.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cAd-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/b44975e353551bdb369305accf4459/.command.log
Size: 54.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cAd-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/78e8d47866ff5ed02e0eed51b6fbb8/fi_workdir/659_cAd-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/b44975e353551bdb369305accf4459/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/b44975e353551bdb369305accf4459/.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: 4806
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4806
=> 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:4806
  => 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: 
ARHGEF18--OR7C1	HAVANA	gene	41978	43043	.	+	.	FI_gene_label "OR7C1^ENSG00000127530.4"  ; ID "ARHGEF18--OR7C1^OR7C1^ENSG00000127530.4"  ; ccdsid "CCDS12317.1"  ; exon_id "ENSE00000873236.2"  ; exon_number 1 ; gene_id "ARHGEF18--OR7C1^OR7C1^ENSG00000127530.4"  ; gene_name OR7C1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183411.3"  ; havana_transcript "OTTHUMT00000466519.2"  ; hgnc_id "HGNC:8373"  ; level 2 ; orig_coord_info "chr19,14799177,14800136,-"  ; protein_id "ENSP00000248073.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGEF18--OR7C1^ENST00000248073.2"  ; transcript_name "OR7C1-201"  ; transcript_support_level NA ; transcript_type protein_coding
ARHGEF18--OR7C1	HAVANA	mRNA	41978	43043	.	+	.	FI_gene_label "OR7C1^ENSG00000127530.4"  ; ID "ARHGEF18--OR7C1^ENST00000248073.2"  ; Parent "ARHGEF18--OR7C1^OR7C1^ENSG00000127530.4"  ; ccdsid "CCDS12317.1"  ; exon_id "ENSE00000873236.2"  ; exon_number 1 ; gene_id "ARHGEF18--OR7C1^OR7C1^ENSG00000127530.4"  ; gene_name OR7C1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183411.3"  ; havana_transcript "OTTHUMT00000466519.2"  ; hgnc_id "HGNC:8373"  ; level 2 ; orig_coord_info "chr19,14799177,14800136,-"  ; protein_id "ENSP00000248073.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGEF18--OR7C1^ENST00000248073.2"  ; transcript_name "OR7C1-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF18--OR7C1	HAVANA	gene	12080	32943	.	+	.	FI_gene_label "ARHGEF18^ENSG00000104880.19"  ; ID "ARHGEF18--OR7C1^ARHGEF18^ENSG00000104880.19"  ; exon_id "ENSE00003546636.1"  ; exon_number 2 ; gene_id "ARHGEF18--OR7C1^ARHGEF18^ENSG00000104880.19"  ; gene_name ARHGEF18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177342.5"  ; havana_transcript "OTTHUMT00000436339.2"  ; hgnc_id "HGNC:17090"  ; level 2 ; orig_coord_info "chr19,7440415,7440482,+"  ; protein_id "ENSP00000319200.8"  ; tag basic appris_alternative_2 ; transcript_id "ARHGEF18--OR7C1^ENST00000319670.14"  ; transcript_name "ARHGEF18-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGEF18--OR7C1	HAVANA	mRNA	12080	32943	.	+	.	FI_gene_label "ARHGEF18^ENSG00000104880.19"  ; ID "ARHGEF18--OR7C1^ENST00000319670.14"  ; Parent "ARHGEF18--OR7C1^ARHGEF18^ENSG00000104880.19"  ; exon_id "ENSE00003546636.1"  ; exon_number 2 ; gene_id "ARHGEF18--OR7C1^ARHGEF18^ENSG00000104880.19"  ; gene_name ARHGEF18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177342.5"  ; havana_transcript "OTTHUMT00000436339.2"  ; hgnc_id "HGNC:17090"  ; level 2 ; orig_coord_info "chr19,7440415,7440482,+"  ; protein_id "ENSP00000319200.8"  ; tag basic appris_alternative_2 ; transcript_id "ARHGEF18--OR7C1^ENST00000319670.14"  ; transcript_name "ARHGEF18-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARL17B--BPTF	HAVANA	gene	23450	66548	.	+	.	FI_gene_label "BPTF^ENSG00000171634.18"  ; ID "ARL17B--BPTF^BPTF^ENSG00000171634.18"  ; ccdsid "CCDS11673.1"  ; exon_id "ENSE00002689718.2"  ; exon_number 1 ; gene_id "ARL17B--BPTF^BPTF^ENSG00000171634.18"  ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6"  ; havana_transcript "OTTHUMT00000255334.3"  ; hgnc_id "HGNC:3581"  ; level 2 ; orig_coord_info "chr17,67825725,67826337,+"  ; protein_id "ENSP00000307208.6"  ; tag basic MANE_Select CCDS ; transcript_id "ARL17B--BPTF^ENST00000306378.11"  ; transcript_name "BPTF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARL17B--BPTF	HAVANA	mRNA	23450	66548	.	+	.	FI_gene_label "BPTF^ENSG00000171634.18"  ; ID "ARL17B--BPTF^ENST00000306378.11"  ; Parent "ARL17B--BPTF^BPTF^ENSG00000171634.18"  ; ccdsid "CCDS11673.1"  ; exon_id "ENSE00002689718.2"  ; exon_number 1 ; gene_id "ARL17B--BPTF^BPTF^ENSG00000171634.18"  ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6"  ; havana_transcript "OTTHUMT00000255334.3"  ; hgnc_id "HGNC:3581"  ; level 2 ; orig_coord_info "chr17,67825725,67826337,+"  ; protein_id "ENSP00000307208.6"  ; tag basic MANE_Select CCDS ; transcript_id "ARL17B--BPTF^ENST00000306378.11"  ; transcript_name "BPTF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARL17B--BPTF	HAVANA	gene	1053	16124	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "ARL17B--BPTF^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "ARL17B--BPTF^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "ARL17B--BPTF^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARL17B--BPTF	HAVANA	mRNA	1053	16124	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "ARL17B--BPTF^ENST00000434041.6"  ; Parent "ARL17B--BPTF^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "ARL17B--BPTF^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "ARL17B--BPTF^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BPTF--ARL17B	HAVANA	gene	1001	44099	.	+	.	FI_gene_label "BPTF^ENSG00000171634.18"  ; ID "BPTF--ARL17B^BPTF^ENSG00000171634.18"  ; ccdsid "CCDS11673.1"  ; exon_id "ENSE00002689718.2"  ; exon_number 1 ; gene_id "BPTF--ARL17B^BPTF^ENSG00000171634.18"  ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6"  ; havana_transcript "OTTHUMT00000255334.3"  ; hgnc_id "HGNC:3581"  ; level 2 ; orig_coord_info "chr17,67825725,67826337,+"  ; protein_id "ENSP00000307208.6"  ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ARL17B^ENST00000306378.11"  ; transcript_name "BPTF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BPTF--ARL17B	HAVANA	mRNA	1001	44099	.	+	.	FI_gene_label "BPTF^ENSG00000171634.18"  ; ID "BPTF--ARL17B^ENST00000306378.11"  ; Parent "BPTF--ARL17B^BPTF^ENSG00000171634.18"  ; ccdsid "CCDS11673.1"  ; exon_id "ENSE00002689718.2"  ; exon_number 1 ; gene_id "BPTF--ARL17B^BPTF^ENSG00000171634.18"  ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6"  ; havana_transcript "OTTHUMT00000255334.3"  ; hgnc_id "HGNC:3581"  ; level 2 ; orig_coord_info "chr17,67825725,67826337,+"  ; protein_id "ENSP00000307208.6"  ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ARL17B^ENST00000306378.11"  ; transcript_name "BPTF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BPTF--ARL17B	HAVANA	gene	47152	62223	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "BPTF--ARL17B^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "BPTF--ARL17B^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "BPTF--ARL17B^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BPTF--ARL17B	HAVANA	mRNA	47152	62223	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "BPTF--ARL17B^ENST00000434041.6"  ; Parent "BPTF--ARL17B^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "BPTF--ARL17B^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "BPTF--ARL17B^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DR1--AL499605.1	HAVANA	gene	1029	6503	.	+	.	FI_gene_label "DR1^ENSG00000117505.13"  ; ID "DR1--AL499605.1^DR1^ENSG00000117505.13"  ; ccdsid "CCDS744.1"  ; exon_id "ENSE00001452215.1"  ; exon_number 2 ; gene_id "DR1--AL499605.1^DR1^ENSG00000117505.13"  ; gene_name DR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010862.3"  ; havana_transcript "OTTHUMT00000029977.1"  ; hgnc_id "HGNC:3017"  ; level 2 ; orig_coord_info "chr1,93346646,93346865,+"  ; protein_id "ENSP00000359290.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DR1--AL499605.1^ENST00000370267.1"  ; transcript_name "DR1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DR1--AL499605.1	HAVANA	mRNA	1029	6503	.	+	.	FI_gene_label "DR1^ENSG00000117505.13"  ; ID "DR1--AL499605.1^ENST00000370267.1"  ; Parent "DR1--AL499605.1^DR1^ENSG00000117505.13"  ; ccdsid "CCDS744.1"  ; exon_id "ENSE00001452215.1"  ; exon_number 2 ; gene_id "DR1--AL499605.1^DR1^ENSG00000117505.13"  ; gene_name DR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010862.3"  ; havana_transcript "OTTHUMT00000029977.1"  ; hgnc_id "HGNC:3017"  ; level 2 ; orig_coord_info "chr1,93346646,93346865,+"  ; protein_id "ENSP00000359290.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DR1--AL499605.1^ENST00000370267.1"  ; transcript_name "DR1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
DR1--AL596327.1	HAVANA	gene	1029	6503	.	+	.	FI_gene_label "DR1^ENSG00000117505.13"  ; ID "DR1--AL596327.1^DR1^ENSG00000117505.13"  ; ccdsid "CCDS744.1"  ; exon_id "ENSE00001452215.1"  ; exon_number 2 ; gene_id "DR1--AL596327.1^DR1^ENSG00000117505.13"  ; gene_name DR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010862.3"  ; havana_transcript "OTTHUMT00000029977.1"  ; hgnc_id "HGNC:3017"  ; level 2 ; orig_coord_info "chr1,93346646,93346865,+"  ; protein_id "ENSP00000359290.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DR1--AL596327.1^ENST00000370267.1"  ; transcript_name "DR1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DR1--AL596327.1	HAVANA	mRNA	1029	6503	.	+	.	FI_gene_label "DR1^ENSG00000117505.13"  ; ID "DR1--AL596327.1^ENST00000370267.1"  ; Parent "DR1--AL596327.1^DR1^ENSG00000117505.13"  ; ccdsid "CCDS744.1"  ; exon_id "ENSE00001452215.1"  ; exon_number 2 ; gene_id "DR1--AL596327.1^DR1^ENSG00000117505.13"  ; gene_name DR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010862.3"  ; havana_transcript "OTTHUMT00000029977.1"  ; hgnc_id "HGNC:3017"  ; level 2 ; orig_coord_info "chr1,93346646,93346865,+"  ; protein_id "ENSP00000359290.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DR1--AL596327.1^ENST00000370267.1"  ; transcript_name "DR1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
LARP4B--SLC45A2	HAVANA	gene	32564	41779	.	+	.	FI_gene_label "SLC45A2^ENSG00000164175.15"  ; ID "LARP4B--SLC45A2^SLC45A2^ENSG00000164175.15"  ; ccdsid "CCDS3901.1"  ; exon_id "ENSE00001953232.2"  ; exon_number 1 ; gene_id "LARP4B--SLC45A2^SLC45A2^ENSG00000164175.15"  ; gene_name SLC45A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090719.6"  ; havana_transcript "OTTHUMT00000207443.3"  ; hgnc_id "HGNC:16472"  ; level 2 ; orig_coord_info "chr5,33984199,33984583,-"  ; protein_id "ENSP00000296589.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "LARP4B--SLC45A2^ENST00000296589.9"  ; transcript_name "SLC45A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LARP4B--SLC45A2	HAVANA	mRNA	32564	41779	.	+	.	FI_gene_label "SLC45A2^ENSG00000164175.15"  ; ID "LARP4B--SLC45A2^ENST00000296589.9"  ; Parent "LARP4B--SLC45A2^SLC45A2^ENSG00000164175.15"  ; ccdsid "CCDS3901.1"  ; exon_id "ENSE00001953232.2"  ; exon_number 1 ; gene_id "LARP4B--SLC45A2^SLC45A2^ENSG00000164175.15"  ; gene_name SLC45A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090719.6"  ; havana_transcript "OTTHUMT00000207443.3"  ; hgnc_id "HGNC:16472"  ; level 2 ; orig_coord_info "chr5,33984199,33984583,-"  ; protein_id "ENSP00000296589.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "LARP4B--SLC45A2^ENST00000296589.9"  ; transcript_name "SLC45A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LARP4B--SLC45A2	HAVANA	gene	1001	27204	.	+	.	FI_gene_label "LARP4B^ENSG00000107929.15"  ; ID "LARP4B--SLC45A2^LARP4B^ENSG00000107929.15"  ; ccdsid "CCDS31131.1"  ; exon_id "ENSE00003703032.1"  ; exon_number 2 ; gene_id "LARP4B--SLC45A2^LARP4B^ENSG00000107929.15"  ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8"  ; havana_transcript "OTTHUMT00000046395.5"  ; hgnc_id "HGNC:28987"  ; level 2 ; orig_coord_info "chr10,885641,885721,-"  ; protein_id "ENSP00000326128.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--SLC45A2^ENST00000316157.8"  ; transcript_name "LARP4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LARP4B--SLC45A2	HAVANA	mRNA	1001	27204	.	+	.	FI_gene_label "LARP4B^ENSG00000107929.15"  ; ID "LARP4B--SLC45A2^ENST00000316157.8"  ; Parent "LARP4B--SLC45A2^LARP4B^ENSG00000107929.15"  ; ccdsid "CCDS31131.1"  ; exon_id "ENSE00003703032.1"  ; exon_number 2 ; gene_id "LARP4B--SLC45A2^LARP4B^ENSG00000107929.15"  ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8"  ; havana_transcript "OTTHUMT00000046395.5"  ; hgnc_id "HGNC:28987"  ; level 2 ; orig_coord_info "chr10,885641,885721,-"  ; protein_id "ENSP00000326128.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--SLC45A2^ENST00000316157.8"  ; transcript_name "LARP4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MDN1--KCNH1	HAVANA	gene	100259	120480	.	+	.	FI_gene_label "KCNH1^ENSG00000143473.13"  ; ID "MDN1--KCNH1^KCNH1^ENSG00000143473.13"  ; ccdsid "CCDS1496.1"  ; exon_id "ENSE00003801336.1"  ; exon_number 1 ; gene_id "MDN1--KCNH1^KCNH1^ENSG00000143473.13"  ; gene_name KCNH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000036309.9"  ; havana_transcript "OTTHUMT00000088332.4"  ; hgnc_id "HGNC:6250"  ; level 2 ; orig_coord_info "chr1,211133867,211133945,-"  ; protein_id "ENSP00000271751.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "MDN1--KCNH1^ENST00000271751.10"  ; transcript_name "KCNH1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MDN1--KCNH1	HAVANA	mRNA	100259	120480	.	+	.	FI_gene_label "KCNH1^ENSG00000143473.13"  ; ID "MDN1--KCNH1^ENST00000271751.10"  ; Parent "MDN1--KCNH1^KCNH1^ENSG00000143473.13"  ; ccdsid "CCDS1496.1"  ; exon_id "ENSE00003801336.1"  ; exon_number 1 ; gene_id "MDN1--KCNH1^KCNH1^ENSG00000143473.13"  ; gene_name KCNH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000036309.9"  ; havana_transcript "OTTHUMT00000088332.4"  ; hgnc_id "HGNC:6250"  ; level 2 ; orig_coord_info "chr1,211133867,211133945,-"  ; protein_id "ENSP00000271751.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "MDN1--KCNH1^ENST00000271751.10"  ; transcript_name "KCNH1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
MDN1--KCNH1	HAVANA	gene	1001	97241	.	+	.	FI_gene_label "MDN1^ENSG00000112159.12"  ; ID "MDN1--KCNH1^MDN1^ENSG00000112159.12"  ; ccdsid "CCDS5024.1"  ; exon_id "ENSE00003846986.1"  ; exon_number 1 ; gene_id "MDN1--KCNH1^MDN1^ENSG00000112159.12"  ; gene_name MDN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015213.4"  ; havana_transcript "OTTHUMT00000041514.3"  ; hgnc_id "HGNC:18302"  ; level 2 ; orig_coord_info "chr6,89819506,89819607,-"  ; protein_id "ENSP00000358400.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDN1--KCNH1^ENST00000369393.8"  ; transcript_name "MDN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MDN1--KCNH1	HAVANA	mRNA	1001	97241	.	+	.	FI_gene_label "MDN1^ENSG00000112159.12"  ; ID "MDN1--KCNH1^ENST00000369393.8"  ; Parent "MDN1--KCNH1^MDN1^ENSG00000112159.12"  ; ccdsid "CCDS5024.1"  ; exon_id "ENSE00003846986.1"  ; exon_number 1 ; gene_id "MDN1--KCNH1^MDN1^ENSG00000112159.12"  ; gene_name MDN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015213.4"  ; havana_transcript "OTTHUMT00000041514.3"  ; hgnc_id "HGNC:18302"  ; level 2 ; orig_coord_info "chr6,89819506,89819607,-"  ; protein_id "ENSP00000358400.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDN1--KCNH1^ENST00000369393.8"  ; transcript_name "MDN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF8--CLCN5	HAVANA	gene	43319	55788	.	+	.	FI_gene_label "CLCN5^ENSG00000171365.17"  ; ID "PHF8--CLCN5^CLCN5^ENSG00000171365.17"  ; ccdsid "CCDS14328.1"  ; exon_id "ENSE00003648075.1"  ; exon_number 2 ; gene_id "PHF8--CLCN5^CLCN5^ENSG00000171365.17"  ; gene_name CLCN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021514.7"  ; havana_transcript "OTTHUMT00000056544.1"  ; hgnc_id "HGNC:2023"  ; level 2 ; orig_coord_info "chrX,50069926,50070030,+"  ; protein_id "ENSP00000304257.2"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PHF8--CLCN5^ENST00000307367.2"  ; transcript_name "CLCN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF8--CLCN5	HAVANA	mRNA	43319	55788	.	+	.	FI_gene_label "CLCN5^ENSG00000171365.17"  ; ID "PHF8--CLCN5^ENST00000307367.2"  ; Parent "PHF8--CLCN5^CLCN5^ENSG00000171365.17"  ; ccdsid "CCDS14328.1"  ; exon_id "ENSE00003648075.1"  ; exon_number 2 ; gene_id "PHF8--CLCN5^CLCN5^ENSG00000171365.17"  ; gene_name CLCN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021514.7"  ; havana_transcript "OTTHUMT00000056544.1"  ; hgnc_id "HGNC:2023"  ; level 2 ; orig_coord_info "chrX,50069926,50070030,+"  ; protein_id "ENSP00000304257.2"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PHF8--CLCN5^ENST00000307367.2"  ; transcript_name "CLCN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF8--CLCN5	HAVANA	gene	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--CLCN5^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--CLCN5^PHF8^ENSG00000172943.20"  ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4"  ; havana_transcript "OTTHUMT00000056785.2"  ; hgnc_id "HGNC:20672"  ; level 1 ; orig_coord_info "chrX,54042631,54042728,-"  ; protein_id "ENSP00000319473.8"  ; tag basic exp_conf CCDS ; transcript_id "PHF8--CLCN5^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF8--CLCN5	HAVANA	mRNA	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--CLCN5^ENST00000322659.12"  ; Parent "PHF8--CLCN5^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--CLCN5^PHF8^ENSG00000172943.20"  ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4"  ; havana_transcript "OTTHUMT00000056785.2"  ; hgnc_id "HGNC:20672"  ; level 1 ; orig_coord_info "chrX,54042631,54042728,-"  ; protein_id "ENSP00000319473.8"  ; tag basic exp_conf CCDS ; transcript_id "PHF8--CLCN5^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PI4KA--LINC02564	HAVANA	gene	1607	51209	.	+	.	FI_gene_label "PI4KA^ENSG00000241973.11"  ; ID "PI4KA--LINC02564^PI4KA^ENSG00000241973.11"  ; ccdsid "CCDS33603.2"  ; exon_id "ENSE00003649653.2"  ; exon_number 1 ; gene_id "PI4KA--LINC02564^PI4KA^ENSG00000241973.11"  ; gene_name PI4KA ; gene_type protein_coding ; havana_gene "OTTHUMG00000167440.4"  ; havana_transcript "OTTHUMT00000075723.6"  ; hgnc_id "HGNC:8983"  ; level 2 ; orig_coord_info "chr22,20858570,20858725,-"  ; protein_id "ENSP00000255882.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PI4KA--LINC02564^ENST00000255882.11"  ; transcript_name "PI4KA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PI4KA--LINC02564	HAVANA	mRNA	1607	51209	.	+	.	FI_gene_label "PI4KA^ENSG00000241973.11"  ; ID "PI4KA--LINC02564^ENST00000255882.11"  ; Parent "PI4KA--LINC02564^PI4KA^ENSG00000241973.11"  ; ccdsid "CCDS33603.2"  ; exon_id "ENSE00003649653.2"  ; exon_number 1 ; gene_id "PI4KA--LINC02564^PI4KA^ENSG00000241973.11"  ; gene_name PI4KA ; gene_type protein_coding ; havana_gene "OTTHUMG00000167440.4"  ; havana_transcript "OTTHUMT00000075723.6"  ; hgnc_id "HGNC:8983"  ; level 2 ; orig_coord_info "chr22,20858570,20858725,-"  ; protein_id "ENSP00000255882.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PI4KA--LINC02564^ENST00000255882.11"  ; transcript_name "PI4KA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTPRK--RSPO3	HAVANA	gene	53093	62586	.	+	.	FI_gene_label "RSPO3^ENSG00000146374.14"  ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14"  ; ccdsid "CCDS5135.1"  ; exon_id "ENSE00001858691.2"  ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14"  ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2"  ; havana_transcript "OTTHUMT00000042111.2"  ; hgnc_id "HGNC:20866"  ; level 2 ; orig_coord_info "chr6,127119193,127119289,+"  ; protein_id "ENSP00000349131.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9"  ; transcript_name "RSPO3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PTPRK--RSPO3	HAVANA	mRNA	53093	62586	.	+	.	FI_gene_label "RSPO3^ENSG00000146374.14"  ; ID "PTPRK--RSPO3^ENST00000356698.9"  ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14"  ; ccdsid "CCDS5135.1"  ; exon_id "ENSE00001858691.2"  ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14"  ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2"  ; havana_transcript "OTTHUMT00000042111.2"  ; hgnc_id "HGNC:20866"  ; level 2 ; orig_coord_info "chr6,127119193,127119289,+"  ; protein_id "ENSP00000349131.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9"  ; transcript_name "RSPO3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTPRK--RSPO3	HAVANA	gene	1034	48764	.	+	.	FI_gene_label "PTPRK^ENSG00000152894.15"  ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15"  ; exon_id "ENSE00002151979.1"  ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15"  ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10"  ; havana_transcript "OTTHUMT00000390045.1"  ; hgnc_id "HGNC:9674"  ; level 2 ; orig_coord_info "chr6,128520259,128520358,-"  ; protein_id "ENSP00000357190.3"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7"  ; transcript_name "PTPRK-203"  ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--RSPO3	HAVANA	mRNA	1034	48764	.	+	.	FI_gene_label "PTPRK^ENSG00000152894.15"  ; ID "PTPRK--RSPO3^ENST00000368207.7"  ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15"  ; exon_id "ENSE00002151979.1"  ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15"  ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10"  ; havana_transcript "OTTHUMT00000390045.1"  ; hgnc_id "HGNC:9674"  ; level 2 ; orig_coord_info "chr6,128520259,128520358,-"  ; protein_id "ENSP00000357190.3"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7"  ; transcript_name "PTPRK-203"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RANBP1--LINC01900	HAVANA	gene	2611	10069	.	+	.	FI_gene_label "RANBP1^ENSG00000099901.17"  ; ID "RANBP1--LINC01900^RANBP1^ENSG00000099901.17"  ; ccdsid "CCDS13775.1"  ; exon_id "ENSE00001953373.1"  ; exon_number 1 ; gene_id "RANBP1--LINC01900^RANBP1^ENSG00000099901.17"  ; gene_name RANBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150490.35"  ; havana_transcript "OTTHUMT00000343733.1"  ; hgnc_id "HGNC:9847"  ; level 2 ; orig_coord_info "chr22,20117650,20117664,+"  ; protein_id "ENSP00000327583.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "RANBP1--LINC01900^ENST00000331821.7"  ; transcript_name "RANBP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RANBP1--LINC01900	HAVANA	mRNA	2611	10069	.	+	.	FI_gene_label "RANBP1^ENSG00000099901.17"  ; ID "RANBP1--LINC01900^ENST00000331821.7"  ; Parent "RANBP1--LINC01900^RANBP1^ENSG00000099901.17"  ; ccdsid "CCDS13775.1"  ; exon_id "ENSE00001953373.1"  ; exon_number 1 ; gene_id "RANBP1--LINC01900^RANBP1^ENSG00000099901.17"  ; gene_name RANBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150490.35"  ; havana_transcript "OTTHUMT00000343733.1"  ; hgnc_id "HGNC:9847"  ; level 2 ; orig_coord_info "chr22,20117650,20117664,+"  ; protein_id "ENSP00000327583.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "RANBP1--LINC01900^ENST00000331821.7"  ; transcript_name "RANBP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TEAD3--LRMDA	HAVANA	gene	1001	11276	.	+	.	FI_gene_label "TEAD3^ENSG00000007866.22"  ; ID "TEAD3--LRMDA^TEAD3^ENSG00000007866.22"  ; ccdsid "CCDS47414.1"  ; exon_id "ENSE00003835150.1"  ; exon_number 2 ; gene_id "TEAD3--LRMDA^TEAD3^ENSG00000007866.22"  ; gene_name TEAD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014571.6"  ; havana_transcript "OTTHUMT00000040298.4"  ; hgnc_id "HGNC:11716"  ; level 2 ; orig_coord_info "chr6,35486461,35486662,-"  ; protein_id "ENSP00000345772.8"  ; tag non_ATG_start basic appris_principal_2 CCDS ; transcript_id "TEAD3--LRMDA^ENST00000338863.13"  ; transcript_name "TEAD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TEAD3--LRMDA	HAVANA	mRNA	1001	11276	.	+	.	FI_gene_label "TEAD3^ENSG00000007866.22"  ; ID "TEAD3--LRMDA^ENST00000338863.13"  ; Parent "TEAD3--LRMDA^TEAD3^ENSG00000007866.22"  ; ccdsid "CCDS47414.1"  ; exon_id "ENSE00003835150.1"  ; exon_number 2 ; gene_id "TEAD3--LRMDA^TEAD3^ENSG00000007866.22"  ; gene_name TEAD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014571.6"  ; havana_transcript "OTTHUMT00000040298.4"  ; hgnc_id "HGNC:11716"  ; level 2 ; orig_coord_info "chr6,35486461,35486662,-"  ; protein_id "ENSP00000345772.8"  ; tag non_ATG_start basic appris_principal_2 CCDS ; transcript_id "TEAD3--LRMDA^ENST00000338863.13"  ; transcript_name "TEAD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TEAD3--LRMDA	HAVANA	gene	18686	37953	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "TEAD3--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "TEAD3--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "TEAD3--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TEAD3--LRMDA	HAVANA	mRNA	18686	37953	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "TEAD3--LRMDA^ENST00000372499.5"  ; Parent "TEAD3--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "TEAD3--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "TEAD3--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-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: 
TTC19--NCOR1	HAVANA	gene	1041	12484	.	+	.	FI_gene_label "TTC19^ENSG00000011295.16"  ; ID "TTC19--NCOR1^TTC19^ENSG00000011295.16"  ; ccdsid "CCDS11174.2"  ; exon_id "ENSE00001013755.5"  ; exon_number 1 ; gene_id "TTC19--NCOR1^TTC19^ENSG00000011295.16"  ; gene_name TTC19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059306.11"  ; havana_transcript "OTTHUMT00000131725.7"  ; hgnc_id "HGNC:26006"  ; level 2 ; orig_coord_info "chr17,15999849,16000032,+"  ; protein_id "ENSP00000261647.5"  ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTC19--NCOR1^ENST00000261647.10"  ; transcript_name "TTC19-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTC19--NCOR1	HAVANA	mRNA	1041	12484	.	+	.	FI_gene_label "TTC19^ENSG00000011295.16"  ; ID "TTC19--NCOR1^ENST00000261647.10"  ; Parent "TTC19--NCOR1^TTC19^ENSG00000011295.16"  ; ccdsid "CCDS11174.2"  ; exon_id "ENSE00001013755.5"  ; exon_number 1 ; gene_id "TTC19--NCOR1^TTC19^ENSG00000011295.16"  ; gene_name TTC19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059306.11"  ; havana_transcript "OTTHUMT00000131725.7"  ; hgnc_id "HGNC:26006"  ; level 2 ; orig_coord_info "chr17,15999849,16000032,+"  ; protein_id "ENSP00000261647.5"  ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTC19--NCOR1^ENST00000261647.10"  ; transcript_name "TTC19-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTC19--NCOR1	HAVANA	gene	18876	74825	.	+	.	FI_gene_label "NCOR1^ENSG00000141027.21"  ; ID "TTC19--NCOR1^NCOR1^ENSG00000141027.21"  ; ccdsid "CCDS11175.1"  ; exon_id "ENSE00003656730.1"  ; exon_number 2 ; gene_id "TTC19--NCOR1^NCOR1^ENSG00000141027.21"  ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12"  ; havana_transcript "OTTHUMT00000131751.6"  ; hgnc_id "HGNC:7672"  ; level 2 ; orig_coord_info "chr17,16194462,16194569,-"  ; protein_id "ENSP00000268712.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "TTC19--NCOR1^ENST00000268712.8"  ; transcript_name "NCOR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTC19--NCOR1	HAVANA	mRNA	18876	74825	.	+	.	FI_gene_label "NCOR1^ENSG00000141027.21"  ; ID "TTC19--NCOR1^ENST00000268712.8"  ; Parent "TTC19--NCOR1^NCOR1^ENSG00000141027.21"  ; ccdsid "CCDS11175.1"  ; exon_id "ENSE00003656730.1"  ; exon_number 2 ; gene_id "TTC19--NCOR1^NCOR1^ENSG00000141027.21"  ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12"  ; havana_transcript "OTTHUMT00000131751.6"  ; hgnc_id "HGNC:7672"  ; level 2 ; orig_coord_info "chr17,16194462,16194569,-"  ; protein_id "ENSP00000268712.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "TTC19--NCOR1^ENST00000268712.8"  ; transcript_name "NCOR1-201"  ; 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: 
AC025884.2--IGH-@-ext	HAVANA	gene	1001	1711	.	+	.	FI_gene_label "AC025884.2^ENSG00000259098.1"  ; ID "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1"  ; exon_id "ENSE00002441536.1"  ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1"  ; gene_name "AC025884.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1"  ; havana_transcript "OTTHUMT00000415152.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr15,22258138,22258848,+"  ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1"  ; transcript_name "AC025884.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
AC025884.2--IGH-@-ext	HAVANA	RNA	1001	1711	.	+	.	FI_gene_label "AC025884.2^ENSG00000259098.1"  ; ID "AC025884.2--IGH-@-ext^ENST00000553429.1"  ; Parent "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1"  ; exon_id "ENSE00002441536.1"  ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1"  ; gene_name "AC025884.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1"  ; havana_transcript "OTTHUMT00000415152.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr15,22258138,22258848,+"  ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1"  ; transcript_name "AC025884.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
AC025884.2--IGH-@-ext	SuperLocus-ext	gene	4712	1296052	.	+	.	FI_gene_label "IGH-@-ext^IGH-.g@-ext"  ; ID "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext"  ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext"  ; gene_name "IGH-@-ext"  ; orig_coord_info "chr14,105583731,106875071,+"  ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext" 
AC025884.2--IGH-@-ext	SuperLocus-ext	RNA	4712	1296052	.	+	.	FI_gene_label "IGH-@-ext^IGH-.g@-ext"  ; ID "AC025884.2--IGH-@-ext^IGH-.t@-ext"  ; Parent "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext"  ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext"  ; gene_name "IGH-@-ext"  ; orig_coord_info "chr14,105583731,106875071,+"  ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext" 
L1 and L2 created: 
BMS1P7--AGAP13P	HAVANA	gene	10576	13938	.	+	.	FI_gene_label "AGAP13P^ENSG00000243289.1"  ; ID "BMS1P7--AGAP13P^AGAP13P^ENSG00000243289.1"  ; exon_id "ENSE00002475142.1"  ; exon_number 1 ; gene_id "BMS1P7--AGAP13P^AGAP13P^ENSG00000243289.1"  ; gene_name AGAP13P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000018095.2"  ; havana_transcript "OTTHUMT00000047819.2"  ; hgnc_id "HGNC:23499"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr10,46816516,46816738,+"  ; tag basic ; transcript_id "BMS1P7--AGAP13P^ENST00000417888.1"  ; transcript_name "AGAP13P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
BMS1P7--AGAP13P	HAVANA	RNA	10576	13938	.	+	.	FI_gene_label "AGAP13P^ENSG00000243289.1"  ; ID "BMS1P7--AGAP13P^ENST00000417888.1"  ; Parent "BMS1P7--AGAP13P^AGAP13P^ENSG00000243289.1"  ; exon_id "ENSE00002475142.1"  ; exon_number 1 ; gene_id "BMS1P7--AGAP13P^AGAP13P^ENSG00000243289.1"  ; gene_name AGAP13P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000018095.2"  ; havana_transcript "OTTHUMT00000047819.2"  ; hgnc_id "HGNC:23499"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr10,46816516,46816738,+"  ; tag basic ; transcript_id "BMS1P7--AGAP13P^ENST00000417888.1"  ; transcript_name "AGAP13P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
BMS1P7--AGAP13P	HAVANA	gene	1001	7575	.	+	.	FI_gene_label "BMS1P7^ENSG00000270025.2"  ; ID "BMS1P7--AGAP13P^BMS1P7^ENSG00000270025.2"  ; exon_id "ENSE00001675840.2"  ; exon_number 1 ; gene_id "BMS1P7--AGAP13P^BMS1P7^ENSG00000270025.2"  ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3"  ; havana_transcript "OTTHUMT00000047911.2"  ; hgnc_id "HGNC:23655"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48059827,48060016,-"  ; tag basic ; transcript_id "BMS1P7--AGAP13P^ENST00000602440.2"  ; transcript_name "BMS1P7-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
BMS1P7--AGAP13P	HAVANA	RNA	1001	7575	.	+	.	FI_gene_label "BMS1P7^ENSG00000270025.2"  ; ID "BMS1P7--AGAP13P^ENST00000602440.2"  ; Parent "BMS1P7--AGAP13P^BMS1P7^ENSG00000270025.2"  ; exon_id "ENSE00001675840.2"  ; exon_number 1 ; gene_id "BMS1P7--AGAP13P^BMS1P7^ENSG00000270025.2"  ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3"  ; havana_transcript "OTTHUMT00000047911.2"  ; hgnc_id "HGNC:23655"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48059827,48060016,-"  ; tag basic ; transcript_id "BMS1P7--AGAP13P^ENST00000602440.2"  ; transcript_name "BMS1P7-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
DR1--AL499605.1	HAVANA	gene	17829	18231	.	+	.	FI_gene_label "AL499605.1^ENSG00000270342.1"  ; ID "DR1--AL499605.1^AL499605.1^ENSG00000270342.1"  ; exon_id "ENSE00003619774.1"  ; exon_number 1 ; gene_id "DR1--AL499605.1^AL499605.1^ENSG00000270342.1"  ; gene_name "AL499605.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184314.1"  ; havana_transcript "OTTHUMT00000468589.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,106544342,106544744,-"  ; tag pseudo_consens basic ; transcript_id "DR1--AL499605.1^ENST00000604628.1"  ; transcript_name "AL499605.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
DR1--AL499605.1	HAVANA	RNA	17829	18231	.	+	.	FI_gene_label "AL499605.1^ENSG00000270342.1"  ; ID "DR1--AL499605.1^ENST00000604628.1"  ; Parent "DR1--AL499605.1^AL499605.1^ENSG00000270342.1"  ; exon_id "ENSE00003619774.1"  ; exon_number 1 ; gene_id "DR1--AL499605.1^AL499605.1^ENSG00000270342.1"  ; gene_name "AL499605.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184314.1"  ; havana_transcript "OTTHUMT00000468589.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,106544342,106544744,-"  ; tag pseudo_consens basic ; transcript_id "DR1--AL499605.1^ENST00000604628.1"  ; transcript_name "AL499605.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
DR1--AL596327.1	HAVANA	gene	17829	18041	.	+	.	FI_gene_label "AL596327.1^ENSG00000270976.1"  ; ID "DR1--AL596327.1^AL596327.1^ENSG00000270976.1"  ; exon_id "ENSE00003558916.1"  ; exon_number 1 ; gene_id "DR1--AL596327.1^AL596327.1^ENSG00000270976.1"  ; gene_name "AL596327.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184318.1"  ; havana_transcript "OTTHUMT00000468593.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr1,106780223,106780435,+"  ; tag basic ; transcript_id "DR1--AL596327.1^ENST00000603629.1"  ; transcript_name "AL596327.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
DR1--AL596327.1	HAVANA	RNA	17829	18041	.	+	.	FI_gene_label "AL596327.1^ENSG00000270976.1"  ; ID "DR1--AL596327.1^ENST00000603629.1"  ; Parent "DR1--AL596327.1^AL596327.1^ENSG00000270976.1"  ; exon_id "ENSE00003558916.1"  ; exon_number 1 ; gene_id "DR1--AL596327.1^AL596327.1^ENSG00000270976.1"  ; gene_name "AL596327.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184318.1"  ; havana_transcript "OTTHUMT00000468593.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr1,106780223,106780435,+"  ; tag basic ; transcript_id "DR1--AL596327.1^ENST00000603629.1"  ; transcript_name "AL596327.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
PI4KA--LINC02564	HAVANA	gene	54232	57641	.	+	.	FI_gene_label "LINC02564^ENSG00000262352.2"  ; ID "PI4KA--LINC02564^LINC02564^ENSG00000262352.2"  ; exon_id "ENSE00002655585.2"  ; exon_number 1 ; gene_id "PI4KA--LINC02564^LINC02564^ENSG00000262352.2"  ; gene_name LINC02564 ; gene_type lncRNA ; havana_gene "OTTHUMG00000177910.2"  ; havana_transcript "OTTHUMT00000439669.2"  ; hgnc_id "HGNC:53604"  ; level 2 ; orig_coord_info "chr18,11125,11595,+"  ; tag basic TAGENE ; transcript_id "PI4KA--LINC02564^ENST00000572573.2"  ; transcript_name "LINC02564-201"  ; transcript_support_level 3 ; transcript_type lncRNA
PI4KA--LINC02564	HAVANA	RNA	54232	57641	.	+	.	FI_gene_label "LINC02564^ENSG00000262352.2"  ; ID "PI4KA--LINC02564^ENST00000572573.2"  ; Parent "PI4KA--LINC02564^LINC02564^ENSG00000262352.2"  ; exon_id "ENSE00002655585.2"  ; exon_number 1 ; gene_id "PI4KA--LINC02564^LINC02564^ENSG00000262352.2"  ; gene_name LINC02564 ; gene_type lncRNA ; havana_gene "OTTHUMG00000177910.2"  ; havana_transcript "OTTHUMT00000439669.2"  ; hgnc_id "HGNC:53604"  ; level 2 ; orig_coord_info "chr18,11125,11595,+"  ; tag basic TAGENE ; transcript_id "PI4KA--LINC02564^ENST00000572573.2"  ; transcript_name "LINC02564-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
RANBP1--LINC01900	HAVANA	gene	15421	16769	.	+	.	FI_gene_label "LINC01900^ENSG00000265758.1"  ; ID "RANBP1--LINC01900^LINC01900^ENSG00000265758.1"  ; exon_id "ENSE00002732333.1"  ; exon_number 1 ; gene_id "RANBP1--LINC01900^LINC01900^ENSG00000265758.1"  ; gene_name LINC01900 ; gene_type lncRNA ; havana_gene "OTTHUMG00000179438.1"  ; havana_transcript "OTTHUMT00000446371.1"  ; hgnc_id "HGNC:52719"  ; level 2 ; orig_coord_info "chr18,22026024,22026110,+"  ; transcript_id "RANBP1--LINC01900^ENST00000584028.1"  ; transcript_name "LINC01900-201"  ; transcript_support_level 2 ; transcript_type lncRNA
RANBP1--LINC01900	HAVANA	RNA	15421	16769	.	+	.	FI_gene_label "LINC01900^ENSG00000265758.1"  ; ID "RANBP1--LINC01900^ENST00000584028.1"  ; Parent "RANBP1--LINC01900^LINC01900^ENSG00000265758.1"  ; exon_id "ENSE00002732333.1"  ; exon_number 1 ; gene_id "RANBP1--LINC01900^LINC01900^ENSG00000265758.1"  ; gene_name LINC01900 ; gene_type lncRNA ; havana_gene "OTTHUMG00000179438.1"  ; havana_transcript "OTTHUMT00000446371.1"  ; hgnc_id "HGNC:52719"  ; level 2 ; orig_coord_info "chr18,22026024,22026110,+"  ; transcript_id "RANBP1--LINC01900^ENST00000584028.1"  ; transcript_name "LINC01900-201"  ; transcript_support_level 2 ; 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
299 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 ------------------------------
479 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 21 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