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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/496978b4c60dd5991b6dc8f7a15c4d/.command.log
Size: 72.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_bhK-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/732d1eb49664ac5d0585e2e03c3ecb/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/496978b4c60dd5991b6dc8f7a15c4d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/496978b4c60dd5991b6dc8f7a15c4d/.command.run
==> STAGING COMPLETE (3 inputs)

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: 2607
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2607
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:2607
  => 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: 
CCDC6--RET	HAVANA	gene	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^ENST00000263102.7"  ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC6--RET	HAVANA	gene	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^ENST00000340058.6"  ; Parent "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--C10orf143	HAVANA	gene	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--C10orf143^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAJC1--C10orf143	HAVANA	mRNA	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--C10orf143^ENST00000376980.8"  ; Parent "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--C10orf143^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--C10orf143	HAVANA	gene	17630	24580	.	+	.	FI_gene_label "C10orf143^ENSG00000237489.5"  ; ID "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5"  ; exon_id "ENSE00001671572.1"  ; exon_number 1 ; gene_id "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5"  ; gene_name C10orf143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019268.5"  ; havana_transcript "OTTHUMT00000051025.2"  ; hgnc_id "HGNC:48677"  ; level 2 ; orig_coord_info "chr10,130110704,130110772,-"  ; protein_id "ENSP00000489817.1"  ; transcript_id "DNAJC1--C10orf143^ENST00000456581.1"  ; transcript_name "C10orf143-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
DNAJC1--C10orf143	HAVANA	mRNA	17630	24580	.	+	.	FI_gene_label "C10orf143^ENSG00000237489.5"  ; ID "DNAJC1--C10orf143^ENST00000456581.1"  ; Parent "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5"  ; exon_id "ENSE00001671572.1"  ; exon_number 1 ; gene_id "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5"  ; gene_name C10orf143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019268.5"  ; havana_transcript "OTTHUMT00000051025.2"  ; hgnc_id "HGNC:48677"  ; level 2 ; orig_coord_info "chr10,130110704,130110772,-"  ; protein_id "ENSP00000489817.1"  ; transcript_id "DNAJC1--C10orf143^ENST00000456581.1"  ; transcript_name "C10orf143-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ECHS1--NEBL	HAVANA	gene	1001	8479	.	+	.	FI_gene_label "ECHS1^ENSG00000127884.5"  ; ID "ECHS1--NEBL^ECHS1^ENSG00000127884.5"  ; ccdsid "CCDS7681.1"  ; exon_id "ENSE00001447396.4"  ; exon_number 1 ; gene_id "ECHS1--NEBL^ECHS1^ENSG00000127884.5"  ; gene_name ECHS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019320.2"  ; havana_transcript "OTTHUMT00000051156.2"  ; hgnc_id "HGNC:3151"  ; level 2 ; orig_coord_info "chr10,133373246,133373333,-"  ; protein_id "ENSP00000357535.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ECHS1--NEBL^ENST00000368547.4"  ; transcript_name "ECHS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ECHS1--NEBL	HAVANA	mRNA	1001	8479	.	+	.	FI_gene_label "ECHS1^ENSG00000127884.5"  ; ID "ECHS1--NEBL^ENST00000368547.4"  ; Parent "ECHS1--NEBL^ECHS1^ENSG00000127884.5"  ; ccdsid "CCDS7681.1"  ; exon_id "ENSE00001447396.4"  ; exon_number 1 ; gene_id "ECHS1--NEBL^ECHS1^ENSG00000127884.5"  ; gene_name ECHS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019320.2"  ; havana_transcript "OTTHUMT00000051156.2"  ; hgnc_id "HGNC:3151"  ; level 2 ; orig_coord_info "chr10,133373246,133373333,-"  ; protein_id "ENSP00000357535.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ECHS1--NEBL^ENST00000368547.4"  ; transcript_name "ECHS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ECHS1--NEBL	HAVANA	gene	36322	73814	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "ECHS1--NEBL^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "ECHS1--NEBL^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "ECHS1--NEBL^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; transcript_support_level 1 ; transcript_type protein_coding
ECHS1--NEBL	HAVANA	mRNA	36322	73814	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "ECHS1--NEBL^ENST00000377122.9"  ; Parent "ECHS1--NEBL^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "ECHS1--NEBL^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "ECHS1--NEBL^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; 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: 
NEBL--CDK1	ENSEMBL	gene	66459	76732	.	+	.	FI_gene_label "CDK1^ENSG00000170312.16"  ; ID "NEBL--CDK1^CDK1^ENSG00000170312.16"  ; ccdsid "CCDS7260.1"  ; exon_id "ENSE00003527529.1"  ; exon_number 2 ; gene_id "NEBL--CDK1^CDK1^ENSG00000170312.16"  ; gene_name CDK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018290.6"  ; hgnc_id "HGNC:1722"  ; level 3 ; orig_coord_info "chr10,60780166,60780202,+"  ; protein_id "ENSP00000325970.4"  ; tag basic CCDS ; transcript_id "NEBL--CDK1^ENST00000316629.8"  ; transcript_name "CDK1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
NEBL--CDK1	ENSEMBL	mRNA	66459	76732	.	+	.	FI_gene_label "CDK1^ENSG00000170312.16"  ; ID "NEBL--CDK1^ENST00000316629.8"  ; Parent "NEBL--CDK1^CDK1^ENSG00000170312.16"  ; ccdsid "CCDS7260.1"  ; exon_id "ENSE00003527529.1"  ; exon_number 2 ; gene_id "NEBL--CDK1^CDK1^ENSG00000170312.16"  ; gene_name CDK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018290.6"  ; hgnc_id "HGNC:1722"  ; level 3 ; orig_coord_info "chr10,60780166,60780202,+"  ; protein_id "ENSP00000325970.4"  ; tag basic CCDS ; transcript_id "NEBL--CDK1^ENST00000316629.8"  ; transcript_name "CDK1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NEBL--CDK1	HAVANA	gene	25843	63335	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "NEBL--CDK1^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "NEBL--CDK1^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "NEBL--CDK1^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; transcript_support_level 1 ; transcript_type protein_coding
NEBL--CDK1	HAVANA	mRNA	25843	63335	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "NEBL--CDK1^ENST00000377122.9"  ; Parent "NEBL--CDK1^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "NEBL--CDK1^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "NEBL--CDK1^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA10	HAVANA	gene	6881	16334	.	+	.	FI_gene_label "PCDHGA10^ENSG00000253846.2"  ; ID "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; ccdsid "CCDS47292.1"  ; exon_id "ENSE00001792208.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2"  ; havana_transcript "OTTHUMT00000374747.1"  ; hgnc_id "HGNC:8697"  ; level 2 ; orig_coord_info "chr5,141413176,141415611,+"  ; protein_id "ENSP00000381611.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; transcript_name "PCDHGA10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA10	HAVANA	mRNA	6881	16334	.	+	.	FI_gene_label "PCDHGA10^ENSG00000253846.2"  ; ID "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; Parent "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; ccdsid "CCDS47292.1"  ; exon_id "ENSE00001792208.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2"  ; havana_transcript "OTTHUMT00000374747.1"  ; hgnc_id "HGNC:8697"  ; level 2 ; orig_coord_info "chr5,141413176,141415611,+"  ; protein_id "ENSP00000381611.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; transcript_name "PCDHGA10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA10	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA10	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA11	HAVANA	gene	6696	15501	.	+	.	FI_gene_label "PCDHGA11^ENSG00000253873.6"  ; ID "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; ccdsid "CCDS47294.1"  ; exon_id "ENSE00001533810.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3"  ; havana_transcript "OTTHUMT00000376974.3"  ; hgnc_id "HGNC:8698"  ; level 2 ; orig_coord_info "chr5,141421228,141423660,+"  ; protein_id "ENSP00000381589.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; transcript_name "PCDHGA11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA11	HAVANA	mRNA	6696	15501	.	+	.	FI_gene_label "PCDHGA11^ENSG00000253873.6"  ; ID "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; Parent "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; ccdsid "CCDS47294.1"  ; exon_id "ENSE00001533810.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3"  ; havana_transcript "OTTHUMT00000376974.3"  ; hgnc_id "HGNC:8698"  ; level 2 ; orig_coord_info "chr5,141421228,141423660,+"  ; protein_id "ENSP00000381589.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; transcript_name "PCDHGA11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA11	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA11	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA12	HAVANA	gene	6692	14584	.	+	.	FI_gene_label "PCDHGA12^ENSG00000253159.3"  ; ID "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; ccdsid "CCDS4260.1"  ; exon_id "ENSE00000814269.5"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6"  ; havana_transcript "OTTHUMT00000251806.3"  ; hgnc_id "HGNC:8699"  ; level 2 ; orig_coord_info "chr5,141430760,141433183,+"  ; protein_id "ENSP00000252085.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; transcript_name "PCDHGA12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA12	HAVANA	mRNA	6692	14584	.	+	.	FI_gene_label "PCDHGA12^ENSG00000253159.3"  ; ID "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; Parent "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; ccdsid "CCDS4260.1"  ; exon_id "ENSE00000814269.5"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6"  ; havana_transcript "OTTHUMT00000251806.3"  ; hgnc_id "HGNC:8699"  ; level 2 ; orig_coord_info "chr5,141430760,141433183,+"  ; protein_id "ENSP00000252085.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; transcript_name "PCDHGA12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA12	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA12	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA8	HAVANA	gene	9168	18348	.	+	.	FI_gene_label "PCDHGA8^ENSG00000253767.3"  ; ID "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; ccdsid "CCDS47291.1"  ; exon_id "ENSE00001533882.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2"  ; havana_transcript "OTTHUMT00000376972.1"  ; hgnc_id "HGNC:8706"  ; level 2 ; orig_coord_info "chr5,141392814,141395237,+"  ; protein_id "ENSP00000381605.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; transcript_name "PCDHGA8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA8	HAVANA	mRNA	9168	18348	.	+	.	FI_gene_label "PCDHGA8^ENSG00000253767.3"  ; ID "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; Parent "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; ccdsid "CCDS47291.1"  ; exon_id "ENSE00001533882.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2"  ; havana_transcript "OTTHUMT00000376972.1"  ; hgnc_id "HGNC:8706"  ; level 2 ; orig_coord_info "chr5,141392814,141395237,+"  ; protein_id "ENSP00000381605.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; transcript_name "PCDHGA8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA8	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA8	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA9	HAVANA	gene	6713	14440	.	+	.	FI_gene_label "PCDHGA9^ENSG00000261934.2"  ; ID "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; ccdsid "CCDS58981.1"  ; exon_id "ENSE00002639131.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2"  ; havana_transcript "OTTHUMT00000437105.1"  ; hgnc_id "HGNC:8707"  ; level 2 ; orig_coord_info "chr5,141402953,141405376,+"  ; protein_id "ENSP00000460274.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; transcript_name "PCDHGA9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA9	HAVANA	mRNA	6713	14440	.	+	.	FI_gene_label "PCDHGA9^ENSG00000261934.2"  ; ID "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; Parent "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; ccdsid "CCDS58981.1"  ; exon_id "ENSE00002639131.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2"  ; havana_transcript "OTTHUMT00000437105.1"  ; hgnc_id "HGNC:8707"  ; level 2 ; orig_coord_info "chr5,141402953,141405376,+"  ; protein_id "ENSP00000460274.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; transcript_name "PCDHGA9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA9	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA9	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB6	HAVANA	gene	6874	16473	.	+	.	FI_gene_label "PCDHGB6^ENSG00000253305.2"  ; ID "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; ccdsid "CCDS54929.1"  ; exon_id "ENSE00002122685.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2"  ; havana_transcript "OTTHUMT00000374746.1"  ; hgnc_id "HGNC:8713"  ; level 2 ; orig_coord_info "chr5,141408203,141410620,+"  ; protein_id "ENSP00000428603.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; transcript_name "PCDHGB6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB6	HAVANA	mRNA	6874	16473	.	+	.	FI_gene_label "PCDHGB6^ENSG00000253305.2"  ; ID "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; Parent "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; ccdsid "CCDS54929.1"  ; exon_id "ENSE00002122685.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2"  ; havana_transcript "OTTHUMT00000374746.1"  ; hgnc_id "HGNC:8713"  ; level 2 ; orig_coord_info "chr5,141408203,141410620,+"  ; protein_id "ENSP00000428603.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; transcript_name "PCDHGB6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB6	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB6	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB7	HAVANA	gene	6724	14653	.	+	.	FI_gene_label "PCDHGB7^ENSG00000254122.3"  ; ID "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; ccdsid "CCDS47293.1"  ; exon_id "ENSE00001533845.4"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2"  ; havana_transcript "OTTHUMT00000376973.2"  ; hgnc_id "HGNC:8714"  ; level 2 ; orig_coord_info "chr5,141417860,141420274,+"  ; protein_id "ENSP00000381594.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; transcript_name "PCDHGB7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB7	HAVANA	mRNA	6724	14653	.	+	.	FI_gene_label "PCDHGB7^ENSG00000254122.3"  ; ID "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; Parent "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; ccdsid "CCDS47293.1"  ; exon_id "ENSE00001533845.4"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2"  ; havana_transcript "OTTHUMT00000376973.2"  ; hgnc_id "HGNC:8714"  ; level 2 ; orig_coord_info "chr5,141417860,141420274,+"  ; protein_id "ENSP00000381594.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; transcript_name "PCDHGB7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB7	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB7	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC3	HAVANA	gene	6711	16897	.	+	.	FI_gene_label "PCDHGC3^ENSG00000240184.7"  ; ID "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; ccdsid "CCDS4261.1"  ; exon_id "ENSE00001199459.7"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8"  ; havana_transcript "OTTHUMT00000251808.5"  ; hgnc_id "HGNC:8716"  ; level 2 ; orig_coord_info "chr5,141476117,141478546,+"  ; protein_id "ENSP00000312070.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; transcript_name "PCDHGC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC3	HAVANA	mRNA	6711	16897	.	+	.	FI_gene_label "PCDHGC3^ENSG00000240184.7"  ; ID "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; Parent "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; ccdsid "CCDS4261.1"  ; exon_id "ENSE00001199459.7"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8"  ; havana_transcript "OTTHUMT00000251808.5"  ; hgnc_id "HGNC:8716"  ; level 2 ; orig_coord_info "chr5,141476117,141478546,+"  ; protein_id "ENSP00000312070.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; transcript_name "PCDHGC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC3	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC3	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC4	HAVANA	gene	6869	14665	.	+	.	FI_gene_label "PCDHGC4^ENSG00000242419.5"  ; ID "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; ccdsid "CCDS4262.1"  ; exon_id "ENSE00001162305.2"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4"  ; havana_transcript "OTTHUMT00000251820.2"  ; hgnc_id "HGNC:8717"  ; level 2 ; orig_coord_info "chr5,141485174,141487615,+"  ; protein_id "ENSP00000306918.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; transcript_name "PCDHGC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC4	HAVANA	mRNA	6869	14665	.	+	.	FI_gene_label "PCDHGC4^ENSG00000242419.5"  ; ID "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; Parent "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; ccdsid "CCDS4262.1"  ; exon_id "ENSE00001162305.2"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4"  ; havana_transcript "OTTHUMT00000251820.2"  ; hgnc_id "HGNC:8717"  ; level 2 ; orig_coord_info "chr5,141485174,141487615,+"  ; protein_id "ENSP00000306918.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; transcript_name "PCDHGC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC4	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC4	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC5	HAVANA	gene	6692	14717	.	+	.	FI_gene_label "PCDHGC5^ENSG00000240764.4"  ; ID "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; ccdsid "CCDS4263.1"  ; exon_id "ENSE00000766474.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2"  ; havana_transcript "OTTHUMT00000251819.2"  ; hgnc_id "HGNC:8718"  ; level 2 ; orig_coord_info "chr5,141489241,141491700,+"  ; protein_id "ENSP00000252087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; transcript_name "PCDHGC5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC5	HAVANA	mRNA	6692	14717	.	+	.	FI_gene_label "PCDHGC5^ENSG00000240764.4"  ; ID "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; Parent "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; ccdsid "CCDS4263.1"  ; exon_id "ENSE00000766474.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2"  ; havana_transcript "OTTHUMT00000251819.2"  ; hgnc_id "HGNC:8718"  ; level 2 ; orig_coord_info "chr5,141489241,141491700,+"  ; protein_id "ENSP00000252087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; transcript_name "PCDHGC5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC5	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC5	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PMS2P5--CCDC146	HAVANA	gene	6874	27241	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P5--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P5--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P5--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P5--CCDC146	HAVANA	mRNA	6874	27241	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P5--CCDC146^ENST00000285871.5"  ; Parent "PMS2P5--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P5--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P5--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^ENST00000302641.8"  ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^ENST00000606293.5"  ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
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: 
TRIM59--IFT80	HAVANA	gene	2416	9154	.	+	.	FI_gene_label "TRIM59^ENSG00000213186.8"  ; ID "TRIM59--IFT80^TRIM59^ENSG00000213186.8"  ; ccdsid "CCDS3190.1"  ; exon_id "ENSE00001192323.6"  ; exon_number 3 ; gene_id "TRIM59--IFT80^TRIM59^ENSG00000213186.8"  ; gene_name TRIM59 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159034.4"  ; havana_transcript "OTTHUMT00000352963.2"  ; hgnc_id "HGNC:30834"  ; level 2 ; orig_coord_info "chr3,160437975,160439183,-"  ; protein_id "ENSP00000311219.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000309784.9"  ; transcript_name "TRIM59-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRIM59--IFT80	HAVANA	mRNA	2416	9154	.	+	.	FI_gene_label "TRIM59^ENSG00000213186.8"  ; ID "TRIM59--IFT80^ENST00000309784.9"  ; Parent "TRIM59--IFT80^TRIM59^ENSG00000213186.8"  ; ccdsid "CCDS3190.1"  ; exon_id "ENSE00001192323.6"  ; exon_number 3 ; gene_id "TRIM59--IFT80^TRIM59^ENSG00000213186.8"  ; gene_name TRIM59 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159034.4"  ; havana_transcript "OTTHUMT00000352963.2"  ; hgnc_id "HGNC:30834"  ; level 2 ; orig_coord_info "chr3,160437975,160439183,-"  ; protein_id "ENSP00000311219.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000309784.9"  ; transcript_name "TRIM59-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRIM59--IFT80	HAVANA	gene	15868	46756	.	+	.	FI_gene_label "IFT80^ENSG00000068885.15"  ; ID "TRIM59--IFT80^IFT80^ENSG00000068885.15"  ; ccdsid "CCDS3188.1"  ; exon_id "ENSE00003486065.1"  ; exon_number 2 ; gene_id "TRIM59--IFT80^IFT80^ENSG00000068885.15"  ; gene_name IFT80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158953.9"  ; havana_transcript "OTTHUMT00000352651.3"  ; hgnc_id "HGNC:29262"  ; level 2 ; orig_coord_info "chr3,160384564,160384600,-"  ; protein_id "ENSP00000312778.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000326448.12"  ; transcript_name "IFT80-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRIM59--IFT80	HAVANA	mRNA	15868	46756	.	+	.	FI_gene_label "IFT80^ENSG00000068885.15"  ; ID "TRIM59--IFT80^ENST00000326448.12"  ; Parent "TRIM59--IFT80^IFT80^ENSG00000068885.15"  ; ccdsid "CCDS3188.1"  ; exon_id "ENSE00003486065.1"  ; exon_number 2 ; gene_id "TRIM59--IFT80^IFT80^ENSG00000068885.15"  ; gene_name IFT80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158953.9"  ; havana_transcript "OTTHUMT00000352651.3"  ; hgnc_id "HGNC:29262"  ; level 2 ; orig_coord_info "chr3,160384564,160384600,-"  ; protein_id "ENSP00000312778.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000326448.12"  ; transcript_name "IFT80-201"  ; 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: 
PMS2P5--CCDC146	HAVANA	gene	1001	3692	.	+	.	FI_gene_label "PMS2P5^ENSG00000123965.13"  ; ID "PMS2P5--CCDC146^PMS2P5^ENSG00000123965.13"  ; exon_id "ENSE00002489954.1"  ; exon_number 1 ; gene_id "PMS2P5--CCDC146^PMS2P5^ENSG00000123965.13"  ; gene_name PMS2P5 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000156014.4"  ; havana_transcript "OTTHUMT00000343742.3"  ; hgnc_id "HGNC:9130"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,74894116,74894257,+"  ; tag basic ; transcript_id "PMS2P5--CCDC146^ENST00000398065.3"  ; transcript_name "PMS2P5-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P5--CCDC146	HAVANA	RNA	1001	3692	.	+	.	FI_gene_label "PMS2P5^ENSG00000123965.13"  ; ID "PMS2P5--CCDC146^ENST00000398065.3"  ; Parent "PMS2P5--CCDC146^PMS2P5^ENSG00000123965.13"  ; exon_id "ENSE00002489954.1"  ; exon_number 1 ; gene_id "PMS2P5--CCDC146^PMS2P5^ENSG00000123965.13"  ; gene_name PMS2P5 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000156014.4"  ; havana_transcript "OTTHUMT00000343742.3"  ; hgnc_id "HGNC:9130"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,74894116,74894257,+"  ; tag basic ; transcript_id "PMS2P5--CCDC146^ENST00000398065.3"  ; transcript_name "PMS2P5-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
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
269 cases fixed where L3 features have parent feature(s) missing
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--------------------------- 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
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------------------------- 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 ------------------------------
475 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 28 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