.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (FFPE_V4_0001_RNA_0001_B23LG7FLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/b2ea0a49ea40fc416969cedb0c54d6/.command.out
Size: 68.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (FFPE_V4_0001_RNA_0001_B23LG7FLT4_1)
Attempt
Content

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 7479
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 7479
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:7479
  => 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: 
AC015911.9--SLFN12L	HAVANA	gene	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L	HAVANA	mRNA	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^ENST00000260908.12"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
BX571818.1--TMEM200A	HAVANA	gene	12785	22570	.	+	.	FI_gene_label "TMEM200A^ENSG00000164484.12"  ; ID "BX571818.1--TMEM200A^TMEM200A^ENSG00000164484.12"  ; ccdsid "CCDS5140.1"  ; exon_id "ENSE00001084680.4"  ; exon_number 3 ; gene_id "BX571818.1--TMEM200A^TMEM200A^ENSG00000164484.12"  ; gene_name TMEM200A ; gene_type protein_coding ; havana_gene "OTTHUMG00000015557.1"  ; havana_transcript "OTTHUMT00000042201.1"  ; hgnc_id "HGNC:21075"  ; level 2 ; orig_coord_info "chr6,130440423,130441895,+"  ; protein_id "ENSP00000296978.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BX571818.1--TMEM200A^ENST00000296978.4"  ; transcript_name "TMEM200A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BX571818.1--TMEM200A	HAVANA	mRNA	12785	22570	.	+	.	FI_gene_label "TMEM200A^ENSG00000164484.12"  ; ID "BX571818.1--TMEM200A^ENST00000296978.4"  ; Parent "BX571818.1--TMEM200A^TMEM200A^ENSG00000164484.12"  ; ccdsid "CCDS5140.1"  ; exon_id "ENSE00001084680.4"  ; exon_number 3 ; gene_id "BX571818.1--TMEM200A^TMEM200A^ENSG00000164484.12"  ; gene_name TMEM200A ; gene_type protein_coding ; havana_gene "OTTHUMG00000015557.1"  ; havana_transcript "OTTHUMT00000042201.1"  ; hgnc_id "HGNC:21075"  ; level 2 ; orig_coord_info "chr6,130440423,130441895,+"  ; protein_id "ENSP00000296978.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BX571818.1--TMEM200A^ENST00000296978.4"  ; transcript_name "TMEM200A-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: 
CD74--ROS1	HAVANA	gene	1219	9629	.	+	.	FI_gene_label "CD74^ENSG00000019582.16"  ; ID "CD74--ROS1^CD74^ENSG00000019582.16"  ; ccdsid "CCDS47309.1"  ; exon_id "ENSE00003588448.1"  ; exon_number 1 ; gene_id "CD74--ROS1^CD74^ENSG00000019582.16"  ; gene_name CD74 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163559.4"  ; havana_transcript "OTTHUMT00000374178.2"  ; hgnc_id "HGNC:1697"  ; level 2 ; orig_coord_info "chr5,150412625,150412749,-"  ; protein_id "ENSP00000009530.7"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "CD74--ROS1^ENST00000009530.12"  ; transcript_name "CD74-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CD74--ROS1	HAVANA	mRNA	1219	9629	.	+	.	FI_gene_label "CD74^ENSG00000019582.16"  ; ID "CD74--ROS1^ENST00000009530.12"  ; Parent "CD74--ROS1^CD74^ENSG00000019582.16"  ; ccdsid "CCDS47309.1"  ; exon_id "ENSE00003588448.1"  ; exon_number 1 ; gene_id "CD74--ROS1^CD74^ENSG00000019582.16"  ; gene_name CD74 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163559.4"  ; havana_transcript "OTTHUMT00000374178.2"  ; hgnc_id "HGNC:1697"  ; level 2 ; orig_coord_info "chr5,150412625,150412749,-"  ; protein_id "ENSP00000009530.7"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "CD74--ROS1^ENST00000009530.12"  ; transcript_name "CD74-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CD74--ROS1	HAVANA	gene	12630	60009	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "CD74--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "CD74--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "CD74--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CD74--ROS1	HAVANA	mRNA	12630	60009	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "CD74--ROS1^ENST00000368507.8"  ; Parent "CD74--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "CD74--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "CD74--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CDV3--MT-RNR2	HAVANA	gene	1001	8278	.	+	.	FI_gene_label "CDV3^ENSG00000091527.16"  ; ID "CDV3--MT-RNR2^CDV3^ENSG00000091527.16"  ; ccdsid "CCDS3079.1"  ; exon_id "ENSE00001346369.4"  ; exon_number 1 ; gene_id "CDV3--MT-RNR2^CDV3^ENSG00000091527.16"  ; gene_name CDV3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159764.13"  ; havana_transcript "OTTHUMT00000357203.1"  ; hgnc_id "HGNC:26928"  ; level 2 ; orig_coord_info "chr3,133574045,133574284,+"  ; protein_id "ENSP00000264993.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CDV3--MT-RNR2^ENST00000264993.8"  ; transcript_name "CDV3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CDV3--MT-RNR2	HAVANA	mRNA	1001	8278	.	+	.	FI_gene_label "CDV3^ENSG00000091527.16"  ; ID "CDV3--MT-RNR2^ENST00000264993.8"  ; Parent "CDV3--MT-RNR2^CDV3^ENSG00000091527.16"  ; ccdsid "CCDS3079.1"  ; exon_id "ENSE00001346369.4"  ; exon_number 1 ; gene_id "CDV3--MT-RNR2^CDV3^ENSG00000091527.16"  ; gene_name CDV3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159764.13"  ; havana_transcript "OTTHUMT00000357203.1"  ; hgnc_id "HGNC:26928"  ; level 2 ; orig_coord_info "chr3,133574045,133574284,+"  ; protein_id "ENSP00000264993.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CDV3--MT-RNR2^ENST00000264993.8"  ; transcript_name "CDV3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EGFR--SEPTIN14	HAVANA	gene	1001	40770	.	+	.	FI_gene_label "EGFR^ENSG00000146648.19"  ; ID "EGFR--SEPTIN14^EGFR^ENSG00000146648.19"  ; ccdsid "CCDS5514.1"  ; exon_id "ENSE00001841347.2"  ; exon_number 1 ; gene_id "EGFR--SEPTIN14^EGFR^ENSG00000146648.19"  ; gene_name EGFR ; gene_type protein_coding ; havana_gene "OTTHUMG00000023661.5"  ; havana_transcript "OTTHUMT00000251456.3"  ; hgnc_id "HGNC:3236"  ; level 2 ; orig_coord_info "chr7,55019278,55019365,+"  ; protein_id "ENSP00000275493.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EGFR--SEPTIN14^ENST00000275493.7"  ; transcript_name "EGFR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EGFR--SEPTIN14	HAVANA	mRNA	1001	40770	.	+	.	FI_gene_label "EGFR^ENSG00000146648.19"  ; ID "EGFR--SEPTIN14^ENST00000275493.7"  ; Parent "EGFR--SEPTIN14^EGFR^ENSG00000146648.19"  ; ccdsid "CCDS5514.1"  ; exon_id "ENSE00001841347.2"  ; exon_number 1 ; gene_id "EGFR--SEPTIN14^EGFR^ENSG00000146648.19"  ; gene_name EGFR ; gene_type protein_coding ; havana_gene "OTTHUMG00000023661.5"  ; havana_transcript "OTTHUMT00000251456.3"  ; hgnc_id "HGNC:3236"  ; level 2 ; orig_coord_info "chr7,55019278,55019365,+"  ; protein_id "ENSP00000275493.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EGFR--SEPTIN14^ENST00000275493.7"  ; transcript_name "EGFR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EGFR--SEPTIN14	HAVANA	gene	43774	57321	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "EGFR--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "EGFR--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EGFR--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
EGFR--SEPTIN14	HAVANA	mRNA	43774	57321	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "EGFR--SEPTIN14^ENST00000388975.4"  ; Parent "EGFR--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "EGFR--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EGFR--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
EML4--ALK	HAVANA	gene	1001	31063	.	+	.	FI_gene_label "EML4^ENSG00000143924.19"  ; ID "EML4--ALK^EML4^ENSG00000143924.19"  ; ccdsid "CCDS1807.1"  ; exon_id "ENSE00001548738.1"  ; exon_number 1 ; gene_id "EML4--ALK^EML4^ENSG00000143924.19"  ; gene_name EML4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128603.7"  ; havana_transcript "OTTHUMT00000250463.4"  ; hgnc_id "HGNC:1316"  ; level 2 ; orig_coord_info "chr2,42169612,42169636,+"  ; protein_id "ENSP00000320663.5"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "EML4--ALK^ENST00000318522.10"  ; transcript_name "EML4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EML4--ALK	HAVANA	mRNA	1001	31063	.	+	.	FI_gene_label "EML4^ENSG00000143924.19"  ; ID "EML4--ALK^ENST00000318522.10"  ; Parent "EML4--ALK^EML4^ENSG00000143924.19"  ; ccdsid "CCDS1807.1"  ; exon_id "ENSE00001548738.1"  ; exon_number 1 ; gene_id "EML4--ALK^EML4^ENSG00000143924.19"  ; gene_name EML4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128603.7"  ; havana_transcript "OTTHUMT00000250463.4"  ; hgnc_id "HGNC:1316"  ; level 2 ; orig_coord_info "chr2,42169612,42169636,+"  ; protein_id "ENSP00000320663.5"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "EML4--ALK^ENST00000318522.10"  ; transcript_name "EML4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EML4--ALK	HAVANA	gene	34064	69068	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "EML4--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "EML4--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EML4--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EML4--ALK	HAVANA	mRNA	34064	69068	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "EML4--ALK^ENST00000389048.8"  ; Parent "EML4--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "EML4--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EML4--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ETV6--NTRK3	HAVANA	gene	13392	15151	.	+	.	FI_gene_label "ETV6^ENSG00000139083.11"  ; ID "ETV6--NTRK3^ETV6^ENSG00000139083.11"  ; exon_id "ENSE00002245284.1"  ; exon_number 1 ; gene_id "ETV6--NTRK3^ETV6^ENSG00000139083.11"  ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3"  ; havana_transcript "OTTHUMT00000400134.1"  ; hgnc_id "HGNC:3495"  ; level 2 ; orig_coord_info "chr12,11885937,11886026,+"  ; protein_id "ENSP00000266427.3"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--NTRK3^ENST00000266427.3"  ; transcript_name "ETV6-201"  ; transcript_support_level 3 ; transcript_type protein_coding
ETV6--NTRK3	HAVANA	mRNA	13392	15151	.	+	.	FI_gene_label "ETV6^ENSG00000139083.11"  ; ID "ETV6--NTRK3^ENST00000266427.3"  ; Parent "ETV6--NTRK3^ETV6^ENSG00000139083.11"  ; exon_id "ENSE00002245284.1"  ; exon_number 1 ; gene_id "ETV6--NTRK3^ETV6^ENSG00000139083.11"  ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3"  ; havana_transcript "OTTHUMT00000400134.1"  ; hgnc_id "HGNC:3495"  ; level 2 ; orig_coord_info "chr12,11885937,11886026,+"  ; protein_id "ENSP00000266427.3"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--NTRK3^ENST00000266427.3"  ; transcript_name "ETV6-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
ETV6--NTRK3	HAVANA	gene	22528	45237	.	+	.	FI_gene_label "NTRK3^ENSG00000140538.16"  ; ID "ETV6--NTRK3^NTRK3^ENSG00000140538.16"  ; ccdsid "CCDS32323.1"  ; exon_id "ENSE00002296343.1"  ; exon_number 1 ; gene_id "ETV6--NTRK3^NTRK3^ENSG00000140538.16"  ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12"  ; havana_transcript "OTTHUMT00000403049.3"  ; hgnc_id "HGNC:8033"  ; level 2 ; orig_coord_info "chr15,88255906,88256153,-"  ; protein_id "ENSP00000318328.3"  ; tag basic CCDS ; transcript_id "ETV6--NTRK3^ENST00000317501.7"  ; transcript_name "NTRK3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ETV6--NTRK3	HAVANA	mRNA	22528	45237	.	+	.	FI_gene_label "NTRK3^ENSG00000140538.16"  ; ID "ETV6--NTRK3^ENST00000317501.7"  ; Parent "ETV6--NTRK3^NTRK3^ENSG00000140538.16"  ; ccdsid "CCDS32323.1"  ; exon_id "ENSE00002296343.1"  ; exon_number 1 ; gene_id "ETV6--NTRK3^NTRK3^ENSG00000140538.16"  ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12"  ; havana_transcript "OTTHUMT00000403049.3"  ; hgnc_id "HGNC:8033"  ; level 2 ; orig_coord_info "chr15,88255906,88256153,-"  ; protein_id "ENSP00000318328.3"  ; tag basic CCDS ; transcript_id "ETV6--NTRK3^ENST00000317501.7"  ; transcript_name "NTRK3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FGFR3--BAIAP2L1	HAVANA	gene	14817	31823	.	+	.	FI_gene_label "BAIAP2L1^ENSG00000006453.14"  ; ID "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; ccdsid "CCDS34687.1"  ; exon_id "ENSE00003618813.2"  ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2"  ; havana_transcript "OTTHUMT00000334681.2"  ; hgnc_id "HGNC:21649"  ; level 2 ; orig_coord_info "chr7,98400802,98400852,-"  ; protein_id "ENSP00000005260.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9"  ; transcript_name "BAIAP2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--BAIAP2L1	HAVANA	mRNA	14817	31823	.	+	.	FI_gene_label "BAIAP2L1^ENSG00000006453.14"  ; ID "FGFR3--BAIAP2L1^ENST00000005260.9"  ; Parent "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; ccdsid "CCDS34687.1"  ; exon_id "ENSE00003618813.2"  ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2"  ; havana_transcript "OTTHUMT00000334681.2"  ; hgnc_id "HGNC:21649"  ; level 2 ; orig_coord_info "chr7,98400802,98400852,-"  ; protein_id "ENSP00000005260.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9"  ; transcript_name "BAIAP2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FGFR3--BAIAP2L1	HAVANA	gene	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--BAIAP2L1^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--BAIAP2L1	HAVANA	mRNA	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--BAIAP2L1^ENST00000260795.8"  ; Parent "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--BAIAP2L1^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGFR3--TACC3	HAVANA	gene	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3	HAVANA	mRNA	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^ENST00000260795.8"  ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGFR3--TACC3	HAVANA	gene	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3	HAVANA	mRNA	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^ENST00000313288.9"  ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KIF5B--RET	HAVANA	gene	1001	24630	.	+	.	FI_gene_label "KIF5B^ENSG00000170759.11"  ; ID "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; ccdsid "CCDS7171.1"  ; exon_id "ENSE00001551533.4"  ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2"  ; havana_transcript "OTTHUMT00000047467.2"  ; hgnc_id "HGNC:6324"  ; level 2 ; orig_coord_info "chr10,32055848,32055973,-"  ; protein_id "ENSP00000307078.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5"  ; transcript_name "KIF5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET	HAVANA	mRNA	1001	24630	.	+	.	FI_gene_label "KIF5B^ENSG00000170759.11"  ; ID "KIF5B--RET^ENST00000302418.5"  ; Parent "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; ccdsid "CCDS7171.1"  ; exon_id "ENSE00001551533.4"  ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2"  ; havana_transcript "OTTHUMT00000047467.2"  ; hgnc_id "HGNC:6324"  ; level 2 ; orig_coord_info "chr10,32055848,32055973,-"  ; protein_id "ENSP00000307078.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5"  ; transcript_name "KIF5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KIF5B--RET	HAVANA	gene	27636	48256	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "KIF5B--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "KIF5B--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 "KIF5B--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET	HAVANA	mRNA	27636	48256	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "KIF5B--RET^ENST00000340058.6"  ; Parent "KIF5B--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "KIF5B--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 "KIF5B--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LMNA--NTRK1	HAVANA	gene	31461	45545	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
LMNA--NTRK1	HAVANA	mRNA	31461	45545	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "LMNA--NTRK1^ENST00000358660.3"  ; Parent "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
LMNA--NTRK1	HAVANA	gene	11719	23624	.	+	.	FI_gene_label "LMNA^ENSG00000160789.23"  ; ID "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; ccdsid "CCDS1129.1"  ; exon_id "ENSE00001554780.1"  ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6"  ; hgnc_id "HGNC:6636"  ; level 2 ; orig_coord_info "chr1,156114919,156115274,+"  ; protein_id "ENSP00000355292.6"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9"  ; transcript_name "LMNA-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LMNA--NTRK1	HAVANA	mRNA	11719	23624	.	+	.	FI_gene_label "LMNA^ENSG00000160789.23"  ; ID "LMNA--NTRK1^ENST00000361308.9"  ; Parent "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; ccdsid "CCDS1129.1"  ; exon_id "ENSE00001554780.1"  ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6"  ; hgnc_id "HGNC:6636"  ; level 2 ; orig_coord_info "chr1,156114919,156115274,+"  ; protein_id "ENSP00000355292.6"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9"  ; transcript_name "LMNA-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NCOA4--RET	HAVANA	gene	17674	38294	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "NCOA4--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "NCOA4--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 "NCOA4--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NCOA4--RET	HAVANA	mRNA	17674	38294	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "NCOA4--RET^ENST00000340058.6"  ; Parent "NCOA4--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "NCOA4--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 "NCOA4--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NCOA4--RET	HAVANA	gene	1017	13344	.	+	.	FI_gene_label "NCOA4^ENSG00000266412.6"  ; ID "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; ccdsid "CCDS73094.1"  ; exon_id "ENSE00002732991.1"  ; exon_number 2 ; gene_id "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; gene_name NCOA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188314.1"  ; havana_transcript "OTTHUMT00000476878.1"  ; hgnc_id "HGNC:7671"  ; level 2 ; orig_coord_info "chr10,46027432,46027465,-"  ; protein_id "ENSP00000463027.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NCOA4--RET^ENST00000578454.5"  ; transcript_name "NCOA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NCOA4--RET	HAVANA	mRNA	1017	13344	.	+	.	FI_gene_label "NCOA4^ENSG00000266412.6"  ; ID "NCOA4--RET^ENST00000578454.5"  ; Parent "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; ccdsid "CCDS73094.1"  ; exon_id "ENSE00002732991.1"  ; exon_number 2 ; gene_id "NCOA4--RET^NCOA4^ENSG00000266412.6"  ; gene_name NCOA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188314.1"  ; havana_transcript "OTTHUMT00000476878.1"  ; hgnc_id "HGNC:7671"  ; level 2 ; orig_coord_info "chr10,46027432,46027465,-"  ; protein_id "ENSP00000463027.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NCOA4--RET^ENST00000578454.5"  ; transcript_name "NCOA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPM1--MT-RNR2	HAVANA	gene	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4"  ; havana_transcript "OTTHUMT00000252858.2"  ; hgnc_id "HGNC:7910"  ; level 2 ; orig_coord_info "chr5,171387949,171388006,+"  ; protein_id "ENSP00000296930.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPM1--MT-RNR2	HAVANA	mRNA	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--MT-RNR2^ENST00000296930.10"  ; Parent "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4"  ; havana_transcript "OTTHUMT00000252858.2"  ; hgnc_id "HGNC:7910"  ; level 2 ; orig_coord_info "chr5,171387949,171388006,+"  ; protein_id "ENSP00000296930.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAX8--PPARG	ENSEMBL	gene	1001	17422	.	+	.	FI_gene_label "PAX8^ENSG00000125618.18"  ; ID "PAX8--PPARG^PAX8^ENSG00000125618.18"  ; ccdsid "CCDS46398.1"  ; exon_id "ENSE00002299701.2"  ; exon_number 2 ; gene_id "PAX8--PPARG^PAX8^ENSG00000125618.18"  ; gene_name PAX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128529.12"  ; hgnc_id "HGNC:8622"  ; level 3 ; orig_coord_info "chr2,113278370,113278394,-"  ; protein_id "ENSP00000263334.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "PAX8--PPARG^ENST00000263334.9"  ; transcript_name "PAX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAX8--PPARG	ENSEMBL	mRNA	1001	17422	.	+	.	FI_gene_label "PAX8^ENSG00000125618.18"  ; ID "PAX8--PPARG^ENST00000263334.9"  ; Parent "PAX8--PPARG^PAX8^ENSG00000125618.18"  ; ccdsid "CCDS46398.1"  ; exon_id "ENSE00002299701.2"  ; exon_number 2 ; gene_id "PAX8--PPARG^PAX8^ENSG00000125618.18"  ; gene_name PAX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128529.12"  ; hgnc_id "HGNC:8622"  ; level 3 ; orig_coord_info "chr2,113278370,113278394,-"  ; protein_id "ENSP00000263334.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "PAX8--PPARG^ENST00000263334.9"  ; transcript_name "PAX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAX8--PPARG	HAVANA	gene	28940	39958	.	+	.	FI_gene_label "PPARG^ENSG00000132170.23"  ; ID "PAX8--PPARG^PPARG^ENSG00000132170.23"  ; ccdsid "CCDS2609.1"  ; exon_id "ENSE00003683648.1"  ; exon_number 1 ; gene_id "PAX8--PPARG^PPARG^ENSG00000132170.23"  ; gene_name PPARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000129764.15"  ; havana_transcript "OTTHUMT00000251979.2"  ; hgnc_id "HGNC:9236"  ; level 2 ; orig_coord_info "chr3,12351593,12351674,+"  ; protein_id "ENSP00000287820.6"  ; tag basic CCDS ; transcript_id "PAX8--PPARG^ENST00000287820.10"  ; transcript_name "PPARG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAX8--PPARG	HAVANA	mRNA	28940	39958	.	+	.	FI_gene_label "PPARG^ENSG00000132170.23"  ; ID "PAX8--PPARG^ENST00000287820.10"  ; Parent "PAX8--PPARG^PPARG^ENSG00000132170.23"  ; ccdsid "CCDS2609.1"  ; exon_id "ENSE00003683648.1"  ; exon_number 1 ; gene_id "PAX8--PPARG^PPARG^ENSG00000132170.23"  ; gene_name PPARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000129764.15"  ; havana_transcript "OTTHUMT00000251979.2"  ; hgnc_id "HGNC:9236"  ; level 2 ; orig_coord_info "chr3,12351593,12351674,+"  ; protein_id "ENSP00000287820.6"  ; tag basic CCDS ; transcript_id "PAX8--PPARG^ENST00000287820.10"  ; transcript_name "PPARG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLC34A2--ROS1	HAVANA	gene	21924	69303	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "SLC34A2--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SLC34A2--ROS1	HAVANA	mRNA	21924	69303	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "SLC34A2--ROS1^ENST00000368507.8"  ; Parent "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "SLC34A2--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SLC34A2--ROS1	HAVANA	gene	2897	18923	.	+	.	FI_gene_label "SLC34A2^ENSG00000157765.13"  ; ID "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; ccdsid "CCDS3435.1"  ; exon_id "ENSE00001034812.5"  ; exon_number 2 ; gene_id "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; gene_name SLC34A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097757.6"  ; havana_transcript "OTTHUMT00000214990.2"  ; hgnc_id "HGNC:11020"  ; level 2 ; orig_coord_info "chr4,25662501,25662612,+"  ; protein_id "ENSP00000371483.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "SLC34A2--ROS1^ENST00000382051.8"  ; transcript_name "SLC34A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC34A2--ROS1	HAVANA	mRNA	2897	18923	.	+	.	FI_gene_label "SLC34A2^ENSG00000157765.13"  ; ID "SLC34A2--ROS1^ENST00000382051.8"  ; Parent "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; ccdsid "CCDS3435.1"  ; exon_id "ENSE00001034812.5"  ; exon_number 2 ; gene_id "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; gene_name SLC34A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097757.6"  ; havana_transcript "OTTHUMT00000214990.2"  ; hgnc_id "HGNC:11020"  ; level 2 ; orig_coord_info "chr4,25662501,25662612,+"  ; protein_id "ENSP00000371483.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "SLC34A2--ROS1^ENST00000382051.8"  ; transcript_name "SLC34A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLC45A3--BRAF	HAVANA	gene	11161	45033	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "SLC45A3--BRAF^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "SLC45A3--BRAF^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "SLC45A3--BRAF^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC45A3--BRAF	HAVANA	mRNA	11161	45033	.	+	.	FI_gene_label "BRAF^ENSG00000157764.14"  ; ID "SLC45A3--BRAF^ENST00000288602.11"  ; Parent "SLC45A3--BRAF^BRAF^ENSG00000157764.14"  ; exon_id "ENSE00003826734.1"  ; exon_number 1 ; gene_id "SLC45A3--BRAF^BRAF^ENSG00000157764.14"  ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6"  ; havana_transcript "OTTHUMT00000496651.1"  ; hgnc_id "HGNC:1097"  ; level 2 ; orig_coord_info "chr7,140924566,140924703,-"  ; protein_id "ENSP00000288602.7"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "SLC45A3--BRAF^ENST00000288602.11"  ; transcript_name "BRAF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLC45A3--BRAF	HAVANA	gene	1001	7963	.	+	.	FI_gene_label "SLC45A3^ENSG00000158715.6"  ; ID "SLC45A3--BRAF^SLC45A3^ENSG00000158715.6"  ; ccdsid "CCDS1458.1"  ; exon_id "ENSE00001443627.1"  ; exon_number 2 ; gene_id "SLC45A3--BRAF^SLC45A3^ENSG00000158715.6"  ; gene_name SLC45A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037223.2"  ; havana_transcript "OTTHUMT00000090619.2"  ; hgnc_id "HGNC:8642"  ; level 2 ; orig_coord_info "chr1,205664485,205664656,-"  ; protein_id "ENSP00000356113.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC45A3--BRAF^ENST00000367145.4"  ; transcript_name "SLC45A3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC45A3--BRAF	HAVANA	mRNA	1001	7963	.	+	.	FI_gene_label "SLC45A3^ENSG00000158715.6"  ; ID "SLC45A3--BRAF^ENST00000367145.4"  ; Parent "SLC45A3--BRAF^SLC45A3^ENSG00000158715.6"  ; ccdsid "CCDS1458.1"  ; exon_id "ENSE00001443627.1"  ; exon_number 2 ; gene_id "SLC45A3--BRAF^SLC45A3^ENSG00000158715.6"  ; gene_name SLC45A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037223.2"  ; havana_transcript "OTTHUMT00000090619.2"  ; hgnc_id "HGNC:8642"  ; level 2 ; orig_coord_info "chr1,205664485,205664656,-"  ; protein_id "ENSP00000356113.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC45A3--BRAF^ENST00000367145.4"  ; transcript_name "SLC45A3-201"  ; 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: 
TFG--NTRK1	HAVANA	gene	1200	22113	.	+	.	FI_gene_label "TFG^ENSG00000114354.15"  ; ID "TFG--NTRK1^TFG^ENSG00000114354.15"  ; ccdsid "CCDS2939.1"  ; exon_id "ENSE00000967215.3"  ; exon_number 2 ; gene_id "TFG--NTRK1^TFG^ENSG00000114354.15"  ; gene_name TFG ; gene_type protein_coding ; havana_gene "OTTHUMG00000159085.4"  ; havana_transcript "OTTHUMT00000353242.2"  ; hgnc_id "HGNC:11758"  ; level 2 ; orig_coord_info "chr3,100713686,100713869,+"  ; protein_id "ENSP00000240851.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TFG--NTRK1^ENST00000240851.9"  ; transcript_name "TFG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TFG--NTRK1	HAVANA	mRNA	1200	22113	.	+	.	FI_gene_label "TFG^ENSG00000114354.15"  ; ID "TFG--NTRK1^ENST00000240851.9"  ; Parent "TFG--NTRK1^TFG^ENSG00000114354.15"  ; ccdsid "CCDS2939.1"  ; exon_id "ENSE00000967215.3"  ; exon_number 2 ; gene_id "TFG--NTRK1^TFG^ENSG00000114354.15"  ; gene_name TFG ; gene_type protein_coding ; havana_gene "OTTHUMG00000159085.4"  ; havana_transcript "OTTHUMT00000353242.2"  ; hgnc_id "HGNC:11758"  ; level 2 ; orig_coord_info "chr3,100713686,100713869,+"  ; protein_id "ENSP00000240851.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TFG--NTRK1^ENST00000240851.9"  ; transcript_name "TFG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TFG--NTRK1	HAVANA	gene	29162	43246	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TFG--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TFG--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TFG--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TFG--NTRK1	HAVANA	mRNA	29162	43246	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TFG--NTRK1^ENST00000358660.3"  ; Parent "TFG--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TFG--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TFG--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; 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: 
TPM3--NTRK1	HAVANA	gene	2360	24514	.	+	.	FI_gene_label "TPM3^ENSG00000143549.21"  ; ID "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; exon_id "ENSE00002024480.1"  ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12"  ; havana_transcript "OTTHUMT00000360295.1"  ; hgnc_id "HGNC:12012"  ; level 2 ; orig_coord_info "chr1,154191902,154192018,-"  ; protein_id "ENSP00000271850.7"  ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11"  ; transcript_name "TPM3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TPM3--NTRK1	HAVANA	mRNA	2360	24514	.	+	.	FI_gene_label "TPM3^ENSG00000143549.21"  ; ID "TPM3--NTRK1^ENST00000271850.11"  ; Parent "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; exon_id "ENSE00002024480.1"  ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12"  ; havana_transcript "OTTHUMT00000360295.1"  ; hgnc_id "HGNC:12012"  ; level 2 ; orig_coord_info "chr1,154191902,154192018,-"  ; protein_id "ENSP00000271850.7"  ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11"  ; transcript_name "TPM3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TPM3--NTRK1	HAVANA	gene	33577	47661	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TPM3--NTRK1	HAVANA	mRNA	33577	47661	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM3--NTRK1^ENST00000358660.3"  ; Parent "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; 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: 
AC015911.9--SLFN12L	HAVANA	gene	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L	HAVANA	RNA	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^ENST00000650652.2"  ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC015911.9--SLFN12L	ENSEMBL	gene	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
AC015911.9--SLFN12L	ENSEMBL	RNA	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^ENST00000675965.1"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
L1 and L2 created: 
BX571818.1--TMEM200A	HAVANA	gene	8685	9440	.	+	.	FI_gene_label "BX571818.1^ENSG00000285417.1"  ; ID "BX571818.1--TMEM200A^BX571818.1^ENSG00000285417.1"  ; exon_id "ENSE00002709709.1"  ; exon_number 1 ; gene_id "BX571818.1--TMEM200A^BX571818.1^ENSG00000285417.1"  ; gene_name "BX571818.1"  ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000184376.4"  ; havana_transcript "OTTHUMT00000468663.1"  ; level 2 ; orig_coord_info "chr1,206061158,206061397,+"  ; transcript_id "BX571818.1--TMEM200A^ENST00000577298.1"  ; transcript_name "BX571818.1-208"  ; transcript_support_level 2 ; transcript_type processed_transcript
BX571818.1--TMEM200A	HAVANA	RNA	8685	9440	.	+	.	FI_gene_label "BX571818.1^ENSG00000285417.1"  ; ID "BX571818.1--TMEM200A^ENST00000577298.1"  ; Parent "BX571818.1--TMEM200A^BX571818.1^ENSG00000285417.1"  ; exon_id "ENSE00002709709.1"  ; exon_number 1 ; gene_id "BX571818.1--TMEM200A^BX571818.1^ENSG00000285417.1"  ; gene_name "BX571818.1"  ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000184376.4"  ; havana_transcript "OTTHUMT00000468663.1"  ; level 2 ; orig_coord_info "chr1,206061158,206061397,+"  ; transcript_id "BX571818.1--TMEM200A^ENST00000577298.1"  ; transcript_name "BX571818.1-208"  ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created: 
CDV3--MT-RNR2	ENSEMBL	gene	11279	12837	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "CDV3--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "CDV3--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "CDV3--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
CDV3--MT-RNR2	ENSEMBL	RNA	11279	12837	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "CDV3--MT-RNR2^ENST00000387347.2"  ; Parent "CDV3--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "CDV3--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "CDV3--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
L1 and L2 created: 
IGL@-ext--MT-RNR2	ENSEMBL	gene	896102	897660	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "IGL@-ext--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "IGL@-ext--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "IGL@-ext--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
IGL@-ext--MT-RNR2	ENSEMBL	RNA	896102	897660	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "IGL@-ext--MT-RNR2^ENST00000387347.2"  ; Parent "IGL@-ext--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "IGL@-ext--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "IGL@-ext--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
L1 and L2 created: 
IGL@-ext--MT-RNR2	SuperLocus-ext	gene	1001	893101	.	+	.	FI_gene_label "IGL@-ext^IGL.g@-ext"  ; ID "IGL@-ext--MT-RNR2^IGL@-ext^IGL.g@-ext"  ; gene_id "IGL@-ext--MT-RNR2^IGL@-ext^IGL.g@-ext"  ; gene_name "IGL@-ext"  ; orig_coord_info "chr22,22030934,22923034,+"  ; transcript_id "IGL@-ext--MT-RNR2^IGL.t@-ext" 
IGL@-ext--MT-RNR2	SuperLocus-ext	RNA	1001	893101	.	+	.	FI_gene_label "IGL@-ext^IGL.g@-ext"  ; ID "IGL@-ext--MT-RNR2^IGL.t@-ext"  ; Parent "IGL@-ext--MT-RNR2^IGL@-ext^IGL.g@-ext"  ; gene_id "IGL@-ext--MT-RNR2^IGL@-ext^IGL.g@-ext"  ; gene_name "IGL@-ext"  ; orig_coord_info "chr22,22030934,22923034,+"  ; transcript_id "IGL@-ext--MT-RNR2^IGL.t@-ext" 
L1 and L2 created: 
NPM1--MT-RNR2	ENSEMBL	gene	18634	20192	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
NPM1--MT-RNR2	ENSEMBL	RNA	18634	20192	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "NPM1--MT-RNR2^ENST00000387347.2"  ; Parent "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
494 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 ------------------------------
1198 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 29 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