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

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/569162e078928faf18627b03c086ac/.command.out
Size: 63.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_ezg-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

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: 6426
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6426
=> 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:6426
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
AC015911.9--SLFN12L	HAVANA	gene	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L	HAVANA	mRNA	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^ENST00000260908.12"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
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: 
AGAP3--BRAF	HAVANA	gene	30511	64383	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "AGAP3--BRAF^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGAP3--BRAF	HAVANA	mRNA	30511	64383	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "AGAP3--BRAF^ENST00000288602.11"  ; Parent "AGAP3--BRAF^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AGAP3--BRAF	HAVANA	gene	6272	14541	.	+	.	FI_gene_label "AGAP3^ENSG00000133612.19"  ; ID "AGAP3--BRAF^AGAP3^ENSG00000133612.19"  ; ccdsid "CCDS78287.1"  ; exon_id "ENSE00001339499.3"  ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19"  ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8"  ; havana_transcript "OTTHUMT00000351912.1"  ; hgnc_id "HGNC:16923"  ; level 2 ; orig_coord_info "chr7,151114771,151115641,+"  ; protein_id "ENSP00000335589.3"  ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7"  ; transcript_name "AGAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGAP3--BRAF	HAVANA	mRNA	6272	14541	.	+	.	FI_gene_label "AGAP3^ENSG00000133612.19"  ; ID "AGAP3--BRAF^ENST00000335367.7"  ; Parent "AGAP3--BRAF^AGAP3^ENSG00000133612.19"  ; ccdsid "CCDS78287.1"  ; exon_id "ENSE00001339499.3"  ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19"  ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8"  ; havana_transcript "OTTHUMT00000351912.1"  ; hgnc_id "HGNC:16923"  ; level 2 ; orig_coord_info "chr7,151114771,151115641,+"  ; protein_id "ENSP00000335589.3"  ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7"  ; transcript_name "AGAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP39--ZNF16	HAVANA	gene	18506	26943	.	+	.	FI_gene_label "ZNF16^ENSG00000170631.15"  ; ID "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15"  ; ccdsid "CCDS6437.1"  ; exon_id "ENSE00003564928.1"  ; exon_number 3 ; gene_id "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15"  ; gene_name ZNF16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165253.3"  ; havana_transcript "OTTHUMT00000382978.1"  ; hgnc_id "HGNC:12947"  ; level 1 ; orig_coord_info "chr8,144946011,144946206,-"  ; protein_id "ENSP00000276816.4"  ; tag alternative_5_UTR basic appris_principal_1 exp_conf CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276816.8"  ; transcript_name "ZNF16-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP39--ZNF16	HAVANA	mRNA	18506	26943	.	+	.	FI_gene_label "ZNF16^ENSG00000170631.15"  ; ID "ARHGAP39--ZNF16^ENST00000276816.8"  ; Parent "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15"  ; ccdsid "CCDS6437.1"  ; exon_id "ENSE00003564928.1"  ; exon_number 3 ; gene_id "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15"  ; gene_name ZNF16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165253.3"  ; havana_transcript "OTTHUMT00000382978.1"  ; hgnc_id "HGNC:12947"  ; level 1 ; orig_coord_info "chr8,144946011,144946206,-"  ; protein_id "ENSP00000276816.4"  ; tag alternative_5_UTR basic appris_principal_1 exp_conf CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276816.8"  ; transcript_name "ZNF16-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP39--ZNF16	HAVANA	gene	1001	15505	.	+	.	FI_gene_label "ARHGAP39^ENSG00000147799.11"  ; ID "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11"  ; ccdsid "CCDS78374.1"  ; exon_id "ENSE00002184188.1"  ; exon_number 1 ; gene_id "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11"  ; gene_name ARHGAP39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165182.1"  ; havana_transcript "OTTHUMT00000382509.1"  ; hgnc_id "HGNC:29351"  ; level 2 ; orig_coord_info "chr8,144605535,144605614,-"  ; protein_id "ENSP00000276826.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276826.5"  ; transcript_name "ARHGAP39-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ARHGAP39--ZNF16	HAVANA	mRNA	1001	15505	.	+	.	FI_gene_label "ARHGAP39^ENSG00000147799.11"  ; ID "ARHGAP39--ZNF16^ENST00000276826.5"  ; Parent "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11"  ; ccdsid "CCDS78374.1"  ; exon_id "ENSE00002184188.1"  ; exon_number 1 ; gene_id "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11"  ; gene_name ARHGAP39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165182.1"  ; havana_transcript "OTTHUMT00000382509.1"  ; hgnc_id "HGNC:29351"  ; level 2 ; orig_coord_info "chr8,144605535,144605614,-"  ; protein_id "ENSP00000276826.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276826.5"  ; transcript_name "ARHGAP39-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ATP11C--MCF2	HAVANA	gene	4133	38542	.	+	.	FI_gene_label "ATP11C^ENSG00000101974.14"  ; ID "ATP11C--MCF2^ATP11C^ENSG00000101974.14"  ; ccdsid "CCDS14668.1"  ; exon_id "ENSE00001415779.1"  ; exon_number 1 ; gene_id "ATP11C--MCF2^ATP11C^ENSG00000101974.14"  ; gene_name ATP11C ; gene_type protein_coding ; havana_gene "OTTHUMG00000022538.7"  ; havana_transcript "OTTHUMT00000354945.1"  ; hgnc_id "HGNC:13554"  ; level 2 ; orig_coord_info "chrX,139832154,139832189,-"  ; protein_id "ENSP00000332756.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000327569.7"  ; transcript_name "ATP11C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP11C--MCF2	HAVANA	mRNA	4133	38542	.	+	.	FI_gene_label "ATP11C^ENSG00000101974.14"  ; ID "ATP11C--MCF2^ENST00000327569.7"  ; Parent "ATP11C--MCF2^ATP11C^ENSG00000101974.14"  ; ccdsid "CCDS14668.1"  ; exon_id "ENSE00001415779.1"  ; exon_number 1 ; gene_id "ATP11C--MCF2^ATP11C^ENSG00000101974.14"  ; gene_name ATP11C ; gene_type protein_coding ; havana_gene "OTTHUMG00000022538.7"  ; havana_transcript "OTTHUMT00000354945.1"  ; hgnc_id "HGNC:13554"  ; level 2 ; orig_coord_info "chrX,139832154,139832189,-"  ; protein_id "ENSP00000332756.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000327569.7"  ; transcript_name "ATP11C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATP11C--MCF2	HAVANA	gene	47570	72966	.	+	.	FI_gene_label "MCF2^ENSG00000101977.21"  ; ID "ATP11C--MCF2^MCF2^ENSG00000101977.21"  ; ccdsid "CCDS55516.1"  ; exon_id "ENSE00001598942.1"  ; exon_number 1 ; gene_id "ATP11C--MCF2^MCF2^ENSG00000101977.21"  ; gene_name MCF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022537.6"  ; havana_transcript "OTTHUMT00000058562.2"  ; hgnc_id "HGNC:6940"  ; level 2 ; orig_coord_info "chrX,139642468,139642518,-"  ; protein_id "ENSP00000342204.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000338585.6"  ; transcript_name "MCF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP11C--MCF2	HAVANA	mRNA	47570	72966	.	+	.	FI_gene_label "MCF2^ENSG00000101977.21"  ; ID "ATP11C--MCF2^ENST00000338585.6"  ; Parent "ATP11C--MCF2^MCF2^ENSG00000101977.21"  ; ccdsid "CCDS55516.1"  ; exon_id "ENSE00001598942.1"  ; exon_number 1 ; gene_id "ATP11C--MCF2^MCF2^ENSG00000101977.21"  ; gene_name MCF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022537.6"  ; havana_transcript "OTTHUMT00000058562.2"  ; hgnc_id "HGNC:6940"  ; level 2 ; orig_coord_info "chrX,139642468,139642518,-"  ; protein_id "ENSP00000342204.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000338585.6"  ; transcript_name "MCF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BRAF--AGAP3	HAVANA	gene	1198	35070	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "BRAF--AGAP3^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "BRAF--AGAP3^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "BRAF--AGAP3^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BRAF--AGAP3	HAVANA	mRNA	1198	35070	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "BRAF--AGAP3^ENST00000288602.11"  ; Parent "BRAF--AGAP3^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "BRAF--AGAP3^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "BRAF--AGAP3^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BRAF--AGAP3	HAVANA	gene	55353	63622	.	+	.	FI_gene_label "AGAP3^ENSG00000133612.19"  ; ID "BRAF--AGAP3^AGAP3^ENSG00000133612.19"  ; ccdsid "CCDS78287.1"  ; exon_id "ENSE00001339499.3"  ; exon_number 1 ; gene_id "BRAF--AGAP3^AGAP3^ENSG00000133612.19"  ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8"  ; havana_transcript "OTTHUMT00000351912.1"  ; hgnc_id "HGNC:16923"  ; level 2 ; orig_coord_info "chr7,151114771,151115641,+"  ; protein_id "ENSP00000335589.3"  ; tag basic CCDS ; transcript_id "BRAF--AGAP3^ENST00000335367.7"  ; transcript_name "AGAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BRAF--AGAP3	HAVANA	mRNA	55353	63622	.	+	.	FI_gene_label "AGAP3^ENSG00000133612.19"  ; ID "BRAF--AGAP3^ENST00000335367.7"  ; Parent "BRAF--AGAP3^AGAP3^ENSG00000133612.19"  ; ccdsid "CCDS78287.1"  ; exon_id "ENSE00001339499.3"  ; exon_number 1 ; gene_id "BRAF--AGAP3^AGAP3^ENSG00000133612.19"  ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8"  ; havana_transcript "OTTHUMT00000351912.1"  ; hgnc_id "HGNC:16923"  ; level 2 ; orig_coord_info "chr7,151114771,151115641,+"  ; protein_id "ENSP00000335589.3"  ; tag basic CCDS ; transcript_id "BRAF--AGAP3^ENST00000335367.7"  ; transcript_name "AGAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CHCHD6--EPB41L1	HAVANA	gene	18841	55808	.	+	.	FI_gene_label "EPB41L1^ENSG00000088367.23"  ; ID "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23"  ; ccdsid "CCDS13272.1"  ; exon_id "ENSE00003546773.1"  ; exon_number 3 ; gene_id "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23"  ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14"  ; havana_transcript "OTTHUMT00000078983.1"  ; hgnc_id "HGNC:3378"  ; level 2 ; orig_coord_info "chr20,36175560,36175715,+"  ; protein_id "ENSP00000202028.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000202028.9"  ; transcript_name "EPB41L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CHCHD6--EPB41L1	HAVANA	mRNA	18841	55808	.	+	.	FI_gene_label "EPB41L1^ENSG00000088367.23"  ; ID "CHCHD6--EPB41L1^ENST00000202028.9"  ; Parent "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23"  ; ccdsid "CCDS13272.1"  ; exon_id "ENSE00003546773.1"  ; exon_number 3 ; gene_id "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23"  ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14"  ; havana_transcript "OTTHUMT00000078983.1"  ; hgnc_id "HGNC:3378"  ; level 2 ; orig_coord_info "chr20,36175560,36175715,+"  ; protein_id "ENSP00000202028.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000202028.9"  ; transcript_name "EPB41L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CHCHD6--EPB41L1	HAVANA	gene	1001	15840	.	+	.	FI_gene_label "CHCHD6^ENSG00000159685.11"  ; ID "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11"  ; ccdsid "CCDS3041.1"  ; exon_id "ENSE00002077922.1"  ; exon_number 1 ; gene_id "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11"  ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3"  ; havana_transcript "OTTHUMT00000356432.2"  ; hgnc_id "HGNC:28184"  ; level 2 ; orig_coord_info "chr3,126704313,126704399,+"  ; protein_id "ENSP00000290913.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000290913.8"  ; transcript_name "CHCHD6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CHCHD6--EPB41L1	HAVANA	mRNA	1001	15840	.	+	.	FI_gene_label "CHCHD6^ENSG00000159685.11"  ; ID "CHCHD6--EPB41L1^ENST00000290913.8"  ; Parent "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11"  ; ccdsid "CCDS3041.1"  ; exon_id "ENSE00002077922.1"  ; exon_number 1 ; gene_id "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11"  ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3"  ; havana_transcript "OTTHUMT00000356432.2"  ; hgnc_id "HGNC:28184"  ; level 2 ; orig_coord_info "chr3,126704313,126704399,+"  ; protein_id "ENSP00000290913.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000290913.8"  ; transcript_name "CHCHD6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DIS3L--MAP2K1	HAVANA	gene	22724	35798	.	+	.	FI_gene_label "MAP2K1^ENSG00000169032.10"  ; ID "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10"  ; ccdsid "CCDS10216.1"  ; exon_id "ENSE00001257104.5"  ; exon_number 1 ; gene_id "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10"  ; gene_name MAP2K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133196.5"  ; havana_transcript "OTTHUMT00000256906.4"  ; hgnc_id "HGNC:6840"  ; level 2 ; orig_coord_info "chr15,66387348,66387427,+"  ; protein_id "ENSP00000302486.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000307102.10"  ; transcript_name "MAP2K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DIS3L--MAP2K1	HAVANA	mRNA	22724	35798	.	+	.	FI_gene_label "MAP2K1^ENSG00000169032.10"  ; ID "DIS3L--MAP2K1^ENST00000307102.10"  ; Parent "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10"  ; ccdsid "CCDS10216.1"  ; exon_id "ENSE00001257104.5"  ; exon_number 1 ; gene_id "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10"  ; gene_name MAP2K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133196.5"  ; havana_transcript "OTTHUMT00000256906.4"  ; hgnc_id "HGNC:6840"  ; level 2 ; orig_coord_info "chr15,66387348,66387427,+"  ; protein_id "ENSP00000302486.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000307102.10"  ; transcript_name "MAP2K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DIS3L--MAP2K1	HAVANA	gene	1001	19648	.	+	.	FI_gene_label "DIS3L^ENSG00000166938.13"  ; ID "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13"  ; ccdsid "CCDS10214.1"  ; exon_id "ENSE00003612725.1"  ; exon_number 2 ; gene_id "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13"  ; gene_name DIS3L ; gene_type protein_coding ; havana_gene "OTTHUMG00000133181.10"  ; havana_transcript "OTTHUMT00000256889.3"  ; hgnc_id "HGNC:28698"  ; level 2 ; orig_coord_info "chr15,66295098,66295141,+"  ; protein_id "ENSP00000321583.5"  ; tag basic CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000319194.9"  ; transcript_name "DIS3L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DIS3L--MAP2K1	HAVANA	mRNA	1001	19648	.	+	.	FI_gene_label "DIS3L^ENSG00000166938.13"  ; ID "DIS3L--MAP2K1^ENST00000319194.9"  ; Parent "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13"  ; ccdsid "CCDS10214.1"  ; exon_id "ENSE00003612725.1"  ; exon_number 2 ; gene_id "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13"  ; gene_name DIS3L ; gene_type protein_coding ; havana_gene "OTTHUMG00000133181.10"  ; havana_transcript "OTTHUMT00000256889.3"  ; hgnc_id "HGNC:28698"  ; level 2 ; orig_coord_info "chr15,66295098,66295141,+"  ; protein_id "ENSP00000321583.5"  ; tag basic CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000319194.9"  ; transcript_name "DIS3L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EPB41L1--CHCHD6	HAVANA	gene	1001	37968	.	+	.	FI_gene_label "EPB41L1^ENSG00000088367.23"  ; ID "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23"  ; ccdsid "CCDS13272.1"  ; exon_id "ENSE00003546773.1"  ; exon_number 3 ; gene_id "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23"  ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14"  ; havana_transcript "OTTHUMT00000078983.1"  ; hgnc_id "HGNC:3378"  ; level 2 ; orig_coord_info "chr20,36175560,36175715,+"  ; protein_id "ENSP00000202028.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000202028.9"  ; transcript_name "EPB41L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EPB41L1--CHCHD6	HAVANA	mRNA	1001	37968	.	+	.	FI_gene_label "EPB41L1^ENSG00000088367.23"  ; ID "EPB41L1--CHCHD6^ENST00000202028.9"  ; Parent "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23"  ; ccdsid "CCDS13272.1"  ; exon_id "ENSE00003546773.1"  ; exon_number 3 ; gene_id "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23"  ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14"  ; havana_transcript "OTTHUMT00000078983.1"  ; hgnc_id "HGNC:3378"  ; level 2 ; orig_coord_info "chr20,36175560,36175715,+"  ; protein_id "ENSP00000202028.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000202028.9"  ; transcript_name "EPB41L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EPB41L1--CHCHD6	HAVANA	gene	43427	58266	.	+	.	FI_gene_label "CHCHD6^ENSG00000159685.11"  ; ID "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11"  ; ccdsid "CCDS3041.1"  ; exon_id "ENSE00002077922.1"  ; exon_number 1 ; gene_id "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11"  ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3"  ; havana_transcript "OTTHUMT00000356432.2"  ; hgnc_id "HGNC:28184"  ; level 2 ; orig_coord_info "chr3,126704313,126704399,+"  ; protein_id "ENSP00000290913.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000290913.8"  ; transcript_name "CHCHD6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EPB41L1--CHCHD6	HAVANA	mRNA	43427	58266	.	+	.	FI_gene_label "CHCHD6^ENSG00000159685.11"  ; ID "EPB41L1--CHCHD6^ENST00000290913.8"  ; Parent "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11"  ; ccdsid "CCDS3041.1"  ; exon_id "ENSE00002077922.1"  ; exon_number 1 ; gene_id "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11"  ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3"  ; havana_transcript "OTTHUMT00000356432.2"  ; hgnc_id "HGNC:28184"  ; level 2 ; orig_coord_info "chr3,126704313,126704399,+"  ; protein_id "ENSP00000290913.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000290913.8"  ; transcript_name "CHCHD6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GPBP1L1--PRDX1	HAVANA	gene	25570	30696	.	+	.	FI_gene_label "PRDX1^ENSG00000117450.15"  ; ID "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15"  ; ccdsid "CCDS522.1"  ; exon_id "ENSE00003648037.1"  ; exon_number 2 ; gene_id "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15"  ; gene_name PRDX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007738.7"  ; hgnc_id "HGNC:9352"  ; level 2 ; orig_coord_info "chr1,45518938,45519043,-"  ; protein_id "ENSP00000262746.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000262746.5"  ; transcript_name "PRDX1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
GPBP1L1--PRDX1	HAVANA	mRNA	25570	30696	.	+	.	FI_gene_label "PRDX1^ENSG00000117450.15"  ; ID "GPBP1L1--PRDX1^ENST00000262746.5"  ; Parent "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15"  ; ccdsid "CCDS522.1"  ; exon_id "ENSE00003648037.1"  ; exon_number 2 ; gene_id "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15"  ; gene_name PRDX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007738.7"  ; hgnc_id "HGNC:9352"  ; level 2 ; orig_coord_info "chr1,45518938,45519043,-"  ; protein_id "ENSP00000262746.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000262746.5"  ; transcript_name "PRDX1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
GPBP1L1--PRDX1	HAVANA	gene	2578	20404	.	+	.	FI_gene_label "GPBP1L1^ENSG00000159592.11"  ; ID "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11"  ; ccdsid "CCDS528.1"  ; exon_id "ENSE00003888808.1"  ; exon_number 3 ; gene_id "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11"  ; gene_name GPBP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040990.3"  ; havana_transcript "OTTHUMT00000098375.1"  ; hgnc_id "HGNC:28843"  ; level 2 ; orig_coord_info "chr1,45659028,45659087,-"  ; protein_id "ENSP00000290795.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000290795.7"  ; transcript_name "GPBP1L1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
GPBP1L1--PRDX1	HAVANA	mRNA	2578	20404	.	+	.	FI_gene_label "GPBP1L1^ENSG00000159592.11"  ; ID "GPBP1L1--PRDX1^ENST00000290795.7"  ; Parent "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11"  ; ccdsid "CCDS528.1"  ; exon_id "ENSE00003888808.1"  ; exon_number 3 ; gene_id "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11"  ; gene_name GPBP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040990.3"  ; havana_transcript "OTTHUMT00000098375.1"  ; hgnc_id "HGNC:28843"  ; level 2 ; orig_coord_info "chr1,45659028,45659087,-"  ; protein_id "ENSP00000290795.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000290795.7"  ; transcript_name "GPBP1L1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MED15--ATXN3	HAVANA	gene	3290	26140	.	+	.	FI_gene_label "MED15^ENSG00000099917.17"  ; ID "MED15--ATXN3^MED15^ENSG00000099917.17"  ; ccdsid "CCDS33602.1"  ; exon_id "ENSE00001871169.1"  ; exon_number 1 ; gene_id "MED15--ATXN3^MED15^ENSG00000099917.17"  ; gene_name MED15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150810.9"  ; havana_transcript "OTTHUMT00000320177.2"  ; hgnc_id "HGNC:14248"  ; level 2 ; orig_coord_info "chr22,20507679,20507746,+"  ; protein_id "ENSP00000263205.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MED15--ATXN3^ENST00000263205.11"  ; transcript_name "MED15-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MED15--ATXN3	HAVANA	mRNA	3290	26140	.	+	.	FI_gene_label "MED15^ENSG00000099917.17"  ; ID "MED15--ATXN3^ENST00000263205.11"  ; Parent "MED15--ATXN3^MED15^ENSG00000099917.17"  ; ccdsid "CCDS33602.1"  ; exon_id "ENSE00001871169.1"  ; exon_number 1 ; gene_id "MED15--ATXN3^MED15^ENSG00000099917.17"  ; gene_name MED15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150810.9"  ; havana_transcript "OTTHUMT00000320177.2"  ; hgnc_id "HGNC:14248"  ; level 2 ; orig_coord_info "chr22,20507679,20507746,+"  ; protein_id "ENSP00000263205.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MED15--ATXN3^ENST00000263205.11"  ; transcript_name "MED15-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MED15--ATXN3	HAVANA	gene	29165	44314	.	+	.	FI_gene_label "ATXN3^ENSG00000066427.24"  ; ID "MED15--ATXN3^ATXN3^ENSG00000066427.24"  ; ccdsid "CCDS32143.1"  ; exon_id "ENSE00002073369.1"  ; exon_number 1 ; gene_id "MED15--ATXN3^ATXN3^ENSG00000066427.24"  ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16"  ; havana_transcript "OTTHUMT00000367924.2"  ; hgnc_id "HGNC:7106"  ; level 2 ; orig_coord_info "chr14,92106529,92106552,-"  ; protein_id "ENSP00000339110.6"  ; tag basic CCDS ; transcript_id "MED15--ATXN3^ENST00000340660.10"  ; transcript_name "ATXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MED15--ATXN3	HAVANA	mRNA	29165	44314	.	+	.	FI_gene_label "ATXN3^ENSG00000066427.24"  ; ID "MED15--ATXN3^ENST00000340660.10"  ; Parent "MED15--ATXN3^ATXN3^ENSG00000066427.24"  ; ccdsid "CCDS32143.1"  ; exon_id "ENSE00002073369.1"  ; exon_number 1 ; gene_id "MED15--ATXN3^ATXN3^ENSG00000066427.24"  ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16"  ; havana_transcript "OTTHUMT00000367924.2"  ; hgnc_id "HGNC:7106"  ; level 2 ; orig_coord_info "chr14,92106529,92106552,-"  ; protein_id "ENSP00000339110.6"  ; tag basic CCDS ; transcript_id "MED15--ATXN3^ENST00000340660.10"  ; transcript_name "ATXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCCA--NALCN-AS1	ENSEMBL	gene	1001	37641	.	+	.	FI_gene_label "PCCA^ENSG00000175198.17"  ; ID "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17"  ; ccdsid "CCDS53878.1"  ; exon_id "ENSE00002300882.1"  ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17"  ; gene_name PCCA ; gene_type protein_coding ; havana_gene "OTTHUMG00000017284.13"  ; hgnc_id "HGNC:8653"  ; level 3 ; orig_coord_info "chr13,100089121,100089225,+"  ; protein_id "ENSP00000365456.3"  ; tag basic CCDS ; transcript_id "PCCA--NALCN-AS1^ENST00000376279.7"  ; transcript_name "PCCA-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PCCA--NALCN-AS1	ENSEMBL	mRNA	1001	37641	.	+	.	FI_gene_label "PCCA^ENSG00000175198.17"  ; ID "PCCA--NALCN-AS1^ENST00000376279.7"  ; Parent "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17"  ; ccdsid "CCDS53878.1"  ; exon_id "ENSE00002300882.1"  ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17"  ; gene_name PCCA ; gene_type protein_coding ; havana_gene "OTTHUMG00000017284.13"  ; hgnc_id "HGNC:8653"  ; level 3 ; orig_coord_info "chr13,100089121,100089225,+"  ; protein_id "ENSP00000365456.3"  ; tag basic CCDS ; transcript_id "PCCA--NALCN-AS1^ENST00000376279.7"  ; transcript_name "PCCA-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PDIA3--STRC	HAVANA	gene	1029	16180	.	+	.	FI_gene_label "PDIA3^ENSG00000167004.13"  ; ID "PDIA3--STRC^PDIA3^ENSG00000167004.13"  ; ccdsid "CCDS10101.1"  ; exon_id "ENSE00001489318.2"  ; exon_number 1 ; gene_id "PDIA3--STRC^PDIA3^ENSG00000167004.13"  ; gene_name PDIA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044444.9"  ; havana_transcript "OTTHUMT00000103532.4"  ; hgnc_id "HGNC:4606"  ; level 2 ; orig_coord_info "chr15,43746540,43746706,+"  ; protein_id "ENSP00000300289.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDIA3--STRC^ENST00000300289.10"  ; transcript_name "PDIA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PDIA3--STRC	HAVANA	mRNA	1029	16180	.	+	.	FI_gene_label "PDIA3^ENSG00000167004.13"  ; ID "PDIA3--STRC^ENST00000300289.10"  ; Parent "PDIA3--STRC^PDIA3^ENSG00000167004.13"  ; ccdsid "CCDS10101.1"  ; exon_id "ENSE00001489318.2"  ; exon_number 1 ; gene_id "PDIA3--STRC^PDIA3^ENSG00000167004.13"  ; gene_name PDIA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044444.9"  ; havana_transcript "OTTHUMT00000103532.4"  ; hgnc_id "HGNC:4606"  ; level 2 ; orig_coord_info "chr15,43746540,43746706,+"  ; protein_id "ENSP00000300289.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDIA3--STRC^ENST00000300289.10"  ; transcript_name "PDIA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PDIA3--STRC	HAVANA	gene	19183	36247	.	+	.	FI_gene_label "STRC^ENSG00000242866.10"  ; ID "PDIA3--STRC^STRC^ENSG00000242866.10"  ; exon_id "ENSE00001642185.1"  ; exon_number 1 ; gene_id "PDIA3--STRC^STRC^ENSG00000242866.10"  ; gene_name STRC ; gene_type protein_coding ; havana_gene "OTTHUMG00000059899.6"  ; havana_transcript "OTTHUMT00000317302.2"  ; hgnc_id "HGNC:16035"  ; level 2 ; orig_coord_info "chr15,43618659,43618722,-"  ; protein_id "ENSP00000415991.1"  ; transcript_id "PDIA3--STRC^ENST00000428650.5"  ; transcript_name "STRC-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
PDIA3--STRC	HAVANA	mRNA	19183	36247	.	+	.	FI_gene_label "STRC^ENSG00000242866.10"  ; ID "PDIA3--STRC^ENST00000428650.5"  ; Parent "PDIA3--STRC^STRC^ENSG00000242866.10"  ; exon_id "ENSE00001642185.1"  ; exon_number 1 ; gene_id "PDIA3--STRC^STRC^ENSG00000242866.10"  ; gene_name STRC ; gene_type protein_coding ; havana_gene "OTTHUMG00000059899.6"  ; havana_transcript "OTTHUMT00000317302.2"  ; hgnc_id "HGNC:16035"  ; level 2 ; orig_coord_info "chr15,43618659,43618722,-"  ; protein_id "ENSP00000415991.1"  ; transcript_id "PDIA3--STRC^ENST00000428650.5"  ; transcript_name "STRC-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
RFNG--IGH@-ext	HAVANA	gene	1021	4930	.	+	.	FI_gene_label "RFNG^ENSG00000169733.12"  ; ID "RFNG--IGH@-ext^RFNG^ENSG00000169733.12"  ; ccdsid "CCDS32773.1"  ; exon_id "ENSE00002222540.2"  ; exon_number 1 ; gene_id "RFNG--IGH@-ext^RFNG^ENSG00000169733.12"  ; gene_name RFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000178512.3"  ; havana_transcript "OTTHUMT00000442263.2"  ; hgnc_id "HGNC:9974"  ; level 2 ; orig_coord_info "chr17,82051500,82051766,-"  ; protein_id "ENSP00000307971.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RFNG--IGH@-ext^ENST00000310496.9"  ; transcript_name "RFNG-201"  ; transcript_support_level 2 ; transcript_type protein_coding
RFNG--IGH@-ext	HAVANA	mRNA	1021	4930	.	+	.	FI_gene_label "RFNG^ENSG00000169733.12"  ; ID "RFNG--IGH@-ext^ENST00000310496.9"  ; Parent "RFNG--IGH@-ext^RFNG^ENSG00000169733.12"  ; ccdsid "CCDS32773.1"  ; exon_id "ENSE00002222540.2"  ; exon_number 1 ; gene_id "RFNG--IGH@-ext^RFNG^ENSG00000169733.12"  ; gene_name RFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000178512.3"  ; havana_transcript "OTTHUMT00000442263.2"  ; hgnc_id "HGNC:9974"  ; level 2 ; orig_coord_info "chr17,82051500,82051766,-"  ; protein_id "ENSP00000307971.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RFNG--IGH@-ext^ENST00000310496.9"  ; transcript_name "RFNG-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^ENST00000326270.13"  ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC015911.9--SLFN12L	HAVANA	gene	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L	HAVANA	RNA	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^ENST00000650652.2"  ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC015911.9--SLFN12L	ENSEMBL	gene	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
AC015911.9--SLFN12L	ENSEMBL	RNA	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^ENST00000675965.1"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
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: 
HERC2P2--AC009563.1	HAVANA	gene	34902	37659	.	+	.	FI_gene_label "AC009563.1^ENSG00000253961.1"  ; ID "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1"  ; exon_id "ENSE00002123895.1"  ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1"  ; gene_name "AC009563.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163915.1"  ; havana_transcript "OTTHUMT00000376382.1"  ; level 1 ; orig_coord_info "chr8,31176692,31176872,-"  ; tag exp_conf ; transcript_id "HERC2P2--AC009563.1^ENST00000521252.1"  ; transcript_name "AC009563.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
HERC2P2--AC009563.1	HAVANA	RNA	34902	37659	.	+	.	FI_gene_label "AC009563.1^ENSG00000253961.1"  ; ID "HERC2P2--AC009563.1^ENST00000521252.1"  ; Parent "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1"  ; exon_id "ENSE00002123895.1"  ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1"  ; gene_name "AC009563.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163915.1"  ; havana_transcript "OTTHUMT00000376382.1"  ; level 1 ; orig_coord_info "chr8,31176692,31176872,-"  ; tag exp_conf ; transcript_id "HERC2P2--AC009563.1^ENST00000521252.1"  ; transcript_name "AC009563.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
HERC2P2--AC009563.1	HAVANA	gene	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--AC009563.1^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
HERC2P2--AC009563.1	HAVANA	RNA	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--AC009563.1^ENST00000613386.4"  ; Parent "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--AC009563.1^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
HERC2P2--AC068672.2	HAVANA	gene	34661	37080	.	+	.	FI_gene_label "AC068672.2^ENSG00000253377.2"  ; ID "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2"  ; exon_id "ENSE00002091619.1"  ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2"  ; gene_name "AC068672.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163916.3"  ; havana_transcript "OTTHUMT00000376384.1"  ; level 2 ; orig_coord_info "chr8,31275596,31275808,+"  ; transcript_id "HERC2P2--AC068672.2^ENST00000524022.1"  ; transcript_name "AC068672.2-201"  ; transcript_support_level 3 ; transcript_type lncRNA
HERC2P2--AC068672.2	HAVANA	RNA	34661	37080	.	+	.	FI_gene_label "AC068672.2^ENSG00000253377.2"  ; ID "HERC2P2--AC068672.2^ENST00000524022.1"  ; Parent "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2"  ; exon_id "ENSE00002091619.1"  ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2"  ; gene_name "AC068672.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163916.3"  ; havana_transcript "OTTHUMT00000376384.1"  ; level 2 ; orig_coord_info "chr8,31275596,31275808,+"  ; transcript_id "HERC2P2--AC068672.2^ENST00000524022.1"  ; transcript_name "AC068672.2-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
HERC2P2--AC068672.2	HAVANA	gene	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--AC068672.2^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
HERC2P2--AC068672.2	HAVANA	RNA	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--AC068672.2^ENST00000613386.4"  ; Parent "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--AC068672.2^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
HERC2P2--KCTD9P6	HAVANA	gene	34607	35697	.	+	.	FI_gene_label "KCTD9P6^ENSG00000229211.3"  ; ID "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3"  ; exon_id "ENSE00002113312.1"  ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3"  ; gene_name KCTD9P6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163896.1"  ; havana_transcript "OTTHUMT00000376252.1"  ; hgnc_id "HGNC:49915"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,31220519,31220984,-"  ; tag pseudo_consens basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000522306.1"  ; transcript_name "KCTD9P6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
HERC2P2--KCTD9P6	HAVANA	RNA	34607	35697	.	+	.	FI_gene_label "KCTD9P6^ENSG00000229211.3"  ; ID "HERC2P2--KCTD9P6^ENST00000522306.1"  ; Parent "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3"  ; exon_id "ENSE00002113312.1"  ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3"  ; gene_name KCTD9P6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163896.1"  ; havana_transcript "OTTHUMT00000376252.1"  ; hgnc_id "HGNC:49915"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,31220519,31220984,-"  ; tag pseudo_consens basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000522306.1"  ; transcript_name "KCTD9P6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
HERC2P2--KCTD9P6	HAVANA	gene	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
HERC2P2--KCTD9P6	HAVANA	RNA	1001	28200	.	+	.	FI_gene_label "HERC2P2^ENSG00000276550.4"  ; ID "HERC2P2--KCTD9P6^ENST00000613386.4"  ; Parent "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4"  ; exon_id "ENSE00003716657.1"  ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4"  ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2"  ; havana_transcript "OTTHUMT00000476788.1"  ; hgnc_id "HGNC:4870"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,22495570,22495672,+"  ; tag basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000613386.4"  ; transcript_name "HERC2P2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
PCCA--NALCN-AS1	HAVANA	gene	40647	49753	.	+	.	FI_gene_label "NALCN-AS1^ENSG00000233009.1"  ; ID "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1"  ; exon_id "ENSE00001597756.1"  ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1"  ; gene_name "NALCN-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017294.1"  ; havana_transcript "OTTHUMT00000045662.1"  ; hgnc_id "HGNC:42743"  ; level 2 ; orig_coord_info "chr13,100708325,100708393,+"  ; tag basic ; transcript_id "PCCA--NALCN-AS1^ENST00000457843.1"  ; transcript_name "NALCN-AS1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
PCCA--NALCN-AS1	HAVANA	RNA	40647	49753	.	+	.	FI_gene_label "NALCN-AS1^ENSG00000233009.1"  ; ID "PCCA--NALCN-AS1^ENST00000457843.1"  ; Parent "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1"  ; exon_id "ENSE00001597756.1"  ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1"  ; gene_name "NALCN-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017294.1"  ; havana_transcript "OTTHUMT00000045662.1"  ; hgnc_id "HGNC:42743"  ; level 2 ; orig_coord_info "chr13,100708325,100708393,+"  ; tag basic ; transcript_id "PCCA--NALCN-AS1^ENST00000457843.1"  ; transcript_name "NALCN-AS1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
RFNG--IGH@-ext	SuperLocus-ext	gene	7931	1299271	.	+	.	FI_gene_label "IGH@-ext^IGH.g@-ext"  ; ID "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext"  ; gene_id "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext"  ; gene_name "IGH@-ext"  ; orig_coord_info "chr14,105583731,106875071,-"  ; transcript_id "RFNG--IGH@-ext^IGH.t@-ext" 
RFNG--IGH@-ext	SuperLocus-ext	RNA	7931	1299271	.	+	.	FI_gene_label "IGH@-ext^IGH.g@-ext"  ; ID "RFNG--IGH@-ext^IGH.t@-ext"  ; Parent "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext"  ; gene_id "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext"  ; gene_name "IGH@-ext"  ; orig_coord_info "chr14,105583731,106875071,-"  ; transcript_id "RFNG--IGH@-ext^IGH.t@-ext" 
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A	HAVANA	RNA	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^ENST00000437428.3"  ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
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
470 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 ------------------------------
923 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 30 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