.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-4fd42c-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/6b45397fafd0002253569798c10c70/.command.log
Size: 67.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-4fd42c-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/629355a3635c55efc941e0bcc1f6ad/fi_workdir/aih-tih-sc-4fd42c-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/6b45397fafd0002253569798c10c70/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/6b45397fafd0002253569798c10c70/.command.run
==> STAGING COMPLETE (3 inputs)

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 5399
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5399
=> 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:5399
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 1 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
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: 
AHNAK--GANAB	HAVANA	gene	2086	27428	.	+	.	FI_gene_label "AHNAK^ENSG00000124942.14"  ; ID "AHNAK--GANAB^AHNAK^ENSG00000124942.14"  ; ccdsid "CCDS44625.1"  ; exon_id "ENSE00001286844.4"  ; exon_number 3 ; gene_id "AHNAK--GANAB^AHNAK^ENSG00000124942.14"  ; gene_name AHNAK ; gene_type protein_coding ; havana_gene "OTTHUMG00000167558.7"  ; havana_transcript "OTTHUMT00000395014.1"  ; hgnc_id "HGNC:347"  ; level 2 ; orig_coord_info "chr11,62535945,62536098,-"  ; protein_id "ENSP00000257247.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "AHNAK--GANAB^ENST00000257247.11"  ; transcript_name "AHNAK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AHNAK--GANAB	HAVANA	mRNA	2086	27428	.	+	.	FI_gene_label "AHNAK^ENSG00000124942.14"  ; ID "AHNAK--GANAB^ENST00000257247.11"  ; Parent "AHNAK--GANAB^AHNAK^ENSG00000124942.14"  ; ccdsid "CCDS44625.1"  ; exon_id "ENSE00001286844.4"  ; exon_number 3 ; gene_id "AHNAK--GANAB^AHNAK^ENSG00000124942.14"  ; gene_name AHNAK ; gene_type protein_coding ; havana_gene "OTTHUMG00000167558.7"  ; havana_transcript "OTTHUMT00000395014.1"  ; hgnc_id "HGNC:347"  ; level 2 ; orig_coord_info "chr11,62535945,62536098,-"  ; protein_id "ENSP00000257247.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "AHNAK--GANAB^ENST00000257247.11"  ; transcript_name "AHNAK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AHNAK--GANAB	HAVANA	gene	30544	43063	.	+	.	FI_gene_label "GANAB^ENSG00000089597.18"  ; ID "AHNAK--GANAB^GANAB^ENSG00000089597.18"  ; ccdsid "CCDS41656.1"  ; exon_id "ENSE00002175558.1"  ; exon_number 1 ; gene_id "AHNAK--GANAB^GANAB^ENSG00000089597.18"  ; gene_name GANAB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167696.7"  ; havana_transcript "OTTHUMT00000395688.2"  ; hgnc_id "HGNC:4138"  ; level 2 ; orig_coord_info "chr11,62646562,62646599,-"  ; protein_id "ENSP00000340466.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "AHNAK--GANAB^ENST00000346178.8"  ; transcript_name "GANAB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AHNAK--GANAB	HAVANA	mRNA	30544	43063	.	+	.	FI_gene_label "GANAB^ENSG00000089597.18"  ; ID "AHNAK--GANAB^ENST00000346178.8"  ; Parent "AHNAK--GANAB^GANAB^ENSG00000089597.18"  ; ccdsid "CCDS41656.1"  ; exon_id "ENSE00002175558.1"  ; exon_number 1 ; gene_id "AHNAK--GANAB^GANAB^ENSG00000089597.18"  ; gene_name GANAB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167696.7"  ; havana_transcript "OTTHUMT00000395688.2"  ; hgnc_id "HGNC:4138"  ; level 2 ; orig_coord_info "chr11,62646562,62646599,-"  ; protein_id "ENSP00000340466.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "AHNAK--GANAB^ENST00000346178.8"  ; transcript_name "GANAB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CDH3--ZFP90	HAVANA	gene	2540	19292	.	+	.	FI_gene_label "CDH3^ENSG00000062038.15"  ; ID "CDH3--ZFP90^CDH3^ENSG00000062038.15"  ; ccdsid "CCDS10868.1"  ; exon_id "ENSE00001822923.2"  ; exon_number 1 ; gene_id "CDH3--ZFP90^CDH3^ENSG00000062038.15"  ; gene_name CDH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137560.8"  ; havana_transcript "OTTHUMT00000268896.4"  ; hgnc_id "HGNC:1762"  ; level 2 ; orig_coord_info "chr16,68645380,68645424,+"  ; protein_id "ENSP00000264012.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH3--ZFP90^ENST00000264012.9"  ; transcript_name "CDH3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CDH3--ZFP90	HAVANA	mRNA	2540	19292	.	+	.	FI_gene_label "CDH3^ENSG00000062038.15"  ; ID "CDH3--ZFP90^ENST00000264012.9"  ; Parent "CDH3--ZFP90^CDH3^ENSG00000062038.15"  ; ccdsid "CCDS10868.1"  ; exon_id "ENSE00001822923.2"  ; exon_number 1 ; gene_id "CDH3--ZFP90^CDH3^ENSG00000062038.15"  ; gene_name CDH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137560.8"  ; havana_transcript "OTTHUMT00000268896.4"  ; hgnc_id "HGNC:1762"  ; level 2 ; orig_coord_info "chr16,68645380,68645424,+"  ; protein_id "ENSP00000264012.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH3--ZFP90^ENST00000264012.9"  ; transcript_name "CDH3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CDH3--ZFP90	ENSEMBL	gene	27949	37656	.	+	.	FI_gene_label "ZFP90^ENSG00000184939.16"  ; ID "CDH3--ZFP90^ZFP90^ENSG00000184939.16"  ; ccdsid "CCDS42183.1"  ; exon_id "ENSE00003512841.1"  ; exon_number 1 ; gene_id "CDH3--ZFP90^ZFP90^ENSG00000184939.16"  ; gene_name ZFP90 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177312.9"  ; hgnc_id "HGNC:23329"  ; level 3 ; orig_coord_info "chr16,68539793,68539825,+"  ; protein_id "ENSP00000381304.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "CDH3--ZFP90^ENST00000398253.6"  ; transcript_name "ZFP90-201"  ; transcript_support_level 4 ; transcript_type protein_coding
CDH3--ZFP90	ENSEMBL	mRNA	27949	37656	.	+	.	FI_gene_label "ZFP90^ENSG00000184939.16"  ; ID "CDH3--ZFP90^ENST00000398253.6"  ; Parent "CDH3--ZFP90^ZFP90^ENSG00000184939.16"  ; ccdsid "CCDS42183.1"  ; exon_id "ENSE00003512841.1"  ; exon_number 1 ; gene_id "CDH3--ZFP90^ZFP90^ENSG00000184939.16"  ; gene_name ZFP90 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177312.9"  ; hgnc_id "HGNC:23329"  ; level 3 ; orig_coord_info "chr16,68539793,68539825,+"  ; protein_id "ENSP00000381304.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "CDH3--ZFP90^ENST00000398253.6"  ; transcript_name "ZFP90-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
CGNL1--TCF12	HAVANA	gene	36093	72831	.	+	.	FI_gene_label "TCF12^ENSG00000140262.18"  ; ID "CGNL1--TCF12^TCF12^ENSG00000140262.18"  ; ccdsid "CCDS10159.1"  ; exon_id "ENSE00003647364.1"  ; exon_number 2 ; gene_id "CGNL1--TCF12^TCF12^ENSG00000140262.18"  ; gene_name TCF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132047.13"  ; havana_transcript "OTTHUMT00000255069.3"  ; hgnc_id "HGNC:11623"  ; level 2 ; orig_coord_info "chr15,56919914,56919988,+"  ; protein_id "ENSP00000267811.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CGNL1--TCF12^ENST00000267811.9"  ; transcript_name "TCF12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CGNL1--TCF12	HAVANA	mRNA	36093	72831	.	+	.	FI_gene_label "TCF12^ENSG00000140262.18"  ; ID "CGNL1--TCF12^ENST00000267811.9"  ; Parent "CGNL1--TCF12^TCF12^ENSG00000140262.18"  ; ccdsid "CCDS10159.1"  ; exon_id "ENSE00003647364.1"  ; exon_number 2 ; gene_id "CGNL1--TCF12^TCF12^ENSG00000140262.18"  ; gene_name TCF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132047.13"  ; havana_transcript "OTTHUMT00000255069.3"  ; hgnc_id "HGNC:11623"  ; level 2 ; orig_coord_info "chr15,56919914,56919988,+"  ; protein_id "ENSP00000267811.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CGNL1--TCF12^ENST00000267811.9"  ; transcript_name "TCF12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CGNL1--TCF12	HAVANA	gene	1539	33090	.	+	.	FI_gene_label "CGNL1^ENSG00000128849.11"  ; ID "CGNL1--TCF12^CGNL1^ENSG00000128849.11"  ; ccdsid "CCDS10161.1"  ; exon_id "ENSE00001103542.1"  ; exon_number 2 ; gene_id "CGNL1--TCF12^CGNL1^ENSG00000128849.11"  ; gene_name CGNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166485.3"  ; havana_transcript "OTTHUMT00000255482.2"  ; hgnc_id "HGNC:25931"  ; level 2 ; orig_coord_info "chr15,57438000,57439601,+"  ; protein_id "ENSP00000281282.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CGNL1--TCF12^ENST00000281282.6"  ; transcript_name "CGNL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CGNL1--TCF12	HAVANA	mRNA	1539	33090	.	+	.	FI_gene_label "CGNL1^ENSG00000128849.11"  ; ID "CGNL1--TCF12^ENST00000281282.6"  ; Parent "CGNL1--TCF12^CGNL1^ENSG00000128849.11"  ; ccdsid "CCDS10161.1"  ; exon_id "ENSE00001103542.1"  ; exon_number 2 ; gene_id "CGNL1--TCF12^CGNL1^ENSG00000128849.11"  ; gene_name CGNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166485.3"  ; havana_transcript "OTTHUMT00000255482.2"  ; hgnc_id "HGNC:25931"  ; level 2 ; orig_coord_info "chr15,57438000,57439601,+"  ; protein_id "ENSP00000281282.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CGNL1--TCF12^ENST00000281282.6"  ; transcript_name "CGNL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FLNB--SLMAP	HAVANA	gene	57753	94861	.	+	.	FI_gene_label "SLMAP^ENSG00000163681.16"  ; ID "FLNB--SLMAP^SLMAP^ENSG00000163681.16"  ; ccdsid "CCDS33774.1"  ; exon_id "ENSE00001518947.1"  ; exon_number 2 ; gene_id "FLNB--SLMAP^SLMAP^ENSG00000163681.16"  ; gene_name SLMAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000133764.5"  ; havana_transcript "OTTHUMT00000258230.1"  ; hgnc_id "HGNC:16643"  ; level 2 ; orig_coord_info "chr3,57757652,57757849,+"  ; protein_id "ENSP00000295951.3"  ; tag basic appris_alternative_1 CCDS ; transcript_id "FLNB--SLMAP^ENST00000295951.7"  ; transcript_name "SLMAP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
FLNB--SLMAP	HAVANA	mRNA	57753	94861	.	+	.	FI_gene_label "SLMAP^ENSG00000163681.16"  ; ID "FLNB--SLMAP^ENST00000295951.7"  ; Parent "FLNB--SLMAP^SLMAP^ENSG00000163681.16"  ; ccdsid "CCDS33774.1"  ; exon_id "ENSE00001518947.1"  ; exon_number 2 ; gene_id "FLNB--SLMAP^SLMAP^ENSG00000163681.16"  ; gene_name SLMAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000133764.5"  ; havana_transcript "OTTHUMT00000258230.1"  ; hgnc_id "HGNC:16643"  ; level 2 ; orig_coord_info "chr3,57757652,57757849,+"  ; protein_id "ENSP00000295951.3"  ; tag basic appris_alternative_1 CCDS ; transcript_id "FLNB--SLMAP^ENST00000295951.7"  ; transcript_name "SLMAP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
FLNB--SLMAP	HAVANA	gene	1023	53972	.	+	.	FI_gene_label "FLNB^ENSG00000136068.15"  ; ID "FLNB--SLMAP^FLNB^ENSG00000136068.15"  ; ccdsid "CCDS2885.1"  ; exon_id "ENSE00000000021.2"  ; exon_number 1 ; gene_id "FLNB--SLMAP^FLNB^ENSG00000136068.15"  ; gene_name FLNB ; gene_type protein_coding ; havana_gene "OTTHUMG00000159158.1"  ; havana_transcript "OTTHUMT00000353569.1"  ; hgnc_id "HGNC:3755"  ; level 2 ; orig_coord_info "chr3,58008565,58008856,+"  ; protein_id "ENSP00000295956.5"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "FLNB--SLMAP^ENST00000295956.9"  ; transcript_name "FLNB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FLNB--SLMAP	HAVANA	mRNA	1023	53972	.	+	.	FI_gene_label "FLNB^ENSG00000136068.15"  ; ID "FLNB--SLMAP^ENST00000295956.9"  ; Parent "FLNB--SLMAP^FLNB^ENSG00000136068.15"  ; ccdsid "CCDS2885.1"  ; exon_id "ENSE00000000021.2"  ; exon_number 1 ; gene_id "FLNB--SLMAP^FLNB^ENSG00000136068.15"  ; gene_name FLNB ; gene_type protein_coding ; havana_gene "OTTHUMG00000159158.1"  ; havana_transcript "OTTHUMT00000353569.1"  ; hgnc_id "HGNC:3755"  ; level 2 ; orig_coord_info "chr3,58008565,58008856,+"  ; protein_id "ENSP00000295956.5"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "FLNB--SLMAP^ENST00000295956.9"  ; transcript_name "FLNB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ISM2--ALKBH1	HAVANA	gene	1001	9384	.	+	.	FI_gene_label "ISM2^ENSG00000100593.18"  ; ID "ISM2--ALKBH1^ISM2^ENSG00000100593.18"  ; exon_id "ENSE00003676816.1"  ; exon_number 1 ; gene_id "ISM2--ALKBH1^ISM2^ENSG00000100593.18"  ; gene_name ISM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158563.6"  ; havana_transcript "OTTHUMT00000351310.2"  ; hgnc_id "HGNC:23176"  ; level 2 ; orig_coord_info "chr14,77498653,77498793,-"  ; protein_id "ENSP00000216481.6"  ; transcript_id "ISM2--ALKBH1^ENST00000216481.10"  ; transcript_name "ISM2-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ISM2--ALKBH1	HAVANA	mRNA	1001	9384	.	+	.	FI_gene_label "ISM2^ENSG00000100593.18"  ; ID "ISM2--ALKBH1^ENST00000216481.10"  ; Parent "ISM2--ALKBH1^ISM2^ENSG00000100593.18"  ; exon_id "ENSE00003676816.1"  ; exon_number 1 ; gene_id "ISM2--ALKBH1^ISM2^ENSG00000100593.18"  ; gene_name ISM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158563.6"  ; havana_transcript "OTTHUMT00000351310.2"  ; hgnc_id "HGNC:23176"  ; level 2 ; orig_coord_info "chr14,77498653,77498793,-"  ; protein_id "ENSP00000216481.6"  ; transcript_id "ISM2--ALKBH1^ENST00000216481.10"  ; transcript_name "ISM2-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ISM2--ALKBH1	HAVANA	gene	12385	21231	.	+	.	FI_gene_label "ALKBH1^ENSG00000100601.10"  ; ID "ISM2--ALKBH1^ALKBH1^ENSG00000100601.10"  ; ccdsid "CCDS32127.1"  ; exon_id "ENSE00002526080.2"  ; exon_number 1 ; gene_id "ISM2--ALKBH1^ALKBH1^ENSG00000100601.10"  ; gene_name ALKBH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171542.2"  ; havana_transcript "OTTHUMT00000414037.2"  ; hgnc_id "HGNC:17911"  ; level 2 ; orig_coord_info "chr14,77707822,77708004,-"  ; protein_id "ENSP00000216489.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ISM2--ALKBH1^ENST00000216489.8"  ; transcript_name "ALKBH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ISM2--ALKBH1	HAVANA	mRNA	12385	21231	.	+	.	FI_gene_label "ALKBH1^ENSG00000100601.10"  ; ID "ISM2--ALKBH1^ENST00000216489.8"  ; Parent "ISM2--ALKBH1^ALKBH1^ENSG00000100601.10"  ; ccdsid "CCDS32127.1"  ; exon_id "ENSE00002526080.2"  ; exon_number 1 ; gene_id "ISM2--ALKBH1^ALKBH1^ENSG00000100601.10"  ; gene_name ALKBH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171542.2"  ; havana_transcript "OTTHUMT00000414037.2"  ; hgnc_id "HGNC:17911"  ; level 2 ; orig_coord_info "chr14,77707822,77708004,-"  ; protein_id "ENSP00000216489.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ISM2--ALKBH1^ENST00000216489.8"  ; transcript_name "ALKBH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ITGA2--ITGA1	HAVANA	gene	36007	82737	.	+	.	FI_gene_label "ITGA1^ENSG00000213949.10"  ; ID "ITGA2--ITGA1^ITGA1^ENSG00000213949.10"  ; ccdsid "CCDS3955.1"  ; exon_id "ENSE00002078767.2"  ; exon_number 1 ; gene_id "ITGA2--ITGA1^ITGA1^ENSG00000213949.10"  ; gene_name ITGA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131163.6"  ; havana_transcript "OTTHUMT00000253855.4"  ; hgnc_id "HGNC:6134"  ; level 2 ; orig_coord_info "chr5,52788354,52788414,+"  ; protein_id "ENSP00000282588.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ITGA2--ITGA1^ENST00000282588.7"  ; transcript_name "ITGA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITGA2--ITGA1	HAVANA	mRNA	36007	82737	.	+	.	FI_gene_label "ITGA1^ENSG00000213949.10"  ; ID "ITGA2--ITGA1^ENST00000282588.7"  ; Parent "ITGA2--ITGA1^ITGA1^ENSG00000213949.10"  ; ccdsid "CCDS3955.1"  ; exon_id "ENSE00002078767.2"  ; exon_number 1 ; gene_id "ITGA2--ITGA1^ITGA1^ENSG00000213949.10"  ; gene_name ITGA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131163.6"  ; havana_transcript "OTTHUMT00000253855.4"  ; hgnc_id "HGNC:6134"  ; level 2 ; orig_coord_info "chr5,52788354,52788414,+"  ; protein_id "ENSP00000282588.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ITGA2--ITGA1^ENST00000282588.7"  ; transcript_name "ITGA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ITGA2--ITGA1	HAVANA	gene	1013	33006	.	+	.	FI_gene_label "ITGA2^ENSG00000164171.11"  ; ID "ITGA2--ITGA1^ITGA2^ENSG00000164171.11"  ; ccdsid "CCDS3957.1"  ; exon_id "ENSE00002047974.2"  ; exon_number 1 ; gene_id "ITGA2--ITGA1^ITGA2^ENSG00000164171.11"  ; gene_name ITGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131165.5"  ; havana_transcript "OTTHUMT00000253857.3"  ; hgnc_id "HGNC:6137"  ; level 2 ; orig_coord_info "chr5,52989469,52989532,+"  ; protein_id "ENSP00000296585.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ITGA2--ITGA1^ENST00000296585.10"  ; transcript_name "ITGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITGA2--ITGA1	HAVANA	mRNA	1013	33006	.	+	.	FI_gene_label "ITGA2^ENSG00000164171.11"  ; ID "ITGA2--ITGA1^ENST00000296585.10"  ; Parent "ITGA2--ITGA1^ITGA2^ENSG00000164171.11"  ; ccdsid "CCDS3957.1"  ; exon_id "ENSE00002047974.2"  ; exon_number 1 ; gene_id "ITGA2--ITGA1^ITGA2^ENSG00000164171.11"  ; gene_name ITGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131165.5"  ; havana_transcript "OTTHUMT00000253857.3"  ; hgnc_id "HGNC:6137"  ; level 2 ; orig_coord_info "chr5,52989469,52989532,+"  ; protein_id "ENSP00000296585.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ITGA2--ITGA1^ENST00000296585.10"  ; transcript_name "ITGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLF13--LINC02352	HAVANA	gene	1001	11301	.	+	.	FI_gene_label "KLF13^ENSG00000169926.11"  ; ID "KLF13--LINC02352^KLF13^ENSG00000169926.11"  ; ccdsid "CCDS10025.1"  ; exon_id "ENSE00001127061.5"  ; exon_number 1 ; gene_id "KLF13--LINC02352^KLF13^ENSG00000169926.11"  ; gene_name KLF13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172224.5"  ; havana_transcript "OTTHUMT00000251381.2"  ; hgnc_id "HGNC:13672"  ; level 2 ; orig_coord_info "chr15,31327213,31327789,+"  ; protein_id "ENSP00000302456.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLF13--LINC02352^ENST00000307145.4"  ; transcript_name "KLF13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLF13--LINC02352	HAVANA	mRNA	1001	11301	.	+	.	FI_gene_label "KLF13^ENSG00000169926.11"  ; ID "KLF13--LINC02352^ENST00000307145.4"  ; Parent "KLF13--LINC02352^KLF13^ENSG00000169926.11"  ; ccdsid "CCDS10025.1"  ; exon_id "ENSE00001127061.5"  ; exon_number 1 ; gene_id "KLF13--LINC02352^KLF13^ENSG00000169926.11"  ; gene_name KLF13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172224.5"  ; havana_transcript "OTTHUMT00000251381.2"  ; hgnc_id "HGNC:13672"  ; level 2 ; orig_coord_info "chr15,31327213,31327789,+"  ; protein_id "ENSP00000302456.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLF13--LINC02352^ENST00000307145.4"  ; transcript_name "KLF13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLF13--TRPM1	HAVANA	gene	21119	51988	.	+	.	FI_gene_label "TRPM1^ENSG00000134160.14"  ; ID "KLF13--TRPM1^TRPM1^ENSG00000134160.14"  ; ccdsid "CCDS58346.1"  ; exon_id "ENSE00002242777.1"  ; exon_number 2 ; gene_id "KLF13--TRPM1^TRPM1^ENSG00000134160.14"  ; gene_name TRPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129267.5"  ; havana_transcript "OTTHUMT00000417166.2"  ; hgnc_id "HGNC:7146"  ; level 1 ; orig_coord_info "chr15,31081353,31081355,-"  ; protein_id "ENSP00000256552.7"  ; tag basic MANE_Select appris_alternative_2 exp_conf CCDS ; transcript_id "KLF13--TRPM1^ENST00000256552.11"  ; transcript_name "TRPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLF13--TRPM1	HAVANA	mRNA	21119	51988	.	+	.	FI_gene_label "TRPM1^ENSG00000134160.14"  ; ID "KLF13--TRPM1^ENST00000256552.11"  ; Parent "KLF13--TRPM1^TRPM1^ENSG00000134160.14"  ; ccdsid "CCDS58346.1"  ; exon_id "ENSE00002242777.1"  ; exon_number 2 ; gene_id "KLF13--TRPM1^TRPM1^ENSG00000134160.14"  ; gene_name TRPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129267.5"  ; havana_transcript "OTTHUMT00000417166.2"  ; hgnc_id "HGNC:7146"  ; level 1 ; orig_coord_info "chr15,31081353,31081355,-"  ; protein_id "ENSP00000256552.7"  ; tag basic MANE_Select appris_alternative_2 exp_conf CCDS ; transcript_id "KLF13--TRPM1^ENST00000256552.11"  ; transcript_name "TRPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLF13--TRPM1	HAVANA	gene	1001	11301	.	+	.	FI_gene_label "KLF13^ENSG00000169926.11"  ; ID "KLF13--TRPM1^KLF13^ENSG00000169926.11"  ; ccdsid "CCDS10025.1"  ; exon_id "ENSE00001127061.5"  ; exon_number 1 ; gene_id "KLF13--TRPM1^KLF13^ENSG00000169926.11"  ; gene_name KLF13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172224.5"  ; havana_transcript "OTTHUMT00000251381.2"  ; hgnc_id "HGNC:13672"  ; level 2 ; orig_coord_info "chr15,31327213,31327789,+"  ; protein_id "ENSP00000302456.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLF13--TRPM1^ENST00000307145.4"  ; transcript_name "KLF13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLF13--TRPM1	HAVANA	mRNA	1001	11301	.	+	.	FI_gene_label "KLF13^ENSG00000169926.11"  ; ID "KLF13--TRPM1^ENST00000307145.4"  ; Parent "KLF13--TRPM1^KLF13^ENSG00000169926.11"  ; ccdsid "CCDS10025.1"  ; exon_id "ENSE00001127061.5"  ; exon_number 1 ; gene_id "KLF13--TRPM1^KLF13^ENSG00000169926.11"  ; gene_name KLF13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172224.5"  ; havana_transcript "OTTHUMT00000251381.2"  ; hgnc_id "HGNC:13672"  ; level 2 ; orig_coord_info "chr15,31327213,31327789,+"  ; protein_id "ENSP00000302456.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLF13--TRPM1^ENST00000307145.4"  ; transcript_name "KLF13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
METAP1--BTF3P13	HAVANA	gene	1063	19945	.	+	.	FI_gene_label "METAP1^ENSG00000164024.12"  ; ID "METAP1--BTF3P13^METAP1^ENSG00000164024.12"  ; ccdsid "CCDS47110.1"  ; exon_id "ENSE00002071619.1"  ; exon_number 1 ; gene_id "METAP1--BTF3P13^METAP1^ENSG00000164024.12"  ; gene_name METAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161231.3"  ; havana_transcript "OTTHUMT00000364237.2"  ; hgnc_id "HGNC:15789"  ; level 2 ; orig_coord_info "chr4,98995754,98995867,+"  ; protein_id "ENSP00000296411.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "METAP1--BTF3P13^ENST00000296411.11"  ; transcript_name "METAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
METAP1--BTF3P13	HAVANA	mRNA	1063	19945	.	+	.	FI_gene_label "METAP1^ENSG00000164024.12"  ; ID "METAP1--BTF3P13^ENST00000296411.11"  ; Parent "METAP1--BTF3P13^METAP1^ENSG00000164024.12"  ; ccdsid "CCDS47110.1"  ; exon_id "ENSE00002071619.1"  ; exon_number 1 ; gene_id "METAP1--BTF3P13^METAP1^ENSG00000164024.12"  ; gene_name METAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161231.3"  ; havana_transcript "OTTHUMT00000364237.2"  ; hgnc_id "HGNC:15789"  ; level 2 ; orig_coord_info "chr4,98995754,98995867,+"  ; protein_id "ENSP00000296411.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "METAP1--BTF3P13^ENST00000296411.11"  ; transcript_name "METAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
METAP1--EIF4E	HAVANA	gene	22987	35463	.	+	.	FI_gene_label "EIF4E^ENSG00000151247.13"  ; ID "METAP1--EIF4E^EIF4E^ENSG00000151247.13"  ; ccdsid "CCDS47109.1"  ; exon_id "ENSE00001609349.1"  ; exon_number 1 ; gene_id "METAP1--EIF4E^EIF4E^ENSG00000151247.13"  ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2"  ; havana_transcript "OTTHUMT00000363740.1"  ; hgnc_id "HGNC:3287"  ; level 2 ; orig_coord_info "chr4,98928895,98928972,-"  ; protein_id "ENSP00000280892.6"  ; tag basic CCDS ; transcript_id "METAP1--EIF4E^ENST00000280892.10"  ; transcript_name "EIF4E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
METAP1--EIF4E	HAVANA	mRNA	22987	35463	.	+	.	FI_gene_label "EIF4E^ENSG00000151247.13"  ; ID "METAP1--EIF4E^ENST00000280892.10"  ; Parent "METAP1--EIF4E^EIF4E^ENSG00000151247.13"  ; ccdsid "CCDS47109.1"  ; exon_id "ENSE00001609349.1"  ; exon_number 1 ; gene_id "METAP1--EIF4E^EIF4E^ENSG00000151247.13"  ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2"  ; havana_transcript "OTTHUMT00000363740.1"  ; hgnc_id "HGNC:3287"  ; level 2 ; orig_coord_info "chr4,98928895,98928972,-"  ; protein_id "ENSP00000280892.6"  ; tag basic CCDS ; transcript_id "METAP1--EIF4E^ENST00000280892.10"  ; transcript_name "EIF4E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
METAP1--EIF4E	HAVANA	gene	1063	19945	.	+	.	FI_gene_label "METAP1^ENSG00000164024.12"  ; ID "METAP1--EIF4E^METAP1^ENSG00000164024.12"  ; ccdsid "CCDS47110.1"  ; exon_id "ENSE00002071619.1"  ; exon_number 1 ; gene_id "METAP1--EIF4E^METAP1^ENSG00000164024.12"  ; gene_name METAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161231.3"  ; havana_transcript "OTTHUMT00000364237.2"  ; hgnc_id "HGNC:15789"  ; level 2 ; orig_coord_info "chr4,98995754,98995867,+"  ; protein_id "ENSP00000296411.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "METAP1--EIF4E^ENST00000296411.11"  ; transcript_name "METAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
METAP1--EIF4E	HAVANA	mRNA	1063	19945	.	+	.	FI_gene_label "METAP1^ENSG00000164024.12"  ; ID "METAP1--EIF4E^ENST00000296411.11"  ; Parent "METAP1--EIF4E^METAP1^ENSG00000164024.12"  ; ccdsid "CCDS47110.1"  ; exon_id "ENSE00002071619.1"  ; exon_number 1 ; gene_id "METAP1--EIF4E^METAP1^ENSG00000164024.12"  ; gene_name METAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161231.3"  ; havana_transcript "OTTHUMT00000364237.2"  ; hgnc_id "HGNC:15789"  ; level 2 ; orig_coord_info "chr4,98995754,98995867,+"  ; protein_id "ENSP00000296411.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "METAP1--EIF4E^ENST00000296411.11"  ; transcript_name "METAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NDE1--BMERB1	HAVANA	gene	28300	42237	.	+	.	FI_gene_label "BMERB1^ENSG00000166780.11"  ; ID "NDE1--BMERB1^BMERB1^ENSG00000166780.11"  ; ccdsid "CCDS10561.1"  ; exon_id "ENSE00002591059.2"  ; exon_number 1 ; gene_id "NDE1--BMERB1^BMERB1^ENSG00000166780.11"  ; gene_name BMERB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129883.6"  ; havana_transcript "OTTHUMT00000252130.3"  ; hgnc_id "HGNC:19213"  ; level 2 ; orig_coord_info "chr16,15434654,15434759,+"  ; protein_id "ENSP00000300006.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDE1--BMERB1^ENST00000300006.9"  ; transcript_name "BMERB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NDE1--BMERB1	HAVANA	mRNA	28300	42237	.	+	.	FI_gene_label "BMERB1^ENSG00000166780.11"  ; ID "NDE1--BMERB1^ENST00000300006.9"  ; Parent "NDE1--BMERB1^BMERB1^ENSG00000166780.11"  ; ccdsid "CCDS10561.1"  ; exon_id "ENSE00002591059.2"  ; exon_number 1 ; gene_id "NDE1--BMERB1^BMERB1^ENSG00000166780.11"  ; gene_name BMERB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129883.6"  ; havana_transcript "OTTHUMT00000252130.3"  ; hgnc_id "HGNC:19213"  ; level 2 ; orig_coord_info "chr16,15434654,15434759,+"  ; protein_id "ENSP00000300006.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDE1--BMERB1^ENST00000300006.9"  ; transcript_name "BMERB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NDE1--BMERB1	HAVANA	gene	3559	21332	.	+	.	FI_gene_label "NDE1^ENSG00000072864.16"  ; ID "NDE1--BMERB1^NDE1^ENSG00000072864.16"  ; ccdsid "CCDS10564.1"  ; exon_id "ENSE00001602389.1"  ; exon_number 2 ; gene_id "NDE1--BMERB1^NDE1^ENSG00000072864.16"  ; gene_name NDE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129885.6"  ; havana_transcript "OTTHUMT00000252132.2"  ; hgnc_id "HGNC:17619"  ; level 2 ; orig_coord_info "chr16,15664779,15664861,+"  ; protein_id "ENSP00000379642.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDE1--BMERB1^ENST00000396354.6"  ; transcript_name "NDE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NDE1--BMERB1	HAVANA	mRNA	3559	21332	.	+	.	FI_gene_label "NDE1^ENSG00000072864.16"  ; ID "NDE1--BMERB1^ENST00000396354.6"  ; Parent "NDE1--BMERB1^NDE1^ENSG00000072864.16"  ; ccdsid "CCDS10564.1"  ; exon_id "ENSE00001602389.1"  ; exon_number 2 ; gene_id "NDE1--BMERB1^NDE1^ENSG00000072864.16"  ; gene_name NDE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129885.6"  ; havana_transcript "OTTHUMT00000252132.2"  ; hgnc_id "HGNC:17619"  ; level 2 ; orig_coord_info "chr16,15664779,15664861,+"  ; protein_id "ENSP00000379642.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDE1--BMERB1^ENST00000396354.6"  ; transcript_name "NDE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NDNF--QRFPR	HAVANA	gene	12241	19729	.	+	.	FI_gene_label "QRFPR^ENSG00000186867.11"  ; ID "NDNF--QRFPR^QRFPR^ENSG00000186867.11"  ; exon_id "ENSE00001518432.2"  ; exon_number 1 ; gene_id "NDNF--QRFPR^QRFPR^ENSG00000186867.11"  ; gene_name QRFPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000133036.4"  ; havana_transcript "OTTHUMT00000364003.1"  ; hgnc_id "HGNC:15565"  ; level 1 ; orig_coord_info "chr4,121380308,121380647,-"  ; protein_id "ENSP00000335610.5"  ; tag basic exp_conf ; transcript_id "NDNF--QRFPR^ENST00000334383.9"  ; transcript_name "QRFPR-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NDNF--QRFPR	HAVANA	mRNA	12241	19729	.	+	.	FI_gene_label "QRFPR^ENSG00000186867.11"  ; ID "NDNF--QRFPR^ENST00000334383.9"  ; Parent "NDNF--QRFPR^QRFPR^ENSG00000186867.11"  ; exon_id "ENSE00001518432.2"  ; exon_number 1 ; gene_id "NDNF--QRFPR^QRFPR^ENSG00000186867.11"  ; gene_name QRFPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000133036.4"  ; havana_transcript "OTTHUMT00000364003.1"  ; hgnc_id "HGNC:15565"  ; level 1 ; orig_coord_info "chr4,121380308,121380647,-"  ; protein_id "ENSP00000335610.5"  ; tag basic exp_conf ; transcript_id "NDNF--QRFPR^ENST00000334383.9"  ; transcript_name "QRFPR-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NDNF--QRFPR	HAVANA	gene	1487	8860	.	+	.	FI_gene_label "NDNF^ENSG00000173376.14"  ; ID "NDNF--QRFPR^NDNF^ENSG00000173376.14"  ; ccdsid "CCDS3717.2"  ; exon_id "ENSE00001784917.1"  ; exon_number 2 ; gene_id "NDNF--QRFPR^NDNF^ENSG00000173376.14"  ; gene_name NDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132973.5"  ; havana_transcript "OTTHUMT00000256532.3"  ; hgnc_id "HGNC:26256"  ; level 2 ; orig_coord_info "chr4,121045650,121045837,-"  ; protein_id "ENSP00000369014.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDNF--QRFPR^ENST00000379692.9"  ; transcript_name "NDNF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NDNF--QRFPR	HAVANA	mRNA	1487	8860	.	+	.	FI_gene_label "NDNF^ENSG00000173376.14"  ; ID "NDNF--QRFPR^ENST00000379692.9"  ; Parent "NDNF--QRFPR^NDNF^ENSG00000173376.14"  ; ccdsid "CCDS3717.2"  ; exon_id "ENSE00001784917.1"  ; exon_number 2 ; gene_id "NDNF--QRFPR^NDNF^ENSG00000173376.14"  ; gene_name NDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132973.5"  ; havana_transcript "OTTHUMT00000256532.3"  ; hgnc_id "HGNC:26256"  ; level 2 ; orig_coord_info "chr4,121045650,121045837,-"  ; protein_id "ENSP00000369014.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDNF--QRFPR^ENST00000379692.9"  ; transcript_name "NDNF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NDNF--TNIP3	HAVANA	gene	15277	29876	.	+	.	FI_gene_label "TNIP3^ENSG00000050730.16"  ; ID "NDNF--TNIP3^TNIP3^ENSG00000050730.16"  ; ccdsid "CCDS3718.1"  ; exon_id "ENSE00002075592.2"  ; exon_number 1 ; gene_id "NDNF--TNIP3^TNIP3^ENSG00000050730.16"  ; gene_name TNIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132969.6"  ; havana_transcript "OTTHUMT00000256527.3"  ; hgnc_id "HGNC:19315"  ; level 2 ; orig_coord_info "chr4,121164060,121164125,-"  ; protein_id "ENSP00000057513.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "NDNF--TNIP3^ENST00000057513.8"  ; transcript_name "TNIP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NDNF--TNIP3	HAVANA	mRNA	15277	29876	.	+	.	FI_gene_label "TNIP3^ENSG00000050730.16"  ; ID "NDNF--TNIP3^ENST00000057513.8"  ; Parent "NDNF--TNIP3^TNIP3^ENSG00000050730.16"  ; ccdsid "CCDS3718.1"  ; exon_id "ENSE00002075592.2"  ; exon_number 1 ; gene_id "NDNF--TNIP3^TNIP3^ENSG00000050730.16"  ; gene_name TNIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132969.6"  ; havana_transcript "OTTHUMT00000256527.3"  ; hgnc_id "HGNC:19315"  ; level 2 ; orig_coord_info "chr4,121164060,121164125,-"  ; protein_id "ENSP00000057513.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "NDNF--TNIP3^ENST00000057513.8"  ; transcript_name "TNIP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NDNF--TNIP3	HAVANA	gene	1487	8860	.	+	.	FI_gene_label "NDNF^ENSG00000173376.14"  ; ID "NDNF--TNIP3^NDNF^ENSG00000173376.14"  ; ccdsid "CCDS3717.2"  ; exon_id "ENSE00001784917.1"  ; exon_number 2 ; gene_id "NDNF--TNIP3^NDNF^ENSG00000173376.14"  ; gene_name NDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132973.5"  ; havana_transcript "OTTHUMT00000256532.3"  ; hgnc_id "HGNC:26256"  ; level 2 ; orig_coord_info "chr4,121045650,121045837,-"  ; protein_id "ENSP00000369014.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDNF--TNIP3^ENST00000379692.9"  ; transcript_name "NDNF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NDNF--TNIP3	HAVANA	mRNA	1487	8860	.	+	.	FI_gene_label "NDNF^ENSG00000173376.14"  ; ID "NDNF--TNIP3^ENST00000379692.9"  ; Parent "NDNF--TNIP3^NDNF^ENSG00000173376.14"  ; ccdsid "CCDS3717.2"  ; exon_id "ENSE00001784917.1"  ; exon_number 2 ; gene_id "NDNF--TNIP3^NDNF^ENSG00000173376.14"  ; gene_name NDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132973.5"  ; havana_transcript "OTTHUMT00000256532.3"  ; hgnc_id "HGNC:26256"  ; level 2 ; orig_coord_info "chr4,121045650,121045837,-"  ; protein_id "ENSP00000369014.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDNF--TNIP3^ENST00000379692.9"  ; transcript_name "NDNF-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTBP3--SUSD1	HAVANA	gene	1636	7412	.	+	.	FI_gene_label "PTBP3^ENSG00000119314.16"  ; ID "PTBP3--SUSD1^PTBP3^ENSG00000119314.16"  ; exon_id "ENSE00001333878.4"  ; exon_number 1 ; gene_id "PTBP3--SUSD1^PTBP3^ENSG00000119314.16"  ; gene_name PTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020503.3"  ; havana_transcript "OTTHUMT00000053674.2"  ; hgnc_id "HGNC:10253"  ; level 2 ; orig_coord_info "chr9,112332784,112332843,-"  ; protein_id "ENSP00000210227.4"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PTBP3--SUSD1^ENST00000210227.4"  ; transcript_name "PTBP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PTBP3--SUSD1	HAVANA	mRNA	1636	7412	.	+	.	FI_gene_label "PTBP3^ENSG00000119314.16"  ; ID "PTBP3--SUSD1^ENST00000210227.4"  ; Parent "PTBP3--SUSD1^PTBP3^ENSG00000119314.16"  ; exon_id "ENSE00001333878.4"  ; exon_number 1 ; gene_id "PTBP3--SUSD1^PTBP3^ENSG00000119314.16"  ; gene_name PTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020503.3"  ; havana_transcript "OTTHUMT00000053674.2"  ; hgnc_id "HGNC:10253"  ; level 2 ; orig_coord_info "chr9,112332784,112332843,-"  ; protein_id "ENSP00000210227.4"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PTBP3--SUSD1^ENST00000210227.4"  ; transcript_name "PTBP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PTBP3--SUSD1	HAVANA	gene	25375	47309	.	+	.	FI_gene_label "SUSD1^ENSG00000106868.17"  ; ID "PTBP3--SUSD1^SUSD1^ENSG00000106868.17"  ; exon_id "ENSE00001706926.1"  ; exon_number 1 ; gene_id "PTBP3--SUSD1^SUSD1^ENSG00000106868.17"  ; gene_name SUSD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020499.5"  ; havana_transcript "OTTHUMT00000053667.2"  ; hgnc_id "HGNC:25413"  ; level 1 ; orig_coord_info "chr9,112175133,112175185,-"  ; protein_id "ENSP00000347558.3"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PTBP3--SUSD1^ENST00000355396.7"  ; transcript_name "SUSD1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PTBP3--SUSD1	HAVANA	mRNA	25375	47309	.	+	.	FI_gene_label "SUSD1^ENSG00000106868.17"  ; ID "PTBP3--SUSD1^ENST00000355396.7"  ; Parent "PTBP3--SUSD1^SUSD1^ENSG00000106868.17"  ; exon_id "ENSE00001706926.1"  ; exon_number 1 ; gene_id "PTBP3--SUSD1^SUSD1^ENSG00000106868.17"  ; gene_name SUSD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020499.5"  ; havana_transcript "OTTHUMT00000053667.2"  ; hgnc_id "HGNC:25413"  ; level 1 ; orig_coord_info "chr9,112175133,112175185,-"  ; protein_id "ENSP00000347558.3"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PTBP3--SUSD1^ENST00000355396.7"  ; transcript_name "SUSD1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RIN2--SLC24A3	HAVANA	gene	1653	26883	.	+	.	FI_gene_label "RIN2^ENSG00000132669.14"  ; ID "RIN2--SLC24A3^RIN2^ENSG00000132669.14"  ; exon_id "ENSE00003602839.1"  ; exon_number 3 ; gene_id "RIN2--SLC24A3^RIN2^ENSG00000132669.14"  ; gene_name RIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031996.3"  ; hgnc_id "HGNC:18750"  ; level 2 ; orig_coord_info "chr20,19889602,19889658,+"  ; protein_id "ENSP00000255006.7"  ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_2 ; transcript_id "RIN2--SLC24A3^ENST00000255006.12"  ; transcript_name "RIN2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
RIN2--SLC24A3	HAVANA	mRNA	1653	26883	.	+	.	FI_gene_label "RIN2^ENSG00000132669.14"  ; ID "RIN2--SLC24A3^ENST00000255006.12"  ; Parent "RIN2--SLC24A3^RIN2^ENSG00000132669.14"  ; exon_id "ENSE00003602839.1"  ; exon_number 3 ; gene_id "RIN2--SLC24A3^RIN2^ENSG00000132669.14"  ; gene_name RIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031996.3"  ; hgnc_id "HGNC:18750"  ; level 2 ; orig_coord_info "chr20,19889602,19889658,+"  ; protein_id "ENSP00000255006.7"  ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_2 ; transcript_id "RIN2--SLC24A3^ENST00000255006.12"  ; transcript_name "RIN2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RIN2--SLC24A3	HAVANA	gene	29885	48954	.	+	.	FI_gene_label "SLC24A3^ENSG00000185052.13"  ; ID "RIN2--SLC24A3^SLC24A3^ENSG00000185052.13"  ; ccdsid "CCDS13140.1"  ; exon_id "ENSE00001704017.2"  ; exon_number 1 ; gene_id "RIN2--SLC24A3^SLC24A3^ENSG00000185052.13"  ; gene_name SLC24A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031993.5"  ; havana_transcript "OTTHUMT00000078207.5"  ; hgnc_id "HGNC:10977"  ; level 2 ; orig_coord_info "chr20,19212843,19212984,+"  ; protein_id "ENSP00000333519.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIN2--SLC24A3^ENST00000328041.11"  ; transcript_name "SLC24A3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RIN2--SLC24A3	HAVANA	mRNA	29885	48954	.	+	.	FI_gene_label "SLC24A3^ENSG00000185052.13"  ; ID "RIN2--SLC24A3^ENST00000328041.11"  ; Parent "RIN2--SLC24A3^SLC24A3^ENSG00000185052.13"  ; ccdsid "CCDS13140.1"  ; exon_id "ENSE00001704017.2"  ; exon_number 1 ; gene_id "RIN2--SLC24A3^SLC24A3^ENSG00000185052.13"  ; gene_name SLC24A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031993.5"  ; havana_transcript "OTTHUMT00000078207.5"  ; hgnc_id "HGNC:10977"  ; level 2 ; orig_coord_info "chr20,19212843,19212984,+"  ; protein_id "ENSP00000333519.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIN2--SLC24A3^ENST00000328041.11"  ; transcript_name "SLC24A3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNU13--LLPH	HAVANA	gene	4331	9276	.	+	.	FI_gene_label "SNU13^ENSG00000100138.15"  ; ID "SNU13--LLPH^SNU13^ENSG00000100138.15"  ; ccdsid "CCDS14022.1"  ; exon_id "ENSE00001388935.4"  ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15"  ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9"  ; havana_transcript "OTTHUMT00000321683.2"  ; hgnc_id "HGNC:7819"  ; level 2 ; orig_coord_info "chr22,41682356,41682358,-"  ; protein_id "ENSP00000215956.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10"  ; transcript_name "SNU13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH	HAVANA	mRNA	4331	9276	.	+	.	FI_gene_label "SNU13^ENSG00000100138.15"  ; ID "SNU13--LLPH^ENST00000215956.10"  ; Parent "SNU13--LLPH^SNU13^ENSG00000100138.15"  ; ccdsid "CCDS14022.1"  ; exon_id "ENSE00001388935.4"  ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15"  ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9"  ; havana_transcript "OTTHUMT00000321683.2"  ; hgnc_id "HGNC:7819"  ; level 2 ; orig_coord_info "chr22,41682356,41682358,-"  ; protein_id "ENSP00000215956.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10"  ; transcript_name "SNU13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNU13--LLPH	HAVANA	gene	13051	23027	.	+	.	FI_gene_label "LLPH^ENSG00000139233.7"  ; ID "SNU13--LLPH^LLPH^ENSG00000139233.7"  ; ccdsid "CCDS8974.1"  ; exon_id "ENSE00003592110.1"  ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7"  ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4"  ; havana_transcript "OTTHUMT00000401752.4"  ; hgnc_id "HGNC:28229"  ; level 2 ; orig_coord_info "chr12,66128896,66129106,-"  ; protein_id "ENSP00000266604.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7"  ; transcript_name "LLPH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH	HAVANA	mRNA	13051	23027	.	+	.	FI_gene_label "LLPH^ENSG00000139233.7"  ; ID "SNU13--LLPH^ENST00000266604.7"  ; Parent "SNU13--LLPH^LLPH^ENSG00000139233.7"  ; ccdsid "CCDS8974.1"  ; exon_id "ENSE00003592110.1"  ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7"  ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4"  ; havana_transcript "OTTHUMT00000401752.4"  ; hgnc_id "HGNC:28229"  ; level 2 ; orig_coord_info "chr12,66128896,66129106,-"  ; protein_id "ENSP00000266604.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7"  ; transcript_name "LLPH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
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: 
ZNF410--DNAL1	HAVANA	gene	25343	38120	.	+	.	FI_gene_label "DNAL1^ENSG00000119661.15"  ; ID "ZNF410--DNAL1^DNAL1^ENSG00000119661.15"  ; exon_id "ENSE00003599576.1"  ; exon_number 5 ; gene_id "ZNF410--DNAL1^DNAL1^ENSG00000119661.15"  ; gene_name DNAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171642.8"  ; havana_transcript "OTTHUMT00000414566.1"  ; hgnc_id "HGNC:23247"  ; level 2 ; orig_coord_info "chr14,73687334,73687385,+"  ; protein_id "ENSP00000310360.3"  ; tag basic ; transcript_id "ZNF410--DNAL1^ENST00000311089.7"  ; transcript_name "DNAL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ZNF410--DNAL1	HAVANA	mRNA	25343	38120	.	+	.	FI_gene_label "DNAL1^ENSG00000119661.15"  ; ID "ZNF410--DNAL1^ENST00000311089.7"  ; Parent "ZNF410--DNAL1^DNAL1^ENSG00000119661.15"  ; exon_id "ENSE00003599576.1"  ; exon_number 5 ; gene_id "ZNF410--DNAL1^DNAL1^ENSG00000119661.15"  ; gene_name DNAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171642.8"  ; havana_transcript "OTTHUMT00000414566.1"  ; hgnc_id "HGNC:23247"  ; level 2 ; orig_coord_info "chr14,73687334,73687385,+"  ; protein_id "ENSP00000310360.3"  ; tag basic ; transcript_id "ZNF410--DNAL1^ENST00000311089.7"  ; transcript_name "DNAL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ZNF410--DNAL1	HAVANA	gene	1189	21965	.	+	.	FI_gene_label "ZNF410^ENSG00000119725.20"  ; ID "ZNF410--DNAL1^ZNF410^ENSG00000119725.20"  ; ccdsid "CCDS55930.1"  ; exon_id "ENSE00003600680.1"  ; exon_number 2 ; gene_id "ZNF410--DNAL1^ZNF410^ENSG00000119725.20"  ; gene_name ZNF410 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171257.5"  ; havana_transcript "OTTHUMT00000412585.1"  ; hgnc_id "HGNC:20144"  ; level 2 ; orig_coord_info "chr14,73892176,73892208,+"  ; protein_id "ENSP00000323293.6"  ; tag basic CCDS ; transcript_id "ZNF410--DNAL1^ENST00000324593.10"  ; transcript_name "ZNF410-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF410--DNAL1	HAVANA	mRNA	1189	21965	.	+	.	FI_gene_label "ZNF410^ENSG00000119725.20"  ; ID "ZNF410--DNAL1^ENST00000324593.10"  ; Parent "ZNF410--DNAL1^ZNF410^ENSG00000119725.20"  ; ccdsid "CCDS55930.1"  ; exon_id "ENSE00003600680.1"  ; exon_number 2 ; gene_id "ZNF410--DNAL1^ZNF410^ENSG00000119725.20"  ; gene_name ZNF410 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171257.5"  ; havana_transcript "OTTHUMT00000412585.1"  ; hgnc_id "HGNC:20144"  ; level 2 ; orig_coord_info "chr14,73892176,73892208,+"  ; protein_id "ENSP00000323293.6"  ; tag basic CCDS ; transcript_id "ZNF410--DNAL1^ENST00000324593.10"  ; transcript_name "ZNF410-201"  ; 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: 
AC136431.1--PKD1P5	HAVANA	gene	9015	30646	.	+	.	FI_gene_label "PKD1P5^ENSG00000254681.6"  ; ID "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; exon_id "ENSE00002185250.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2"  ; havana_transcript "OTTHUMT00000388923.1"  ; hgnc_id "HGNC:30069"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr16,18401584,18401940,-"  ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5"  ; transcript_name "PKD1P5-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AC136431.1--PKD1P5	HAVANA	RNA	9015	30646	.	+	.	FI_gene_label "PKD1P5^ENSG00000254681.6"  ; ID "AC136431.1--PKD1P5^ENST00000532415.5"  ; Parent "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; exon_id "ENSE00002185250.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2"  ; havana_transcript "OTTHUMT00000388923.1"  ; hgnc_id "HGNC:30069"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr16,18401584,18401940,-"  ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5"  ; transcript_name "PKD1P5-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC136431.1--PKD1P5	HAVANA	gene	1001	6014	.	+	.	FI_gene_label "AC136431.1^ENSG00000260126.2"  ; ID "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; exon_id "ENSE00003856180.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; gene_name "AC136431.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2"  ; havana_transcript "OTTHUMT00000436080.2"  ; level 2 ; orig_coord_info "chr16,16499533,16499619,+"  ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2"  ; transcript_name "AC136431.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
AC136431.1--PKD1P5	HAVANA	RNA	1001	6014	.	+	.	FI_gene_label "AC136431.1^ENSG00000260126.2"  ; ID "AC136431.1--PKD1P5^ENST00000567465.2"  ; Parent "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; exon_id "ENSE00003856180.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; gene_name "AC136431.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2"  ; havana_transcript "OTTHUMT00000436080.2"  ; level 2 ; orig_coord_info "chr16,16499533,16499619,+"  ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2"  ; transcript_name "AC136431.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
KLF13--LINC02352	HAVANA	gene	20148	24272	.	+	.	FI_gene_label "LINC02352^ENSG00000259448.3"  ; ID "KLF13--LINC02352^LINC02352^ENSG00000259448.3"  ; exon_id "ENSE00002553693.1"  ; exon_number 1 ; gene_id "KLF13--LINC02352^LINC02352^ENSG00000259448.3"  ; gene_name LINC02352 ; gene_type lncRNA ; havana_gene "OTTHUMG00000172222.3"  ; havana_transcript "OTTHUMT00000417390.1"  ; hgnc_id "HGNC:53274"  ; level 2 ; orig_coord_info "chr15,31216021,31216037,+"  ; tag dotter_confirmed ; transcript_id "KLF13--LINC02352^ENST00000557928.1"  ; transcript_name "LINC02352-201"  ; transcript_support_level 5 ; transcript_type lncRNA
KLF13--LINC02352	HAVANA	RNA	20148	24272	.	+	.	FI_gene_label "LINC02352^ENSG00000259448.3"  ; ID "KLF13--LINC02352^ENST00000557928.1"  ; Parent "KLF13--LINC02352^LINC02352^ENSG00000259448.3"  ; exon_id "ENSE00002553693.1"  ; exon_number 1 ; gene_id "KLF13--LINC02352^LINC02352^ENSG00000259448.3"  ; gene_name LINC02352 ; gene_type lncRNA ; havana_gene "OTTHUMG00000172222.3"  ; havana_transcript "OTTHUMT00000417390.1"  ; hgnc_id "HGNC:53274"  ; level 2 ; orig_coord_info "chr15,31216021,31216037,+"  ; tag dotter_confirmed ; transcript_id "KLF13--LINC02352^ENST00000557928.1"  ; transcript_name "LINC02352-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
METAP1--BTF3P13	HAVANA	gene	22946	23435	.	+	.	FI_gene_label "BTF3P13^ENSG00000227118.3"  ; ID "METAP1--BTF3P13^BTF3P13^ENSG00000227118.3"  ; exon_id "ENSE00002024060.1"  ; exon_number 1 ; gene_id "METAP1--BTF3P13^BTF3P13^ENSG00000227118.3"  ; gene_name BTF3P13 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161089.1"  ; havana_transcript "OTTHUMT00000363738.1"  ; hgnc_id "HGNC:1128"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr4,98740742,98741231,+"  ; tag pseudo_consens basic ; transcript_id "METAP1--BTF3P13^ENST00000513224.1"  ; transcript_name "BTF3P13-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
METAP1--BTF3P13	HAVANA	RNA	22946	23435	.	+	.	FI_gene_label "BTF3P13^ENSG00000227118.3"  ; ID "METAP1--BTF3P13^ENST00000513224.1"  ; Parent "METAP1--BTF3P13^BTF3P13^ENSG00000227118.3"  ; exon_id "ENSE00002024060.1"  ; exon_number 1 ; gene_id "METAP1--BTF3P13^BTF3P13^ENSG00000227118.3"  ; gene_name BTF3P13 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161089.1"  ; havana_transcript "OTTHUMT00000363738.1"  ; hgnc_id "HGNC:1128"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr4,98740742,98741231,+"  ; tag pseudo_consens basic ; transcript_id "METAP1--BTF3P13^ENST00000513224.1"  ; transcript_name "BTF3P13-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
399 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 1 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
967 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 1 second) ------                   


GFF3 file parsed