.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-150e73-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/49ce5bbe898efe38e01d1bcb3c775a/.command.log
Size: 57.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-150e73-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/49ce5bbe898efe38e01d1bcb3c775a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/0bc62a229ae6fa8a61d556e66e7571/fi_workdir/aih-tih-sc-150e73-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/49ce5bbe898efe38e01d1bcb3c775a/.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: 4572
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4572
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:4572
  => 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: 
ACTBP6--ACTB	HAVANA	gene	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ACTBP6--ACTB	HAVANA	mRNA	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ENST00000414620.1"  ; Parent "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
AGO2--TRAPPC9	HAVANA	gene	1001	34934	.	+	.	FI_gene_label "AGO2^ENSG00000123908.12"  ; ID "AGO2--TRAPPC9^AGO2^ENSG00000123908.12"  ; ccdsid "CCDS6380.1"  ; exon_id "ENSE00002115766.2"  ; exon_number 1 ; gene_id "AGO2--TRAPPC9^AGO2^ENSG00000123908.12"  ; gene_name AGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164232.7"  ; havana_transcript "OTTHUMT00000377866.6"  ; hgnc_id "HGNC:3263"  ; level 2 ; orig_coord_info "chr8,140635485,140635506,-"  ; protein_id "ENSP00000220592.5"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000220592.10"  ; transcript_name "AGO2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGO2--TRAPPC9	HAVANA	mRNA	1001	34934	.	+	.	FI_gene_label "AGO2^ENSG00000123908.12"  ; ID "AGO2--TRAPPC9^ENST00000220592.10"  ; Parent "AGO2--TRAPPC9^AGO2^ENSG00000123908.12"  ; ccdsid "CCDS6380.1"  ; exon_id "ENSE00002115766.2"  ; exon_number 1 ; gene_id "AGO2--TRAPPC9^AGO2^ENSG00000123908.12"  ; gene_name AGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164232.7"  ; havana_transcript "OTTHUMT00000377866.6"  ; hgnc_id "HGNC:3263"  ; level 2 ; orig_coord_info "chr8,140635485,140635506,-"  ; protein_id "ENSP00000220592.5"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000220592.10"  ; transcript_name "AGO2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AGO2--TRAPPC9	HAVANA	gene	38770	79875	.	+	.	FI_gene_label "TRAPPC9^ENSG00000167632.18"  ; ID "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18"  ; ccdsid "CCDS55278.1"  ; exon_id "ENSE00003610885.1"  ; exon_number 2 ; gene_id "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18"  ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10"  ; havana_transcript "OTTHUMT00000497841.1"  ; hgnc_id "HGNC:30832"  ; level 2 ; orig_coord_info "chr8,140450790,140451373,-"  ; protein_id "ENSP00000405060.3"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000438773.4"  ; transcript_name "TRAPPC9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGO2--TRAPPC9	HAVANA	mRNA	38770	79875	.	+	.	FI_gene_label "TRAPPC9^ENSG00000167632.18"  ; ID "AGO2--TRAPPC9^ENST00000438773.4"  ; Parent "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18"  ; ccdsid "CCDS55278.1"  ; exon_id "ENSE00003610885.1"  ; exon_number 2 ; gene_id "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18"  ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10"  ; havana_transcript "OTTHUMT00000497841.1"  ; hgnc_id "HGNC:30832"  ; level 2 ; orig_coord_info "chr8,140450790,140451373,-"  ; protein_id "ENSP00000405060.3"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000438773.4"  ; transcript_name "TRAPPC9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCL28--RN7SL1	HAVANA	gene	1001	7684	.	+	.	FI_gene_label "CCL28^ENSG00000151882.11"  ; ID "CCL28--RN7SL1^CCL28^ENSG00000151882.11"  ; ccdsid "CCDS3944.1"  ; exon_id "ENSE00001489205.3"  ; exon_number 1 ; gene_id "CCL28--RN7SL1^CCL28^ENSG00000151882.11"  ; gene_name CCL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094811.3"  ; havana_transcript "OTTHUMT00000211631.2"  ; hgnc_id "HGNC:17700"  ; level 2 ; orig_coord_info "chr5,43412253,43412316,-"  ; protein_id "ENSP00000354416.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCL28--RN7SL1^ENST00000361115.4"  ; transcript_name "CCL28-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCL28--RN7SL1	HAVANA	mRNA	1001	7684	.	+	.	FI_gene_label "CCL28^ENSG00000151882.11"  ; ID "CCL28--RN7SL1^ENST00000361115.4"  ; Parent "CCL28--RN7SL1^CCL28^ENSG00000151882.11"  ; ccdsid "CCDS3944.1"  ; exon_id "ENSE00001489205.3"  ; exon_number 1 ; gene_id "CCL28--RN7SL1^CCL28^ENSG00000151882.11"  ; gene_name CCL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094811.3"  ; havana_transcript "OTTHUMT00000211631.2"  ; hgnc_id "HGNC:17700"  ; level 2 ; orig_coord_info "chr5,43412253,43412316,-"  ; protein_id "ENSP00000354416.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCL28--RN7SL1^ENST00000361115.4"  ; transcript_name "CCL28-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CERS6--ABCB11	HAVANA	gene	1024	17424	.	+	.	FI_gene_label "CERS6^ENSG00000172292.15"  ; ID "CERS6--ABCB11^CERS6^ENSG00000172292.15"  ; ccdsid "CCDS2228.1"  ; exon_id "ENSE00002561332.2"  ; exon_number 1 ; gene_id "CERS6--ABCB11^CERS6^ENSG00000172292.15"  ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4"  ; havana_transcript "OTTHUMT00000255235.3"  ; hgnc_id "HGNC:23826"  ; level 2 ; orig_coord_info "chr2,168456449,168456618,+"  ; protein_id "ENSP00000306579.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--ABCB11^ENST00000305747.11"  ; transcript_name "CERS6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CERS6--ABCB11	HAVANA	mRNA	1024	17424	.	+	.	FI_gene_label "CERS6^ENSG00000172292.15"  ; ID "CERS6--ABCB11^ENST00000305747.11"  ; Parent "CERS6--ABCB11^CERS6^ENSG00000172292.15"  ; ccdsid "CCDS2228.1"  ; exon_id "ENSE00002561332.2"  ; exon_number 1 ; gene_id "CERS6--ABCB11^CERS6^ENSG00000172292.15"  ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4"  ; havana_transcript "OTTHUMT00000255235.3"  ; hgnc_id "HGNC:23826"  ; level 2 ; orig_coord_info "chr2,168456449,168456618,+"  ; protein_id "ENSP00000306579.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--ABCB11^ENST00000305747.11"  ; transcript_name "CERS6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CERS6--ABCB11	HAVANA	gene	34796	51471	.	+	.	FI_gene_label "ABCB11^ENSG00000073734.10"  ; ID "CERS6--ABCB11^ABCB11^ENSG00000073734.10"  ; exon_id "ENSE00001803468.1"  ; exon_number 1 ; gene_id "CERS6--ABCB11^ABCB11^ENSG00000073734.10"  ; gene_name ABCB11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154039.5"  ; havana_transcript "OTTHUMT00000333618.2"  ; hgnc_id "HGNC:42"  ; level 2 ; orig_coord_info "chr2,168971847,168972032,-"  ; protein_id "ENSP00000416058.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CERS6--ABCB11^ENST00000439188.1"  ; transcript_name "ABCB11-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
CERS6--ABCB11	HAVANA	mRNA	34796	51471	.	+	.	FI_gene_label "ABCB11^ENSG00000073734.10"  ; ID "CERS6--ABCB11^ENST00000439188.1"  ; Parent "CERS6--ABCB11^ABCB11^ENSG00000073734.10"  ; exon_id "ENSE00001803468.1"  ; exon_number 1 ; gene_id "CERS6--ABCB11^ABCB11^ENSG00000073734.10"  ; gene_name ABCB11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154039.5"  ; havana_transcript "OTTHUMT00000333618.2"  ; hgnc_id "HGNC:42"  ; level 2 ; orig_coord_info "chr2,168971847,168972032,-"  ; protein_id "ENSP00000416058.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CERS6--ABCB11^ENST00000439188.1"  ; transcript_name "ABCB11-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
CERS6--DHRS9	HAVANA	gene	1024	17424	.	+	.	FI_gene_label "CERS6^ENSG00000172292.15"  ; ID "CERS6--DHRS9^CERS6^ENSG00000172292.15"  ; ccdsid "CCDS2228.1"  ; exon_id "ENSE00002561332.2"  ; exon_number 1 ; gene_id "CERS6--DHRS9^CERS6^ENSG00000172292.15"  ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4"  ; havana_transcript "OTTHUMT00000255235.3"  ; hgnc_id "HGNC:23826"  ; level 2 ; orig_coord_info "chr2,168456449,168456618,+"  ; protein_id "ENSP00000306579.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--DHRS9^ENST00000305747.11"  ; transcript_name "CERS6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CERS6--DHRS9	HAVANA	mRNA	1024	17424	.	+	.	FI_gene_label "CERS6^ENSG00000172292.15"  ; ID "CERS6--DHRS9^ENST00000305747.11"  ; Parent "CERS6--DHRS9^CERS6^ENSG00000172292.15"  ; ccdsid "CCDS2228.1"  ; exon_id "ENSE00002561332.2"  ; exon_number 1 ; gene_id "CERS6--DHRS9^CERS6^ENSG00000172292.15"  ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4"  ; havana_transcript "OTTHUMT00000255235.3"  ; hgnc_id "HGNC:23826"  ; level 2 ; orig_coord_info "chr2,168456449,168456618,+"  ; protein_id "ENSP00000306579.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--DHRS9^ENST00000305747.11"  ; transcript_name "CERS6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CERS6--DHRS9	HAVANA	gene	22353	33271	.	+	.	FI_gene_label "DHRS9^ENSG00000073737.17"  ; ID "CERS6--DHRS9^DHRS9^ENSG00000073737.17"  ; ccdsid "CCDS2231.1"  ; exon_id "ENSE00003585749.1"  ; exon_number 3 ; gene_id "CERS6--DHRS9^DHRS9^ENSG00000073737.17"  ; gene_name DHRS9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132180.9"  ; havana_transcript "OTTHUMT00000255232.1"  ; hgnc_id "HGNC:16888"  ; level 2 ; orig_coord_info "chr2,169081582,169081894,+"  ; protein_id "ENSP00000350154.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "CERS6--DHRS9^ENST00000357546.6"  ; transcript_name "DHRS9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CERS6--DHRS9	HAVANA	mRNA	22353	33271	.	+	.	FI_gene_label "DHRS9^ENSG00000073737.17"  ; ID "CERS6--DHRS9^ENST00000357546.6"  ; Parent "CERS6--DHRS9^DHRS9^ENSG00000073737.17"  ; ccdsid "CCDS2231.1"  ; exon_id "ENSE00003585749.1"  ; exon_number 3 ; gene_id "CERS6--DHRS9^DHRS9^ENSG00000073737.17"  ; gene_name DHRS9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132180.9"  ; havana_transcript "OTTHUMT00000255232.1"  ; hgnc_id "HGNC:16888"  ; level 2 ; orig_coord_info "chr2,169081582,169081894,+"  ; protein_id "ENSP00000350154.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "CERS6--DHRS9^ENST00000357546.6"  ; transcript_name "DHRS9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPNE4--ACP3	HAVANA	gene	32505	45388	.	+	.	FI_gene_label "ACP3^ENSG00000014257.16"  ; ID "CPNE4--ACP3^ACP3^ENSG00000014257.16"  ; ccdsid "CCDS3073.1"  ; exon_id "ENSE00001922674.1"  ; exon_number 1 ; gene_id "CPNE4--ACP3^ACP3^ENSG00000014257.16"  ; gene_name ACP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159650.6"  ; havana_transcript "OTTHUMT00000356699.3"  ; hgnc_id "HGNC:125"  ; level 2 ; orig_coord_info "chr3,132317457,132317576,+"  ; protein_id "ENSP00000337471.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CPNE4--ACP3^ENST00000336375.10"  ; transcript_name "ACP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ACP3	HAVANA	mRNA	32505	45388	.	+	.	FI_gene_label "ACP3^ENSG00000014257.16"  ; ID "CPNE4--ACP3^ENST00000336375.10"  ; Parent "CPNE4--ACP3^ACP3^ENSG00000014257.16"  ; ccdsid "CCDS3073.1"  ; exon_id "ENSE00001922674.1"  ; exon_number 1 ; gene_id "CPNE4--ACP3^ACP3^ENSG00000014257.16"  ; gene_name ACP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159650.6"  ; havana_transcript "OTTHUMT00000356699.3"  ; hgnc_id "HGNC:125"  ; level 2 ; orig_coord_info "chr3,132317457,132317576,+"  ; protein_id "ENSP00000337471.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CPNE4--ACP3^ENST00000336375.10"  ; transcript_name "ACP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPNE4--ACP3	ENSEMBL	gene	6503	29459	.	+	.	FI_gene_label "CPNE4^ENSG00000196353.11"  ; ID "CPNE4--ACP3^CPNE4^ENSG00000196353.11"  ; ccdsid "CCDS3072.1"  ; exon_id "ENSE00003536115.1"  ; exon_number 2 ; gene_id "CPNE4--ACP3^CPNE4^ENSG00000196353.11"  ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14"  ; hgnc_id "HGNC:2317"  ; level 3 ; orig_coord_info "chr3,131905264,131905443,-"  ; protein_id "ENSP00000411904.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ACP3^ENST00000429747.5"  ; transcript_name "CPNE4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ACP3	ENSEMBL	mRNA	6503	29459	.	+	.	FI_gene_label "CPNE4^ENSG00000196353.11"  ; ID "CPNE4--ACP3^ENST00000429747.5"  ; Parent "CPNE4--ACP3^CPNE4^ENSG00000196353.11"  ; ccdsid "CCDS3072.1"  ; exon_id "ENSE00003536115.1"  ; exon_number 2 ; gene_id "CPNE4--ACP3^CPNE4^ENSG00000196353.11"  ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14"  ; hgnc_id "HGNC:2317"  ; level 3 ; orig_coord_info "chr3,131905264,131905443,-"  ; protein_id "ENSP00000411904.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ACP3^ENST00000429747.5"  ; transcript_name "CPNE4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GPR39--AC010974.2	HAVANA	gene	1001	7766	.	+	.	FI_gene_label "GPR39^ENSG00000183840.7"  ; ID "GPR39--AC010974.2^GPR39^ENSG00000183840.7"  ; ccdsid "CCDS2170.1"  ; exon_id "ENSE00001315513.3"  ; exon_number 1 ; gene_id "GPR39--AC010974.2^GPR39^ENSG00000183840.7"  ; gene_name GPR39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131679.3"  ; havana_transcript "OTTHUMT00000254582.2"  ; hgnc_id "HGNC:4496"  ; level 2 ; orig_coord_info "chr2,132417043,132417898,+"  ; protein_id "ENSP00000327417.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPR39--AC010974.2^ENST00000329321.4"  ; transcript_name "GPR39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GPR39--AC010974.2	HAVANA	mRNA	1001	7766	.	+	.	FI_gene_label "GPR39^ENSG00000183840.7"  ; ID "GPR39--AC010974.2^ENST00000329321.4"  ; Parent "GPR39--AC010974.2^GPR39^ENSG00000183840.7"  ; ccdsid "CCDS2170.1"  ; exon_id "ENSE00001315513.3"  ; exon_number 1 ; gene_id "GPR39--AC010974.2^GPR39^ENSG00000183840.7"  ; gene_name GPR39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131679.3"  ; havana_transcript "OTTHUMT00000254582.2"  ; hgnc_id "HGNC:4496"  ; level 2 ; orig_coord_info "chr2,132417043,132417898,+"  ; protein_id "ENSP00000327417.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPR39--AC010974.2^ENST00000329321.4"  ; transcript_name "GPR39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^ENST00000240618.11"  ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^ENST00000309384.2"  ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC00665--WDR62	HAVANA	gene	25529	56982	.	+	.	FI_gene_label "WDR62^ENSG00000075702.19"  ; ID "LINC00665--WDR62^WDR62^ENSG00000075702.19"  ; ccdsid "CCDS33001.1"  ; exon_id "ENSE00002287575.1"  ; exon_number 1 ; gene_id "LINC00665--WDR62^WDR62^ENSG00000075702.19"  ; gene_name WDR62 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048139.9"  ; havana_transcript "OTTHUMT00000457436.1"  ; hgnc_id "HGNC:24502"  ; level 2 ; orig_coord_info "chr19,36054972,36055148,+"  ; protein_id "ENSP00000270301.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "LINC00665--WDR62^ENST00000270301.12"  ; transcript_name "WDR62-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LINC00665--WDR62	HAVANA	mRNA	25529	56982	.	+	.	FI_gene_label "WDR62^ENSG00000075702.19"  ; ID "LINC00665--WDR62^ENST00000270301.12"  ; Parent "LINC00665--WDR62^WDR62^ENSG00000075702.19"  ; ccdsid "CCDS33001.1"  ; exon_id "ENSE00002287575.1"  ; exon_number 1 ; gene_id "LINC00665--WDR62^WDR62^ENSG00000075702.19"  ; gene_name WDR62 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048139.9"  ; havana_transcript "OTTHUMT00000457436.1"  ; hgnc_id "HGNC:24502"  ; level 2 ; orig_coord_info "chr19,36054972,36055148,+"  ; protein_id "ENSP00000270301.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "LINC00665--WDR62^ENST00000270301.12"  ; transcript_name "WDR62-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MAL2--DIPK1A	HAVANA	gene	13031	20286	.	+	.	FI_gene_label "DIPK1A^ENSG00000154511.12"  ; ID "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12"  ; ccdsid "CCDS44173.1"  ; exon_id "ENSE00001882462.2"  ; exon_number 1 ; gene_id "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12"  ; gene_name DIPK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000010894.3"  ; havana_transcript "OTTHUMT00000030046.3"  ; hgnc_id "HGNC:32213"  ; level 2 ; orig_coord_info "chr1,92961376,92961429,-"  ; protein_id "ENSP00000359333.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAL2--DIPK1A^ENST00000370310.5"  ; transcript_name "DIPK1A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MAL2--DIPK1A	HAVANA	mRNA	13031	20286	.	+	.	FI_gene_label "DIPK1A^ENSG00000154511.12"  ; ID "MAL2--DIPK1A^ENST00000370310.5"  ; Parent "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12"  ; ccdsid "CCDS44173.1"  ; exon_id "ENSE00001882462.2"  ; exon_number 1 ; gene_id "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12"  ; gene_name DIPK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000010894.3"  ; havana_transcript "OTTHUMT00000030046.3"  ; hgnc_id "HGNC:32213"  ; level 2 ; orig_coord_info "chr1,92961376,92961429,-"  ; protein_id "ENSP00000359333.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAL2--DIPK1A^ENST00000370310.5"  ; transcript_name "DIPK1A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
MAL2--DIPK1A	HAVANA	gene	1001	7825	.	+	.	FI_gene_label "MAL2^ENSG00000147676.14"  ; ID "MAL2--DIPK1A^MAL2^ENSG00000147676.14"  ; exon_id "ENSE00003500807.1"  ; exon_number 3 ; gene_id "MAL2--DIPK1A^MAL2^ENSG00000147676.14"  ; gene_name MAL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164973.5"  ; havana_transcript "OTTHUMT00000383353.2"  ; hgnc_id "HGNC:13634"  ; level 2 ; orig_coord_info "chr8,119221659,119221757,+"  ; protein_id "ENSP00000483044.1"  ; tag alternative_5_UTR basic ; transcript_id "MAL2--DIPK1A^ENST00000522112.6"  ; transcript_name "MAL2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
MAL2--DIPK1A	HAVANA	mRNA	1001	7825	.	+	.	FI_gene_label "MAL2^ENSG00000147676.14"  ; ID "MAL2--DIPK1A^ENST00000522112.6"  ; Parent "MAL2--DIPK1A^MAL2^ENSG00000147676.14"  ; exon_id "ENSE00003500807.1"  ; exon_number 3 ; gene_id "MAL2--DIPK1A^MAL2^ENSG00000147676.14"  ; gene_name MAL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164973.5"  ; havana_transcript "OTTHUMT00000383353.2"  ; hgnc_id "HGNC:13634"  ; level 2 ; orig_coord_info "chr8,119221659,119221757,+"  ; protein_id "ENSP00000483044.1"  ; tag alternative_5_UTR basic ; transcript_id "MAL2--DIPK1A^ENST00000522112.6"  ; transcript_name "MAL2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
PHF8--CBX1P4	HAVANA	gene	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--CBX1P4^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--CBX1P4^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--CBX1P4^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF8--CBX1P4	HAVANA	mRNA	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--CBX1P4^ENST00000322659.12"  ; Parent "PHF8--CBX1P4^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--CBX1P4^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--CBX1P4^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF8--REPS2	HAVANA	gene	35093	62864	.	+	.	FI_gene_label "REPS2^ENSG00000169891.18"  ; ID "PHF8--REPS2^REPS2^ENSG00000169891.18"  ; ccdsid "CCDS43919.1"  ; exon_id "ENSE00001956325.1"  ; exon_number 1 ; gene_id "PHF8--REPS2^REPS2^ENSG00000169891.18"  ; gene_name REPS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021199.4"  ; havana_transcript "OTTHUMT00000055924.3"  ; hgnc_id "HGNC:9963"  ; level 2 ; orig_coord_info "chrX,16946862,16947134,+"  ; protein_id "ENSP00000306033.7"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PHF8--REPS2^ENST00000303843.7"  ; transcript_name "REPS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF8--REPS2	HAVANA	mRNA	35093	62864	.	+	.	FI_gene_label "REPS2^ENSG00000169891.18"  ; ID "PHF8--REPS2^ENST00000303843.7"  ; Parent "PHF8--REPS2^REPS2^ENSG00000169891.18"  ; ccdsid "CCDS43919.1"  ; exon_id "ENSE00001956325.1"  ; exon_number 1 ; gene_id "PHF8--REPS2^REPS2^ENSG00000169891.18"  ; gene_name REPS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021199.4"  ; havana_transcript "OTTHUMT00000055924.3"  ; hgnc_id "HGNC:9963"  ; level 2 ; orig_coord_info "chrX,16946862,16947134,+"  ; protein_id "ENSP00000306033.7"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PHF8--REPS2^ENST00000303843.7"  ; transcript_name "REPS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF8--REPS2	HAVANA	gene	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--REPS2^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--REPS2^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--REPS2^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF8--REPS2	HAVANA	mRNA	4110	26409	.	+	.	FI_gene_label "PHF8^ENSG00000172943.20"  ; ID "PHF8--REPS2^ENST00000322659.12"  ; Parent "PHF8--REPS2^PHF8^ENSG00000172943.20"  ; ccdsid "CCDS55419.1"  ; exon_id "ENSE00003602569.1"  ; exon_number 2 ; gene_id "PHF8--REPS2^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--REPS2^ENST00000322659.12"  ; transcript_name "PHF8-201"  ; 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: 
TTBK2--SH2D3A	HAVANA	gene	36731	47573	.	+	.	FI_gene_label "SH2D3A^ENSG00000125731.13"  ; ID "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13"  ; ccdsid "CCDS12173.1"  ; exon_id "ENSE00003633486.1"  ; exon_number 2 ; gene_id "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13"  ; gene_name SH2D3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000181868.3"  ; havana_transcript "OTTHUMT00000458016.2"  ; hgnc_id "HGNC:16885"  ; level 2 ; orig_coord_info "chr19,6763680,6763748,-"  ; protein_id "ENSP00000245908.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000245908.11"  ; transcript_name "SH2D3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTBK2--SH2D3A	HAVANA	mRNA	36731	47573	.	+	.	FI_gene_label "SH2D3A^ENSG00000125731.13"  ; ID "TTBK2--SH2D3A^ENST00000245908.11"  ; Parent "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13"  ; ccdsid "CCDS12173.1"  ; exon_id "ENSE00003633486.1"  ; exon_number 2 ; gene_id "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13"  ; gene_name SH2D3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000181868.3"  ; havana_transcript "OTTHUMT00000458016.2"  ; hgnc_id "HGNC:16885"  ; level 2 ; orig_coord_info "chr19,6763680,6763748,-"  ; protein_id "ENSP00000245908.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000245908.11"  ; transcript_name "SH2D3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTBK2--SH2D3A	HAVANA	gene	1032	33702	.	+	.	FI_gene_label "TTBK2^ENSG00000128881.17"  ; ID "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17"  ; ccdsid "CCDS42029.1"  ; exon_id "ENSE00003688715.1"  ; exon_number 2 ; gene_id "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17"  ; gene_name TTBK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175802.5"  ; havana_transcript "OTTHUMT00000431106.3"  ; hgnc_id "HGNC:19141"  ; level 2 ; orig_coord_info "chr15,42878549,42878617,-"  ; protein_id "ENSP00000267890.6"  ; tag basic MANE_Select CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000267890.11"  ; transcript_name "TTBK2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TTBK2--SH2D3A	HAVANA	mRNA	1032	33702	.	+	.	FI_gene_label "TTBK2^ENSG00000128881.17"  ; ID "TTBK2--SH2D3A^ENST00000267890.11"  ; Parent "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17"  ; ccdsid "CCDS42029.1"  ; exon_id "ENSE00003688715.1"  ; exon_number 2 ; gene_id "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17"  ; gene_name TTBK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175802.5"  ; havana_transcript "OTTHUMT00000431106.3"  ; hgnc_id "HGNC:19141"  ; level 2 ; orig_coord_info "chr15,42878549,42878617,-"  ; protein_id "ENSP00000267890.6"  ; tag basic MANE_Select CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000267890.11"  ; transcript_name "TTBK2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TTC6--MIPOL1	ENSEMBL	gene	25637	41624	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTC6--MIPOL1^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTC6--MIPOL1^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTC6--MIPOL1^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TTC6--MIPOL1	ENSEMBL	mRNA	25637	41624	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTC6--MIPOL1^ENST00000267368.11"  ; Parent "TTC6--MIPOL1^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTC6--MIPOL1^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTC6--MIPOL1^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TTC6--MIPOL1	HAVANA	gene	55184	98633	.	+	.	FI_gene_label "MIPOL1^ENSG00000151338.18"  ; ID "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18"  ; ccdsid "CCDS9664.1"  ; exon_id "ENSE00003679602.1"  ; exon_number 4 ; gene_id "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18"  ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3"  ; havana_transcript "OTTHUMT00000276734.1"  ; hgnc_id "HGNC:21460"  ; level 2 ; orig_coord_info "chr14,37247889,37247907,+"  ; protein_id "ENSP00000333539.7"  ; tag basic appris_principal_2 CCDS ; transcript_id "TTC6--MIPOL1^ENST00000327441.11"  ; transcript_name "MIPOL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTC6--MIPOL1	HAVANA	mRNA	55184	98633	.	+	.	FI_gene_label "MIPOL1^ENSG00000151338.18"  ; ID "TTC6--MIPOL1^ENST00000327441.11"  ; Parent "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18"  ; ccdsid "CCDS9664.1"  ; exon_id "ENSE00003679602.1"  ; exon_number 4 ; gene_id "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18"  ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3"  ; havana_transcript "OTTHUMT00000276734.1"  ; hgnc_id "HGNC:21460"  ; level 2 ; orig_coord_info "chr14,37247889,37247907,+"  ; protein_id "ENSP00000333539.7"  ; tag basic appris_principal_2 CCDS ; transcript_id "TTC6--MIPOL1^ENST00000327441.11"  ; transcript_name "MIPOL1-201"  ; 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: 
WDR92--PPP3R1	HAVANA	gene	18563	27322	.	+	.	FI_gene_label "PPP3R1^ENSG00000221823.11"  ; ID "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11"  ; ccdsid "CCDS46310.1"  ; exon_id "ENSE00001191356.5"  ; exon_number 1 ; gene_id "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11"  ; gene_name PPP3R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129561.9"  ; havana_transcript "OTTHUMT00000326765.5"  ; hgnc_id "HGNC:9317"  ; level 2 ; orig_coord_info "chr2,68252125,68252127,-"  ; protein_id "ENSP00000234310.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000234310.8"  ; transcript_name "PPP3R1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WDR92--PPP3R1	HAVANA	mRNA	18563	27322	.	+	.	FI_gene_label "PPP3R1^ENSG00000221823.11"  ; ID "WDR92--PPP3R1^ENST00000234310.8"  ; Parent "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11"  ; ccdsid "CCDS46310.1"  ; exon_id "ENSE00001191356.5"  ; exon_number 1 ; gene_id "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11"  ; gene_name PPP3R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129561.9"  ; havana_transcript "OTTHUMT00000326765.5"  ; hgnc_id "HGNC:9317"  ; level 2 ; orig_coord_info "chr2,68252125,68252127,-"  ; protein_id "ENSP00000234310.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000234310.8"  ; transcript_name "PPP3R1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
WDR92--PPP3R1	HAVANA	gene	1023	12125	.	+	.	FI_gene_label "WDR92^ENSG00000243667.7"  ; ID "WDR92--PPP3R1^WDR92^ENSG00000243667.7"  ; ccdsid "CCDS1884.1"  ; exon_id "ENSE00001738493.3"  ; exon_number 1 ; gene_id "WDR92--PPP3R1^WDR92^ENSG00000243667.7"  ; gene_name WDR92 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152561.6"  ; havana_transcript "OTTHUMT00000251754.4"  ; hgnc_id "HGNC:25176"  ; level 2 ; orig_coord_info "chr2,68157261,68157443,-"  ; protein_id "ENSP00000295121.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000295121.11"  ; transcript_name "WDR92-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WDR92--PPP3R1	HAVANA	mRNA	1023	12125	.	+	.	FI_gene_label "WDR92^ENSG00000243667.7"  ; ID "WDR92--PPP3R1^ENST00000295121.11"  ; Parent "WDR92--PPP3R1^WDR92^ENSG00000243667.7"  ; ccdsid "CCDS1884.1"  ; exon_id "ENSE00001738493.3"  ; exon_number 1 ; gene_id "WDR92--PPP3R1^WDR92^ENSG00000243667.7"  ; gene_name WDR92 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152561.6"  ; havana_transcript "OTTHUMT00000251754.4"  ; hgnc_id "HGNC:25176"  ; level 2 ; orig_coord_info "chr2,68157261,68157443,-"  ; protein_id "ENSP00000295121.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000295121.11"  ; transcript_name "WDR92-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF875--ZNF793	HAVANA	gene	10040	20910	.	+	.	FI_gene_label "ZNF875^ENSG00000181666.18"  ; ID "ZNF875--ZNF793^ZNF875^ENSG00000181666.18"  ; ccdsid "CCDS12502.1"  ; exon_id "ENSE00001337429.2"  ; exon_number 3 ; gene_id "ZNF875--ZNF793^ZNF875^ENSG00000181666.18"  ; gene_name ZNF875 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181937.8"  ; havana_transcript "OTTHUMT00000458375.1"  ; hgnc_id "HGNC:4928"  ; level 2 ; orig_coord_info "chr19,37344685,37344774,+"  ; protein_id "ENSP00000315505.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000324411.8"  ; transcript_name "ZNF875-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF875--ZNF793	HAVANA	mRNA	10040	20910	.	+	.	FI_gene_label "ZNF875^ENSG00000181666.18"  ; ID "ZNF875--ZNF793^ENST00000324411.8"  ; Parent "ZNF875--ZNF793^ZNF875^ENSG00000181666.18"  ; ccdsid "CCDS12502.1"  ; exon_id "ENSE00001337429.2"  ; exon_number 3 ; gene_id "ZNF875--ZNF793^ZNF875^ENSG00000181666.18"  ; gene_name ZNF875 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181937.8"  ; havana_transcript "OTTHUMT00000458375.1"  ; hgnc_id "HGNC:4928"  ; level 2 ; orig_coord_info "chr19,37344685,37344774,+"  ; protein_id "ENSP00000315505.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000324411.8"  ; transcript_name "ZNF875-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF875--ZNF793	ENSEMBL	gene	29565	41594	.	+	.	FI_gene_label "ZNF793^ENSG00000188227.13"  ; ID "ZNF875--ZNF793^ZNF793^ENSG00000188227.13"  ; ccdsid "CCDS46062.1"  ; exon_id "ENSE00001806128.1"  ; exon_number 1 ; gene_id "ZNF875--ZNF793^ZNF793^ENSG00000188227.13"  ; gene_name ZNF793 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182003.5"  ; hgnc_id "HGNC:33115"  ; level 3 ; orig_coord_info "chr19,37523440,37523454,+"  ; protein_id "ENSP00000396402.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000445217.5"  ; transcript_name "ZNF793-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ZNF875--ZNF793	ENSEMBL	mRNA	29565	41594	.	+	.	FI_gene_label "ZNF793^ENSG00000188227.13"  ; ID "ZNF875--ZNF793^ENST00000445217.5"  ; Parent "ZNF875--ZNF793^ZNF793^ENSG00000188227.13"  ; ccdsid "CCDS46062.1"  ; exon_id "ENSE00001806128.1"  ; exon_number 1 ; gene_id "ZNF875--ZNF793^ZNF793^ENSG00000188227.13"  ; gene_name ZNF793 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182003.5"  ; hgnc_id "HGNC:33115"  ; level 3 ; orig_coord_info "chr19,37523440,37523454,+"  ; protein_id "ENSP00000396402.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000445217.5"  ; transcript_name "ZNF793-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ACTBP6--ACTB	HAVANA	gene	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ACTBP6--ACTB	HAVANA	RNA	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ENST00000520036.1"  ; Parent "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
CCL28--RN7SL1	ENSEMBL	gene	12525	12823	.	+	.	FI_gene_label "RN7SL1^ENSG00000276168.1"  ; ID "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1"  ; exon_id "ENSE00003741348.1"  ; exon_number 1 ; gene_id "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1"  ; gene_name RN7SL1 ; gene_type misc_RNA ; hgnc_id "HGNC:10038"  ; level 3 ; orig_coord_info "chr14,49586580,49586878,+"  ; tag basic ; transcript_id "CCL28--RN7SL1^ENST00000618786.1"  ; transcript_name "RN7SL1-201"  ; transcript_support_level NA ; transcript_type misc_RNA
CCL28--RN7SL1	ENSEMBL	RNA	12525	12823	.	+	.	FI_gene_label "RN7SL1^ENSG00000276168.1"  ; ID "CCL28--RN7SL1^ENST00000618786.1"  ; Parent "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1"  ; exon_id "ENSE00003741348.1"  ; exon_number 1 ; gene_id "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1"  ; gene_name RN7SL1 ; gene_type misc_RNA ; hgnc_id "HGNC:10038"  ; level 3 ; orig_coord_info "chr14,49586580,49586878,+"  ; tag basic ; transcript_id "CCL28--RN7SL1^ENST00000618786.1"  ; transcript_name "RN7SL1-201"  ; transcript_support_level NA ; transcript_type misc_RNA
L1 and L2 created: 
GPR39--AC010974.2	HAVANA	gene	10767	14791	.	+	.	FI_gene_label "AC010974.2^ENSG00000286068.1"  ; ID "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1"  ; exon_id "ENSE00003850879.1"  ; exon_number 1 ; gene_id "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1"  ; gene_name "AC010974.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192755.1"  ; havana_transcript "OTTHUMT00000499024.1"  ; level 2 ; orig_coord_info "chr2,132685224,132685548,+"  ; tag basic ; transcript_id "GPR39--AC010974.2^ENST00000651100.1"  ; transcript_name "AC010974.2-201"  ; transcript_type lncRNA
GPR39--AC010974.2	HAVANA	RNA	10767	14791	.	+	.	FI_gene_label "AC010974.2^ENSG00000286068.1"  ; ID "GPR39--AC010974.2^ENST00000651100.1"  ; Parent "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1"  ; exon_id "ENSE00003850879.1"  ; exon_number 1 ; gene_id "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1"  ; gene_name "AC010974.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192755.1"  ; havana_transcript "OTTHUMT00000499024.1"  ; level 2 ; orig_coord_info "chr2,132685224,132685548,+"  ; tag basic ; transcript_id "GPR39--AC010974.2^ENST00000651100.1"  ; transcript_name "AC010974.2-201"  ; transcript_type lncRNA
L1 and L2 created: 
LINC00665--WDR62	HAVANA	gene	1037	15549	.	+	.	FI_gene_label "LINC00665^ENSG00000232677.9"  ; ID "LINC00665--WDR62^LINC00665^ENSG00000232677.9"  ; exon_id "ENSE00003882974.1"  ; exon_number 1 ; gene_id "LINC00665--WDR62^LINC00665^ENSG00000232677.9"  ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6"  ; havana_transcript "OTTHUMT00000109548.1"  ; hgnc_id "HGNC:44323"  ; level 1 ; orig_coord_info "chr19,36331447,36331734,-"  ; tag exp_conf ; transcript_id "LINC00665--WDR62^ENST00000412740.7"  ; transcript_name "LINC00665-201"  ; transcript_support_level 3 ; transcript_type lncRNA
LINC00665--WDR62	HAVANA	RNA	1037	15549	.	+	.	FI_gene_label "LINC00665^ENSG00000232677.9"  ; ID "LINC00665--WDR62^ENST00000412740.7"  ; Parent "LINC00665--WDR62^LINC00665^ENSG00000232677.9"  ; exon_id "ENSE00003882974.1"  ; exon_number 1 ; gene_id "LINC00665--WDR62^LINC00665^ENSG00000232677.9"  ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6"  ; havana_transcript "OTTHUMT00000109548.1"  ; hgnc_id "HGNC:44323"  ; level 1 ; orig_coord_info "chr19,36331447,36331734,-"  ; tag exp_conf ; transcript_id "LINC00665--WDR62^ENST00000412740.7"  ; transcript_name "LINC00665-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PHF8--CBX1P4	HAVANA	gene	34889	35345	.	+	.	FI_gene_label "CBX1P4^ENSG00000214321.3"  ; ID "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3"  ; exon_id "ENSE00001785430.1"  ; exon_number 1 ; gene_id "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3"  ; gene_name CBX1P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021201.1"  ; havana_transcript "OTTHUMT00000055929.1"  ; hgnc_id "HGNC:38658"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chrX,17282637,17283093,+"  ; tag pseudo_consens basic ; transcript_id "PHF8--CBX1P4^ENST00000439415.1"  ; transcript_name "CBX1P4-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
PHF8--CBX1P4	HAVANA	RNA	34889	35345	.	+	.	FI_gene_label "CBX1P4^ENSG00000214321.3"  ; ID "PHF8--CBX1P4^ENST00000439415.1"  ; Parent "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3"  ; exon_id "ENSE00001785430.1"  ; exon_number 1 ; gene_id "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3"  ; gene_name CBX1P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021201.1"  ; havana_transcript "OTTHUMT00000055929.1"  ; hgnc_id "HGNC:38658"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chrX,17282637,17283093,+"  ; tag pseudo_consens basic ; transcript_id "PHF8--CBX1P4^ENST00000439415.1"  ; transcript_name "CBX1P4-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
352 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 ------------------------------
777 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 28 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