944.4"  ; hgnc_id "HGNC:12034"  ; level 2 ; orig_coord_info "chr17,28744113,28744255,+"  ; protein_id "ENSP00000262395.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRAF4--AC011840.1^ENST00000262395.10"  ; transcript_name "TRAF4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRAF4--AC011840.1	HAVANA	mRNA	1007	7728	.	+	.	FI_gene_label "TRAF4^ENSG00000076604.15"  ; ID "TRAF4--AC011840.1^ENST00000262395.10"  ; Parent "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15"  ; ccdsid "CCDS11243.1"  ; exon_id "ENSE00002729975.2"  ; exon_number 1 ; gene_id "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15"  ; gene_name TRAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132677.8"  ; havana_transcript "OTTHUMT00000255944.4"  ; hgnc_id "HGNC:12034"  ; level 2 ; orig_coord_info "chr17,28744113,28744255,+"  ; protein_id "ENSP00000262395.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRAF4--AC011840.1^ENST00000262395.10"  ; transcript_name "TRAF4-201"  ; 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: 
AL669831.1--SEPTIN14	HAVANA	gene	2344	8334	.	+	.	FI_gene_label "AL669831.1^ENSG00000228327.3"  ; ID "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3"  ; exon_id "ENSE00001630466.1"  ; exon_number 1 ; gene_id "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3"  ; gene_name "AL669831.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2"  ; havana_transcript "OTTHUMT00000488438.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,774171,774280,-"  ; tag basic ; transcript_id "AL669831.1--SEPTIN14^ENST00000428504.2"  ; transcript_name "AL669831.1-202"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AL669831.1--SEPTIN14	HAVANA	RNA	2344	8334	.	+	.	FI_gene_label "AL669831.1^ENSG00000228327.3"  ; ID "AL669831.1--SEPTIN14^ENST00000428504.2"  ; Parent "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3"  ; exon_id "ENSE00001630466.1"  ; exon_number 1 ; gene_id "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3"  ; gene_name "AL669831.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2"  ; havana_transcript "OTTHUMT00000488438.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,774171,774280,-"  ; tag basic ; transcript_id "AL669831.1--SEPTIN14^ENST00000428504.2"  ; transcript_name "AL669831.1-202"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
AL669831.4--SEPTIN14	HAVANA	RNA	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^ENST00000447500.4"  ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
GTF2A1L--STON1-GTF2A1L	HAVANA	gene	14395	15764	.	+	.	FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21"  ; ID "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21"  ; exon_id "ENSE00001916353.1"  ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21"  ; gene_name "STON1-GTF2A1L"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6"  ; havana_transcript "OTTHUMT00000325207.1"  ; hgnc_id "HGNC:30651"  ; level 1 ; orig_coord_info "chr2,48768954,48769121,+"  ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5"  ; transcript_name "STON1-GTF2A1L-205"  ; transcript_support_level 5 ; transcript_type processed_transcript
GTF2A1L--STON1-GTF2A1L	HAVANA	RNA	14395	15764	.	+	.	FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21"  ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5"  ; Parent "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21"  ; exon_id "ENSE00001916353.1"  ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21"  ; gene_name "STON1-GTF2A1L"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6"  ; havana_transcript "OTTHUMT00000325207.1"  ; hgnc_id "HGNC:30651"  ; level 1 ; orig_coord_info "chr2,48768954,48769121,+"  ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5"  ; transcript_name "STON1-GTF2A1L-205"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
MYO18A--KRT18P55	HAVANA	gene	52133	56897	.	+	.	FI_gene_label "KRT18P55^ENSG00000265480.5"  ; ID "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5"  ; exon_id "ENSE00002724983.1"  ; exon_number 1 ; gene_id "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5"  ; gene_name KRT18P55 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000179422.3"  ; havana_transcript "OTTHUMT00000446194.1"  ; hgnc_id "HGNC:26874"  ; level 2 ; orig_coord_info "chr17,28306976,28307382,-"  ; tag basic ; transcript_id "MYO18A--KRT18P55^ENST00000577198.5"  ; transcript_name "KRT18P55-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
MYO18A--KRT18P55	HAVANA	RNA	52133	56897	.	+	.	FI_gene_label "KRT18P55^ENSG00000265480.5"  ; ID "MYO18A--KRT18P55^ENST00000577198.5"  ; Parent "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5"  ; exon_id "ENSE00002724983.1"  ; exon_number 1 ; gene_id "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5"  ; gene_name KRT18P55 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000179422.3"  ; havana_transcript "OTTHUMT00000446194.1"  ; hgnc_id "HGNC:26874"  ; level 2 ; orig_coord_info "chr17,28306976,28307382,-"  ; tag basic ; transcript_id "MYO18A--KRT18P55^ENST00000577198.5"  ; transcript_name "KRT18P55-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
RNF135--AC005552.1	HAVANA	gene	11372	12033	.	+	.	FI_gene_label "AC005552.1^ENSG00000264174.1"  ; ID "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1"  ; exon_id "ENSE00002719564.1"  ; exon_number 1 ; gene_id "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1"  ; gene_name "AC005552.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179768.1"  ; havana_transcript "OTTHUMT00000448011.1"  ; level 2 ; orig_coord_info "chr17,34725509,34726170,-"  ; tag basic ; transcript_id "RNF135--AC005552.1^ENST00000577556.1"  ; transcript_name "AC005552.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
RNF135--AC005552.1	HAVANA	RNA	11372	12033	.	+	.	FI_gene_label "AC005552.1^ENSG00000264174.1"  ; ID "RNF135--AC005552.1^ENST00000577556.1"  ; Parent "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1"  ; exon_id "ENSE00002719564.1"  ; exon_number 1 ; gene_id "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1"  ; gene_name "AC005552.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179768.1"  ; havana_transcript "OTTHUMT00000448011.1"  ; level 2 ; orig_coord_info "chr17,34725509,34726170,-"  ; tag basic ; transcript_id "RNF135--AC005552.1^ENST00000577556.1"  ; transcript_name "AC005552.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
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
L1 and L2 created: 
TRAF4--AC011840.1	HAVANA	gene	10729	13673	.	+	.	FI_gene_label "AC011840.1^ENSG00000231421.8"  ; ID "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8"  ; exon_id "ENSE00001595653.2"  ; exon_number 1 ; gene_id "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8"  ; gene_name "AC011840.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000132806.4"  ; havana_transcript "OTTHUMT00000256223.3"  ; level 2 ; orig_coord_info "chr17,30576006,30577000,-"  ; tag basic TAGENE ; transcript_id "TRAF4--AC011840.1^ENST00000436477.7"  ; transcript_name "AC011840.1-202"  ; transcript_support_level 2 ; transcript_type lncRNA
TRAF4--AC011840.1	HAVANA	RNA	10729	13673	.	+	.	FI_gene_label "AC011840.1^ENSG00000231421.8"  ; ID "TRAF4--AC011840.1^ENST00000436477.7"  ; Parent "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8"  ; exon_id "ENSE00001595653.2"  ; exon_number 1 ; gene_id "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8"  ; gene_name "AC011840.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000132806.4"  ; havana_transcript "OTTHUMT00000256223.3"  ; level 2 ; orig_coord_info "chr17,30576006,30577000,-"  ; tag basic TAGENE ; transcript_id "TRAF4--AC011840.1^ENST00000436477.7"  ; transcript_name "AC011840.1-202"  ; transcript_support_level 2 ; transcript_type lncRNA
215 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 ------------------------------
385 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 24 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
Lets remove isoform PLEKHG1--MTHFD1L^ENST00000643692.1
1 identical isoforms removed
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 0 second) ------                   


GFF3 file parsed