File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/58134775552d0d705989eeb6696871/.command.out
Size
63.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_eu1-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

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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: 5536
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5536
=> 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:5536
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
ABCE1--ZNF330	HAVANA	gene	21712	32165	.	+	.	FI_gene_label "ZNF330^ENSG00000109445.11"  ; ID "ABCE1--ZNF330^ZNF330^ENSG00000109445.11"  ; ccdsid "CCDS3754.1"  ; exon_id "ENSE00003845998.1"  ; exon_number 2 ; gene_id "ABCE1--ZNF330^ZNF330^ENSG00000109445.11"  ; gene_name ZNF330 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133413.9"  ; havana_transcript "OTTHUMT00000257271.3"  ; hgnc_id "HGNC:15462"  ; level 2 ; orig_coord_info "chr4,141222372,141222491,+"  ; protein_id "ENSP00000262990.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABCE1--ZNF330^ENST00000262990.9"  ; transcript_name "ZNF330-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ABCE1--ZNF330	HAVANA	mRNA	21712	32165	.	+	.	FI_gene_label "ZNF330^ENSG00000109445.11"  ; ID "ABCE1--ZNF330^ENST00000262990.9"  ; Parent "ABCE1--ZNF330^ZNF330^ENSG00000109445.11"  ; ccdsid "CCDS3754.1"  ; exon_id "ENSE00003845998.1"  ; exon_number 2 ; gene_id "ABCE1--ZNF330^ZNF330^ENSG00000109445.11"  ; gene_name ZNF330 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133413.9"  ; havana_transcript "OTTHUMT00000257271.3"  ; hgnc_id "HGNC:15462"  ; level 2 ; orig_coord_info "chr4,141222372,141222491,+"  ; protein_id "ENSP00000262990.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABCE1--ZNF330^ENST00000262990.9"  ; transcript_name "ZNF330-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ABCE1--ZNF330	HAVANA	gene	1024	18703	.	+	.	FI_gene_label "ABCE1^ENSG00000164163.11"  ; ID "ABCE1--ZNF330^ABCE1^ENSG00000164163.11"  ; ccdsid "CCDS34071.1"  ; exon_id "ENSE00003592817.1"  ; exon_number 2 ; gene_id "ABCE1--ZNF330^ABCE1^ENSG00000164163.11"  ; gene_name ABCE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161478.4"  ; havana_transcript "OTTHUMT00000365104.2"  ; hgnc_id "HGNC:69"  ; level 2 ; orig_coord_info "chr4,145104413,145104515,+"  ; protein_id "ENSP00000296577.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABCE1--ZNF330^ENST00000296577.9"  ; transcript_name "ABCE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ABCE1--ZNF330	HAVANA	mRNA	1024	18703	.	+	.	FI_gene_label "ABCE1^ENSG00000164163.11"  ; ID "ABCE1--ZNF330^ENST00000296577.9"  ; Parent "ABCE1--ZNF330^ABCE1^ENSG00000164163.11"  ; ccdsid "CCDS34071.1"  ; exon_id "ENSE00003592817.1"  ; exon_number 2 ; gene_id "ABCE1--ZNF330^ABCE1^ENSG00000164163.11"  ; gene_name ABCE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161478.4"  ; havana_transcript "OTTHUMT00000365104.2"  ; hgnc_id "HGNC:69"  ; level 2 ; orig_coord_info "chr4,145104413,145104515,+"  ; protein_id "ENSP00000296577.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABCE1--ZNF330^ENST00000296577.9"  ; transcript_name "ABCE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARPC1B--CPA5	HAVANA	gene	18647	27611	.	+	.	FI_gene_label "CPA5^ENSG00000158525.16"  ; ID "ARPC1B--CPA5^CPA5^ENSG00000158525.16"  ; ccdsid "CCDS5819.1"  ; exon_id "ENSE00001901540.1"  ; exon_number 1 ; gene_id "ARPC1B--CPA5^CPA5^ENSG00000158525.16"  ; gene_name CPA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157824.3"  ; havana_transcript "OTTHUMT00000349714.1"  ; hgnc_id "HGNC:15722"  ; level 2 ; orig_coord_info "chr7,130346486,130346601,+"  ; protein_id "ENSP00000376907.3"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARPC1B--CPA5^ENST00000393213.7"  ; transcript_name "CPA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARPC1B--CPA5	HAVANA	mRNA	18647	27611	.	+	.	FI_gene_label "CPA5^ENSG00000158525.16"  ; ID "ARPC1B--CPA5^ENST00000393213.7"  ; Parent "ARPC1B--CPA5^CPA5^ENSG00000158525.16"  ; ccdsid "CCDS5819.1"  ; exon_id "ENSE00001901540.1"  ; exon_number 1 ; gene_id "ARPC1B--CPA5^CPA5^ENSG00000158525.16"  ; gene_name CPA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157824.3"  ; havana_transcript "OTTHUMT00000349714.1"  ; hgnc_id "HGNC:15722"  ; level 2 ; orig_coord_info "chr7,130346486,130346601,+"  ; protein_id "ENSP00000376907.3"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARPC1B--CPA5^ENST00000393213.7"  ; transcript_name "CPA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARPC1B--CPA5	HAVANA	gene	1011	7904	.	+	.	FI_gene_label "ARPC1B^ENSG00000130429.15"  ; ID "ARPC1B--CPA5^ARPC1B^ENSG00000130429.15"  ; exon_id "ENSE00003598946.1"  ; exon_number 2 ; gene_id "ARPC1B--CPA5^ARPC1B^ENSG00000130429.15"  ; gene_name ARPC1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000154552.34"  ; havana_transcript "OTTHUMT00000335898.2"  ; hgnc_id "HGNC:704"  ; level 2 ; orig_coord_info "chr7,99385715,99385778,+"  ; protein_id "ENSP00000398620.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "ARPC1B--CPA5^ENST00000414376.5"  ; transcript_name "ARPC1B-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ARPC1B--CPA5	HAVANA	mRNA	1011	7904	.	+	.	FI_gene_label "ARPC1B^ENSG00000130429.15"  ; ID "ARPC1B--CPA5^ENST00000414376.5"  ; Parent "ARPC1B--CPA5^ARPC1B^ENSG00000130429.15"  ; exon_id "ENSE00003598946.1"  ; exon_number 2 ; gene_id "ARPC1B--CPA5^ARPC1B^ENSG00000130429.15"  ; gene_name ARPC1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000154552.34"  ; havana_transcript "OTTHUMT00000335898.2"  ; hgnc_id "HGNC:704"  ; level 2 ; orig_coord_info "chr7,99385715,99385778,+"  ; protein_id "ENSP00000398620.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "ARPC1B--CPA5^ENST00000414376.5"  ; transcript_name "ARPC1B-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
CNNM3--TANC1	HAVANA	gene	14119	49742	.	+	.	FI_gene_label "TANC1^ENSG00000115183.15"  ; ID "CNNM3--TANC1^TANC1^ENSG00000115183.15"  ; ccdsid "CCDS42766.1"  ; exon_id "ENSE00003715868.1"  ; exon_number 3 ; gene_id "CNNM3--TANC1^TANC1^ENSG00000115183.15"  ; gene_name TANC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153945.3"  ; havana_transcript "OTTHUMT00000333135.2"  ; hgnc_id "HGNC:29364"  ; level 2 ; orig_coord_info "chr2,159065911,159065971,+"  ; protein_id "ENSP00000263635.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNNM3--TANC1^ENST00000263635.8"  ; transcript_name "TANC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CNNM3--TANC1	HAVANA	mRNA	14119	49742	.	+	.	FI_gene_label "TANC1^ENSG00000115183.15"  ; ID "CNNM3--TANC1^ENST00000263635.8"  ; Parent "CNNM3--TANC1^TANC1^ENSG00000115183.15"  ; ccdsid "CCDS42766.1"  ; exon_id "ENSE00003715868.1"  ; exon_number 3 ; gene_id "CNNM3--TANC1^TANC1^ENSG00000115183.15"  ; gene_name TANC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153945.3"  ; havana_transcript "OTTHUMT00000333135.2"  ; hgnc_id "HGNC:29364"  ; level 2 ; orig_coord_info "chr2,159065911,159065971,+"  ; protein_id "ENSP00000263635.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNNM3--TANC1^ENST00000263635.8"  ; transcript_name "TANC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CNNM3--TANC1	HAVANA	gene	1024	11118	.	+	.	FI_gene_label "CNNM3^ENSG00000168763.16"  ; ID "CNNM3--TANC1^CNNM3^ENSG00000168763.16"  ; ccdsid "CCDS2025.1"  ; exon_id "ENSE00001853337.2"  ; exon_number 1 ; gene_id "CNNM3--TANC1^CNNM3^ENSG00000168763.16"  ; gene_name CNNM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130531.4"  ; havana_transcript "OTTHUMT00000252952.3"  ; hgnc_id "HGNC:104"  ; level 2 ; orig_coord_info "chr2,96816278,96817502,+"  ; protein_id "ENSP00000305449.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNNM3--TANC1^ENST00000305510.4"  ; transcript_name "CNNM3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CNNM3--TANC1	HAVANA	mRNA	1024	11118	.	+	.	FI_gene_label "CNNM3^ENSG00000168763.16"  ; ID "CNNM3--TANC1^ENST00000305510.4"  ; Parent "CNNM3--TANC1^CNNM3^ENSG00000168763.16"  ; ccdsid "CCDS2025.1"  ; exon_id "ENSE00001853337.2"  ; exon_number 1 ; gene_id "CNNM3--TANC1^CNNM3^ENSG00000168763.16"  ; gene_name CNNM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130531.4"  ; havana_transcript "OTTHUMT00000252952.3"  ; hgnc_id "HGNC:104"  ; level 2 ; orig_coord_info "chr2,96816278,96817502,+"  ; protein_id "ENSP00000305449.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNNM3--TANC1^ENST00000305510.4"  ; transcript_name "CNNM3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IQGAP1--AKAP13	HAVANA	gene	1001	41690	.	+	.	FI_gene_label "IQGAP1^ENSG00000140575.13"  ; ID "IQGAP1--AKAP13^IQGAP1^ENSG00000140575.13"  ; ccdsid "CCDS10362.1"  ; exon_id "ENSE00001304261.8"  ; exon_number 1 ; gene_id "IQGAP1--AKAP13^IQGAP1^ENSG00000140575.13"  ; gene_name IQGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149832.6"  ; havana_transcript "OTTHUMT00000313493.2"  ; hgnc_id "HGNC:6110"  ; level 2 ; orig_coord_info "chr15,90388342,90388396,+"  ; protein_id "ENSP00000268182.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IQGAP1--AKAP13^ENST00000268182.10"  ; transcript_name "IQGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IQGAP1--AKAP13	HAVANA	mRNA	1001	41690	.	+	.	FI_gene_label "IQGAP1^ENSG00000140575.13"  ; ID "IQGAP1--AKAP13^ENST00000268182.10"  ; Parent "IQGAP1--AKAP13^IQGAP1^ENSG00000140575.13"  ; ccdsid "CCDS10362.1"  ; exon_id "ENSE00001304261.8"  ; exon_number 1 ; gene_id "IQGAP1--AKAP13^IQGAP1^ENSG00000140575.13"  ; gene_name IQGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149832.6"  ; havana_transcript "OTTHUMT00000313493.2"  ; hgnc_id "HGNC:6110"  ; level 2 ; orig_coord_info "chr15,90388342,90388396,+"  ; protein_id "ENSP00000268182.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IQGAP1--AKAP13^ENST00000268182.10"  ; transcript_name "IQGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IQGAP1--AKAP13	HAVANA	gene	44849	101839	.	+	.	FI_gene_label "AKAP13^ENSG00000170776.22"  ; ID "IQGAP1--AKAP13^AKAP13^ENSG00000170776.22"  ; ccdsid "CCDS32320.1"  ; exon_id "ENSE00002705517.1"  ; exon_number 2 ; gene_id "IQGAP1--AKAP13^AKAP13^ENSG00000170776.22"  ; gene_name AKAP13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172205.3"  ; havana_transcript "OTTHUMT00000417319.1"  ; hgnc_id "HGNC:371"  ; level 2 ; orig_coord_info "chr15,85485721,85485753,+"  ; protein_id "ENSP00000354718.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IQGAP1--AKAP13^ENST00000361243.6"  ; transcript_name "AKAP13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IQGAP1--AKAP13	HAVANA	mRNA	44849	101839	.	+	.	FI_gene_label "AKAP13^ENSG00000170776.22"  ; ID "IQGAP1--AKAP13^ENST00000361243.6"  ; Parent "IQGAP1--AKAP13^AKAP13^ENSG00000170776.22"  ; ccdsid "CCDS32320.1"  ; exon_id "ENSE00002705517.1"  ; exon_number 2 ; gene_id "IQGAP1--AKAP13^AKAP13^ENSG00000170776.22"  ; gene_name AKAP13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172205.3"  ; havana_transcript "OTTHUMT00000417319.1"  ; hgnc_id "HGNC:371"  ; level 2 ; orig_coord_info "chr15,85485721,85485753,+"  ; protein_id "ENSP00000354718.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IQGAP1--AKAP13^ENST00000361243.6"  ; transcript_name "AKAP13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LFNG--STRIP2	HAVANA	gene	4537	10893	.	+	.	FI_gene_label "LFNG^ENSG00000106003.13"  ; ID "LFNG--STRIP2^LFNG^ENSG00000106003.13"  ; ccdsid "CCDS34587.1"  ; exon_id "ENSE00001329541.4"  ; exon_number 1 ; gene_id "LFNG--STRIP2^LFNG^ENSG00000106003.13"  ; gene_name LFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000152043.2"  ; havana_transcript "OTTHUMT00000325021.2"  ; hgnc_id "HGNC:6560"  ; level 2 ; orig_coord_info "chr7,2519862,2520293,+"  ; protein_id "ENSP00000222725.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LFNG--STRIP2^ENST00000222725.10"  ; transcript_name "LFNG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LFNG--STRIP2	HAVANA	mRNA	4537	10893	.	+	.	FI_gene_label "LFNG^ENSG00000106003.13"  ; ID "LFNG--STRIP2^ENST00000222725.10"  ; Parent "LFNG--STRIP2^LFNG^ENSG00000106003.13"  ; ccdsid "CCDS34587.1"  ; exon_id "ENSE00001329541.4"  ; exon_number 1 ; gene_id "LFNG--STRIP2^LFNG^ENSG00000106003.13"  ; gene_name LFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000152043.2"  ; havana_transcript "OTTHUMT00000325021.2"  ; hgnc_id "HGNC:6560"  ; level 2 ; orig_coord_info "chr7,2519862,2520293,+"  ; protein_id "ENSP00000222725.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LFNG--STRIP2^ENST00000222725.10"  ; transcript_name "LFNG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
LFNG--STRIP2	HAVANA	gene	14642	37428	.	+	.	FI_gene_label "STRIP2^ENSG00000128578.10"  ; ID "LFNG--STRIP2^STRIP2^ENSG00000128578.10"  ; ccdsid "CCDS34752.1"  ; exon_id "ENSE00001712110.2"  ; exon_number 1 ; gene_id "LFNG--STRIP2^STRIP2^ENSG00000128578.10"  ; gene_name STRIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157695.2"  ; havana_transcript "OTTHUMT00000349418.2"  ; hgnc_id "HGNC:22209"  ; level 2 ; orig_coord_info "chr7,129434473,129434601,+"  ; protein_id "ENSP00000249344.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LFNG--STRIP2^ENST00000249344.7"  ; transcript_name "STRIP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LFNG--STRIP2	HAVANA	mRNA	14642	37428	.	+	.	FI_gene_label "STRIP2^ENSG00000128578.10"  ; ID "LFNG--STRIP2^ENST00000249344.7"  ; Parent "LFNG--STRIP2^STRIP2^ENSG00000128578.10"  ; ccdsid "CCDS34752.1"  ; exon_id "ENSE00001712110.2"  ; exon_number 1 ; gene_id "LFNG--STRIP2^STRIP2^ENSG00000128578.10"  ; gene_name STRIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157695.2"  ; havana_transcript "OTTHUMT00000349418.2"  ; hgnc_id "HGNC:22209"  ; level 2 ; orig_coord_info "chr7,129434473,129434601,+"  ; protein_id "ENSP00000249344.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LFNG--STRIP2^ENST00000249344.7"  ; transcript_name "STRIP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRIG1--CLTC	HAVANA	gene	31200	65735	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "LRIG1--CLTC^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "LRIG1--CLTC^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRIG1--CLTC^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LRIG1--CLTC	HAVANA	mRNA	31200	65735	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "LRIG1--CLTC^ENST00000269122.8"  ; Parent "LRIG1--CLTC^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "LRIG1--CLTC^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRIG1--CLTC^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRIG1--CLTC	HAVANA	gene	1242	27993	.	+	.	FI_gene_label "LRIG1^ENSG00000144749.14"  ; ID "LRIG1--CLTC^LRIG1^ENSG00000144749.14"  ; ccdsid "CCDS33783.1"  ; exon_id "ENSE00001888452.2"  ; exon_number 1 ; gene_id "LRIG1--CLTC^LRIG1^ENSG00000144749.14"  ; gene_name LRIG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158727.1"  ; havana_transcript "OTTHUMT00000351930.1"  ; hgnc_id "HGNC:17360"  ; level 2 ; orig_coord_info "chr3,66500190,66500407,-"  ; protein_id "ENSP00000273261.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRIG1--CLTC^ENST00000273261.8"  ; transcript_name "LRIG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LRIG1--CLTC	HAVANA	mRNA	1242	27993	.	+	.	FI_gene_label "LRIG1^ENSG00000144749.14"  ; ID "LRIG1--CLTC^ENST00000273261.8"  ; Parent "LRIG1--CLTC^LRIG1^ENSG00000144749.14"  ; ccdsid "CCDS33783.1"  ; exon_id "ENSE00001888452.2"  ; exon_number 1 ; gene_id "LRIG1--CLTC^LRIG1^ENSG00000144749.14"  ; gene_name LRIG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158727.1"  ; havana_transcript "OTTHUMT00000351930.1"  ; hgnc_id "HGNC:17360"  ; level 2 ; orig_coord_info "chr3,66500190,66500407,-"  ; protein_id "ENSP00000273261.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRIG1--CLTC^ENST00000273261.8"  ; transcript_name "LRIG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
OTUD4--ZNF330	HAVANA	gene	33073	43526	.	+	.	FI_gene_label "ZNF330^ENSG00000109445.11"  ; ID "OTUD4--ZNF330^ZNF330^ENSG00000109445.11"  ; ccdsid "CCDS3754.1"  ; exon_id "ENSE00003845998.1"  ; exon_number 2 ; gene_id "OTUD4--ZNF330^ZNF330^ENSG00000109445.11"  ; gene_name ZNF330 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133413.9"  ; havana_transcript "OTTHUMT00000257271.3"  ; hgnc_id "HGNC:15462"  ; level 2 ; orig_coord_info "chr4,141222372,141222491,+"  ; protein_id "ENSP00000262990.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "OTUD4--ZNF330^ENST00000262990.9"  ; transcript_name "ZNF330-201"  ; transcript_support_level 1 ; transcript_type protein_coding
OTUD4--ZNF330	HAVANA	mRNA	33073	43526	.	+	.	FI_gene_label "ZNF330^ENSG00000109445.11"  ; ID "OTUD4--ZNF330^ENST00000262990.9"  ; Parent "OTUD4--ZNF330^ZNF330^ENSG00000109445.11"  ; ccdsid "CCDS3754.1"  ; exon_id "ENSE00003845998.1"  ; exon_number 2 ; gene_id "OTUD4--ZNF330^ZNF330^ENSG00000109445.11"  ; gene_name ZNF330 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133413.9"  ; havana_transcript "OTTHUMT00000257271.3"  ; hgnc_id "HGNC:15462"  ; level 2 ; orig_coord_info "chr4,141222372,141222491,+"  ; protein_id "ENSP00000262990.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "OTUD4--ZNF330^ENST00000262990.9"  ; transcript_name "ZNF330-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
OTUD4--ZNF330	HAVANA	gene	1001	27593	.	+	.	FI_gene_label "OTUD4^ENSG00000164164.17"  ; ID "OTUD4--ZNF330^OTUD4^ENSG00000164164.17"  ; exon_id "ENSE00002042731.2"  ; exon_number 1 ; gene_id "OTUD4--ZNF330^OTUD4^ENSG00000164164.17"  ; gene_name OTUD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161480.8"  ; havana_transcript "OTTHUMT00000365117.4"  ; hgnc_id "HGNC:24949"  ; level 2 ; orig_coord_info "chr4,145179815,145179973,-"  ; protein_id "ENSP00000395487.2"  ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_1 ; transcript_id "OTUD4--ZNF330^ENST00000447906.8"  ; transcript_name "OTUD4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
OTUD4--ZNF330	HAVANA	mRNA	1001	27593	.	+	.	FI_gene_label "OTUD4^ENSG00000164164.17"  ; ID "OTUD4--ZNF330^ENST00000447906.8"  ; Parent "OTUD4--ZNF330^OTUD4^ENSG00000164164.17"  ; exon_id "ENSE00002042731.2"  ; exon_number 1 ; gene_id "OTUD4--ZNF330^OTUD4^ENSG00000164164.17"  ; gene_name OTUD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161480.8"  ; havana_transcript "OTTHUMT00000365117.4"  ; hgnc_id "HGNC:24949"  ; level 2 ; orig_coord_info "chr4,145179815,145179973,-"  ; protein_id "ENSP00000395487.2"  ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_1 ; transcript_id "OTUD4--ZNF330^ENST00000447906.8"  ; transcript_name "OTUD4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PACS2--PTCD3	HAVANA	gene	33058	58932	.	+	.	FI_gene_label "PTCD3^ENSG00000132300.19"  ; ID "PACS2--PTCD3^PTCD3^ENSG00000132300.19"  ; ccdsid "CCDS33235.1"  ; exon_id "ENSE00001616986.2"  ; exon_number 1 ; gene_id "PACS2--PTCD3^PTCD3^ENSG00000132300.19"  ; gene_name PTCD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153168.6"  ; havana_transcript "OTTHUMT00000329854.2"  ; hgnc_id "HGNC:24717"  ; level 2 ; orig_coord_info "chr2,86106248,86106351,+"  ; protein_id "ENSP00000254630.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PACS2--PTCD3^ENST00000254630.12"  ; transcript_name "PTCD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PACS2--PTCD3	HAVANA	mRNA	33058	58932	.	+	.	FI_gene_label "PTCD3^ENSG00000132300.19"  ; ID "PACS2--PTCD3^ENST00000254630.12"  ; Parent "PACS2--PTCD3^PTCD3^ENSG00000132300.19"  ; ccdsid "CCDS33235.1"  ; exon_id "ENSE00001616986.2"  ; exon_number 1 ; gene_id "PACS2--PTCD3^PTCD3^ENSG00000132300.19"  ; gene_name PTCD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153168.6"  ; havana_transcript "OTTHUMT00000329854.2"  ; hgnc_id "HGNC:24717"  ; level 2 ; orig_coord_info "chr2,86106248,86106351,+"  ; protein_id "ENSP00000254630.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PACS2--PTCD3^ENST00000254630.12"  ; transcript_name "PTCD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PACS2--PTCD3	HAVANA	gene	2418	27104	.	+	.	FI_gene_label "PACS2^ENSG00000179364.14"  ; ID "PACS2--PTCD3^PACS2^ENSG00000179364.14"  ; ccdsid "CCDS32168.1"  ; exon_id "ENSE00002400785.1"  ; exon_number 1 ; gene_id "PACS2--PTCD3^PACS2^ENSG00000179364.14"  ; gene_name PACS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170450.3"  ; havana_transcript "OTTHUMT00000409209.1"  ; hgnc_id "HGNC:23794"  ; level 2 ; orig_coord_info "chr14,105314919,105315037,+"  ; protein_id "ENSP00000321834.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "PACS2--PTCD3^ENST00000325438.12"  ; transcript_name "PACS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PACS2--PTCD3	HAVANA	mRNA	2418	27104	.	+	.	FI_gene_label "PACS2^ENSG00000179364.14"  ; ID "PACS2--PTCD3^ENST00000325438.12"  ; Parent "PACS2--PTCD3^PACS2^ENSG00000179364.14"  ; ccdsid "CCDS32168.1"  ; exon_id "ENSE00002400785.1"  ; exon_number 1 ; gene_id "PACS2--PTCD3^PACS2^ENSG00000179364.14"  ; gene_name PACS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170450.3"  ; havana_transcript "OTTHUMT00000409209.1"  ; hgnc_id "HGNC:23794"  ; level 2 ; orig_coord_info "chr14,105314919,105315037,+"  ; protein_id "ENSP00000321834.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "PACS2--PTCD3^ENST00000325438.12"  ; transcript_name "PACS2-201"  ; transcript_support_level 1 ; 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: 
PDZRN3--LINC00877	HAVANA	gene	1001	23093	.	+	.	FI_gene_label "PDZRN3^ENSG00000121440.15"  ; ID "PDZRN3--LINC00877^PDZRN3^ENSG00000121440.15"  ; ccdsid "CCDS33789.1"  ; exon_id "ENSE00001890354.2"  ; exon_number 1 ; gene_id "PDZRN3--LINC00877^PDZRN3^ENSG00000121440.15"  ; gene_name PDZRN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158865.6"  ; havana_transcript "OTTHUMT00000352460.2"  ; hgnc_id "HGNC:17704"  ; level 2 ; orig_coord_info "chr3,73624103,73624825,-"  ; protein_id "ENSP00000263666.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDZRN3--LINC00877^ENST00000263666.9"  ; transcript_name "PDZRN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PDZRN3--LINC00877	HAVANA	mRNA	1001	23093	.	+	.	FI_gene_label "PDZRN3^ENSG00000121440.15"  ; ID "PDZRN3--LINC00877^ENST00000263666.9"  ; Parent "PDZRN3--LINC00877^PDZRN3^ENSG00000121440.15"  ; ccdsid "CCDS33789.1"  ; exon_id "ENSE00001890354.2"  ; exon_number 1 ; gene_id "PDZRN3--LINC00877^PDZRN3^ENSG00000121440.15"  ; gene_name PDZRN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158865.6"  ; havana_transcript "OTTHUMT00000352460.2"  ; hgnc_id "HGNC:17704"  ; level 2 ; orig_coord_info "chr3,73624103,73624825,-"  ; protein_id "ENSP00000263666.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDZRN3--LINC00877^ENST00000263666.9"  ; transcript_name "PDZRN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PDZRN3--RN7SL271P	HAVANA	gene	1001	23093	.	+	.	FI_gene_label "PDZRN3^ENSG00000121440.15"  ; ID "PDZRN3--RN7SL271P^PDZRN3^ENSG00000121440.15"  ; ccdsid "CCDS33789.1"  ; exon_id "ENSE00001890354.2"  ; exon_number 1 ; gene_id "PDZRN3--RN7SL271P^PDZRN3^ENSG00000121440.15"  ; gene_name PDZRN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158865.6"  ; havana_transcript "OTTHUMT00000352460.2"  ; hgnc_id "HGNC:17704"  ; level 2 ; orig_coord_info "chr3,73624103,73624825,-"  ; protein_id "ENSP00000263666.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDZRN3--RN7SL271P^ENST00000263666.9"  ; transcript_name "PDZRN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PDZRN3--RN7SL271P	HAVANA	mRNA	1001	23093	.	+	.	FI_gene_label "PDZRN3^ENSG00000121440.15"  ; ID "PDZRN3--RN7SL271P^ENST00000263666.9"  ; Parent "PDZRN3--RN7SL271P^PDZRN3^ENSG00000121440.15"  ; ccdsid "CCDS33789.1"  ; exon_id "ENSE00001890354.2"  ; exon_number 1 ; gene_id "PDZRN3--RN7SL271P^PDZRN3^ENSG00000121440.15"  ; gene_name PDZRN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158865.6"  ; havana_transcript "OTTHUMT00000352460.2"  ; hgnc_id "HGNC:17704"  ; level 2 ; orig_coord_info "chr3,73624103,73624825,-"  ; protein_id "ENSP00000263666.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDZRN3--RN7SL271P^ENST00000263666.9"  ; transcript_name "PDZRN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTEN--AUNIP	HAVANA	gene	1001	20660	.	+	.	FI_gene_label "PTEN^ENSG00000171862.11"  ; ID "PTEN--AUNIP^PTEN^ENSG00000171862.11"  ; ccdsid "CCDS31238.1"  ; exon_id "ENSE00001456562.4"  ; exon_number 1 ; gene_id "PTEN--AUNIP^PTEN^ENSG00000171862.11"  ; gene_name PTEN ; gene_type protein_coding ; havana_gene "OTTHUMG00000018688.3"  ; havana_transcript "OTTHUMT00000049241.2"  ; hgnc_id "HGNC:9588"  ; level 2 ; orig_coord_info "chr10,87864470,87864548,+"  ; protein_id "ENSP00000361021.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTEN--AUNIP^ENST00000371953.8"  ; transcript_name "PTEN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PTEN--AUNIP	HAVANA	mRNA	1001	20660	.	+	.	FI_gene_label "PTEN^ENSG00000171862.11"  ; ID "PTEN--AUNIP^ENST00000371953.8"  ; Parent "PTEN--AUNIP^PTEN^ENSG00000171862.11"  ; ccdsid "CCDS31238.1"  ; exon_id "ENSE00001456562.4"  ; exon_number 1 ; gene_id "PTEN--AUNIP^PTEN^ENSG00000171862.11"  ; gene_name PTEN ; gene_type protein_coding ; havana_gene "OTTHUMG00000018688.3"  ; havana_transcript "OTTHUMT00000049241.2"  ; hgnc_id "HGNC:9588"  ; level 2 ; orig_coord_info "chr10,87864470,87864548,+"  ; protein_id "ENSP00000361021.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTEN--AUNIP^ENST00000371953.8"  ; transcript_name "PTEN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTEN--AUNIP	HAVANA	gene	23662	27822	.	+	.	FI_gene_label "AUNIP^ENSG00000127423.11"  ; ID "PTEN--AUNIP^AUNIP^ENSG00000127423.11"  ; ccdsid "CCDS266.1"  ; exon_id "ENSE00001463075.4"  ; exon_number 1 ; gene_id "PTEN--AUNIP^AUNIP^ENSG00000127423.11"  ; gene_name AUNIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000007372.2"  ; havana_transcript "OTTHUMT00000019309.2"  ; hgnc_id "HGNC:28363"  ; level 2 ; orig_coord_info "chr1,25859280,25859357,-"  ; protein_id "ENSP00000363416.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTEN--AUNIP^ENST00000374298.4"  ; transcript_name "AUNIP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PTEN--AUNIP	HAVANA	mRNA	23662	27822	.	+	.	FI_gene_label "AUNIP^ENSG00000127423.11"  ; ID "PTEN--AUNIP^ENST00000374298.4"  ; Parent "PTEN--AUNIP^AUNIP^ENSG00000127423.11"  ; ccdsid "CCDS266.1"  ; exon_id "ENSE00001463075.4"  ; exon_number 1 ; gene_id "PTEN--AUNIP^AUNIP^ENSG00000127423.11"  ; gene_name AUNIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000007372.2"  ; havana_transcript "OTTHUMT00000019309.2"  ; hgnc_id "HGNC:28363"  ; level 2 ; orig_coord_info "chr1,25859280,25859357,-"  ; protein_id "ENSP00000363416.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTEN--AUNIP^ENST00000374298.4"  ; transcript_name "AUNIP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TANC1--TMEM266	HAVANA	gene	1001	36624	.	+	.	FI_gene_label "TANC1^ENSG00000115183.15"  ; ID "TANC1--TMEM266^TANC1^ENSG00000115183.15"  ; ccdsid "CCDS42766.1"  ; exon_id "ENSE00003715868.1"  ; exon_number 3 ; gene_id "TANC1--TMEM266^TANC1^ENSG00000115183.15"  ; gene_name TANC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153945.3"  ; havana_transcript "OTTHUMT00000333135.2"  ; hgnc_id "HGNC:29364"  ; level 2 ; orig_coord_info "chr2,159065911,159065971,+"  ; protein_id "ENSP00000263635.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TANC1--TMEM266^ENST00000263635.8"  ; transcript_name "TANC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TANC1--TMEM266	HAVANA	mRNA	1001	36624	.	+	.	FI_gene_label "TANC1^ENSG00000115183.15"  ; ID "TANC1--TMEM266^ENST00000263635.8"  ; Parent "TANC1--TMEM266^TANC1^ENSG00000115183.15"  ; ccdsid "CCDS42766.1"  ; exon_id "ENSE00003715868.1"  ; exon_number 3 ; gene_id "TANC1--TMEM266^TANC1^ENSG00000115183.15"  ; gene_name TANC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153945.3"  ; havana_transcript "OTTHUMT00000333135.2"  ; hgnc_id "HGNC:29364"  ; level 2 ; orig_coord_info "chr2,159065911,159065971,+"  ; protein_id "ENSP00000263635.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TANC1--TMEM266^ENST00000263635.8"  ; transcript_name "TANC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TANC1--TMEM266	HAVANA	gene	39652	56859	.	+	.	FI_gene_label "TMEM266^ENSG00000169758.13"  ; ID "TANC1--TMEM266^TMEM266^ENSG00000169758.13"  ; ccdsid "CCDS10289.2"  ; exon_id "ENSE00002569427.1"  ; exon_number 2 ; gene_id "TANC1--TMEM266^TMEM266^ENSG00000169758.13"  ; gene_name TMEM266 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142918.7"  ; havana_transcript "OTTHUMT00000286637.3"  ; hgnc_id "HGNC:26763"  ; level 1 ; orig_coord_info "chr15,76134264,76134301,+"  ; protein_id "ENSP00000373594.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "TANC1--TMEM266^ENST00000388942.8"  ; transcript_name "TMEM266-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TANC1--TMEM266	HAVANA	mRNA	39652	56859	.	+	.	FI_gene_label "TMEM266^ENSG00000169758.13"  ; ID "TANC1--TMEM266^ENST00000388942.8"  ; Parent "TANC1--TMEM266^TMEM266^ENSG00000169758.13"  ; ccdsid "CCDS10289.2"  ; exon_id "ENSE00002569427.1"  ; exon_number 2 ; gene_id "TANC1--TMEM266^TMEM266^ENSG00000169758.13"  ; gene_name TMEM266 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142918.7"  ; havana_transcript "OTTHUMT00000286637.3"  ; hgnc_id "HGNC:26763"  ; level 1 ; orig_coord_info "chr15,76134264,76134301,+"  ; protein_id "ENSP00000373594.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "TANC1--TMEM266^ENST00000388942.8"  ; transcript_name "TMEM266-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TMPRSS2--ERG	HAVANA	gene	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ENST00000288319.12"  ; Parent "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMPRSS2--ERG	HAVANA	gene	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^ENST00000332149.10"  ; Parent "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTC6--TTLL5	ENSEMBL	gene	25637	41624	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTC6--TTLL5^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTC6--TTLL5^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTC6--TTLL5^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TTC6--TTLL5	ENSEMBL	mRNA	25637	41624	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTC6--TTLL5^ENST00000267368.11"  ; Parent "TTC6--TTLL5^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTC6--TTLL5^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTC6--TTLL5^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TTC6--TTLL5	HAVANA	gene	57609	70098	.	+	.	FI_gene_label "TTLL5^ENSG00000119685.20"  ; ID "TTC6--TTLL5^TTLL5^ENSG00000119685.20"  ; exon_id "ENSE00003625930.1"  ; exon_number 2 ; gene_id "TTC6--TTLL5^TTLL5^ENSG00000119685.20"  ; gene_name TTLL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171611.6"  ; havana_transcript "OTTHUMT00000414452.1"  ; hgnc_id "HGNC:19963"  ; level 2 ; orig_coord_info "chr14,75663150,75663223,+"  ; protein_id "ENSP00000286650.5"  ; tag basic ; transcript_id "TTC6--TTLL5^ENST00000286650.9"  ; transcript_name "TTLL5-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TTC6--TTLL5	HAVANA	mRNA	57609	70098	.	+	.	FI_gene_label "TTLL5^ENSG00000119685.20"  ; ID "TTC6--TTLL5^ENST00000286650.9"  ; Parent "TTC6--TTLL5^TTLL5^ENSG00000119685.20"  ; exon_id "ENSE00003625930.1"  ; exon_number 2 ; gene_id "TTC6--TTLL5^TTLL5^ENSG00000119685.20"  ; gene_name TTLL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171611.6"  ; havana_transcript "OTTHUMT00000414452.1"  ; hgnc_id "HGNC:19963"  ; level 2 ; orig_coord_info "chr14,75663150,75663223,+"  ; protein_id "ENSP00000286650.5"  ; tag basic ; transcript_id "TTC6--TTLL5^ENST00000286650.9"  ; transcript_name "TTLL5-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TTLL5--TTC6	ENSEMBL	gene	80500	96487	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTLL5--TTC6^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTLL5--TTC6^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTLL5--TTC6^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TTLL5--TTC6	ENSEMBL	mRNA	80500	96487	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "TTLL5--TTC6^ENST00000267368.11"  ; Parent "TTLL5--TTC6^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "TTLL5--TTC6^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "TTLL5--TTC6^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TTLL5--TTC6	HAVANA	gene	3463	15952	.	+	.	FI_gene_label "TTLL5^ENSG00000119685.20"  ; ID "TTLL5--TTC6^TTLL5^ENSG00000119685.20"  ; exon_id "ENSE00003625930.1"  ; exon_number 2 ; gene_id "TTLL5--TTC6^TTLL5^ENSG00000119685.20"  ; gene_name TTLL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171611.6"  ; havana_transcript "OTTHUMT00000414452.1"  ; hgnc_id "HGNC:19963"  ; level 2 ; orig_coord_info "chr14,75663150,75663223,+"  ; protein_id "ENSP00000286650.5"  ; tag basic ; transcript_id "TTLL5--TTC6^ENST00000286650.9"  ; transcript_name "TTLL5-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TTLL5--TTC6	HAVANA	mRNA	3463	15952	.	+	.	FI_gene_label "TTLL5^ENSG00000119685.20"  ; ID "TTLL5--TTC6^ENST00000286650.9"  ; Parent "TTLL5--TTC6^TTLL5^ENSG00000119685.20"  ; exon_id "ENSE00003625930.1"  ; exon_number 2 ; gene_id "TTLL5--TTC6^TTLL5^ENSG00000119685.20"  ; gene_name TTLL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171611.6"  ; havana_transcript "OTTHUMT00000414452.1"  ; hgnc_id "HGNC:19963"  ; level 2 ; orig_coord_info "chr14,75663150,75663223,+"  ; protein_id "ENSP00000286650.5"  ; tag basic ; transcript_id "TTLL5--TTC6^ENST00000286650.9"  ; transcript_name "TTLL5-201"  ; transcript_support_level 2 ; 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: 
ZFHX3--LINC01572	HAVANA	gene	21649	45862	.	+	.	FI_gene_label "ZFHX3^ENSG00000140836.17"  ; ID "ZFHX3--LINC01572^ZFHX3^ENSG00000140836.17"  ; ccdsid "CCDS10908.1"  ; exon_id "ENSE00001171638.5"  ; exon_number 2 ; gene_id "ZFHX3--LINC01572^ZFHX3^ENSG00000140836.17"  ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7"  ; havana_transcript "OTTHUMT00000269008.2"  ; hgnc_id "HGNC:777"  ; level 2 ; orig_coord_info "chr16,72957427,72960145,-"  ; protein_id "ENSP00000268489.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--LINC01572^ENST00000268489.10"  ; transcript_name "ZFHX3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFHX3--LINC01572	HAVANA	mRNA	21649	45862	.	+	.	FI_gene_label "ZFHX3^ENSG00000140836.17"  ; ID "ZFHX3--LINC01572^ENST00000268489.10"  ; Parent "ZFHX3--LINC01572^ZFHX3^ENSG00000140836.17"  ; ccdsid "CCDS10908.1"  ; exon_id "ENSE00001171638.5"  ; exon_number 2 ; gene_id "ZFHX3--LINC01572^ZFHX3^ENSG00000140836.17"  ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7"  ; havana_transcript "OTTHUMT00000269008.2"  ; hgnc_id "HGNC:777"  ; level 2 ; orig_coord_info "chr16,72957427,72960145,-"  ; protein_id "ENSP00000268489.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--LINC01572^ENST00000268489.10"  ; transcript_name "ZFHX3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF236--SYN2	HAVANA	gene	2107	41277	.	+	.	FI_gene_label "ZNF236^ENSG00000130856.17"  ; ID "ZNF236--SYN2^ZNF236^ENSG00000130856.17"  ; ccdsid "CCDS42447.1"  ; exon_id "ENSE00001349209.1"  ; exon_number 1 ; gene_id "ZNF236--SYN2^ZNF236^ENSG00000130856.17"  ; gene_name ZNF236 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179331.3"  ; havana_transcript "OTTHUMT00000445776.1"  ; hgnc_id "HGNC:13028"  ; level 2 ; orig_coord_info "chr18,76824358,76824406,+"  ; protein_id "ENSP00000253159.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF236--SYN2^ENST00000253159.12"  ; transcript_name "ZNF236-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF236--SYN2	HAVANA	mRNA	2107	41277	.	+	.	FI_gene_label "ZNF236^ENSG00000130856.17"  ; ID "ZNF236--SYN2^ENST00000253159.12"  ; Parent "ZNF236--SYN2^ZNF236^ENSG00000130856.17"  ; ccdsid "CCDS42447.1"  ; exon_id "ENSE00001349209.1"  ; exon_number 1 ; gene_id "ZNF236--SYN2^ZNF236^ENSG00000130856.17"  ; gene_name ZNF236 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179331.3"  ; havana_transcript "OTTHUMT00000445776.1"  ; hgnc_id "HGNC:13028"  ; level 2 ; orig_coord_info "chr18,76824358,76824406,+"  ; protein_id "ENSP00000253159.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF236--SYN2^ENST00000253159.12"  ; transcript_name "ZNF236-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF236--SYN2	HAVANA	gene	55874	62877	.	+	.	FI_gene_label "SYN2^ENSG00000157152.17"  ; ID "ZNF236--SYN2^SYN2^ENSG00000157152.17"  ; exon_id "ENSE00001771105.1"  ; exon_number 1 ; gene_id "ZNF236--SYN2^SYN2^ENSG00000157152.17"  ; gene_name SYN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155335.10"  ; havana_transcript "OTTHUMT00000339723.2"  ; hgnc_id "HGNC:11495"  ; level 2 ; orig_coord_info "chr3,12161545,12161608,+"  ; protein_id "ENSP00000480038.1"  ; tag mRNA_start_NF cds_start_NF not_organism_supported ; transcript_id "ZNF236--SYN2^ENST00000425297.2"  ; transcript_name "SYN2-202"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
ZNF236--SYN2	HAVANA	mRNA	55874	62877	.	+	.	FI_gene_label "SYN2^ENSG00000157152.17"  ; ID "ZNF236--SYN2^ENST00000425297.2"  ; Parent "ZNF236--SYN2^SYN2^ENSG00000157152.17"  ; exon_id "ENSE00001771105.1"  ; exon_number 1 ; gene_id "ZNF236--SYN2^SYN2^ENSG00000157152.17"  ; gene_name SYN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155335.10"  ; havana_transcript "OTTHUMT00000339723.2"  ; hgnc_id "HGNC:11495"  ; level 2 ; orig_coord_info "chr3,12161545,12161608,+"  ; protein_id "ENSP00000480038.1"  ; tag mRNA_start_NF cds_start_NF not_organism_supported ; transcript_id "ZNF236--SYN2^ENST00000425297.2"  ; transcript_name "SYN2-202"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
PDZRN3--LINC00877	HAVANA	gene	34006	38689	.	+	.	FI_gene_label "LINC00877^ENSG00000241163.8"  ; ID "PDZRN3--LINC00877^LINC00877^ENSG00000241163.8"  ; exon_id "ENSE00001812226.1"  ; exon_number 1 ; gene_id "PDZRN3--LINC00877^LINC00877^ENSG00000241163.8"  ; gene_name LINC00877 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158784.20"  ; havana_transcript "OTTHUMT00000352212.2"  ; hgnc_id "HGNC:27706"  ; level 2 ; orig_coord_info "chr3,72100788,72100869,-"  ; transcript_id "PDZRN3--LINC00877^ENST00000462492.5"  ; transcript_name "LINC00877-201"  ; transcript_support_level 3 ; transcript_type lncRNA
PDZRN3--LINC00877	HAVANA	RNA	34006	38689	.	+	.	FI_gene_label "LINC00877^ENSG00000241163.8"  ; ID "PDZRN3--LINC00877^ENST00000462492.5"  ; Parent "PDZRN3--LINC00877^LINC00877^ENSG00000241163.8"  ; exon_id "ENSE00001812226.1"  ; exon_number 1 ; gene_id "PDZRN3--LINC00877^LINC00877^ENSG00000241163.8"  ; gene_name LINC00877 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158784.20"  ; havana_transcript "OTTHUMT00000352212.2"  ; hgnc_id "HGNC:27706"  ; level 2 ; orig_coord_info "chr3,72100788,72100869,-"  ; transcript_id "PDZRN3--LINC00877^ENST00000462492.5"  ; transcript_name "LINC00877-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PDZRN3--RN7SL271P	ENSEMBL	gene	26094	26388	.	+	.	FI_gene_label "RN7SL271P^ENSG00000239250.3"  ; ID "PDZRN3--RN7SL271P^RN7SL271P^ENSG00000239250.3"  ; exon_id "ENSE00001835209.3"  ; exon_number 1 ; gene_id "PDZRN3--RN7SL271P^RN7SL271P^ENSG00000239250.3"  ; gene_name RN7SL271P ; gene_type misc_RNA ; hgnc_id "HGNC:46287"  ; level 3 ; orig_coord_info "chr3,71827177,71827471,+"  ; tag basic ; transcript_id "PDZRN3--RN7SL271P^ENST00000487601.3"  ; transcript_name "RN7SL271P-201"  ; transcript_support_level NA ; transcript_type misc_RNA
PDZRN3--RN7SL271P	ENSEMBL	RNA	26094	26388	.	+	.	FI_gene_label "RN7SL271P^ENSG00000239250.3"  ; ID "PDZRN3--RN7SL271P^ENST00000487601.3"  ; Parent "PDZRN3--RN7SL271P^RN7SL271P^ENSG00000239250.3"  ; exon_id "ENSE00001835209.3"  ; exon_number 1 ; gene_id "PDZRN3--RN7SL271P^RN7SL271P^ENSG00000239250.3"  ; gene_name RN7SL271P ; gene_type misc_RNA ; hgnc_id "HGNC:46287"  ; level 3 ; orig_coord_info "chr3,71827177,71827471,+"  ; tag basic ; transcript_id "PDZRN3--RN7SL271P^ENST00000487601.3"  ; transcript_name "RN7SL271P-201"  ; transcript_support_level NA ; transcript_type misc_RNA
L1 and L2 created: 
ZFHX3--LINC01572	HAVANA	gene	48873	65849	.	+	.	FI_gene_label "LINC01572^ENSG00000261008.7"  ; ID "ZFHX3--LINC01572^LINC01572^ENSG00000261008.7"  ; exon_id "ENSE00002594094.1"  ; exon_number 1 ; gene_id "ZFHX3--LINC01572^LINC01572^ENSG00000261008.7"  ; gene_name LINC01572 ; gene_type lncRNA ; havana_gene "OTTHUMG00000173457.17"  ; havana_transcript "OTTHUMT00000423195.2"  ; hgnc_id "HGNC:51385"  ; level 2 ; orig_coord_info "chr16,72664892,72665004,-"  ; tag basic ; transcript_id "ZFHX3--LINC01572^ENST00000561611.2"  ; transcript_name "LINC01572-201"  ; transcript_support_level 3 ; transcript_type lncRNA
ZFHX3--LINC01572	HAVANA	RNA	48873	65849	.	+	.	FI_gene_label "LINC01572^ENSG00000261008.7"  ; ID "ZFHX3--LINC01572^ENST00000561611.2"  ; Parent "ZFHX3--LINC01572^LINC01572^ENSG00000261008.7"  ; exon_id "ENSE00002594094.1"  ; exon_number 1 ; gene_id "ZFHX3--LINC01572^LINC01572^ENSG00000261008.7"  ; gene_name LINC01572 ; gene_type lncRNA ; havana_gene "OTTHUMG00000173457.17"  ; havana_transcript "OTTHUMT00000423195.2"  ; hgnc_id "HGNC:51385"  ; level 2 ; orig_coord_info "chr16,72664892,72665004,-"  ; tag basic ; transcript_id "ZFHX3--LINC01572^ENST00000561611.2"  ; transcript_name "LINC01572-201"  ; transcript_support_level 3 ; transcript_type lncRNA
428 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 ------------------------------
644 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

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

------------------------ Check12: all level1 locations -------------------------
We fixed 32 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed