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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/cd9c51aceedfee21fe3b6ba5c0e4ac/.command.log
Size: 67.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_epP-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/ad8bffc16787de3d3b7ab3b8e9f9ce/fi_workdir/659_epP-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/cd9c51aceedfee21fe3b6ba5c0e4ac/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/cd9c51aceedfee21fe3b6ba5c0e4ac/.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: 3644
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3644
=> 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:3644
  => 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: 
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: 
AL669831.4--SEPTIN14	HAVANA	gene	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AL669831.4--SEPTIN14	HAVANA	mRNA	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^ENST00000388975.4"  ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ANGEL1--AL365295.1	HAVANA	gene	3286	16903	.	+	.	FI_gene_label "ANGEL1^ENSG00000013523.11"  ; ID "ANGEL1--AL365295.1^ANGEL1^ENSG00000013523.11"  ; ccdsid "CCDS9852.1"  ; exon_id "ENSE00000808471.5"  ; exon_number 1 ; gene_id "ANGEL1--AL365295.1^ANGEL1^ENSG00000013523.11"  ; gene_name ANGEL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171494.9"  ; havana_transcript "OTTHUMT00000413712.5"  ; hgnc_id "HGNC:19961"  ; level 2 ; orig_coord_info "chr14,76812764,76812827,-"  ; protein_id "ENSP00000251089.3"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANGEL1--AL365295.1^ENST00000251089.8"  ; transcript_name "ANGEL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ANGEL1--AL365295.1	HAVANA	mRNA	3286	16903	.	+	.	FI_gene_label "ANGEL1^ENSG00000013523.11"  ; ID "ANGEL1--AL365295.1^ENST00000251089.8"  ; Parent "ANGEL1--AL365295.1^ANGEL1^ENSG00000013523.11"  ; ccdsid "CCDS9852.1"  ; exon_id "ENSE00000808471.5"  ; exon_number 1 ; gene_id "ANGEL1--AL365295.1^ANGEL1^ENSG00000013523.11"  ; gene_name ANGEL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171494.9"  ; havana_transcript "OTTHUMT00000413712.5"  ; hgnc_id "HGNC:19961"  ; level 2 ; orig_coord_info "chr14,76812764,76812827,-"  ; protein_id "ENSP00000251089.3"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANGEL1--AL365295.1^ENST00000251089.8"  ; transcript_name "ANGEL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B	HAVANA	mRNA	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^ENST00000308284.10"  ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CXADR--AC010378.1	HAVANA	gene	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--AC010378.1^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--AC010378.1^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--AC010378.1^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CXADR--AC010378.1	HAVANA	mRNA	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--AC010378.1^ENST00000284878.12"  ; Parent "CXADR--AC010378.1^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--AC010378.1^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--AC010378.1^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CXADR--AP000457.1	HAVANA	gene	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--AP000457.1^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--AP000457.1^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--AP000457.1^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CXADR--AP000457.1	HAVANA	mRNA	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--AP000457.1^ENST00000284878.12"  ; Parent "CXADR--AP000457.1^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--AP000457.1^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--AP000457.1^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CXADR--RNU6-113P	HAVANA	gene	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--RNU6-113P^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--RNU6-113P^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--RNU6-113P^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CXADR--RNU6-113P	HAVANA	mRNA	1001	12106	.	+	.	FI_gene_label "CXADR^ENSG00000154639.19"  ; ID "CXADR--RNU6-113P^ENST00000284878.12"  ; Parent "CXADR--RNU6-113P^CXADR^ENSG00000154639.19"  ; ccdsid "CCDS33519.1"  ; exon_id "ENSE00001356018.5"  ; exon_number 1 ; gene_id "CXADR--RNU6-113P^CXADR^ENSG00000154639.19"  ; gene_name CXADR ; gene_type protein_coding ; havana_gene "OTTHUMG00000074508.4"  ; havana_transcript "OTTHUMT00000158209.2"  ; hgnc_id "HGNC:2559"  ; level 2 ; orig_coord_info "chr21,17513130,17513172,+"  ; protein_id "ENSP00000284878.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CXADR--RNU6-113P^ENST00000284878.12"  ; transcript_name "CXADR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EXOC4--LRGUK	HAVANA	gene	1006	38283	.	+	.	FI_gene_label "EXOC4^ENSG00000131558.15"  ; ID "EXOC4--LRGUK^EXOC4^ENSG00000131558.15"  ; ccdsid "CCDS5829.1"  ; exon_id "ENSE00003845393.1"  ; exon_number 1 ; gene_id "EXOC4--LRGUK^EXOC4^ENSG00000131558.15"  ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5"  ; havana_transcript "OTTHUMT00000339182.2"  ; hgnc_id "HGNC:30389"  ; level 2 ; orig_coord_info "chr7,133253102,133253187,+"  ; protein_id "ENSP00000253861.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--LRGUK^ENST00000253861.5"  ; transcript_name "EXOC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EXOC4--LRGUK	HAVANA	mRNA	1006	38283	.	+	.	FI_gene_label "EXOC4^ENSG00000131558.15"  ; ID "EXOC4--LRGUK^ENST00000253861.5"  ; Parent "EXOC4--LRGUK^EXOC4^ENSG00000131558.15"  ; ccdsid "CCDS5829.1"  ; exon_id "ENSE00003845393.1"  ; exon_number 1 ; gene_id "EXOC4--LRGUK^EXOC4^ENSG00000131558.15"  ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5"  ; havana_transcript "OTTHUMT00000339182.2"  ; hgnc_id "HGNC:30389"  ; level 2 ; orig_coord_info "chr7,133253102,133253187,+"  ; protein_id "ENSP00000253861.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--LRGUK^ENST00000253861.5"  ; transcript_name "EXOC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EXOC4--LRGUK	HAVANA	gene	42112	67910	.	+	.	FI_gene_label "LRGUK^ENSG00000155530.3"  ; ID "EXOC4--LRGUK^LRGUK^ENSG00000155530.3"  ; ccdsid "CCDS5830.1"  ; exon_id "ENSE00001821313.1"  ; exon_number 1 ; gene_id "EXOC4--LRGUK^LRGUK^ENSG00000155530.3"  ; gene_name LRGUK ; gene_type protein_coding ; havana_gene "OTTHUMG00000155320.3"  ; havana_transcript "OTTHUMT00000339442.1"  ; hgnc_id "HGNC:21964"  ; level 2 ; orig_coord_info "chr7,134127368,134127664,+"  ; protein_id "ENSP00000285928.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "EXOC4--LRGUK^ENST00000285928.2"  ; transcript_name "LRGUK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EXOC4--LRGUK	HAVANA	mRNA	42112	67910	.	+	.	FI_gene_label "LRGUK^ENSG00000155530.3"  ; ID "EXOC4--LRGUK^ENST00000285928.2"  ; Parent "EXOC4--LRGUK^LRGUK^ENSG00000155530.3"  ; ccdsid "CCDS5830.1"  ; exon_id "ENSE00001821313.1"  ; exon_number 1 ; gene_id "EXOC4--LRGUK^LRGUK^ENSG00000155530.3"  ; gene_name LRGUK ; gene_type protein_coding ; havana_gene "OTTHUMG00000155320.3"  ; havana_transcript "OTTHUMT00000339442.1"  ; hgnc_id "HGNC:21964"  ; level 2 ; orig_coord_info "chr7,134127368,134127664,+"  ; protein_id "ENSP00000285928.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "EXOC4--LRGUK^ENST00000285928.2"  ; transcript_name "LRGUK-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: 
LINC02438--USP4	HAVANA	gene	9872	37636	.	+	.	FI_gene_label "USP4^ENSG00000114316.13"  ; ID "LINC02438--USP4^USP4^ENSG00000114316.13"  ; ccdsid "CCDS2793.1"  ; exon_id "ENSE00000861562.7"  ; exon_number 1 ; gene_id "LINC02438--USP4^USP4^ENSG00000114316.13"  ; gene_name USP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156825.3"  ; havana_transcript "OTTHUMT00000346069.2"  ; hgnc_id "HGNC:12627"  ; level 2 ; orig_coord_info "chr3,49339924,49340024,-"  ; protein_id "ENSP00000265560.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LINC02438--USP4^ENST00000265560.9"  ; transcript_name "USP4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC02438--USP4	HAVANA	mRNA	9872	37636	.	+	.	FI_gene_label "USP4^ENSG00000114316.13"  ; ID "LINC02438--USP4^ENST00000265560.9"  ; Parent "LINC02438--USP4^USP4^ENSG00000114316.13"  ; ccdsid "CCDS2793.1"  ; exon_id "ENSE00000861562.7"  ; exon_number 1 ; gene_id "LINC02438--USP4^USP4^ENSG00000114316.13"  ; gene_name USP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156825.3"  ; havana_transcript "OTTHUMT00000346069.2"  ; hgnc_id "HGNC:12627"  ; level 2 ; orig_coord_info "chr3,49339924,49340024,-"  ; protein_id "ENSP00000265560.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LINC02438--USP4^ENST00000265560.9"  ; transcript_name "USP4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NCOA4--RET	HAVANA	gene	17674	38294	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "NCOA4--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "NCOA4--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "NCOA4--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NCOA4--RET	HAVANA	mRNA	17674	38294	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "NCOA4--RET^ENST00000340058.6"  ; Parent "NCOA4--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "NCOA4--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "NCOA4--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NCOA4--RET	HAVANA	gene	1017	13344	.	+	.	FI_gene_label "NCOA4^ENSG00000266412.6"  ; ID "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; ccdsid "CCDS73094.1"  ; exon_id "ENSE00002732991.1"  ; exon_number 2 ; gene_id "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; gene_name NCOA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188314.1"  ; havana_transcript "OTTHUMT00000476878.1"  ; hgnc_id "HGNC:7671"  ; level 2 ; orig_coord_info "chr10,46027432,46027465,-"  ; protein_id "ENSP00000463027.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NCOA4--RET^ENST00000578454.5"  ; transcript_name "NCOA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NCOA4--RET	HAVANA	mRNA	1017	13344	.	+	.	FI_gene_label "NCOA4^ENSG00000266412.6"  ; ID "NCOA4--RET^ENST00000578454.5"  ; Parent "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; ccdsid "CCDS73094.1"  ; exon_id "ENSE00002732991.1"  ; exon_number 2 ; gene_id "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; gene_name NCOA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188314.1"  ; havana_transcript "OTTHUMT00000476878.1"  ; hgnc_id "HGNC:7671"  ; level 2 ; orig_coord_info "chr10,46027432,46027465,-"  ; protein_id "ENSP00000463027.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NCOA4--RET^ENST00000578454.5"  ; transcript_name "NCOA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ENST00000264990.11"  ; Parent "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^ENST00000337331.10"  ; Parent "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146	HAVANA	mRNA	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^ENST00000285871.5"  ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SEC24B--MCUB	HAVANA	gene	1044	27878	.	+	.	FI_gene_label "SEC24B^ENSG00000138802.11"  ; ID "SEC24B--MCUB^SEC24B^ENSG00000138802.11"  ; ccdsid "CCDS47124.1"  ; exon_id "ENSE00002081193.1"  ; exon_number 1 ; gene_id "SEC24B--MCUB^SEC24B^ENSG00000138802.11"  ; gene_name SEC24B ; gene_type protein_coding ; havana_gene "OTTHUMG00000161372.3"  ; havana_transcript "OTTHUMT00000364693.2"  ; hgnc_id "HGNC:10704"  ; level 2 ; orig_coord_info "chr4,109433870,109434002,+"  ; protein_id "ENSP00000265175.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SEC24B--MCUB^ENST00000265175.5"  ; transcript_name "SEC24B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SEC24B--MCUB	HAVANA	mRNA	1044	27878	.	+	.	FI_gene_label "SEC24B^ENSG00000138802.11"  ; ID "SEC24B--MCUB^ENST00000265175.5"  ; Parent "SEC24B--MCUB^SEC24B^ENSG00000138802.11"  ; ccdsid "CCDS47124.1"  ; exon_id "ENSE00002081193.1"  ; exon_number 1 ; gene_id "SEC24B--MCUB^SEC24B^ENSG00000138802.11"  ; gene_name SEC24B ; gene_type protein_coding ; havana_gene "OTTHUMG00000161372.3"  ; havana_transcript "OTTHUMT00000364693.2"  ; hgnc_id "HGNC:10704"  ; level 2 ; orig_coord_info "chr4,109433870,109434002,+"  ; protein_id "ENSP00000265175.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SEC24B--MCUB^ENST00000265175.5"  ; transcript_name "SEC24B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SEC24B--MCUB	HAVANA	gene	30916	42986	.	+	.	FI_gene_label "MCUB^ENSG00000005059.16"  ; ID "SEC24B--MCUB^MCUB^ENSG00000005059.16"  ; ccdsid "CCDS3683.2"  ; exon_id "ENSE00002034107.2"  ; exon_number 1 ; gene_id "SEC24B--MCUB^MCUB^ENSG00000005059.16"  ; gene_name MCUB ; gene_type protein_coding ; havana_gene "OTTHUMG00000161103.3"  ; havana_transcript "OTTHUMT00000254865.3"  ; hgnc_id "HGNC:26076"  ; level 2 ; orig_coord_info "chr4,109560338,109560436,+"  ; protein_id "ENSP00000378145.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SEC24B--MCUB^ENST00000394650.7"  ; transcript_name "MCUB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SEC24B--MCUB	HAVANA	mRNA	30916	42986	.	+	.	FI_gene_label "MCUB^ENSG00000005059.16"  ; ID "SEC24B--MCUB^ENST00000394650.7"  ; Parent "SEC24B--MCUB^MCUB^ENSG00000005059.16"  ; ccdsid "CCDS3683.2"  ; exon_id "ENSE00002034107.2"  ; exon_number 1 ; gene_id "SEC24B--MCUB^MCUB^ENSG00000005059.16"  ; gene_name MCUB ; gene_type protein_coding ; havana_gene "OTTHUMG00000161103.3"  ; havana_transcript "OTTHUMT00000254865.3"  ; hgnc_id "HGNC:26076"  ; level 2 ; orig_coord_info "chr4,109560338,109560436,+"  ; protein_id "ENSP00000378145.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SEC24B--MCUB^ENST00000394650.7"  ; transcript_name "MCUB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLCO1B3--SLCO1B7	ENSEMBL	gene	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLCO1B3--SLCO1B7	ENSEMBL	mRNA	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^ENST00000403751.8"  ; Parent "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^ENST00000404752.6"  ; Parent "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
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: 
TKT--ARHGAP27	ENSEMBL	gene	22757	25997	.	+	.	FI_gene_label "ARHGAP27^ENSG00000159314.11"  ; ID "TKT--ARHGAP27^ARHGAP27^ENSG00000159314.11"  ; ccdsid "CCDS32670.1"  ; exon_id "ENSE00002406214.1"  ; exon_number 4 ; gene_id "TKT--ARHGAP27^ARHGAP27^ENSG00000159314.11"  ; gene_name ARHGAP27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166982.6"  ; hgnc_id "HGNC:31813"  ; level 3 ; orig_coord_info "chr17,45429491,45430279,-"  ; protein_id "ENSP00000290470.3"  ; tag basic CCDS ; transcript_id "TKT--ARHGAP27^ENST00000290470.3"  ; transcript_name "ARHGAP27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TKT--ARHGAP27	ENSEMBL	mRNA	22757	25997	.	+	.	FI_gene_label "ARHGAP27^ENSG00000159314.11"  ; ID "TKT--ARHGAP27^ENST00000290470.3"  ; Parent "TKT--ARHGAP27^ARHGAP27^ENSG00000159314.11"  ; ccdsid "CCDS32670.1"  ; exon_id "ENSE00002406214.1"  ; exon_number 4 ; gene_id "TKT--ARHGAP27^ARHGAP27^ENSG00000159314.11"  ; gene_name ARHGAP27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166982.6"  ; hgnc_id "HGNC:31813"  ; level 3 ; orig_coord_info "chr17,45429491,45430279,-"  ; protein_id "ENSP00000290470.3"  ; tag basic CCDS ; transcript_id "TKT--ARHGAP27^ENST00000290470.3"  ; transcript_name "ARHGAP27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TKT--ARHGAP27	ENSEMBL	gene	1040	17304	.	+	.	FI_gene_label "TKT^ENSG00000163931.16"  ; ID "TKT--ARHGAP27^TKT^ENSG00000163931.16"  ; exon_id "ENSE00003716652.1"  ; exon_number 6 ; gene_id "TKT--ARHGAP27^TKT^ENSG00000163931.16"  ; gene_name TKT ; gene_type protein_coding ; havana_gene "OTTHUMG00000158192.3"  ; hgnc_id "HGNC:11834"  ; level 3 ; orig_coord_info "chr3,53234983,53235113,-"  ; protein_id "ENSP00000296289.7"  ; tag basic ; transcript_id "TKT--ARHGAP27^ENST00000296289.10"  ; transcript_name "TKT-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TKT--ARHGAP27	ENSEMBL	mRNA	1040	17304	.	+	.	FI_gene_label "TKT^ENSG00000163931.16"  ; ID "TKT--ARHGAP27^ENST00000296289.10"  ; Parent "TKT--ARHGAP27^TKT^ENSG00000163931.16"  ; exon_id "ENSE00003716652.1"  ; exon_number 6 ; gene_id "TKT--ARHGAP27^TKT^ENSG00000163931.16"  ; gene_name TKT ; gene_type protein_coding ; havana_gene "OTTHUMG00000158192.3"  ; hgnc_id "HGNC:11834"  ; level 3 ; orig_coord_info "chr3,53234983,53235113,-"  ; protein_id "ENSP00000296289.7"  ; tag basic ; transcript_id "TKT--ARHGAP27^ENST00000296289.10"  ; transcript_name "TKT-201"  ; transcript_support_level 5 ; 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: 
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: 
AL669831.4--SEPTIN14	HAVANA	gene	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
AL669831.4--SEPTIN14	HAVANA	RNA	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^ENST00000447500.4"  ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
ANGEL1--AL365295.1	HAVANA	gene	36202	44763	.	+	.	FI_gene_label "AL365295.1^ENSG00000237356.7"  ; ID "ANGEL1--AL365295.1^AL365295.1^ENSG00000237356.7"  ; exon_id "ENSE00001653377.1"  ; exon_number 1 ; gene_id "ANGEL1--AL365295.1^AL365295.1^ENSG00000237356.7"  ; gene_name "AL365295.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000133700.25"  ; havana_transcript "OTTHUMT00000316369.1"  ; level 2 ; orig_coord_info "chr14,53369381,53369501,+"  ; transcript_id "ANGEL1--AL365295.1^ENST00000425648.1"  ; transcript_name "AL365295.1-205"  ; transcript_support_level 4 ; transcript_type lncRNA
ANGEL1--AL365295.1	HAVANA	RNA	36202	44763	.	+	.	FI_gene_label "AL365295.1^ENSG00000237356.7"  ; ID "ANGEL1--AL365295.1^ENST00000425648.1"  ; Parent "ANGEL1--AL365295.1^AL365295.1^ENSG00000237356.7"  ; exon_id "ENSE00001653377.1"  ; exon_number 1 ; gene_id "ANGEL1--AL365295.1^AL365295.1^ENSG00000237356.7"  ; gene_name "AL365295.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000133700.25"  ; havana_transcript "OTTHUMT00000316369.1"  ; level 2 ; orig_coord_info "chr14,53369381,53369501,+"  ; transcript_id "ANGEL1--AL365295.1^ENST00000425648.1"  ; transcript_name "AL365295.1-205"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B	HAVANA	RNA	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^ENST00000462729.2"  ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created: 
CXADR--AC010378.1	HAVANA	gene	16535	19621	.	+	.	FI_gene_label "AC010378.1^ENSG00000286403.1"  ; ID "CXADR--AC010378.1^AC010378.1^ENSG00000286403.1"  ; exon_id "ENSE00003856647.1"  ; exon_number 1 ; gene_id "CXADR--AC010378.1^AC010378.1^ENSG00000286403.1"  ; gene_name "AC010378.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194731.1"  ; havana_transcript "OTTHUMT00000521300.1"  ; level 2 ; orig_coord_info "chr5,139503242,139503813,+"  ; tag basic TAGENE ; transcript_id "CXADR--AC010378.1^ENST00000657350.1"  ; transcript_name "AC010378.1-201"  ; transcript_type lncRNA
CXADR--AC010378.1	HAVANA	RNA	16535	19621	.	+	.	FI_gene_label "AC010378.1^ENSG00000286403.1"  ; ID "CXADR--AC010378.1^ENST00000657350.1"  ; Parent "CXADR--AC010378.1^AC010378.1^ENSG00000286403.1"  ; exon_id "ENSE00003856647.1"  ; exon_number 1 ; gene_id "CXADR--AC010378.1^AC010378.1^ENSG00000286403.1"  ; gene_name "AC010378.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194731.1"  ; havana_transcript "OTTHUMT00000521300.1"  ; level 2 ; orig_coord_info "chr5,139503242,139503813,+"  ; tag basic TAGENE ; transcript_id "CXADR--AC010378.1^ENST00000657350.1"  ; transcript_name "AC010378.1-201"  ; transcript_type lncRNA
L1 and L2 created: 
CXADR--AP000457.1	HAVANA	gene	16535	16912	.	+	.	FI_gene_label "AP000457.1^ENSG00000278181.1"  ; ID "CXADR--AP000457.1^AP000457.1^ENSG00000278181.1"  ; exon_id "ENSE00003748822.1"  ; exon_number 1 ; gene_id "CXADR--AP000457.1^AP000457.1^ENSG00000278181.1"  ; gene_name "AP000457.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000187954.1"  ; havana_transcript "OTTHUMT00000475732.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr21,17296219,17296596,+"  ; tag basic ; transcript_id "CXADR--AP000457.1^ENST00000620221.1"  ; transcript_name "AP000457.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
CXADR--AP000457.1	HAVANA	RNA	16535	16912	.	+	.	FI_gene_label "AP000457.1^ENSG00000278181.1"  ; ID "CXADR--AP000457.1^ENST00000620221.1"  ; Parent "CXADR--AP000457.1^AP000457.1^ENSG00000278181.1"  ; exon_id "ENSE00003748822.1"  ; exon_number 1 ; gene_id "CXADR--AP000457.1^AP000457.1^ENSG00000278181.1"  ; gene_name "AP000457.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000187954.1"  ; havana_transcript "OTTHUMT00000475732.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr21,17296219,17296596,+"  ; tag basic ; transcript_id "CXADR--AP000457.1^ENST00000620221.1"  ; transcript_name "AP000457.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
CXADR--RNU6-113P	ENSEMBL	gene	16535	16635	.	+	.	FI_gene_label "RNU6-113P^ENSG00000252462.1"  ; ID "CXADR--RNU6-113P^RNU6-113P^ENSG00000252462.1"  ; exon_id "ENSE00002088930.1"  ; exon_number 1 ; gene_id "CXADR--RNU6-113P^RNU6-113P^ENSG00000252462.1"  ; gene_name "RNU6-113P"  ; gene_type snRNA ; hgnc_id "HGNC:47076"  ; level 3 ; orig_coord_info "chr21,17431547,17431647,+"  ; tag basic ; transcript_id "CXADR--RNU6-113P^ENST00000516653.1"  ; transcript_name "RNU6-113P-201"  ; transcript_support_level NA ; transcript_type snRNA
CXADR--RNU6-113P	ENSEMBL	RNA	16535	16635	.	+	.	FI_gene_label "RNU6-113P^ENSG00000252462.1"  ; ID "CXADR--RNU6-113P^ENST00000516653.1"  ; Parent "CXADR--RNU6-113P^RNU6-113P^ENSG00000252462.1"  ; exon_id "ENSE00002088930.1"  ; exon_number 1 ; gene_id "CXADR--RNU6-113P^RNU6-113P^ENSG00000252462.1"  ; gene_name "RNU6-113P"  ; gene_type snRNA ; hgnc_id "HGNC:47076"  ; level 3 ; orig_coord_info "chr21,17431547,17431647,+"  ; tag basic ; transcript_id "CXADR--RNU6-113P^ENST00000516653.1"  ; transcript_name "RNU6-113P-201"  ; transcript_support_level NA ; transcript_type snRNA
L1 and L2 created: 
LINC02438--USP4	HAVANA	gene	1001	6212	.	+	.	FI_gene_label "LINC02438^ENSG00000248238.2"  ; ID "LINC02438--USP4^LINC02438^ENSG00000248238.2"  ; exon_id "ENSE00002077368.1"  ; exon_number 1 ; gene_id "LINC02438--USP4^LINC02438^ENSG00000248238.2"  ; gene_name LINC02438 ; gene_type lncRNA ; havana_gene "OTTHUMG00000160243.2"  ; havana_transcript "OTTHUMT00000359858.1"  ; hgnc_id "HGNC:53370"  ; level 2 ; orig_coord_info "chr4,19456646,19456994,-"  ; tag basic ; transcript_id "LINC02438--USP4^ENST00000505347.1"  ; transcript_name "LINC02438-201"  ; transcript_support_level 3 ; transcript_type lncRNA
LINC02438--USP4	HAVANA	RNA	1001	6212	.	+	.	FI_gene_label "LINC02438^ENSG00000248238.2"  ; ID "LINC02438--USP4^ENST00000505347.1"  ; Parent "LINC02438--USP4^LINC02438^ENSG00000248238.2"  ; exon_id "ENSE00002077368.1"  ; exon_number 1 ; gene_id "LINC02438--USP4^LINC02438^ENSG00000248238.2"  ; gene_name LINC02438 ; gene_type lncRNA ; havana_gene "OTTHUMG00000160243.2"  ; havana_transcript "OTTHUMT00000359858.1"  ; hgnc_id "HGNC:53370"  ; level 2 ; orig_coord_info "chr4,19456646,19456994,-"  ; tag basic ; transcript_id "LINC02438--USP4^ENST00000505347.1"  ; transcript_name "LINC02438-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146	HAVANA	RNA	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^ENST00000333674.5"  ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
SLCO1B3--SLCO1B7	HAVANA	gene	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
SLCO1B3--SLCO1B7	HAVANA	RNA	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
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: 
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
316 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 ------------------------------
502 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 32 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