.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_6i-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/67d2bb7bf3ad735b7a181001bdedda/.command.out
Size: 57.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_6i-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: 3535
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3535
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:3535
  => 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: 
AC026412.1--LPCAT1	HAVANA	gene	13046	31181	.	+	.	FI_gene_label "LPCAT1^ENSG00000153395.10"  ; ID "AC026412.1--LPCAT1^LPCAT1^ENSG00000153395.10"  ; ccdsid "CCDS3864.1"  ; exon_id "ENSE00001814690.2"  ; exon_number 1 ; gene_id "AC026412.1--LPCAT1^LPCAT1^ENSG00000153395.10"  ; gene_name LPCAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131017.5"  ; havana_transcript "OTTHUMT00000304032.2"  ; hgnc_id "HGNC:25718"  ; level 2 ; orig_coord_info "chr5,1523710,1523844,-"  ; protein_id "ENSP00000283415.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026412.1--LPCAT1^ENST00000283415.4"  ; transcript_name "LPCAT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC026412.1--LPCAT1	HAVANA	mRNA	13046	31181	.	+	.	FI_gene_label "LPCAT1^ENSG00000153395.10"  ; ID "AC026412.1--LPCAT1^ENST00000283415.4"  ; Parent "AC026412.1--LPCAT1^LPCAT1^ENSG00000153395.10"  ; ccdsid "CCDS3864.1"  ; exon_id "ENSE00001814690.2"  ; exon_number 1 ; gene_id "AC026412.1--LPCAT1^LPCAT1^ENSG00000153395.10"  ; gene_name LPCAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131017.5"  ; havana_transcript "OTTHUMT00000304032.2"  ; hgnc_id "HGNC:25718"  ; level 2 ; orig_coord_info "chr5,1523710,1523844,-"  ; protein_id "ENSP00000283415.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026412.1--LPCAT1^ENST00000283415.4"  ; transcript_name "LPCAT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARL13B--AC021055.1	HAVANA	gene	1004	19994	.	+	.	FI_gene_label "ARL13B^ENSG00000169379.17"  ; ID "ARL13B--AC021055.1^ARL13B^ENSG00000169379.17"  ; ccdsid "CCDS2924.1"  ; exon_id "ENSE00003528537.1"  ; exon_number 1 ; gene_id "ARL13B--AC021055.1^ARL13B^ENSG00000169379.17"  ; gene_name ARL13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000159012.5"  ; havana_transcript "OTTHUMT00000352900.1"  ; hgnc_id "HGNC:25419"  ; level 2 ; orig_coord_info "chr3,93980424,93980482,+"  ; protein_id "ENSP00000306225.7"  ; tag basic CCDS ; transcript_id "ARL13B--AC021055.1^ENST00000303097.11"  ; transcript_name "ARL13B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARL13B--AC021055.1	HAVANA	mRNA	1004	19994	.	+	.	FI_gene_label "ARL13B^ENSG00000169379.17"  ; ID "ARL13B--AC021055.1^ENST00000303097.11"  ; Parent "ARL13B--AC021055.1^ARL13B^ENSG00000169379.17"  ; ccdsid "CCDS2924.1"  ; exon_id "ENSE00003528537.1"  ; exon_number 1 ; gene_id "ARL13B--AC021055.1^ARL13B^ENSG00000169379.17"  ; gene_name ARL13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000159012.5"  ; havana_transcript "OTTHUMT00000352900.1"  ; hgnc_id "HGNC:25419"  ; level 2 ; orig_coord_info "chr3,93980424,93980482,+"  ; protein_id "ENSP00000306225.7"  ; tag basic CCDS ; transcript_id "ARL13B--AC021055.1^ENST00000303097.11"  ; transcript_name "ARL13B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARL13B--LINC02031	HAVANA	gene	1004	19994	.	+	.	FI_gene_label "ARL13B^ENSG00000169379.17"  ; ID "ARL13B--LINC02031^ARL13B^ENSG00000169379.17"  ; ccdsid "CCDS2924.1"  ; exon_id "ENSE00003528537.1"  ; exon_number 1 ; gene_id "ARL13B--LINC02031^ARL13B^ENSG00000169379.17"  ; gene_name ARL13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000159012.5"  ; havana_transcript "OTTHUMT00000352900.1"  ; hgnc_id "HGNC:25419"  ; level 2 ; orig_coord_info "chr3,93980424,93980482,+"  ; protein_id "ENSP00000306225.7"  ; tag basic CCDS ; transcript_id "ARL13B--LINC02031^ENST00000303097.11"  ; transcript_name "ARL13B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARL13B--LINC02031	HAVANA	mRNA	1004	19994	.	+	.	FI_gene_label "ARL13B^ENSG00000169379.17"  ; ID "ARL13B--LINC02031^ENST00000303097.11"  ; Parent "ARL13B--LINC02031^ARL13B^ENSG00000169379.17"  ; ccdsid "CCDS2924.1"  ; exon_id "ENSE00003528537.1"  ; exon_number 1 ; gene_id "ARL13B--LINC02031^ARL13B^ENSG00000169379.17"  ; gene_name ARL13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000159012.5"  ; havana_transcript "OTTHUMT00000352900.1"  ; hgnc_id "HGNC:25419"  ; level 2 ; orig_coord_info "chr3,93980424,93980482,+"  ; protein_id "ENSP00000306225.7"  ; tag basic CCDS ; transcript_id "ARL13B--LINC02031^ENST00000303097.11"  ; transcript_name "ARL13B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COP1--UBAP2L	ENSEMBL	gene	29247	57570	.	+	.	FI_gene_label "UBAP2L^ENSG00000143569.19"  ; ID "COP1--UBAP2L^UBAP2L^ENSG00000143569.19"  ; ccdsid "CCDS81381.1"  ; exon_id "ENSE00003894600.1"  ; exon_number 2 ; gene_id "COP1--UBAP2L^UBAP2L^ENSG00000143569.19"  ; gene_name UBAP2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035983.6"  ; hgnc_id "HGNC:29877"  ; level 3 ; orig_coord_info "chr1,154225124,154225213,+"  ; protein_id "ENSP00000271877.8"  ; tag basic CCDS ; transcript_id "COP1--UBAP2L^ENST00000271877.11"  ; transcript_name "UBAP2L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
COP1--UBAP2L	ENSEMBL	mRNA	29247	57570	.	+	.	FI_gene_label "UBAP2L^ENSG00000143569.19"  ; ID "COP1--UBAP2L^ENST00000271877.11"  ; Parent "COP1--UBAP2L^UBAP2L^ENSG00000143569.19"  ; ccdsid "CCDS81381.1"  ; exon_id "ENSE00003894600.1"  ; exon_number 2 ; gene_id "COP1--UBAP2L^UBAP2L^ENSG00000143569.19"  ; gene_name UBAP2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035983.6"  ; hgnc_id "HGNC:29877"  ; level 3 ; orig_coord_info "chr1,154225124,154225213,+"  ; protein_id "ENSP00000271877.8"  ; tag basic CCDS ; transcript_id "COP1--UBAP2L^ENST00000271877.11"  ; transcript_name "UBAP2L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
COP1--UBAP2L	HAVANA	gene	1309	25254	.	+	.	FI_gene_label "COP1^ENSG00000143207.21"  ; ID "COP1--UBAP2L^COP1^ENSG00000143207.21"  ; ccdsid "CCDS44279.1"  ; exon_id "ENSE00002179931.1"  ; exon_number 1 ; gene_id "COP1--UBAP2L^COP1^ENSG00000143207.21"  ; gene_name COP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034986.7"  ; havana_transcript "OTTHUMT00000393314.2"  ; hgnc_id "HGNC:17440"  ; level 2 ; orig_coord_info "chr1,176206572,176206978,-"  ; protein_id "ENSP00000310943.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "COP1--UBAP2L^ENST00000308769.12"  ; transcript_name "COP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COP1--UBAP2L	HAVANA	mRNA	1309	25254	.	+	.	FI_gene_label "COP1^ENSG00000143207.21"  ; ID "COP1--UBAP2L^ENST00000308769.12"  ; Parent "COP1--UBAP2L^COP1^ENSG00000143207.21"  ; ccdsid "CCDS44279.1"  ; exon_id "ENSE00002179931.1"  ; exon_number 1 ; gene_id "COP1--UBAP2L^COP1^ENSG00000143207.21"  ; gene_name COP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034986.7"  ; havana_transcript "OTTHUMT00000393314.2"  ; hgnc_id "HGNC:17440"  ; level 2 ; orig_coord_info "chr1,176206572,176206978,-"  ; protein_id "ENSP00000310943.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "COP1--UBAP2L^ENST00000308769.12"  ; transcript_name "COP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPNE4--ADGRG7	HAVANA	gene	32467	49835	.	+	.	FI_gene_label "ADGRG7^ENSG00000144820.8"  ; ID "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8"  ; ccdsid "CCDS2938.1"  ; exon_id "ENSE00001225273.6"  ; exon_number 1 ; gene_id "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8"  ; gene_name ADGRG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159083.2"  ; havana_transcript "OTTHUMT00000353236.2"  ; hgnc_id "HGNC:19241"  ; level 2 ; orig_coord_info "chr3,100609857,100609971,+"  ; protein_id "ENSP00000273352.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000273352.8"  ; transcript_name "ADGRG7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ADGRG7	HAVANA	mRNA	32467	49835	.	+	.	FI_gene_label "ADGRG7^ENSG00000144820.8"  ; ID "CPNE4--ADGRG7^ENST00000273352.8"  ; Parent "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8"  ; ccdsid "CCDS2938.1"  ; exon_id "ENSE00001225273.6"  ; exon_number 1 ; gene_id "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8"  ; gene_name ADGRG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159083.2"  ; havana_transcript "OTTHUMT00000353236.2"  ; hgnc_id "HGNC:19241"  ; level 2 ; orig_coord_info "chr3,100609857,100609971,+"  ; protein_id "ENSP00000273352.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000273352.8"  ; transcript_name "ADGRG7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPNE4--ADGRG7	ENSEMBL	gene	6503	29459	.	+	.	FI_gene_label "CPNE4^ENSG00000196353.11"  ; ID "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11"  ; ccdsid "CCDS3072.1"  ; exon_id "ENSE00003536115.1"  ; exon_number 2 ; gene_id "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11"  ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14"  ; hgnc_id "HGNC:2317"  ; level 3 ; orig_coord_info "chr3,131905264,131905443,-"  ; protein_id "ENSP00000411904.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000429747.5"  ; transcript_name "CPNE4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ADGRG7	ENSEMBL	mRNA	6503	29459	.	+	.	FI_gene_label "CPNE4^ENSG00000196353.11"  ; ID "CPNE4--ADGRG7^ENST00000429747.5"  ; Parent "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11"  ; ccdsid "CCDS3072.1"  ; exon_id "ENSE00003536115.1"  ; exon_number 2 ; gene_id "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11"  ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14"  ; hgnc_id "HGNC:2317"  ; level 3 ; orig_coord_info "chr3,131905264,131905443,-"  ; protein_id "ENSP00000411904.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000429747.5"  ; transcript_name "CPNE4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DAPK2--RAD51B	ENSEMBL	gene	5533	30352	.	+	.	FI_gene_label "DAPK2^ENSG00000035664.11"  ; ID "DAPK2--RAD51B^DAPK2^ENSG00000035664.11"  ; ccdsid "CCDS10188.1"  ; exon_id "ENSE00003473652.1"  ; exon_number 1 ; gene_id "DAPK2--RAD51B^DAPK2^ENSG00000035664.11"  ; gene_name DAPK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132947.5"  ; hgnc_id "HGNC:2675"  ; level 3 ; orig_coord_info "chr15,64040170,64040261,-"  ; protein_id "ENSP00000261891.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "DAPK2--RAD51B^ENST00000261891.7"  ; transcript_name "DAPK2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DAPK2--RAD51B	ENSEMBL	mRNA	5533	30352	.	+	.	FI_gene_label "DAPK2^ENSG00000035664.11"  ; ID "DAPK2--RAD51B^ENST00000261891.7"  ; Parent "DAPK2--RAD51B^DAPK2^ENSG00000035664.11"  ; ccdsid "CCDS10188.1"  ; exon_id "ENSE00003473652.1"  ; exon_number 1 ; gene_id "DAPK2--RAD51B^DAPK2^ENSG00000035664.11"  ; gene_name DAPK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132947.5"  ; hgnc_id "HGNC:2675"  ; level 3 ; orig_coord_info "chr15,64040170,64040261,-"  ; protein_id "ENSP00000261891.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "DAPK2--RAD51B^ENST00000261891.7"  ; transcript_name "DAPK2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
DAPK2--RAD51B	ENSEMBL	gene	33386	44112	.	+	.	FI_gene_label "RAD51B^ENSG00000182185.18"  ; ID "DAPK2--RAD51B^RAD51B^ENSG00000182185.18"  ; exon_id "ENSE00001518458.1"  ; exon_number 2 ; gene_id "DAPK2--RAD51B^RAD51B^ENSG00000182185.18"  ; gene_name RAD51B ; gene_type protein_coding ; havana_gene "OTTHUMG00000157530.6"  ; hgnc_id "HGNC:9822"  ; level 3 ; orig_coord_info "chr14,67823544,67823627,+"  ; protein_id "ENSP00000375101.4"  ; tag basic ; transcript_id "DAPK2--RAD51B^ENST00000390683.7"  ; transcript_name "RAD51B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DAPK2--RAD51B	ENSEMBL	mRNA	33386	44112	.	+	.	FI_gene_label "RAD51B^ENSG00000182185.18"  ; ID "DAPK2--RAD51B^ENST00000390683.7"  ; Parent "DAPK2--RAD51B^RAD51B^ENSG00000182185.18"  ; exon_id "ENSE00001518458.1"  ; exon_number 2 ; gene_id "DAPK2--RAD51B^RAD51B^ENSG00000182185.18"  ; gene_name RAD51B ; gene_type protein_coding ; havana_gene "OTTHUMG00000157530.6"  ; hgnc_id "HGNC:9822"  ; level 3 ; orig_coord_info "chr14,67823544,67823627,+"  ; protein_id "ENSP00000375101.4"  ; tag basic ; transcript_id "DAPK2--RAD51B^ENST00000390683.7"  ; transcript_name "RAD51B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^ENST00000616325.1"  ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
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: 
TMPRSS2--ERG	HAVANA	gene	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ENST00000288319.12"  ; Parent "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMPRSS2--ERG	HAVANA	gene	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^ENST00000332149.10"  ; Parent "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; 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: 
ZNF292--AL357522.1	HAVANA	gene	2428	24040	.	+	.	FI_gene_label "ZNF292^ENSG00000188994.13"  ; ID "ZNF292--AL357522.1^ZNF292^ENSG00000188994.13"  ; exon_id "ENSE00002097352.1"  ; exon_number 1 ; gene_id "ZNF292--AL357522.1^ZNF292^ENSG00000188994.13"  ; gene_name ZNF292 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015164.7"  ; havana_transcript "OTTHUMT00000041428.2"  ; hgnc_id "HGNC:18410"  ; level 2 ; orig_coord_info "chr6,87155592,87155759,+"  ; protein_id "ENSP00000342847.4"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "ZNF292--AL357522.1^ENST00000339907.8"  ; transcript_name "ZNF292-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ZNF292--AL357522.1	HAVANA	mRNA	2428	24040	.	+	.	FI_gene_label "ZNF292^ENSG00000188994.13"  ; ID "ZNF292--AL357522.1^ENST00000339907.8"  ; Parent "ZNF292--AL357522.1^ZNF292^ENSG00000188994.13"  ; exon_id "ENSE00002097352.1"  ; exon_number 1 ; gene_id "ZNF292--AL357522.1^ZNF292^ENSG00000188994.13"  ; gene_name ZNF292 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015164.7"  ; havana_transcript "OTTHUMT00000041428.2"  ; hgnc_id "HGNC:18410"  ; level 2 ; orig_coord_info "chr6,87155592,87155759,+"  ; protein_id "ENSP00000342847.4"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "ZNF292--AL357522.1^ENST00000339907.8"  ; transcript_name "ZNF292-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ZNF292--NPM1P10	HAVANA	gene	2428	24040	.	+	.	FI_gene_label "ZNF292^ENSG00000188994.13"  ; ID "ZNF292--NPM1P10^ZNF292^ENSG00000188994.13"  ; exon_id "ENSE00002097352.1"  ; exon_number 1 ; gene_id "ZNF292--NPM1P10^ZNF292^ENSG00000188994.13"  ; gene_name ZNF292 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015164.7"  ; havana_transcript "OTTHUMT00000041428.2"  ; hgnc_id "HGNC:18410"  ; level 2 ; orig_coord_info "chr6,87155592,87155759,+"  ; protein_id "ENSP00000342847.4"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "ZNF292--NPM1P10^ENST00000339907.8"  ; transcript_name "ZNF292-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ZNF292--NPM1P10	HAVANA	mRNA	2428	24040	.	+	.	FI_gene_label "ZNF292^ENSG00000188994.13"  ; ID "ZNF292--NPM1P10^ENST00000339907.8"  ; Parent "ZNF292--NPM1P10^ZNF292^ENSG00000188994.13"  ; exon_id "ENSE00002097352.1"  ; exon_number 1 ; gene_id "ZNF292--NPM1P10^ZNF292^ENSG00000188994.13"  ; gene_name ZNF292 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015164.7"  ; havana_transcript "OTTHUMT00000041428.2"  ; hgnc_id "HGNC:18410"  ; level 2 ; orig_coord_info "chr6,87155592,87155759,+"  ; protein_id "ENSP00000342847.4"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "ZNF292--NPM1P10^ENST00000339907.8"  ; transcript_name "ZNF292-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
AC026412.1--LPCAT1	HAVANA	gene	1022	4928	.	+	.	FI_gene_label "AC026412.1^ENSG00000188002.10"  ; ID "AC026412.1--LPCAT1^AC026412.1^ENSG00000188002.10"  ; exon_id "ENSE00002322149.1"  ; exon_number 1 ; gene_id "AC026412.1--LPCAT1^AC026412.1^ENSG00000188002.10"  ; gene_name "AC026412.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161734.4"  ; havana_transcript "OTTHUMT00000365921.1"  ; level 2 ; orig_coord_info "chr5,1633808,1633984,-"  ; transcript_id "AC026412.1--LPCAT1^ENST00000343123.4"  ; transcript_name "AC026412.1-207"  ; transcript_support_level 1 ; transcript_type processed_transcript
AC026412.1--LPCAT1	HAVANA	RNA	1022	4928	.	+	.	FI_gene_label "AC026412.1^ENSG00000188002.10"  ; ID "AC026412.1--LPCAT1^ENST00000343123.4"  ; Parent "AC026412.1--LPCAT1^AC026412.1^ENSG00000188002.10"  ; exon_id "ENSE00002322149.1"  ; exon_number 1 ; gene_id "AC026412.1--LPCAT1^AC026412.1^ENSG00000188002.10"  ; gene_name "AC026412.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161734.4"  ; havana_transcript "OTTHUMT00000365921.1"  ; level 2 ; orig_coord_info "chr5,1633808,1633984,-"  ; transcript_id "AC026412.1--LPCAT1^ENST00000343123.4"  ; transcript_name "AC026412.1-207"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
ARL13B--AC021055.1	HAVANA	gene	23394	25280	.	+	.	FI_gene_label "AC021055.1^ENSG00000287941.1"  ; ID "ARL13B--AC021055.1^AC021055.1^ENSG00000287941.1"  ; exon_id "ENSE00003878763.1"  ; exon_number 1 ; gene_id "ARL13B--AC021055.1^AC021055.1^ENSG00000287941.1"  ; gene_name "AC021055.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195739.1"  ; havana_transcript "OTTHUMT00000528537.1"  ; level 2 ; orig_coord_info "chr3,182617764,182617810,-"  ; tag basic TAGENE ; transcript_id "ARL13B--AC021055.1^ENST00000661576.1"  ; transcript_name "AC021055.1-201"  ; transcript_type lncRNA
ARL13B--AC021055.1	HAVANA	RNA	23394	25280	.	+	.	FI_gene_label "AC021055.1^ENSG00000287941.1"  ; ID "ARL13B--AC021055.1^ENST00000661576.1"  ; Parent "ARL13B--AC021055.1^AC021055.1^ENSG00000287941.1"  ; exon_id "ENSE00003878763.1"  ; exon_number 1 ; gene_id "ARL13B--AC021055.1^AC021055.1^ENSG00000287941.1"  ; gene_name "AC021055.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195739.1"  ; havana_transcript "OTTHUMT00000528537.1"  ; level 2 ; orig_coord_info "chr3,182617764,182617810,-"  ; tag basic TAGENE ; transcript_id "ARL13B--AC021055.1^ENST00000661576.1"  ; transcript_name "AC021055.1-201"  ; transcript_type lncRNA
L1 and L2 created: 
ARL13B--LINC02031	HAVANA	gene	23394	26381	.	+	.	FI_gene_label "LINC02031^ENSG00000238837.3"  ; ID "ARL13B--LINC02031^LINC02031^ENSG00000238837.3"  ; exon_id "ENSE00001834055.1"  ; exon_number 1 ; gene_id "ARL13B--LINC02031^LINC02031^ENSG00000238837.3"  ; gene_name LINC02031 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158297.2"  ; havana_transcript "OTTHUMT00000350610.2"  ; hgnc_id "HGNC:52865"  ; level 2 ; orig_coord_info "chr3,182644214,182644315,+"  ; tag basic ; transcript_id "ARL13B--LINC02031^ENST00000492416.2"  ; transcript_name "LINC02031-201"  ; transcript_support_level 4 ; transcript_type lncRNA
ARL13B--LINC02031	HAVANA	RNA	23394	26381	.	+	.	FI_gene_label "LINC02031^ENSG00000238837.3"  ; ID "ARL13B--LINC02031^ENST00000492416.2"  ; Parent "ARL13B--LINC02031^LINC02031^ENSG00000238837.3"  ; exon_id "ENSE00001834055.1"  ; exon_number 1 ; gene_id "ARL13B--LINC02031^LINC02031^ENSG00000238837.3"  ; gene_name LINC02031 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158297.2"  ; havana_transcript "OTTHUMT00000350610.2"  ; hgnc_id "HGNC:52865"  ; level 2 ; orig_coord_info "chr3,182644214,182644315,+"  ; tag basic ; transcript_id "ARL13B--LINC02031^ENST00000492416.2"  ; transcript_name "LINC02031-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
ZNF292--AL357522.1	HAVANA	gene	31809	40454	.	+	.	FI_gene_label "AL357522.1^ENSG00000287616.1"  ; ID "ZNF292--AL357522.1^AL357522.1^ENSG00000287616.1"  ; exon_id "ENSE00003882655.1"  ; exon_number 1 ; gene_id "ZNF292--AL357522.1^AL357522.1^ENSG00000287616.1"  ; gene_name "AL357522.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195526.1"  ; havana_transcript "OTTHUMT00000527407.1"  ; level 2 ; orig_coord_info "chr6,104527274,104527413,-"  ; tag TAGENE ; transcript_id "ZNF292--AL357522.1^ENST00000654628.1"  ; transcript_name "AL357522.1-201"  ; transcript_type lncRNA
ZNF292--AL357522.1	HAVANA	RNA	31809	40454	.	+	.	FI_gene_label "AL357522.1^ENSG00000287616.1"  ; ID "ZNF292--AL357522.1^ENST00000654628.1"  ; Parent "ZNF292--AL357522.1^AL357522.1^ENSG00000287616.1"  ; exon_id "ENSE00003882655.1"  ; exon_number 1 ; gene_id "ZNF292--AL357522.1^AL357522.1^ENSG00000287616.1"  ; gene_name "AL357522.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195526.1"  ; havana_transcript "OTTHUMT00000527407.1"  ; level 2 ; orig_coord_info "chr6,104527274,104527413,-"  ; tag TAGENE ; transcript_id "ZNF292--AL357522.1^ENST00000654628.1"  ; transcript_name "AL357522.1-201"  ; transcript_type lncRNA
L1 and L2 created: 
ZNF292--NPM1P10	HAVANA	gene	31064	32287	.	+	.	FI_gene_label "NPM1P10^ENSG00000214428.3"  ; ID "ZNF292--NPM1P10^NPM1P10^ENSG00000214428.3"  ; exon_id "ENSE00002667708.1"  ; exon_number 1 ; gene_id "ZNF292--NPM1P10^NPM1P10^ENSG00000214428.3"  ; gene_name NPM1P10 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000015284.2"  ; havana_transcript "OTTHUMT00000041639.2"  ; hgnc_id "HGNC:7912"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr6,104026612,104026763,-"  ; tag pseudo_consens basic ; transcript_id "ZNF292--NPM1P10^ENST00000398310.3"  ; transcript_name "NPM1P10-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ZNF292--NPM1P10	HAVANA	RNA	31064	32287	.	+	.	FI_gene_label "NPM1P10^ENSG00000214428.3"  ; ID "ZNF292--NPM1P10^ENST00000398310.3"  ; Parent "ZNF292--NPM1P10^NPM1P10^ENSG00000214428.3"  ; exon_id "ENSE00002667708.1"  ; exon_number 1 ; gene_id "ZNF292--NPM1P10^NPM1P10^ENSG00000214428.3"  ; gene_name NPM1P10 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000015284.2"  ; havana_transcript "OTTHUMT00000041639.2"  ; hgnc_id "HGNC:7912"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr6,104026612,104026763,-"  ; tag pseudo_consens basic ; transcript_id "ZNF292--NPM1P10^ENST00000398310.3"  ; transcript_name "NPM1P10-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
288 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- 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 1 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 ------------------------------
657 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 23 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 1 second) ------                   


GFF3 file parsed