.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-45523c-R1_A23YTGFLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/371adfee8611fd1b051a6741e4cdf9/.command.out
Size: 66.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-45523c-R1_A23YTGFLT4_1)
Attempt
Content

Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file

 ------------------------------------------------------------------------------
|   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: 6153
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6153
=> 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:6153
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
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: 
CPSF7--AP005139.1	HAVANA	gene	1121	13344	.	+	.	FI_gene_label "CPSF7^ENSG00000149532.16"  ; ID "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16"  ; ccdsid "CCDS8006.2"  ; exon_id "ENSE00001745275.1"  ; exon_number 1 ; gene_id "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16"  ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5"  ; havana_transcript "OTTHUMT00000347830.2"  ; hgnc_id "HGNC:30098"  ; level 2 ; orig_coord_info "chr11,61429757,61429830,-"  ; protein_id "ENSP00000345412.4"  ; tag basic CCDS ; transcript_id "CPSF7--AP005139.1^ENST00000340437.8"  ; transcript_name "CPSF7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPSF7--AP005139.1	HAVANA	mRNA	1121	13344	.	+	.	FI_gene_label "CPSF7^ENSG00000149532.16"  ; ID "CPSF7--AP005139.1^ENST00000340437.8"  ; Parent "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16"  ; ccdsid "CCDS8006.2"  ; exon_id "ENSE00001745275.1"  ; exon_number 1 ; gene_id "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16"  ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5"  ; havana_transcript "OTTHUMT00000347830.2"  ; hgnc_id "HGNC:30098"  ; level 2 ; orig_coord_info "chr11,61429757,61429830,-"  ; protein_id "ENSP00000345412.4"  ; tag basic CCDS ; transcript_id "CPSF7--AP005139.1^ENST00000340437.8"  ; transcript_name "CPSF7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPSF7--PIEZO2	HAVANA	gene	17326	83462	.	+	.	FI_gene_label "PIEZO2^ENSG00000154864.13"  ; ID "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13"  ; exon_id "ENSE00002236501.2"  ; exon_number 1 ; gene_id "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13"  ; gene_name PIEZO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178507.14"  ; havana_transcript "OTTHUMT00000254528.5"  ; hgnc_id "HGNC:26270"  ; level 2 ; orig_coord_info "chr18,11148525,11148588,-"  ; protein_id "ENSP00000303316.6"  ; tag basic ; transcript_id "CPSF7--PIEZO2^ENST00000302079.10"  ; transcript_name "PIEZO2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CPSF7--PIEZO2	HAVANA	mRNA	17326	83462	.	+	.	FI_gene_label "PIEZO2^ENSG00000154864.13"  ; ID "CPSF7--PIEZO2^ENST00000302079.10"  ; Parent "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13"  ; exon_id "ENSE00002236501.2"  ; exon_number 1 ; gene_id "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13"  ; gene_name PIEZO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178507.14"  ; havana_transcript "OTTHUMT00000254528.5"  ; hgnc_id "HGNC:26270"  ; level 2 ; orig_coord_info "chr18,11148525,11148588,-"  ; protein_id "ENSP00000303316.6"  ; tag basic ; transcript_id "CPSF7--PIEZO2^ENST00000302079.10"  ; transcript_name "PIEZO2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CPSF7--PIEZO2	HAVANA	gene	1121	13344	.	+	.	FI_gene_label "CPSF7^ENSG00000149532.16"  ; ID "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16"  ; ccdsid "CCDS8006.2"  ; exon_id "ENSE00001745275.1"  ; exon_number 1 ; gene_id "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16"  ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5"  ; havana_transcript "OTTHUMT00000347830.2"  ; hgnc_id "HGNC:30098"  ; level 2 ; orig_coord_info "chr11,61429757,61429830,-"  ; protein_id "ENSP00000345412.4"  ; tag basic CCDS ; transcript_id "CPSF7--PIEZO2^ENST00000340437.8"  ; transcript_name "CPSF7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPSF7--PIEZO2	HAVANA	mRNA	1121	13344	.	+	.	FI_gene_label "CPSF7^ENSG00000149532.16"  ; ID "CPSF7--PIEZO2^ENST00000340437.8"  ; Parent "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16"  ; ccdsid "CCDS8006.2"  ; exon_id "ENSE00001745275.1"  ; exon_number 1 ; gene_id "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16"  ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5"  ; havana_transcript "OTTHUMT00000347830.2"  ; hgnc_id "HGNC:30098"  ; level 2 ; orig_coord_info "chr11,61429757,61429830,-"  ; protein_id "ENSP00000345412.4"  ; tag basic CCDS ; transcript_id "CPSF7--PIEZO2^ENST00000340437.8"  ; transcript_name "CPSF7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DDX5--SMURF2	HAVANA	gene	2911	10946	.	+	.	FI_gene_label "DDX5^ENSG00000108654.16"  ; ID "DDX5--SMURF2^DDX5^ENSG00000108654.16"  ; ccdsid "CCDS11659.1"  ; exon_id "ENSE00003466024.1"  ; exon_number 1 ; gene_id "DDX5--SMURF2^DDX5^ENSG00000108654.16"  ; gene_name DDX5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178936.11"  ; havana_transcript "OTTHUMT00000444030.2"  ; hgnc_id "HGNC:2746"  ; level 2 ; orig_coord_info "chr17,64506076,64506119,-"  ; protein_id "ENSP00000225792.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000225792.10"  ; transcript_name "DDX5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DDX5--SMURF2	HAVANA	mRNA	2911	10946	.	+	.	FI_gene_label "DDX5^ENSG00000108654.16"  ; ID "DDX5--SMURF2^ENST00000225792.10"  ; Parent "DDX5--SMURF2^DDX5^ENSG00000108654.16"  ; ccdsid "CCDS11659.1"  ; exon_id "ENSE00003466024.1"  ; exon_number 1 ; gene_id "DDX5--SMURF2^DDX5^ENSG00000108654.16"  ; gene_name DDX5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178936.11"  ; havana_transcript "OTTHUMT00000444030.2"  ; hgnc_id "HGNC:2746"  ; level 2 ; orig_coord_info "chr17,64506076,64506119,-"  ; protein_id "ENSP00000225792.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000225792.10"  ; transcript_name "DDX5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DDX5--SMURF2	HAVANA	gene	13947	40224	.	+	.	FI_gene_label "SMURF2^ENSG00000108854.16"  ; ID "DDX5--SMURF2^SMURF2^ENSG00000108854.16"  ; ccdsid "CCDS32707.1"  ; exon_id "ENSE00001331843.8"  ; exon_number 1 ; gene_id "DDX5--SMURF2^SMURF2^ENSG00000108854.16"  ; gene_name SMURF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179189.3"  ; havana_transcript "OTTHUMT00000445227.2"  ; hgnc_id "HGNC:16809"  ; level 2 ; orig_coord_info "chr17,64661829,64661880,-"  ; protein_id "ENSP00000262435.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000262435.14"  ; transcript_name "SMURF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DDX5--SMURF2	HAVANA	mRNA	13947	40224	.	+	.	FI_gene_label "SMURF2^ENSG00000108854.16"  ; ID "DDX5--SMURF2^ENST00000262435.14"  ; Parent "DDX5--SMURF2^SMURF2^ENSG00000108854.16"  ; ccdsid "CCDS32707.1"  ; exon_id "ENSE00001331843.8"  ; exon_number 1 ; gene_id "DDX5--SMURF2^SMURF2^ENSG00000108854.16"  ; gene_name SMURF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179189.3"  ; havana_transcript "OTTHUMT00000445227.2"  ; hgnc_id "HGNC:16809"  ; level 2 ; orig_coord_info "chr17,64661829,64661880,-"  ; protein_id "ENSP00000262435.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000262435.14"  ; transcript_name "SMURF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DHX38--WWOX	HAVANA	gene	1235	18399	.	+	.	FI_gene_label "DHX38^ENSG00000140829.12"  ; ID "DHX38--WWOX^DHX38^ENSG00000140829.12"  ; ccdsid "CCDS10907.1"  ; exon_id "ENSE00000945215.1"  ; exon_number 2 ; gene_id "DHX38--WWOX^DHX38^ENSG00000140829.12"  ; gene_name DHX38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137596.7"  ; havana_transcript "OTTHUMT00000269004.4"  ; hgnc_id "HGNC:17211"  ; level 2 ; orig_coord_info "chr16,72096158,72096480,+"  ; protein_id "ENSP00000268482.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX38--WWOX^ENST00000268482.8"  ; transcript_name "DHX38-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DHX38--WWOX	HAVANA	mRNA	1235	18399	.	+	.	FI_gene_label "DHX38^ENSG00000140829.12"  ; ID "DHX38--WWOX^ENST00000268482.8"  ; Parent "DHX38--WWOX^DHX38^ENSG00000140829.12"  ; ccdsid "CCDS10907.1"  ; exon_id "ENSE00000945215.1"  ; exon_number 2 ; gene_id "DHX38--WWOX^DHX38^ENSG00000140829.12"  ; gene_name DHX38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137596.7"  ; havana_transcript "OTTHUMT00000269004.4"  ; hgnc_id "HGNC:17211"  ; level 2 ; orig_coord_info "chr16,72096158,72096480,+"  ; protein_id "ENSP00000268482.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX38--WWOX^ENST00000268482.8"  ; transcript_name "DHX38-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DHX38--WWOX	HAVANA	gene	21649	39167	.	+	.	FI_gene_label "WWOX^ENSG00000186153.17"  ; ID "DHX38--WWOX^WWOX^ENSG00000186153.17"  ; ccdsid "CCDS42197.1"  ; exon_id "ENSE00002598693.1"  ; exon_number 1 ; gene_id "DHX38--WWOX^WWOX^ENSG00000186153.17"  ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3"  ; havana_transcript "OTTHUMT00000434020.1"  ; hgnc_id "HGNC:12799"  ; level 2 ; orig_coord_info "chr16,78099779,78099885,+"  ; protein_id "ENSP00000348119.3"  ; tag basic CCDS ; transcript_id "DHX38--WWOX^ENST00000355860.7"  ; transcript_name "WWOX-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DHX38--WWOX	HAVANA	mRNA	21649	39167	.	+	.	FI_gene_label "WWOX^ENSG00000186153.17"  ; ID "DHX38--WWOX^ENST00000355860.7"  ; Parent "DHX38--WWOX^WWOX^ENSG00000186153.17"  ; ccdsid "CCDS42197.1"  ; exon_id "ENSE00002598693.1"  ; exon_number 1 ; gene_id "DHX38--WWOX^WWOX^ENSG00000186153.17"  ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3"  ; havana_transcript "OTTHUMT00000434020.1"  ; hgnc_id "HGNC:12799"  ; level 2 ; orig_coord_info "chr16,78099779,78099885,+"  ; protein_id "ENSP00000348119.3"  ; tag basic CCDS ; transcript_id "DHX38--WWOX^ENST00000355860.7"  ; transcript_name "WWOX-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ERC1--RASSF7	HAVANA	gene	1730	37441	.	+	.	FI_gene_label "ERC1^ENSG00000082805.20"  ; ID "ERC1--RASSF7^ERC1^ENSG00000082805.20"  ; exon_id "ENSE00001318114.5"  ; exon_number 2 ; gene_id "ERC1--RASSF7^ERC1^ENSG00000082805.20"  ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14"  ; havana_transcript "OTTHUMT00000398378.1"  ; hgnc_id "HGNC:17072"  ; level 2 ; orig_coord_info "chr12,1027904,1028572,+"  ; protein_id "ENSP00000340054.6"  ; transcript_id "ERC1--RASSF7^ENST00000347735.10"  ; transcript_name "ERC1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ERC1--RASSF7	HAVANA	mRNA	1730	37441	.	+	.	FI_gene_label "ERC1^ENSG00000082805.20"  ; ID "ERC1--RASSF7^ENST00000347735.10"  ; Parent "ERC1--RASSF7^ERC1^ENSG00000082805.20"  ; exon_id "ENSE00001318114.5"  ; exon_number 2 ; gene_id "ERC1--RASSF7^ERC1^ENSG00000082805.20"  ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14"  ; havana_transcript "OTTHUMT00000398378.1"  ; hgnc_id "HGNC:17072"  ; level 2 ; orig_coord_info "chr12,1027904,1028572,+"  ; protein_id "ENSP00000340054.6"  ; transcript_id "ERC1--RASSF7^ENST00000347735.10"  ; transcript_name "ERC1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ERC1--RASSF7	HAVANA	gene	45360	48416	.	+	.	FI_gene_label "RASSF7^ENSG00000099849.15"  ; ID "ERC1--RASSF7^RASSF7^ENSG00000099849.15"  ; ccdsid "CCDS44506.1"  ; exon_id "ENSE00001694199.1"  ; exon_number 2 ; gene_id "ERC1--RASSF7^RASSF7^ENSG00000099849.15"  ; gene_name RASSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132004.5"  ; havana_transcript "OTTHUMT00000254970.2"  ; hgnc_id "HGNC:1166"  ; level 2 ; orig_coord_info "chr11,561769,561892,+"  ; protein_id "ENSP00000380712.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ERC1--RASSF7^ENST00000397582.7"  ; transcript_name "RASSF7-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ERC1--RASSF7	HAVANA	mRNA	45360	48416	.	+	.	FI_gene_label "RASSF7^ENSG00000099849.15"  ; ID "ERC1--RASSF7^ENST00000397582.7"  ; Parent "ERC1--RASSF7^RASSF7^ENSG00000099849.15"  ; ccdsid "CCDS44506.1"  ; exon_id "ENSE00001694199.1"  ; exon_number 2 ; gene_id "ERC1--RASSF7^RASSF7^ENSG00000099849.15"  ; gene_name RASSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132004.5"  ; havana_transcript "OTTHUMT00000254970.2"  ; hgnc_id "HGNC:1166"  ; level 2 ; orig_coord_info "chr11,561769,561892,+"  ; protein_id "ENSP00000380712.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ERC1--RASSF7^ENST00000397582.7"  ; transcript_name "RASSF7-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1	HAVANA	mRNA	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^ENST00000350221.4"  ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KIAA1958--NTRK2	HAVANA	gene	22318	60261	.	+	.	FI_gene_label "NTRK2^ENSG00000148053.17"  ; ID "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17"  ; ccdsid "CCDS6671.1"  ; exon_id "ENSE00001343633.1"  ; exon_number 2 ; gene_id "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17"  ; gene_name NTRK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020120.3"  ; havana_transcript "OTTHUMT00000052885.2"  ; hgnc_id "HGNC:8032"  ; level 2 ; orig_coord_info "chr9,84670749,84670960,+"  ; protein_id "ENSP00000277120.3"  ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_1 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000277120.8"  ; transcript_name "NTRK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIAA1958--NTRK2	HAVANA	mRNA	22318	60261	.	+	.	FI_gene_label "NTRK2^ENSG00000148053.17"  ; ID "KIAA1958--NTRK2^ENST00000277120.8"  ; Parent "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17"  ; ccdsid "CCDS6671.1"  ; exon_id "ENSE00001343633.1"  ; exon_number 2 ; gene_id "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17"  ; gene_name NTRK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020120.3"  ; havana_transcript "OTTHUMT00000052885.2"  ; hgnc_id "HGNC:8032"  ; level 2 ; orig_coord_info "chr9,84670749,84670960,+"  ; protein_id "ENSP00000277120.3"  ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_1 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000277120.8"  ; transcript_name "NTRK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KIAA1958--NTRK2	HAVANA	gene	1001	18139	.	+	.	FI_gene_label "KIAA1958^ENSG00000165185.15"  ; ID "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15"  ; ccdsid "CCDS35108.1"  ; exon_id "ENSE00001410398.2"  ; exon_number 2 ; gene_id "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15"  ; gene_name KIAA1958 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020508.1"  ; havana_transcript "OTTHUMT00000053690.1"  ; hgnc_id "HGNC:23427"  ; level 2 ; orig_coord_info "chr9,112574081,112575251,+"  ; protein_id "ENSP00000336940.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000337530.11"  ; transcript_name "KIAA1958-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIAA1958--NTRK2	HAVANA	mRNA	1001	18139	.	+	.	FI_gene_label "KIAA1958^ENSG00000165185.15"  ; ID "KIAA1958--NTRK2^ENST00000337530.11"  ; Parent "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15"  ; ccdsid "CCDS35108.1"  ; exon_id "ENSE00001410398.2"  ; exon_number 2 ; gene_id "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15"  ; gene_name KIAA1958 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020508.1"  ; havana_transcript "OTTHUMT00000053690.1"  ; hgnc_id "HGNC:23427"  ; level 2 ; orig_coord_info "chr9,112574081,112575251,+"  ; protein_id "ENSP00000336940.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000337530.11"  ; transcript_name "KIAA1958-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LMNTD2--ERC1	HAVANA	gene	1001	6889	.	+	.	FI_gene_label "LMNTD2^ENSG00000185522.9"  ; ID "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9"  ; ccdsid "CCDS7701.1"  ; exon_id "ENSE00001296983.2"  ; exon_number 1 ; gene_id "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9"  ; gene_name LMNTD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132005.5"  ; havana_transcript "OTTHUMT00000254973.3"  ; hgnc_id "HGNC:28561"  ; level 2 ; orig_coord_info "chr11,560683,560716,-"  ; protein_id "ENSP00000331167.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LMNTD2--ERC1^ENST00000329451.8"  ; transcript_name "LMNTD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LMNTD2--ERC1	HAVANA	mRNA	1001	6889	.	+	.	FI_gene_label "LMNTD2^ENSG00000185522.9"  ; ID "LMNTD2--ERC1^ENST00000329451.8"  ; Parent "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9"  ; ccdsid "CCDS7701.1"  ; exon_id "ENSE00001296983.2"  ; exon_number 1 ; gene_id "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9"  ; gene_name LMNTD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132005.5"  ; havana_transcript "OTTHUMT00000254973.3"  ; hgnc_id "HGNC:28561"  ; level 2 ; orig_coord_info "chr11,560683,560716,-"  ; protein_id "ENSP00000331167.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LMNTD2--ERC1^ENST00000329451.8"  ; transcript_name "LMNTD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LMNTD2--ERC1	HAVANA	gene	10619	46330	.	+	.	FI_gene_label "ERC1^ENSG00000082805.20"  ; ID "LMNTD2--ERC1^ERC1^ENSG00000082805.20"  ; exon_id "ENSE00001318114.5"  ; exon_number 2 ; gene_id "LMNTD2--ERC1^ERC1^ENSG00000082805.20"  ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14"  ; havana_transcript "OTTHUMT00000398378.1"  ; hgnc_id "HGNC:17072"  ; level 2 ; orig_coord_info "chr12,1027904,1028572,+"  ; protein_id "ENSP00000340054.6"  ; transcript_id "LMNTD2--ERC1^ENST00000347735.10"  ; transcript_name "ERC1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
LMNTD2--ERC1	HAVANA	mRNA	10619	46330	.	+	.	FI_gene_label "ERC1^ENSG00000082805.20"  ; ID "LMNTD2--ERC1^ENST00000347735.10"  ; Parent "LMNTD2--ERC1^ERC1^ENSG00000082805.20"  ; exon_id "ENSE00001318114.5"  ; exon_number 2 ; gene_id "LMNTD2--ERC1^ERC1^ENSG00000082805.20"  ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14"  ; havana_transcript "OTTHUMT00000398378.1"  ; hgnc_id "HGNC:17072"  ; level 2 ; orig_coord_info "chr12,1027904,1028572,+"  ; protein_id "ENSP00000340054.6"  ; transcript_id "LMNTD2--ERC1^ENST00000347735.10"  ; transcript_name "ERC1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
NAE1--CAPNS2	HAVANA	gene	2144	19536	.	+	.	FI_gene_label "NAE1^ENSG00000159593.15"  ; ID "NAE1--CAPNS2^NAE1^ENSG00000159593.15"  ; ccdsid "CCDS10820.1"  ; exon_id "ENSE00003672944.1"  ; exon_number 1 ; gene_id "NAE1--CAPNS2^NAE1^ENSG00000159593.15"  ; gene_name NAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137513.8"  ; havana_transcript "OTTHUMT00000268832.2"  ; hgnc_id "HGNC:621"  ; level 2 ; orig_coord_info "chr16,66830847,66830899,-"  ; protein_id "ENSP00000290810.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000290810.8"  ; transcript_name "NAE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NAE1--CAPNS2	HAVANA	mRNA	2144	19536	.	+	.	FI_gene_label "NAE1^ENSG00000159593.15"  ; ID "NAE1--CAPNS2^ENST00000290810.8"  ; Parent "NAE1--CAPNS2^NAE1^ENSG00000159593.15"  ; ccdsid "CCDS10820.1"  ; exon_id "ENSE00003672944.1"  ; exon_number 1 ; gene_id "NAE1--CAPNS2^NAE1^ENSG00000159593.15"  ; gene_name NAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137513.8"  ; havana_transcript "OTTHUMT00000268832.2"  ; hgnc_id "HGNC:621"  ; level 2 ; orig_coord_info "chr16,66830847,66830899,-"  ; protein_id "ENSP00000290810.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000290810.8"  ; transcript_name "NAE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NAE1--CAPNS2	HAVANA	gene	22540	23543	.	+	.	FI_gene_label "CAPNS2^ENSG00000256812.2"  ; ID "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2"  ; ccdsid "CCDS54010.1"  ; exon_id "ENSE00002251412.2"  ; exon_number 1 ; gene_id "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2"  ; gene_name CAPNS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167812.2"  ; havana_transcript "OTTHUMT00000396391.2"  ; hgnc_id "HGNC:16371"  ; level 2 ; orig_coord_info "chr16,55566757,55567500,+"  ; protein_id "ENSP00000400882.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000457326.3"  ; transcript_name "CAPNS2-201"  ; transcript_support_level NA ; transcript_type protein_coding
NAE1--CAPNS2	HAVANA	mRNA	22540	23543	.	+	.	FI_gene_label "CAPNS2^ENSG00000256812.2"  ; ID "NAE1--CAPNS2^ENST00000457326.3"  ; Parent "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2"  ; ccdsid "CCDS54010.1"  ; exon_id "ENSE00002251412.2"  ; exon_number 1 ; gene_id "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2"  ; gene_name CAPNS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167812.2"  ; havana_transcript "OTTHUMT00000396391.2"  ; hgnc_id "HGNC:16371"  ; level 2 ; orig_coord_info "chr16,55566757,55567500,+"  ; protein_id "ENSP00000400882.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000457326.3"  ; transcript_name "CAPNS2-201"  ; transcript_support_level NA ; 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: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--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: 
TXNL4B--CARMIL2	HAVANA	gene	1812	7811	.	+	.	FI_gene_label "TXNL4B^ENSG00000140830.9"  ; ID "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9"  ; ccdsid "CCDS10906.1"  ; exon_id "ENSE00000945241.1"  ; exon_number 2 ; gene_id "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9"  ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3"  ; havana_transcript "OTTHUMT00000269007.3"  ; hgnc_id "HGNC:26041"  ; level 2 ; orig_coord_info "chr16,72090618,72090749,-"  ; protein_id "ENSP00000268483.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000268483.8"  ; transcript_name "TXNL4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CARMIL2	HAVANA	mRNA	1812	7811	.	+	.	FI_gene_label "TXNL4B^ENSG00000140830.9"  ; ID "TXNL4B--CARMIL2^ENST00000268483.8"  ; Parent "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9"  ; ccdsid "CCDS10906.1"  ; exon_id "ENSE00000945241.1"  ; exon_number 2 ; gene_id "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9"  ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3"  ; havana_transcript "OTTHUMT00000269007.3"  ; hgnc_id "HGNC:26041"  ; level 2 ; orig_coord_info "chr16,72090618,72090749,-"  ; protein_id "ENSP00000268483.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000268483.8"  ; transcript_name "TXNL4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TXNL4B--CARMIL2	HAVANA	gene	12037	24332	.	+	.	FI_gene_label "CARMIL2^ENSG00000159753.14"  ; ID "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14"  ; ccdsid "CCDS45513.1"  ; exon_id "ENSE00003304989.2"  ; exon_number 1 ; gene_id "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14"  ; gene_name CARMIL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184043.3"  ; havana_transcript "OTTHUMT00000467858.2"  ; hgnc_id "HGNC:27089"  ; level 2 ; orig_coord_info "chr16,67645247,67645286,+"  ; protein_id "ENSP00000334958.5"  ; tag basic MANE_Select CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000334583.11"  ; transcript_name "CARMIL2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CARMIL2	HAVANA	mRNA	12037	24332	.	+	.	FI_gene_label "CARMIL2^ENSG00000159753.14"  ; ID "TXNL4B--CARMIL2^ENST00000334583.11"  ; Parent "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14"  ; ccdsid "CCDS45513.1"  ; exon_id "ENSE00003304989.2"  ; exon_number 1 ; gene_id "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14"  ; gene_name CARMIL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184043.3"  ; havana_transcript "OTTHUMT00000467858.2"  ; hgnc_id "HGNC:27089"  ; level 2 ; orig_coord_info "chr16,67645247,67645286,+"  ; protein_id "ENSP00000334958.5"  ; tag basic MANE_Select CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000334583.11"  ; transcript_name "CARMIL2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TXNL4B--CTCF	HAVANA	gene	11940	34463	.	+	.	FI_gene_label "CTCF^ENSG00000102974.16"  ; ID "TXNL4B--CTCF^CTCF^ENSG00000102974.16"  ; ccdsid "CCDS10841.1"  ; exon_id "ENSE00002242686.1"  ; exon_number 3 ; gene_id "TXNL4B--CTCF^CTCF^ENSG00000102974.16"  ; gene_name CTCF ; gene_type protein_coding ; havana_gene "OTTHUMG00000137539.7"  ; havana_transcript "OTTHUMT00000268870.4"  ; hgnc_id "HGNC:13723"  ; level 2 ; orig_coord_info "chr16,67610833,67611613,+"  ; protein_id "ENSP00000264010.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000264010.10"  ; transcript_name "CTCF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CTCF	HAVANA	mRNA	11940	34463	.	+	.	FI_gene_label "CTCF^ENSG00000102974.16"  ; ID "TXNL4B--CTCF^ENST00000264010.10"  ; Parent "TXNL4B--CTCF^CTCF^ENSG00000102974.16"  ; ccdsid "CCDS10841.1"  ; exon_id "ENSE00002242686.1"  ; exon_number 3 ; gene_id "TXNL4B--CTCF^CTCF^ENSG00000102974.16"  ; gene_name CTCF ; gene_type protein_coding ; havana_gene "OTTHUMG00000137539.7"  ; havana_transcript "OTTHUMT00000268870.4"  ; hgnc_id "HGNC:13723"  ; level 2 ; orig_coord_info "chr16,67610833,67611613,+"  ; protein_id "ENSP00000264010.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000264010.10"  ; transcript_name "CTCF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TXNL4B--CTCF	HAVANA	gene	1812	7811	.	+	.	FI_gene_label "TXNL4B^ENSG00000140830.9"  ; ID "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9"  ; ccdsid "CCDS10906.1"  ; exon_id "ENSE00000945241.1"  ; exon_number 2 ; gene_id "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9"  ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3"  ; havana_transcript "OTTHUMT00000269007.3"  ; hgnc_id "HGNC:26041"  ; level 2 ; orig_coord_info "chr16,72090618,72090749,-"  ; protein_id "ENSP00000268483.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000268483.8"  ; transcript_name "TXNL4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CTCF	HAVANA	mRNA	1812	7811	.	+	.	FI_gene_label "TXNL4B^ENSG00000140830.9"  ; ID "TXNL4B--CTCF^ENST00000268483.8"  ; Parent "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9"  ; ccdsid "CCDS10906.1"  ; exon_id "ENSE00000945241.1"  ; exon_number 2 ; gene_id "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9"  ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3"  ; havana_transcript "OTTHUMT00000269007.3"  ; hgnc_id "HGNC:26041"  ; level 2 ; orig_coord_info "chr16,72090618,72090749,-"  ; protein_id "ENSP00000268483.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000268483.8"  ; transcript_name "TXNL4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
WWP2--MPHOSPH6	HAVANA	gene	37937	45966	.	+	.	FI_gene_label "MPHOSPH6^ENSG00000135698.10"  ; ID "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10"  ; ccdsid "CCDS10937.1"  ; exon_id "ENSE00000920946.5"  ; exon_number 1 ; gene_id "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10"  ; gene_name MPHOSPH6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137632.3"  ; havana_transcript "OTTHUMT00000269058.2"  ; hgnc_id "HGNC:7214"  ; level 2 ; orig_coord_info "chr16,82170125,82170175,-"  ; protein_id "ENSP00000258169.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000258169.9"  ; transcript_name "MPHOSPH6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WWP2--MPHOSPH6	HAVANA	mRNA	37937	45966	.	+	.	FI_gene_label "MPHOSPH6^ENSG00000135698.10"  ; ID "WWP2--MPHOSPH6^ENST00000258169.9"  ; Parent "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10"  ; ccdsid "CCDS10937.1"  ; exon_id "ENSE00000920946.5"  ; exon_number 1 ; gene_id "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10"  ; gene_name MPHOSPH6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137632.3"  ; havana_transcript "OTTHUMT00000269058.2"  ; hgnc_id "HGNC:7214"  ; level 2 ; orig_coord_info "chr16,82170125,82170175,-"  ; protein_id "ENSP00000258169.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000258169.9"  ; transcript_name "MPHOSPH6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
WWP2--MPHOSPH6	ENSEMBL	gene	10833	34936	.	+	.	FI_gene_label "WWP2^ENSG00000198373.13"  ; ID "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13"  ; ccdsid "CCDS58476.1"  ; exon_id "ENSE00003538515.1"  ; exon_number 2 ; gene_id "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13"  ; gene_name WWP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137573.3"  ; hgnc_id "HGNC:16804"  ; level 3 ; orig_coord_info "chr16,69840134,69840263,+"  ; protein_id "ENSP00000348283.3"  ; tag basic CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000356003.6"  ; transcript_name "WWP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
WWP2--MPHOSPH6	ENSEMBL	mRNA	10833	34936	.	+	.	FI_gene_label "WWP2^ENSG00000198373.13"  ; ID "WWP2--MPHOSPH6^ENST00000356003.6"  ; Parent "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13"  ; ccdsid "CCDS58476.1"  ; exon_id "ENSE00003538515.1"  ; exon_number 2 ; gene_id "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13"  ; gene_name WWP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137573.3"  ; hgnc_id "HGNC:16804"  ; level 3 ; orig_coord_info "chr16,69840134,69840263,+"  ; protein_id "ENSP00000348283.3"  ; tag basic CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000356003.6"  ; transcript_name "WWP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ZFHX3--CNTNAP4	HAVANA	gene	21649	45862	.	+	.	FI_gene_label "ZFHX3^ENSG00000140836.17"  ; ID "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17"  ; ccdsid "CCDS10908.1"  ; exon_id "ENSE00001171638.5"  ; exon_number 2 ; gene_id "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17"  ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7"  ; havana_transcript "OTTHUMT00000269008.2"  ; hgnc_id "HGNC:777"  ; level 2 ; orig_coord_info "chr16,72957427,72960145,-"  ; protein_id "ENSP00000268489.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--CNTNAP4^ENST00000268489.10"  ; transcript_name "ZFHX3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFHX3--CNTNAP4	HAVANA	mRNA	21649	45862	.	+	.	FI_gene_label "ZFHX3^ENSG00000140836.17"  ; ID "ZFHX3--CNTNAP4^ENST00000268489.10"  ; Parent "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17"  ; ccdsid "CCDS10908.1"  ; exon_id "ENSE00001171638.5"  ; exon_number 2 ; gene_id "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17"  ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7"  ; havana_transcript "OTTHUMT00000269008.2"  ; hgnc_id "HGNC:777"  ; level 2 ; orig_coord_info "chr16,72957427,72960145,-"  ; protein_id "ENSP00000268489.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--CNTNAP4^ENST00000268489.10"  ; transcript_name "ZFHX3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZFHX3--CNTNAP4	ENSEMBL	gene	48863	78570	.	+	.	FI_gene_label "CNTNAP4^ENSG00000152910.19"  ; ID "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19"  ; exon_id "ENSE00001629021.3"  ; exon_number 1 ; gene_id "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19"  ; gene_name CNTNAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137617.8"  ; hgnc_id "HGNC:18747"  ; level 3 ; orig_coord_info "chr16,76277663,76277747,+"  ; protein_id "ENSP00000306893.9"  ; tag basic appris_alternative_1 ; transcript_id "ZFHX3--CNTNAP4^ENST00000307431.12"  ; transcript_name "CNTNAP4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ZFHX3--CNTNAP4	ENSEMBL	mRNA	48863	78570	.	+	.	FI_gene_label "CNTNAP4^ENSG00000152910.19"  ; ID "ZFHX3--CNTNAP4^ENST00000307431.12"  ; Parent "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19"  ; exon_id "ENSE00001629021.3"  ; exon_number 1 ; gene_id "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19"  ; gene_name CNTNAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137617.8"  ; hgnc_id "HGNC:18747"  ; level 3 ; orig_coord_info "chr16,76277663,76277747,+"  ; protein_id "ENSP00000306893.9"  ; tag basic appris_alternative_1 ; transcript_id "ZFHX3--CNTNAP4^ENST00000307431.12"  ; transcript_name "CNTNAP4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
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: 
CPSF7--AP005139.1	HAVANA	gene	16345	18907	.	+	.	FI_gene_label "AP005139.1^ENSG00000263682.1"  ; ID "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1"  ; exon_id "ENSE00002684615.1"  ; exon_number 1 ; gene_id "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1"  ; gene_name "AP005139.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000178558.2"  ; havana_transcript "OTTHUMT00000442454.2"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr18,11326270,11326789,+"  ; tag pseudo_consens basic ; transcript_id "CPSF7--AP005139.1^ENST00000580702.1"  ; transcript_name "AP005139.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
CPSF7--AP005139.1	HAVANA	RNA	16345	18907	.	+	.	FI_gene_label "AP005139.1^ENSG00000263682.1"  ; ID "CPSF7--AP005139.1^ENST00000580702.1"  ; Parent "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1"  ; exon_id "ENSE00002684615.1"  ; exon_number 1 ; gene_id "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1"  ; gene_name "AP005139.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000178558.2"  ; havana_transcript "OTTHUMT00000442454.2"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr18,11326270,11326789,+"  ; tag pseudo_consens basic ; transcript_id "CPSF7--AP005139.1^ENST00000580702.1"  ; transcript_name "AP005139.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1	HAVANA	RNA	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^ENST00000558209.1"  ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; 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: 
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
451 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 ------------------------------
944 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 30 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed