.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/2b91b1d07a477b4e8543ce8ba22bc9/.command.log
Size: 71.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/095574670fe8223870f738518dc448/fi_workdir/aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/2b91b1d07a477b4e8543ce8ba22bc9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/2b91b1d07a477b4e8543ce8ba22bc9/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
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                          ------ 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: 3229
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3229
=> 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:3229
  => 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: 
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: 
ACSF2--AC018521.3	HAVANA	gene	1061	14951	.	+	.	FI_gene_label "ACSF2^ENSG00000167107.13"  ; ID "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13"  ; ccdsid "CCDS11567.1"  ; exon_id "ENSE00003678158.1"  ; exon_number 1 ; gene_id "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13"  ; gene_name ACSF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162128.5"  ; havana_transcript "OTTHUMT00000367423.3"  ; hgnc_id "HGNC:26101"  ; level 2 ; orig_coord_info "chr17,50426262,50426389,+"  ; protein_id "ENSP00000300441.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACSF2--AC018521.3^ENST00000300441.9"  ; transcript_name "ACSF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ACSF2--AC018521.3	HAVANA	mRNA	1061	14951	.	+	.	FI_gene_label "ACSF2^ENSG00000167107.13"  ; ID "ACSF2--AC018521.3^ENST00000300441.9"  ; Parent "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13"  ; ccdsid "CCDS11567.1"  ; exon_id "ENSE00003678158.1"  ; exon_number 1 ; gene_id "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13"  ; gene_name ACSF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162128.5"  ; havana_transcript "OTTHUMT00000367423.3"  ; hgnc_id "HGNC:26101"  ; level 2 ; orig_coord_info "chr17,50426262,50426389,+"  ; protein_id "ENSP00000300441.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACSF2--AC018521.3^ENST00000300441.9"  ; transcript_name "ACSF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ASCC2--ANKFN1	HAVANA	gene	1031	28012	.	+	.	FI_gene_label "ASCC2^ENSG00000100325.15"  ; ID "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15"  ; ccdsid "CCDS13869.1"  ; exon_id "ENSE00003557333.1"  ; exon_number 2 ; gene_id "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15"  ; gene_name ASCC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067658.7"  ; havana_transcript "OTTHUMT00000145221.4"  ; hgnc_id "HGNC:24103"  ; level 2 ; orig_coord_info "chr22,29832245,29832325,-"  ; protein_id "ENSP00000305502.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000307790.8"  ; transcript_name "ASCC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ASCC2--ANKFN1	HAVANA	mRNA	1031	28012	.	+	.	FI_gene_label "ASCC2^ENSG00000100325.15"  ; ID "ASCC2--ANKFN1^ENST00000307790.8"  ; Parent "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15"  ; ccdsid "CCDS13869.1"  ; exon_id "ENSE00003557333.1"  ; exon_number 2 ; gene_id "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15"  ; gene_name ASCC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067658.7"  ; havana_transcript "OTTHUMT00000145221.4"  ; hgnc_id "HGNC:24103"  ; level 2 ; orig_coord_info "chr22,29832245,29832325,-"  ; protein_id "ENSP00000305502.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000307790.8"  ; transcript_name "ASCC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ASCC2--ANKFN1	HAVANA	gene	37793	72255	.	+	.	FI_gene_label "ANKFN1^ENSG00000153930.12"  ; ID "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12"  ; ccdsid "CCDS32686.1"  ; exon_id "ENSE00001239155.3"  ; exon_number 1 ; gene_id "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12"  ; gene_name ANKFN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155010.6"  ; havana_transcript "OTTHUMT00000338043.1"  ; hgnc_id "HGNC:26766"  ; level 2 ; orig_coord_info "chr17,56153510,56153530,+"  ; protein_id "ENSP00000321627.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000318698.6"  ; transcript_name "ANKFN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ASCC2--ANKFN1	HAVANA	mRNA	37793	72255	.	+	.	FI_gene_label "ANKFN1^ENSG00000153930.12"  ; ID "ASCC2--ANKFN1^ENST00000318698.6"  ; Parent "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12"  ; ccdsid "CCDS32686.1"  ; exon_id "ENSE00001239155.3"  ; exon_number 1 ; gene_id "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12"  ; gene_name ANKFN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155010.6"  ; havana_transcript "OTTHUMT00000338043.1"  ; hgnc_id "HGNC:26766"  ; level 2 ; orig_coord_info "chr17,56153510,56153530,+"  ; protein_id "ENSP00000321627.2"  ; tag basic appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000318698.6"  ; transcript_name "ANKFN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
BCR--CABIN1	HAVANA	gene	41099	88248	.	+	.	FI_gene_label "CABIN1^ENSG00000099991.18"  ; ID "BCR--CABIN1^CABIN1^ENSG00000099991.18"  ; ccdsid "CCDS13823.1"  ; exon_id "ENSE00001361081.2"  ; exon_number 2 ; gene_id "BCR--CABIN1^CABIN1^ENSG00000099991.18"  ; gene_name CABIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150797.6"  ; havana_transcript "OTTHUMT00000340949.3"  ; hgnc_id "HGNC:24187"  ; level 2 ; orig_coord_info "chr22,24035518,24035520,+"  ; protein_id "ENSP00000263119.5"  ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "BCR--CABIN1^ENST00000263119.10"  ; transcript_name "CABIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BCR--CABIN1	HAVANA	mRNA	41099	88248	.	+	.	FI_gene_label "CABIN1^ENSG00000099991.18"  ; ID "BCR--CABIN1^ENST00000263119.10"  ; Parent "BCR--CABIN1^CABIN1^ENSG00000099991.18"  ; ccdsid "CCDS13823.1"  ; exon_id "ENSE00001361081.2"  ; exon_number 2 ; gene_id "BCR--CABIN1^CABIN1^ENSG00000099991.18"  ; gene_name CABIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150797.6"  ; havana_transcript "OTTHUMT00000340949.3"  ; hgnc_id "HGNC:24187"  ; level 2 ; orig_coord_info "chr22,24035518,24035520,+"  ; protein_id "ENSP00000263119.5"  ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "BCR--CABIN1^ENST00000263119.10"  ; transcript_name "CABIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BCR--CABIN1	HAVANA	gene	1806	37986	.	+	.	FI_gene_label "BCR^ENSG00000186716.21"  ; ID "BCR--CABIN1^BCR^ENSG00000186716.21"  ; ccdsid "CCDS13806.1"  ; exon_id "ENSE00001897802.2"  ; exon_number 1 ; gene_id "BCR--CABIN1^BCR^ENSG00000186716.21"  ; gene_name BCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000150655.5"  ; havana_transcript "OTTHUMT00000075819.2"  ; hgnc_id "HGNC:1014"  ; level 2 ; orig_coord_info "chr22,23180961,23182239,+"  ; protein_id "ENSP00000303507.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCR--CABIN1^ENST00000305877.13"  ; transcript_name "BCR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BCR--CABIN1	HAVANA	mRNA	1806	37986	.	+	.	FI_gene_label "BCR^ENSG00000186716.21"  ; ID "BCR--CABIN1^ENST00000305877.13"  ; Parent "BCR--CABIN1^BCR^ENSG00000186716.21"  ; ccdsid "CCDS13806.1"  ; exon_id "ENSE00001897802.2"  ; exon_number 1 ; gene_id "BCR--CABIN1^BCR^ENSG00000186716.21"  ; gene_name BCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000150655.5"  ; havana_transcript "OTTHUMT00000075819.2"  ; hgnc_id "HGNC:1014"  ; level 2 ; orig_coord_info "chr22,23180961,23182239,+"  ; protein_id "ENSP00000303507.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCR--CABIN1^ENST00000305877.13"  ; transcript_name "BCR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C17orf80--LINC00469	HAVANA	gene	1001	7545	.	+	.	FI_gene_label "C17orf80^ENSG00000141219.15"  ; ID "C17orf80--LINC00469^C17orf80^ENSG00000141219.15"  ; ccdsid "CCDS74145.1"  ; exon_id "ENSE00001340095.1"  ; exon_number 3 ; gene_id "C17orf80--LINC00469^C17orf80^ENSG00000141219.15"  ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2"  ; havana_transcript "OTTHUMT00000441887.1"  ; hgnc_id "HGNC:29601"  ; level 2 ; orig_coord_info "chr17,73235483,73236995,+"  ; protein_id "ENSP00000255557.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "C17orf80--LINC00469^ENST00000255557.8"  ; transcript_name "C17orf80-201"  ; transcript_support_level 2 ; transcript_type protein_coding
C17orf80--LINC00469	HAVANA	mRNA	1001	7545	.	+	.	FI_gene_label "C17orf80^ENSG00000141219.15"  ; ID "C17orf80--LINC00469^ENST00000255557.8"  ; Parent "C17orf80--LINC00469^C17orf80^ENSG00000141219.15"  ; ccdsid "CCDS74145.1"  ; exon_id "ENSE00001340095.1"  ; exon_number 3 ; gene_id "C17orf80--LINC00469^C17orf80^ENSG00000141219.15"  ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2"  ; havana_transcript "OTTHUMT00000441887.1"  ; hgnc_id "HGNC:29601"  ; level 2 ; orig_coord_info "chr17,73235483,73236995,+"  ; protein_id "ENSP00000255557.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "C17orf80--LINC00469^ENST00000255557.8"  ; transcript_name "C17orf80-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CEP112--AC134698.1	HAVANA	gene	29887	41644	.	+	.	FI_gene_label "CEP112^ENSG00000154240.17"  ; ID "CEP112--AC134698.1^CEP112^ENSG00000154240.17"  ; ccdsid "CCDS32711.1"  ; exon_id "ENSE00001276658.7"  ; exon_number 1 ; gene_id "CEP112--AC134698.1^CEP112^ENSG00000154240.17"  ; gene_name CEP112 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179474.6"  ; havana_transcript "OTTHUMT00000446583.1"  ; hgnc_id "HGNC:28514"  ; level 2 ; orig_coord_info "chr17,65826138,65826299,-"  ; protein_id "ENSP00000320592.5"  ; tag basic CCDS ; transcript_id "CEP112--AC134698.1^ENST00000317442.12"  ; transcript_name "CEP112-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CEP112--AC134698.1	HAVANA	mRNA	29887	41644	.	+	.	FI_gene_label "CEP112^ENSG00000154240.17"  ; ID "CEP112--AC134698.1^ENST00000317442.12"  ; Parent "CEP112--AC134698.1^CEP112^ENSG00000154240.17"  ; ccdsid "CCDS32711.1"  ; exon_id "ENSE00001276658.7"  ; exon_number 1 ; gene_id "CEP112--AC134698.1^CEP112^ENSG00000154240.17"  ; gene_name CEP112 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179474.6"  ; havana_transcript "OTTHUMT00000446583.1"  ; hgnc_id "HGNC:28514"  ; level 2 ; orig_coord_info "chr17,65826138,65826299,-"  ; protein_id "ENSP00000320592.5"  ; tag basic CCDS ; transcript_id "CEP112--AC134698.1^ENST00000317442.12"  ; transcript_name "CEP112-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COX6CP1--COX6C	HAVANA	gene	4239	10289	.	+	.	FI_gene_label "COX6C^ENSG00000164919.11"  ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; ccdsid "CCDS6284.1"  ; exon_id "ENSE00002129072.1"  ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6"  ; havana_transcript "OTTHUMT00000379835.1"  ; hgnc_id "HGNC:2285"  ; level 2 ; orig_coord_info "chr8,99891908,99892021,-"  ; protein_id "ENSP00000297564.2"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6"  ; transcript_name "COX6C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
COX6CP1--COX6C	HAVANA	mRNA	4239	10289	.	+	.	FI_gene_label "COX6C^ENSG00000164919.11"  ; ID "COX6CP1--COX6C^ENST00000297564.6"  ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; ccdsid "CCDS6284.1"  ; exon_id "ENSE00002129072.1"  ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6"  ; havana_transcript "OTTHUMT00000379835.1"  ; hgnc_id "HGNC:2285"  ; level 2 ; orig_coord_info "chr8,99891908,99892021,-"  ; protein_id "ENSP00000297564.2"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6"  ; transcript_name "COX6C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CSNK1D--C17orf80	HAVANA	gene	24148	30692	.	+	.	FI_gene_label "C17orf80^ENSG00000141219.15"  ; ID "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15"  ; ccdsid "CCDS74145.1"  ; exon_id "ENSE00001340095.1"  ; exon_number 3 ; gene_id "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15"  ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2"  ; havana_transcript "OTTHUMT00000441887.1"  ; hgnc_id "HGNC:29601"  ; level 2 ; orig_coord_info "chr17,73235483,73236995,+"  ; protein_id "ENSP00000255557.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "CSNK1D--C17orf80^ENST00000255557.8"  ; transcript_name "C17orf80-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CSNK1D--C17orf80	HAVANA	mRNA	24148	30692	.	+	.	FI_gene_label "C17orf80^ENSG00000141219.15"  ; ID "CSNK1D--C17orf80^ENST00000255557.8"  ; Parent "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15"  ; ccdsid "CCDS74145.1"  ; exon_id "ENSE00001340095.1"  ; exon_number 3 ; gene_id "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15"  ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2"  ; havana_transcript "OTTHUMT00000441887.1"  ; hgnc_id "HGNC:29601"  ; level 2 ; orig_coord_info "chr17,73235483,73236995,+"  ; protein_id "ENSP00000255557.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "CSNK1D--C17orf80^ENST00000255557.8"  ; transcript_name "C17orf80-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CSNK1D--C17orf80	HAVANA	gene	6457	17094	.	+	.	FI_gene_label "CSNK1D^ENSG00000141551.14"  ; ID "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14"  ; exon_id "ENSE00002716627.1"  ; exon_number 1 ; gene_id "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14"  ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2"  ; havana_transcript "OTTHUMT00000442642.1"  ; hgnc_id "HGNC:2452"  ; level 2 ; orig_coord_info "chr17,82255429,82255516,-"  ; protein_id "ENSP00000269361.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CSNK1D--C17orf80^ENST00000269361.11"  ; transcript_name "CSNK1D-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
CSNK1D--C17orf80	HAVANA	mRNA	6457	17094	.	+	.	FI_gene_label "CSNK1D^ENSG00000141551.14"  ; ID "CSNK1D--C17orf80^ENST00000269361.11"  ; Parent "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14"  ; exon_id "ENSE00002716627.1"  ; exon_number 1 ; gene_id "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14"  ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2"  ; havana_transcript "OTTHUMT00000442642.1"  ; hgnc_id "HGNC:2452"  ; level 2 ; orig_coord_info "chr17,82255429,82255516,-"  ; protein_id "ENSP00000269361.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CSNK1D--C17orf80^ENST00000269361.11"  ; transcript_name "CSNK1D-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
EIF4E--AP002026.1	HAVANA	gene	1042	13518	.	+	.	FI_gene_label "EIF4E^ENSG00000151247.13"  ; ID "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13"  ; ccdsid "CCDS47109.1"  ; exon_id "ENSE00001609349.1"  ; exon_number 1 ; gene_id "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13"  ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2"  ; havana_transcript "OTTHUMT00000363740.1"  ; hgnc_id "HGNC:3287"  ; level 2 ; orig_coord_info "chr4,98928895,98928972,-"  ; protein_id "ENSP00000280892.6"  ; tag basic CCDS ; transcript_id "EIF4E--AP002026.1^ENST00000280892.10"  ; transcript_name "EIF4E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EIF4E--AP002026.1	HAVANA	mRNA	1042	13518	.	+	.	FI_gene_label "EIF4E^ENSG00000151247.13"  ; ID "EIF4E--AP002026.1^ENST00000280892.10"  ; Parent "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13"  ; ccdsid "CCDS47109.1"  ; exon_id "ENSE00001609349.1"  ; exon_number 1 ; gene_id "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13"  ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2"  ; havana_transcript "OTTHUMT00000363740.1"  ; hgnc_id "HGNC:3287"  ; level 2 ; orig_coord_info "chr4,98928895,98928972,-"  ; protein_id "ENSP00000280892.6"  ; tag basic CCDS ; transcript_id "EIF4E--AP002026.1^ENST00000280892.10"  ; transcript_name "EIF4E-201"  ; transcript_support_level 1 ; 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: 
KLRC4--KLRK1	HAVANA	gene	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^ENST00000240618.11"  ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^ENST00000309384.2"  ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
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: 
PLXNA3--AC245140.3	HAVANA	gene	1001	19691	.	+	.	FI_gene_label "PLXNA3^ENSG00000130827.6"  ; ID "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6"  ; ccdsid "CCDS14752.1"  ; exon_id "ENSE00001450662.1"  ; exon_number 2 ; gene_id "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6"  ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6"  ; havana_transcript "OTTHUMT00000081634.3"  ; hgnc_id "HGNC:9101"  ; level 2 ; orig_coord_info "chrX,154460184,154460777,+"  ; protein_id "ENSP00000358696.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--AC245140.3^ENST00000369682.4"  ; transcript_name "PLXNA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLXNA3--AC245140.3	HAVANA	mRNA	1001	19691	.	+	.	FI_gene_label "PLXNA3^ENSG00000130827.6"  ; ID "PLXNA3--AC245140.3^ENST00000369682.4"  ; Parent "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6"  ; ccdsid "CCDS14752.1"  ; exon_id "ENSE00001450662.1"  ; exon_number 2 ; gene_id "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6"  ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6"  ; havana_transcript "OTTHUMT00000081634.3"  ; hgnc_id "HGNC:9101"  ; level 2 ; orig_coord_info "chrX,154460184,154460777,+"  ; protein_id "ENSP00000358696.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--AC245140.3^ENST00000369682.4"  ; transcript_name "PLXNA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PLXNA3--EMD	HAVANA	gene	1001	19691	.	+	.	FI_gene_label "PLXNA3^ENSG00000130827.6"  ; ID "PLXNA3--EMD^PLXNA3^ENSG00000130827.6"  ; ccdsid "CCDS14752.1"  ; exon_id "ENSE00001450662.1"  ; exon_number 2 ; gene_id "PLXNA3--EMD^PLXNA3^ENSG00000130827.6"  ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6"  ; havana_transcript "OTTHUMT00000081634.3"  ; hgnc_id "HGNC:9101"  ; level 2 ; orig_coord_info "chrX,154460184,154460777,+"  ; protein_id "ENSP00000358696.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--EMD^ENST00000369682.4"  ; transcript_name "PLXNA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLXNA3--EMD	HAVANA	mRNA	1001	19691	.	+	.	FI_gene_label "PLXNA3^ENSG00000130827.6"  ; ID "PLXNA3--EMD^ENST00000369682.4"  ; Parent "PLXNA3--EMD^PLXNA3^ENSG00000130827.6"  ; ccdsid "CCDS14752.1"  ; exon_id "ENSE00001450662.1"  ; exon_number 2 ; gene_id "PLXNA3--EMD^PLXNA3^ENSG00000130827.6"  ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6"  ; havana_transcript "OTTHUMT00000081634.3"  ; hgnc_id "HGNC:9101"  ; level 2 ; orig_coord_info "chrX,154460184,154460777,+"  ; protein_id "ENSP00000358696.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--EMD^ENST00000369682.4"  ; transcript_name "PLXNA3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PLXNA3--EMD	HAVANA	gene	22692	24710	.	+	.	FI_gene_label "EMD^ENSG00000102119.11"  ; ID "PLXNA3--EMD^EMD^ENSG00000102119.11"  ; exon_id "ENSE00001909734.1"  ; exon_number 1 ; gene_id "PLXNA3--EMD^EMD^ENSG00000102119.11"  ; gene_name EMD ; gene_type protein_coding ; havana_gene "OTTHUMG00000033186.6"  ; havana_transcript "OTTHUMT00000130306.1"  ; hgnc_id "HGNC:3331"  ; level 2 ; orig_coord_info "chrX,154379485,154379566,+"  ; protein_id "ENSP00000358850.3"  ; tag basic ; transcript_id "PLXNA3--EMD^ENST00000369835.3"  ; transcript_name "EMD-201"  ; transcript_support_level 3 ; transcript_type protein_coding
PLXNA3--EMD	HAVANA	mRNA	22692	24710	.	+	.	FI_gene_label "EMD^ENSG00000102119.11"  ; ID "PLXNA3--EMD^ENST00000369835.3"  ; Parent "PLXNA3--EMD^EMD^ENSG00000102119.11"  ; exon_id "ENSE00001909734.1"  ; exon_number 1 ; gene_id "PLXNA3--EMD^EMD^ENSG00000102119.11"  ; gene_name EMD ; gene_type protein_coding ; havana_gene "OTTHUMG00000033186.6"  ; havana_transcript "OTTHUMT00000130306.1"  ; hgnc_id "HGNC:3331"  ; level 2 ; orig_coord_info "chrX,154379485,154379566,+"  ; protein_id "ENSP00000358850.3"  ; tag basic ; transcript_id "PLXNA3--EMD^ENST00000369835.3"  ; transcript_name "EMD-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
SLC16A5--CSNK1D	HAVANA	gene	19340	29977	.	+	.	FI_gene_label "CSNK1D^ENSG00000141551.14"  ; ID "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14"  ; exon_id "ENSE00002716627.1"  ; exon_number 1 ; gene_id "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14"  ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2"  ; havana_transcript "OTTHUMT00000442642.1"  ; hgnc_id "HGNC:2452"  ; level 2 ; orig_coord_info "chr17,82255429,82255516,-"  ; protein_id "ENSP00000269361.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SLC16A5--CSNK1D^ENST00000269361.11"  ; transcript_name "CSNK1D-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
SLC16A5--CSNK1D	HAVANA	mRNA	19340	29977	.	+	.	FI_gene_label "CSNK1D^ENSG00000141551.14"  ; ID "SLC16A5--CSNK1D^ENST00000269361.11"  ; Parent "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14"  ; exon_id "ENSE00002716627.1"  ; exon_number 1 ; gene_id "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14"  ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2"  ; havana_transcript "OTTHUMT00000442642.1"  ; hgnc_id "HGNC:2452"  ; level 2 ; orig_coord_info "chr17,82255429,82255516,-"  ; protein_id "ENSP00000269361.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SLC16A5--CSNK1D^ENST00000269361.11"  ; transcript_name "CSNK1D-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
SLC16A5--CSNK1D	HAVANA	gene	1228	10883	.	+	.	FI_gene_label "SLC16A5^ENSG00000170190.16"  ; ID "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16"  ; ccdsid "CCDS11713.1"  ; exon_id "ENSE00003508349.1"  ; exon_number 3 ; gene_id "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16"  ; gene_name SLC16A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179277.5"  ; havana_transcript "OTTHUMT00000445545.2"  ; hgnc_id "HGNC:10926"  ; level 2 ; orig_coord_info "chr17,75093637,75093835,+"  ; protein_id "ENSP00000330141.4"  ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SLC16A5--CSNK1D^ENST00000329783.9"  ; transcript_name "SLC16A5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC16A5--CSNK1D	HAVANA	mRNA	1228	10883	.	+	.	FI_gene_label "SLC16A5^ENSG00000170190.16"  ; ID "SLC16A5--CSNK1D^ENST00000329783.9"  ; Parent "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16"  ; ccdsid "CCDS11713.1"  ; exon_id "ENSE00003508349.1"  ; exon_number 3 ; gene_id "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16"  ; gene_name SLC16A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179277.5"  ; havana_transcript "OTTHUMT00000445545.2"  ; hgnc_id "HGNC:10926"  ; level 2 ; orig_coord_info "chr17,75093637,75093835,+"  ; protein_id "ENSP00000330141.4"  ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SLC16A5--CSNK1D^ENST00000329783.9"  ; transcript_name "SLC16A5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLX4IP--FRG1DP	HAVANA	gene	1001	14056	.	+	.	FI_gene_label "SLX4IP^ENSG00000149346.15"  ; ID "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15"  ; ccdsid "CCDS33439.1"  ; exon_id "ENSE00001175305.1"  ; exon_number 2 ; gene_id "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15"  ; gene_name SLX4IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000031873.6"  ; havana_transcript "OTTHUMT00000078000.5"  ; hgnc_id "HGNC:16225"  ; level 2 ; orig_coord_info "chr20,10458205,10458231,+"  ; protein_id "ENSP00000335557.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLX4IP--FRG1DP^ENST00000334534.10"  ; transcript_name "SLX4IP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLX4IP--FRG1DP	HAVANA	mRNA	1001	14056	.	+	.	FI_gene_label "SLX4IP^ENSG00000149346.15"  ; ID "SLX4IP--FRG1DP^ENST00000334534.10"  ; Parent "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15"  ; ccdsid "CCDS33439.1"  ; exon_id "ENSE00001175305.1"  ; exon_number 2 ; gene_id "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15"  ; gene_name SLX4IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000031873.6"  ; havana_transcript "OTTHUMT00000078000.5"  ; hgnc_id "HGNC:16225"  ; level 2 ; orig_coord_info "chr20,10458205,10458231,+"  ; protein_id "ENSP00000335557.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLX4IP--FRG1DP^ENST00000334534.10"  ; transcript_name "SLX4IP-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: 
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: 
ACSF2--AC018521.3	HAVANA	gene	17960	19775	.	+	.	FI_gene_label "AC018521.3^ENSG00000264243.1"  ; ID "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1"  ; exon_id "ENSE00002694001.1"  ; exon_number 1 ; gene_id "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1"  ; gene_name "AC018521.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000178291.1"  ; havana_transcript "OTTHUMT00000441396.1"  ; level 2 ; orig_coord_info "chr17,47863342,47863419,+"  ; tag basic ; transcript_id "ACSF2--AC018521.3^ENST00000581213.1"  ; transcript_name "AC018521.3-201"  ; transcript_support_level 1 ; transcript_type lncRNA
ACSF2--AC018521.3	HAVANA	RNA	17960	19775	.	+	.	FI_gene_label "AC018521.3^ENSG00000264243.1"  ; ID "ACSF2--AC018521.3^ENST00000581213.1"  ; Parent "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1"  ; exon_id "ENSE00002694001.1"  ; exon_number 1 ; gene_id "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1"  ; gene_name "AC018521.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000178291.1"  ; havana_transcript "OTTHUMT00000441396.1"  ; level 2 ; orig_coord_info "chr17,47863342,47863419,+"  ; tag basic ; transcript_id "ACSF2--AC018521.3^ENST00000581213.1"  ; transcript_name "AC018521.3-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
C17orf80--LINC00469	HAVANA	gene	13258	18525	.	+	.	FI_gene_label "LINC00469^ENSG00000177338.14"  ; ID "C17orf80--LINC00469^LINC00469^ENSG00000177338.14"  ; exon_id "ENSE00001556257.1"  ; exon_number 1 ; gene_id "C17orf80--LINC00469^LINC00469^ENSG00000177338.14"  ; gene_name LINC00469 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167833.4"  ; havana_transcript "OTTHUMT00000396490.1"  ; hgnc_id "HGNC:26863"  ; level 2 ; orig_coord_info "chr17,73828448,73828520,-"  ; tag basic ; transcript_id "C17orf80--LINC00469^ENST00000321800.11"  ; transcript_name "LINC00469-201"  ; transcript_support_level 1 ; transcript_type lncRNA
C17orf80--LINC00469	HAVANA	RNA	13258	18525	.	+	.	FI_gene_label "LINC00469^ENSG00000177338.14"  ; ID "C17orf80--LINC00469^ENST00000321800.11"  ; Parent "C17orf80--LINC00469^LINC00469^ENSG00000177338.14"  ; exon_id "ENSE00001556257.1"  ; exon_number 1 ; gene_id "C17orf80--LINC00469^LINC00469^ENSG00000177338.14"  ; gene_name LINC00469 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167833.4"  ; havana_transcript "OTTHUMT00000396490.1"  ; hgnc_id "HGNC:26863"  ; level 2 ; orig_coord_info "chr17,73828448,73828520,-"  ; tag basic ; transcript_id "C17orf80--LINC00469^ENST00000321800.11"  ; transcript_name "LINC00469-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
CEP112--AC134698.1	HAVANA	gene	44924	49566	.	+	.	FI_gene_label "AC134698.1^ENSG00000250637.2"  ; ID "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2"  ; exon_id "ENSE00002076945.1"  ; exon_number 1 ; gene_id "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2"  ; gene_name "AC134698.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160408.2"  ; havana_transcript "OTTHUMT00000360482.2"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr8,43442902,43443081,+"  ; tag basic ; transcript_id "CEP112--AC134698.1^ENST00000511619.2"  ; transcript_name "AC134698.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
CEP112--AC134698.1	HAVANA	RNA	44924	49566	.	+	.	FI_gene_label "AC134698.1^ENSG00000250637.2"  ; ID "CEP112--AC134698.1^ENST00000511619.2"  ; Parent "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2"  ; exon_id "ENSE00002076945.1"  ; exon_number 1 ; gene_id "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2"  ; gene_name "AC134698.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160408.2"  ; havana_transcript "OTTHUMT00000360482.2"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr8,43442902,43443081,+"  ; tag basic ; transcript_id "CEP112--AC134698.1^ENST00000511619.2"  ; transcript_name "AC134698.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
COX6CP1--COX6C	HAVANA	gene	1001	1215	.	+	.	FI_gene_label "COX6CP1^ENSG00000260318.1"  ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; exon_id "ENSE00002587981.1"  ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1"  ; havana_transcript "OTTHUMT00000421521.1"  ; hgnc_id "HGNC:2286"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,11903923,11904137,-"  ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1"  ; transcript_name "COX6CP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
COX6CP1--COX6C	HAVANA	RNA	1001	1215	.	+	.	FI_gene_label "COX6CP1^ENSG00000260318.1"  ; ID "COX6CP1--COX6C^ENST00000564972.1"  ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; exon_id "ENSE00002587981.1"  ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1"  ; havana_transcript "OTTHUMT00000421521.1"  ; hgnc_id "HGNC:2286"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,11903923,11904137,-"  ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1"  ; transcript_name "COX6CP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
EIF4E--AP002026.1	HAVANA	gene	18154	19918	.	+	.	FI_gene_label "AP002026.1^ENSG00000246090.7"  ; ID "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7"  ; exon_id "ENSE00001962097.2"  ; exon_number 1 ; gene_id "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7"  ; gene_name "AP002026.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000161232.6"  ; havana_transcript "OTTHUMT00000364249.1"  ; level 2 ; orig_coord_info "chr4,99088951,99089284,+"  ; transcript_id "EIF4E--AP002026.1^ENST00000499178.2"  ; transcript_name "AP002026.1-202"  ; transcript_support_level 3 ; transcript_type lncRNA
EIF4E--AP002026.1	HAVANA	RNA	18154	19918	.	+	.	FI_gene_label "AP002026.1^ENSG00000246090.7"  ; ID "EIF4E--AP002026.1^ENST00000499178.2"  ; Parent "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7"  ; exon_id "ENSE00001962097.2"  ; exon_number 1 ; gene_id "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7"  ; gene_name "AP002026.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000161232.6"  ; havana_transcript "OTTHUMT00000364249.1"  ; level 2 ; orig_coord_info "chr4,99088951,99089284,+"  ; transcript_id "EIF4E--AP002026.1^ENST00000499178.2"  ; transcript_name "AP002026.1-202"  ; transcript_support_level 3 ; transcript_type lncRNA
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: 
PLXNA3--AC245140.3	HAVANA	gene	22692	24371	.	+	.	FI_gene_label "AC245140.3^ENSG00000285018.1"  ; ID "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1"  ; exon_id "ENSE00003819558.1"  ; exon_number 1 ; gene_id "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1"  ; gene_name "AC245140.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192605.1"  ; havana_transcript "OTTHUMT00000497131.1"  ; level 2 ; orig_coord_info "chrX,154374595,154374727,+"  ; tag basic ; transcript_id "PLXNA3--AC245140.3^ENST00000644854.1"  ; transcript_name "AC245140.3-201"  ; transcript_type lncRNA
PLXNA3--AC245140.3	HAVANA	RNA	22692	24371	.	+	.	FI_gene_label "AC245140.3^ENSG00000285018.1"  ; ID "PLXNA3--AC245140.3^ENST00000644854.1"  ; Parent "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1"  ; exon_id "ENSE00003819558.1"  ; exon_number 1 ; gene_id "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1"  ; gene_name "AC245140.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192605.1"  ; havana_transcript "OTTHUMT00000497131.1"  ; level 2 ; orig_coord_info "chrX,154374595,154374727,+"  ; tag basic ; transcript_id "PLXNA3--AC245140.3^ENST00000644854.1"  ; transcript_name "AC245140.3-201"  ; transcript_type lncRNA
L1 and L2 created: 
SLX4IP--FRG1DP	HAVANA	gene	18591	27121	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "SLX4IP--FRG1DP^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
SLX4IP--FRG1DP	HAVANA	RNA	18591	27121	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "SLX4IP--FRG1DP^ENST00000635586.1"  ; Parent "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "SLX4IP--FRG1DP^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
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
353 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 ------------------------------
506 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
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---------------------- Check13: remove identical isoforms ----------------------
None found
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GFF3 file parsed