.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-606237-R1_A23WJ53LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/40aa337ef01ebe1172ed1c401e8692/.command.out
Size: 78.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-606237-R1_A23WJ53LT4_1)
Attempt
Content

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: 4418
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4418
=> 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:4418
  => 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: 
ADAM9--ZMAT4	HAVANA	gene	42020	55703	.	+	.	FI_gene_label "ZMAT4^ENSG00000165061.15"  ; ID "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15"  ; ccdsid "CCDS34885.1"  ; exon_id "ENSE00003606486.1"  ; exon_number 2 ; gene_id "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15"  ; gene_name ZMAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164049.3"  ; havana_transcript "OTTHUMT00000376950.2"  ; hgnc_id "HGNC:25844"  ; level 2 ; orig_coord_info "chr8,40825575,40825676,-"  ; protein_id "ENSP00000297737.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--ZMAT4^ENST00000297737.11"  ; transcript_name "ZMAT4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ADAM9--ZMAT4	HAVANA	mRNA	42020	55703	.	+	.	FI_gene_label "ZMAT4^ENSG00000165061.15"  ; ID "ADAM9--ZMAT4^ENST00000297737.11"  ; Parent "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15"  ; ccdsid "CCDS34885.1"  ; exon_id "ENSE00003606486.1"  ; exon_number 2 ; gene_id "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15"  ; gene_name ZMAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164049.3"  ; havana_transcript "OTTHUMT00000376950.2"  ; hgnc_id "HGNC:25844"  ; level 2 ; orig_coord_info "chr8,40825575,40825676,-"  ; protein_id "ENSP00000297737.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--ZMAT4^ENST00000297737.11"  ; transcript_name "ZMAT4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ADAM9--ZMAT4	HAVANA	gene	1273	38711	.	+	.	FI_gene_label "ADAM9^ENSG00000168615.13"  ; ID "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13"  ; exon_id "ENSE00001854428.1"  ; exon_number 1 ; gene_id "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13"  ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5"  ; havana_transcript "OTTHUMT00000357297.1"  ; hgnc_id "HGNC:216"  ; level 2 ; orig_coord_info "chr8,38997064,38997160,+"  ; protein_id "ENSP00000369249.3"  ; transcript_id "ADAM9--ZMAT4^ENST00000379917.7"  ; transcript_name "ADAM9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ADAM9--ZMAT4	HAVANA	mRNA	1273	38711	.	+	.	FI_gene_label "ADAM9^ENSG00000168615.13"  ; ID "ADAM9--ZMAT4^ENST00000379917.7"  ; Parent "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13"  ; exon_id "ENSE00001854428.1"  ; exon_number 1 ; gene_id "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13"  ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5"  ; havana_transcript "OTTHUMT00000357297.1"  ; hgnc_id "HGNC:216"  ; level 2 ; orig_coord_info "chr8,38997064,38997160,+"  ; protein_id "ENSP00000369249.3"  ; transcript_id "ADAM9--ZMAT4^ENST00000379917.7"  ; transcript_name "ADAM9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
AXIN1--GGA2	HAVANA	gene	1001	16032	.	+	.	FI_gene_label "AXIN1^ENSG00000103126.15"  ; ID "AXIN1--GGA2^AXIN1^ENSG00000103126.15"  ; ccdsid "CCDS10405.1"  ; exon_id "ENSE00001331290.2"  ; exon_number 2 ; gene_id "AXIN1--GGA2^AXIN1^ENSG00000103126.15"  ; gene_name AXIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000064930.5"  ; havana_transcript "OTTHUMT00000139441.4"  ; hgnc_id "HGNC:903"  ; level 2 ; orig_coord_info "chr16,346148,347025,-"  ; protein_id "ENSP00000262320.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AXIN1--GGA2^ENST00000262320.8"  ; transcript_name "AXIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AXIN1--GGA2	HAVANA	mRNA	1001	16032	.	+	.	FI_gene_label "AXIN1^ENSG00000103126.15"  ; ID "AXIN1--GGA2^ENST00000262320.8"  ; Parent "AXIN1--GGA2^AXIN1^ENSG00000103126.15"  ; ccdsid "CCDS10405.1"  ; exon_id "ENSE00001331290.2"  ; exon_number 2 ; gene_id "AXIN1--GGA2^AXIN1^ENSG00000103126.15"  ; gene_name AXIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000064930.5"  ; havana_transcript "OTTHUMT00000139441.4"  ; hgnc_id "HGNC:903"  ; level 2 ; orig_coord_info "chr16,346148,347025,-"  ; protein_id "ENSP00000262320.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AXIN1--GGA2^ENST00000262320.8"  ; transcript_name "AXIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AXIN1--GGA2	HAVANA	gene	21289	41972	.	+	.	FI_gene_label "GGA2^ENSG00000103365.15"  ; ID "AXIN1--GGA2^GGA2^ENSG00000103365.15"  ; ccdsid "CCDS10611.1"  ; exon_id "ENSE00003495136.1"  ; exon_number 1 ; gene_id "AXIN1--GGA2^GGA2^ENSG00000103365.15"  ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5"  ; havana_transcript "OTTHUMT00000214019.1"  ; hgnc_id "HGNC:16064"  ; level 2 ; orig_coord_info "chr16,23510321,23510411,-"  ; protein_id "ENSP00000311962.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AXIN1--GGA2^ENST00000309859.8"  ; transcript_name "GGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AXIN1--GGA2	HAVANA	mRNA	21289	41972	.	+	.	FI_gene_label "GGA2^ENSG00000103365.15"  ; ID "AXIN1--GGA2^ENST00000309859.8"  ; Parent "AXIN1--GGA2^GGA2^ENSG00000103365.15"  ; ccdsid "CCDS10611.1"  ; exon_id "ENSE00003495136.1"  ; exon_number 1 ; gene_id "AXIN1--GGA2^GGA2^ENSG00000103365.15"  ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5"  ; havana_transcript "OTTHUMT00000214019.1"  ; hgnc_id "HGNC:16064"  ; level 2 ; orig_coord_info "chr16,23510321,23510411,-"  ; protein_id "ENSP00000311962.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AXIN1--GGA2^ENST00000309859.8"  ; transcript_name "GGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COX6CP1--COX6C	HAVANA	gene	4239	10289	.	+	.	FI_gene_label "COX6C^ENSG00000164919.11"  ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; ccdsid "CCDS6284.1"  ; exon_id "ENSE00002129072.1"  ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6"  ; havana_transcript "OTTHUMT00000379835.1"  ; hgnc_id "HGNC:2285"  ; level 2 ; orig_coord_info "chr8,99891908,99892021,-"  ; protein_id "ENSP00000297564.2"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6"  ; transcript_name "COX6C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
COX6CP1--COX6C	HAVANA	mRNA	4239	10289	.	+	.	FI_gene_label "COX6C^ENSG00000164919.11"  ; ID "COX6CP1--COX6C^ENST00000297564.6"  ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; ccdsid "CCDS6284.1"  ; exon_id "ENSE00002129072.1"  ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11"  ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6"  ; havana_transcript "OTTHUMT00000379835.1"  ; hgnc_id "HGNC:2285"  ; level 2 ; orig_coord_info "chr8,99891908,99892021,-"  ; protein_id "ENSP00000297564.2"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6"  ; transcript_name "COX6C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B	HAVANA	mRNA	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^ENST00000308284.10"  ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DCTN5--MRPL28	HAVANA	gene	23801	27370	.	+	.	FI_gene_label "MRPL28^ENSG00000086504.17"  ; ID "DCTN5--MRPL28^MRPL28^ENSG00000086504.17"  ; ccdsid "CCDS32349.1"  ; exon_id "ENSE00003622338.1"  ; exon_number 2 ; gene_id "DCTN5--MRPL28^MRPL28^ENSG00000086504.17"  ; gene_name MRPL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047994.9"  ; havana_transcript "OTTHUMT00000139285.3"  ; hgnc_id "HGNC:14484"  ; level 2 ; orig_coord_info "chr16,369931,370218,-"  ; protein_id "ENSP00000199706.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000199706.13"  ; transcript_name "MRPL28-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DCTN5--MRPL28	HAVANA	mRNA	23801	27370	.	+	.	FI_gene_label "MRPL28^ENSG00000086504.17"  ; ID "DCTN5--MRPL28^ENST00000199706.13"  ; Parent "DCTN5--MRPL28^MRPL28^ENSG00000086504.17"  ; ccdsid "CCDS32349.1"  ; exon_id "ENSE00003622338.1"  ; exon_number 2 ; gene_id "DCTN5--MRPL28^MRPL28^ENSG00000086504.17"  ; gene_name MRPL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047994.9"  ; havana_transcript "OTTHUMT00000139285.3"  ; hgnc_id "HGNC:14484"  ; level 2 ; orig_coord_info "chr16,369931,370218,-"  ; protein_id "ENSP00000199706.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000199706.13"  ; transcript_name "MRPL28-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DCTN5--MRPL28	HAVANA	gene	1001	20049	.	+	.	FI_gene_label "DCTN5^ENSG00000166847.10"  ; ID "DCTN5--MRPL28^DCTN5^ENSG00000166847.10"  ; ccdsid "CCDS10615.1"  ; exon_id "ENSE00001830153.2"  ; exon_number 1 ; gene_id "DCTN5--MRPL28^DCTN5^ENSG00000166847.10"  ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7"  ; havana_transcript "OTTHUMT00000254497.3"  ; hgnc_id "HGNC:24594"  ; level 2 ; orig_coord_info "chr16,23641543,23641590,+"  ; protein_id "ENSP00000300087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000300087.7"  ; transcript_name "DCTN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DCTN5--MRPL28	HAVANA	mRNA	1001	20049	.	+	.	FI_gene_label "DCTN5^ENSG00000166847.10"  ; ID "DCTN5--MRPL28^ENST00000300087.7"  ; Parent "DCTN5--MRPL28^DCTN5^ENSG00000166847.10"  ; ccdsid "CCDS10615.1"  ; exon_id "ENSE00001830153.2"  ; exon_number 1 ; gene_id "DCTN5--MRPL28^DCTN5^ENSG00000166847.10"  ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7"  ; havana_transcript "OTTHUMT00000254497.3"  ; hgnc_id "HGNC:24594"  ; level 2 ; orig_coord_info "chr16,23641543,23641590,+"  ; protein_id "ENSP00000300087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000300087.7"  ; transcript_name "DCTN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GGA2--WARS2-AS1	HAVANA	gene	3257	23940	.	+	.	FI_gene_label "GGA2^ENSG00000103365.15"  ; ID "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15"  ; ccdsid "CCDS10611.1"  ; exon_id "ENSE00003495136.1"  ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15"  ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5"  ; havana_transcript "OTTHUMT00000214019.1"  ; hgnc_id "HGNC:16064"  ; level 2 ; orig_coord_info "chr16,23510321,23510411,-"  ; protein_id "ENSP00000311962.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA2--WARS2-AS1^ENST00000309859.8"  ; transcript_name "GGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GGA2--WARS2-AS1	HAVANA	mRNA	3257	23940	.	+	.	FI_gene_label "GGA2^ENSG00000103365.15"  ; ID "GGA2--WARS2-AS1^ENST00000309859.8"  ; Parent "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15"  ; ccdsid "CCDS10611.1"  ; exon_id "ENSE00003495136.1"  ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15"  ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5"  ; havana_transcript "OTTHUMT00000214019.1"  ; hgnc_id "HGNC:16064"  ; level 2 ; orig_coord_info "chr16,23510321,23510411,-"  ; protein_id "ENSP00000311962.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA2--WARS2-AS1^ENST00000309859.8"  ; transcript_name "GGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP3K1--LMNB1	HAVANA	gene	25964	39721	.	+	.	FI_gene_label "LMNB1^ENSG00000113368.12"  ; ID "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12"  ; ccdsid "CCDS4140.1"  ; exon_id "ENSE00001294154.7"  ; exon_number 1 ; gene_id "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12"  ; gene_name LMNB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128969.8"  ; havana_transcript "OTTHUMT00000250956.3"  ; hgnc_id "HGNC:6637"  ; level 2 ; orig_coord_info "chr5,126777509,126777867,+"  ; protein_id "ENSP00000261366.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000261366.10"  ; transcript_name "LMNB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--LMNB1	HAVANA	mRNA	25964	39721	.	+	.	FI_gene_label "LMNB1^ENSG00000113368.12"  ; ID "MAP3K1--LMNB1^ENST00000261366.10"  ; Parent "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12"  ; ccdsid "CCDS4140.1"  ; exon_id "ENSE00001294154.7"  ; exon_number 1 ; gene_id "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12"  ; gene_name LMNB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128969.8"  ; havana_transcript "OTTHUMT00000250956.3"  ; hgnc_id "HGNC:6637"  ; level 2 ; orig_coord_info "chr5,126777509,126777867,+"  ; protein_id "ENSP00000261366.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000261366.10"  ; transcript_name "LMNB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP3K1--LMNB1	HAVANA	gene	1001	22450	.	+	.	FI_gene_label "MAP3K1^ENSG00000095015.6"  ; ID "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6"  ; ccdsid "CCDS43318.1"  ; exon_id "ENSE00001538799.4"  ; exon_number 1 ; gene_id "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6"  ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3"  ; havana_transcript "OTTHUMT00000132309.3"  ; hgnc_id "HGNC:6848"  ; level 1 ; orig_coord_info "chr5,56815574,56816055,+"  ; protein_id "ENSP00000382423.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000399503.4"  ; transcript_name "MAP3K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--LMNB1	HAVANA	mRNA	1001	22450	.	+	.	FI_gene_label "MAP3K1^ENSG00000095015.6"  ; ID "MAP3K1--LMNB1^ENST00000399503.4"  ; Parent "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6"  ; ccdsid "CCDS43318.1"  ; exon_id "ENSE00001538799.4"  ; exon_number 1 ; gene_id "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6"  ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3"  ; havana_transcript "OTTHUMT00000132309.3"  ; hgnc_id "HGNC:6848"  ; level 1 ; orig_coord_info "chr5,56815574,56816055,+"  ; protein_id "ENSP00000382423.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000399503.4"  ; transcript_name "MAP3K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP3K1--MARCHF3	HAVANA	gene	25451	36559	.	+	.	FI_gene_label "MARCHF3^ENSG00000173926.6"  ; ID "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6"  ; ccdsid "CCDS4141.1"  ; exon_id "ENSE00003676575.1"  ; exon_number 2 ; gene_id "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6"  ; gene_name MARCHF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128968.4"  ; havana_transcript "OTTHUMT00000250955.3"  ; hgnc_id "HGNC:28728"  ; level 2 ; orig_coord_info "chr5,126917984,126918171,-"  ; protein_id "ENSP00000309141.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000308660.6"  ; transcript_name "MARCHF3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--MARCHF3	HAVANA	mRNA	25451	36559	.	+	.	FI_gene_label "MARCHF3^ENSG00000173926.6"  ; ID "MAP3K1--MARCHF3^ENST00000308660.6"  ; Parent "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6"  ; ccdsid "CCDS4141.1"  ; exon_id "ENSE00003676575.1"  ; exon_number 2 ; gene_id "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6"  ; gene_name MARCHF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128968.4"  ; havana_transcript "OTTHUMT00000250955.3"  ; hgnc_id "HGNC:28728"  ; level 2 ; orig_coord_info "chr5,126917984,126918171,-"  ; protein_id "ENSP00000309141.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000308660.6"  ; transcript_name "MARCHF3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP3K1--MARCHF3	HAVANA	gene	1001	22450	.	+	.	FI_gene_label "MAP3K1^ENSG00000095015.6"  ; ID "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6"  ; ccdsid "CCDS43318.1"  ; exon_id "ENSE00001538799.4"  ; exon_number 1 ; gene_id "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6"  ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3"  ; havana_transcript "OTTHUMT00000132309.3"  ; hgnc_id "HGNC:6848"  ; level 1 ; orig_coord_info "chr5,56815574,56816055,+"  ; protein_id "ENSP00000382423.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000399503.4"  ; transcript_name "MAP3K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--MARCHF3	HAVANA	mRNA	1001	22450	.	+	.	FI_gene_label "MAP3K1^ENSG00000095015.6"  ; ID "MAP3K1--MARCHF3^ENST00000399503.4"  ; Parent "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6"  ; ccdsid "CCDS43318.1"  ; exon_id "ENSE00001538799.4"  ; exon_number 1 ; gene_id "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6"  ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3"  ; havana_transcript "OTTHUMT00000132309.3"  ; hgnc_id "HGNC:6848"  ; level 1 ; orig_coord_info "chr5,56815574,56816055,+"  ; protein_id "ENSP00000382423.3"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000399503.4"  ; transcript_name "MAP3K1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PDE7A--CLVS1	HAVANA	gene	32042	48239	.	+	.	FI_gene_label "CLVS1^ENSG00000177182.11"  ; ID "PDE7A--CLVS1^CLVS1^ENSG00000177182.11"  ; ccdsid "CCDS6176.1"  ; exon_id "ENSE00001087276.4"  ; exon_number 2 ; gene_id "PDE7A--CLVS1^CLVS1^ENSG00000177182.11"  ; gene_name CLVS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164334.8"  ; havana_transcript "OTTHUMT00000378326.2"  ; hgnc_id "HGNC:23139"  ; level 2 ; orig_coord_info "chr8,61299828,61300282,+"  ; protein_id "ENSP00000325506.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000325897.5"  ; transcript_name "CLVS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PDE7A--CLVS1	HAVANA	mRNA	32042	48239	.	+	.	FI_gene_label "CLVS1^ENSG00000177182.11"  ; ID "PDE7A--CLVS1^ENST00000325897.5"  ; Parent "PDE7A--CLVS1^CLVS1^ENSG00000177182.11"  ; ccdsid "CCDS6176.1"  ; exon_id "ENSE00001087276.4"  ; exon_number 2 ; gene_id "PDE7A--CLVS1^CLVS1^ENSG00000177182.11"  ; gene_name CLVS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164334.8"  ; havana_transcript "OTTHUMT00000378326.2"  ; hgnc_id "HGNC:23139"  ; level 2 ; orig_coord_info "chr8,61299828,61300282,+"  ; protein_id "ENSP00000325506.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000325897.5"  ; transcript_name "CLVS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PDE7A--CLVS1	HAVANA	gene	4228	22817	.	+	.	FI_gene_label "PDE7A^ENSG00000205268.11"  ; ID "PDE7A--CLVS1^PDE7A^ENSG00000205268.11"  ; ccdsid "CCDS34901.1"  ; exon_id "ENSE00001480936.4"  ; exon_number 1 ; gene_id "PDE7A--CLVS1^PDE7A^ENSG00000205268.11"  ; gene_name PDE7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000164469.3"  ; havana_transcript "OTTHUMT00000378906.1"  ; hgnc_id "HGNC:8791"  ; level 2 ; orig_coord_info "chr8,65788882,65788941,-"  ; protein_id "ENSP00000368730.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000379419.8"  ; transcript_name "PDE7A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PDE7A--CLVS1	HAVANA	mRNA	4228	22817	.	+	.	FI_gene_label "PDE7A^ENSG00000205268.11"  ; ID "PDE7A--CLVS1^ENST00000379419.8"  ; Parent "PDE7A--CLVS1^PDE7A^ENSG00000205268.11"  ; ccdsid "CCDS34901.1"  ; exon_id "ENSE00001480936.4"  ; exon_number 1 ; gene_id "PDE7A--CLVS1^PDE7A^ENSG00000205268.11"  ; gene_name PDE7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000164469.3"  ; havana_transcript "OTTHUMT00000378906.1"  ; hgnc_id "HGNC:8791"  ; level 2 ; orig_coord_info "chr8,65788882,65788941,-"  ; protein_id "ENSP00000368730.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000379419.8"  ; transcript_name "PDE7A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RAB11FIP3--DCTN5	HAVANA	gene	1001	19602	.	+	.	FI_gene_label "RAB11FIP3^ENSG00000090565.17"  ; ID "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17"  ; ccdsid "CCDS32351.1"  ; exon_id "ENSE00002222336.2"  ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17"  ; gene_name RAB11FIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047843.9"  ; havana_transcript "OTTHUMT00000109066.5"  ; hgnc_id "HGNC:17224"  ; level 2 ; orig_coord_info "chr16,426007,426720,+"  ; protein_id "ENSP00000262305.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000262305.9"  ; transcript_name "RAB11FIP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAB11FIP3--DCTN5	HAVANA	mRNA	1001	19602	.	+	.	FI_gene_label "RAB11FIP3^ENSG00000090565.17"  ; ID "RAB11FIP3--DCTN5^ENST00000262305.9"  ; Parent "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17"  ; ccdsid "CCDS32351.1"  ; exon_id "ENSE00002222336.2"  ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17"  ; gene_name RAB11FIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047843.9"  ; havana_transcript "OTTHUMT00000109066.5"  ; hgnc_id "HGNC:17224"  ; level 2 ; orig_coord_info "chr16,426007,426720,+"  ; protein_id "ENSP00000262305.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000262305.9"  ; transcript_name "RAB11FIP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAB11FIP3--DCTN5	HAVANA	gene	22603	41651	.	+	.	FI_gene_label "DCTN5^ENSG00000166847.10"  ; ID "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10"  ; ccdsid "CCDS10615.1"  ; exon_id "ENSE00001830153.2"  ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10"  ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7"  ; havana_transcript "OTTHUMT00000254497.3"  ; hgnc_id "HGNC:24594"  ; level 2 ; orig_coord_info "chr16,23641543,23641590,+"  ; protein_id "ENSP00000300087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000300087.7"  ; transcript_name "DCTN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAB11FIP3--DCTN5	HAVANA	mRNA	22603	41651	.	+	.	FI_gene_label "DCTN5^ENSG00000166847.10"  ; ID "RAB11FIP3--DCTN5^ENST00000300087.7"  ; Parent "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10"  ; ccdsid "CCDS10615.1"  ; exon_id "ENSE00001830153.2"  ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10"  ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7"  ; havana_transcript "OTTHUMT00000254497.3"  ; hgnc_id "HGNC:24594"  ; level 2 ; orig_coord_info "chr16,23641543,23641590,+"  ; protein_id "ENSP00000300087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000300087.7"  ; transcript_name "DCTN5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4	HAVANA	gene	15043	21268	.	+	.	FI_gene_label "RBM4^ENSG00000173933.21"  ; ID "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; ccdsid "CCDS41676.1"  ; exon_id "ENSE00003513724.1"  ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7"  ; havana_transcript "OTTHUMT00000334210.2"  ; hgnc_id "HGNC:9901"  ; level 2 ; orig_coord_info "chr11,66639712,66640123,+"  ; protein_id "ENSP00000309166.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12"  ; transcript_name "RBM4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4	HAVANA	mRNA	15043	21268	.	+	.	FI_gene_label "RBM4^ENSG00000173933.21"  ; ID "RBM14--RBM4^ENST00000310092.12"  ; Parent "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; ccdsid "CCDS41676.1"  ; exon_id "ENSE00003513724.1"  ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7"  ; havana_transcript "OTTHUMT00000334210.2"  ; hgnc_id "HGNC:9901"  ; level 2 ; orig_coord_info "chr11,66639712,66640123,+"  ; protein_id "ENSP00000309166.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12"  ; transcript_name "RBM4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4	HAVANA	gene	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5"  ; havana_transcript "OTTHUMT00000277128.1"  ; hgnc_id "HGNC:14219"  ; level 2 ; orig_coord_info "chr11,66616721,66617057,+"  ; protein_id "ENSP00000311747.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4	HAVANA	mRNA	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4^ENST00000310137.5"  ; Parent "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5"  ; havana_transcript "OTTHUMT00000277128.1"  ; hgnc_id "HGNC:14219"  ; level 2 ; orig_coord_info "chr11,66616721,66617057,+"  ; protein_id "ENSP00000311747.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCML2--AC095353.1	HAVANA	gene	1001	20080	.	+	.	FI_gene_label "SCML2^ENSG00000102098.19"  ; ID "SCML2--AC095353.1^SCML2^ENSG00000102098.19"  ; ccdsid "CCDS14185.1"  ; exon_id "ENSE00002285630.1"  ; exon_number 2 ; gene_id "SCML2--AC095353.1^SCML2^ENSG00000102098.19"  ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4"  ; havana_transcript "OTTHUMT00000055941.2"  ; hgnc_id "HGNC:10581"  ; level 2 ; orig_coord_info "chrX,18334050,18334071,-"  ; protein_id "ENSP00000251900.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC095353.1^ENST00000251900.9"  ; transcript_name "SCML2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCML2--AC095353.1	HAVANA	mRNA	1001	20080	.	+	.	FI_gene_label "SCML2^ENSG00000102098.19"  ; ID "SCML2--AC095353.1^ENST00000251900.9"  ; Parent "SCML2--AC095353.1^SCML2^ENSG00000102098.19"  ; ccdsid "CCDS14185.1"  ; exon_id "ENSE00002285630.1"  ; exon_number 2 ; gene_id "SCML2--AC095353.1^SCML2^ENSG00000102098.19"  ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4"  ; havana_transcript "OTTHUMT00000055941.2"  ; hgnc_id "HGNC:10581"  ; level 2 ; orig_coord_info "chrX,18334050,18334071,-"  ; protein_id "ENSP00000251900.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC095353.1^ENST00000251900.9"  ; transcript_name "SCML2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCML2--AC110995.1	HAVANA	gene	1001	20080	.	+	.	FI_gene_label "SCML2^ENSG00000102098.19"  ; ID "SCML2--AC110995.1^SCML2^ENSG00000102098.19"  ; ccdsid "CCDS14185.1"  ; exon_id "ENSE00002285630.1"  ; exon_number 2 ; gene_id "SCML2--AC110995.1^SCML2^ENSG00000102098.19"  ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4"  ; havana_transcript "OTTHUMT00000055941.2"  ; hgnc_id "HGNC:10581"  ; level 2 ; orig_coord_info "chrX,18334050,18334071,-"  ; protein_id "ENSP00000251900.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC110995.1^ENST00000251900.9"  ; transcript_name "SCML2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCML2--AC110995.1	HAVANA	mRNA	1001	20080	.	+	.	FI_gene_label "SCML2^ENSG00000102098.19"  ; ID "SCML2--AC110995.1^ENST00000251900.9"  ; Parent "SCML2--AC110995.1^SCML2^ENSG00000102098.19"  ; ccdsid "CCDS14185.1"  ; exon_id "ENSE00002285630.1"  ; exon_number 2 ; gene_id "SCML2--AC110995.1^SCML2^ENSG00000102098.19"  ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4"  ; havana_transcript "OTTHUMT00000055941.2"  ; hgnc_id "HGNC:10581"  ; level 2 ; orig_coord_info "chrX,18334050,18334071,-"  ; protein_id "ENSP00000251900.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC110995.1^ENST00000251900.9"  ; transcript_name "SCML2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLCO1B3--SLCO1B7	ENSEMBL	gene	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLCO1B3--SLCO1B7	ENSEMBL	mRNA	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNX29--MRTFB	ENSEMBL	gene	42313	78553	.	+	.	FI_gene_label "MRTFB^ENSG00000186260.17"  ; ID "SNX29--MRTFB^MRTFB^ENSG00000186260.17"  ; ccdsid "CCDS32391.1"  ; exon_id "ENSE00003525727.1"  ; exon_number 2 ; gene_id "SNX29--MRTFB^MRTFB^ENSG00000186260.17"  ; gene_name MRTFB ; gene_type protein_coding ; havana_gene "OTTHUMG00000177379.3"  ; hgnc_id "HGNC:29819"  ; level 3 ; orig_coord_info "chr16,14140607,14140760,+"  ; protein_id "ENSP00000339086.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SNX29--MRTFB^ENST00000318282.9"  ; transcript_name "MRTFB-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SNX29--MRTFB	ENSEMBL	mRNA	42313	78553	.	+	.	FI_gene_label "MRTFB^ENSG00000186260.17"  ; ID "SNX29--MRTFB^ENST00000318282.9"  ; Parent "SNX29--MRTFB^MRTFB^ENSG00000186260.17"  ; ccdsid "CCDS32391.1"  ; exon_id "ENSE00003525727.1"  ; exon_number 2 ; gene_id "SNX29--MRTFB^MRTFB^ENSG00000186260.17"  ; gene_name MRTFB ; gene_type protein_coding ; havana_gene "OTTHUMG00000177379.3"  ; hgnc_id "HGNC:29819"  ; level 3 ; orig_coord_info "chr16,14140607,14140760,+"  ; protein_id "ENSP00000339086.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SNX29--MRTFB^ENST00000318282.9"  ; transcript_name "MRTFB-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SNX29--MRTFB	HAVANA	gene	23819	27354	.	+	.	FI_gene_label "SNX29^ENSG00000048471.14"  ; ID "SNX29--MRTFB^SNX29^ENSG00000048471.14"  ; exon_id "ENSE00002616399.1"  ; exon_number 1 ; gene_id "SNX29--MRTFB^SNX29^ENSG00000048471.14"  ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4"  ; havana_transcript "OTTHUMT00000422625.1"  ; hgnc_id "HGNC:30542"  ; level 2 ; orig_coord_info "chr16,12356253,12356279,+"  ; protein_id "ENSP00000455327.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--MRTFB^ENST00000562510.1"  ; transcript_name "SNX29-201"  ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--MRTFB	HAVANA	mRNA	23819	27354	.	+	.	FI_gene_label "SNX29^ENSG00000048471.14"  ; ID "SNX29--MRTFB^ENST00000562510.1"  ; Parent "SNX29--MRTFB^SNX29^ENSG00000048471.14"  ; exon_id "ENSE00002616399.1"  ; exon_number 1 ; gene_id "SNX29--MRTFB^SNX29^ENSG00000048471.14"  ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4"  ; havana_transcript "OTTHUMT00000422625.1"  ; hgnc_id "HGNC:30542"  ; level 2 ; orig_coord_info "chr16,12356253,12356279,+"  ; protein_id "ENSP00000455327.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--MRTFB^ENST00000562510.1"  ; transcript_name "SNX29-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STARD13--MTUS2	HAVANA	gene	7683	28646	.	+	.	FI_gene_label "STARD13^ENSG00000133121.21"  ; ID "STARD13--MTUS2^STARD13^ENSG00000133121.21"  ; ccdsid "CCDS9349.1"  ; exon_id "ENSE00001333091.2"  ; exon_number 1 ; gene_id "STARD13--MTUS2^STARD13^ENSG00000133121.21"  ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8"  ; havana_transcript "OTTHUMT00000044439.3"  ; hgnc_id "HGNC:19164"  ; level 2 ; orig_coord_info "chr13,33185878,33186022,-"  ; protein_id "ENSP00000255486.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--MTUS2^ENST00000255486.8"  ; transcript_name "STARD13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STARD13--MTUS2	HAVANA	mRNA	7683	28646	.	+	.	FI_gene_label "STARD13^ENSG00000133121.21"  ; ID "STARD13--MTUS2^ENST00000255486.8"  ; Parent "STARD13--MTUS2^STARD13^ENSG00000133121.21"  ; ccdsid "CCDS9349.1"  ; exon_id "ENSE00001333091.2"  ; exon_number 1 ; gene_id "STARD13--MTUS2^STARD13^ENSG00000133121.21"  ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8"  ; havana_transcript "OTTHUMT00000044439.3"  ; hgnc_id "HGNC:19164"  ; level 2 ; orig_coord_info "chr13,33185878,33186022,-"  ; protein_id "ENSP00000255486.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--MTUS2^ENST00000255486.8"  ; transcript_name "STARD13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STARD13--MTUS2	HAVANA	gene	44573	55337	.	+	.	FI_gene_label "MTUS2^ENSG00000132938.22"  ; ID "STARD13--MTUS2^MTUS2^ENSG00000132938.22"  ; ccdsid "CCDS41874.1"  ; exon_id "ENSE00001486334.1"  ; exon_number 1 ; gene_id "STARD13--MTUS2^MTUS2^ENSG00000132938.22"  ; gene_name MTUS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016657.6"  ; havana_transcript "OTTHUMT00000044335.2"  ; hgnc_id "HGNC:20595"  ; level 2 ; orig_coord_info "chr13,29428843,29428896,+"  ; protein_id "ENSP00000370186.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "STARD13--MTUS2^ENST00000380808.6"  ; transcript_name "MTUS2-202"  ; transcript_support_level 1 ; transcript_type protein_coding
STARD13--MTUS2	HAVANA	mRNA	44573	55337	.	+	.	FI_gene_label "MTUS2^ENSG00000132938.22"  ; ID "STARD13--MTUS2^ENST00000380808.6"  ; Parent "STARD13--MTUS2^MTUS2^ENSG00000132938.22"  ; ccdsid "CCDS41874.1"  ; exon_id "ENSE00001486334.1"  ; exon_number 1 ; gene_id "STARD13--MTUS2^MTUS2^ENSG00000132938.22"  ; gene_name MTUS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016657.6"  ; havana_transcript "OTTHUMT00000044335.2"  ; hgnc_id "HGNC:20595"  ; level 2 ; orig_coord_info "chr13,29428843,29428896,+"  ; protein_id "ENSP00000370186.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "STARD13--MTUS2^ENST00000380808.6"  ; transcript_name "MTUS2-202"  ; 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: 
TARS3--TM2D3	HAVANA	gene	29125	36112	.	+	.	FI_gene_label "TM2D3^ENSG00000184277.13"  ; ID "TARS3--TM2D3^TM2D3^ENSG00000184277.13"  ; ccdsid "CCDS10393.1"  ; exon_id "ENSE00001838012.2"  ; exon_number 1 ; gene_id "TARS3--TM2D3^TM2D3^ENSG00000184277.13"  ; gene_name TM2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149872.5"  ; havana_transcript "OTTHUMT00000313623.2"  ; hgnc_id "HGNC:24128"  ; level 2 ; orig_coord_info "chr15,101652271,101652361,-"  ; protein_id "ENSP00000330433.3"  ; tag basic MANE_Select CCDS ; transcript_id "TARS3--TM2D3^ENST00000333202.8"  ; transcript_name "TM2D3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TARS3--TM2D3	HAVANA	mRNA	29125	36112	.	+	.	FI_gene_label "TM2D3^ENSG00000184277.13"  ; ID "TARS3--TM2D3^ENST00000333202.8"  ; Parent "TARS3--TM2D3^TM2D3^ENSG00000184277.13"  ; ccdsid "CCDS10393.1"  ; exon_id "ENSE00001838012.2"  ; exon_number 1 ; gene_id "TARS3--TM2D3^TM2D3^ENSG00000184277.13"  ; gene_name TM2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149872.5"  ; havana_transcript "OTTHUMT00000313623.2"  ; hgnc_id "HGNC:24128"  ; level 2 ; orig_coord_info "chr15,101652271,101652361,-"  ; protein_id "ENSP00000330433.3"  ; tag basic MANE_Select CCDS ; transcript_id "TARS3--TM2D3^ENST00000333202.8"  ; transcript_name "TM2D3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TARS3--TM2D3	HAVANA	gene	1001	26114	.	+	.	FI_gene_label "TARS3^ENSG00000185418.16"  ; ID "TARS3--TM2D3^TARS3^ENSG00000185418.16"  ; ccdsid "CCDS10394.1"  ; exon_id "ENSE00001876578.2"  ; exon_number 1 ; gene_id "TARS3--TM2D3^TARS3^ENSG00000185418.16"  ; gene_name TARS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149869.6"  ; havana_transcript "OTTHUMT00000313619.4"  ; hgnc_id "HGNC:24728"  ; level 2 ; orig_coord_info "chr15,101724091,101724387,-"  ; protein_id "ENSP00000338093.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TARS3--TM2D3^ENST00000335968.8"  ; transcript_name "TARS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TARS3--TM2D3	HAVANA	mRNA	1001	26114	.	+	.	FI_gene_label "TARS3^ENSG00000185418.16"  ; ID "TARS3--TM2D3^ENST00000335968.8"  ; Parent "TARS3--TM2D3^TARS3^ENSG00000185418.16"  ; ccdsid "CCDS10394.1"  ; exon_id "ENSE00001876578.2"  ; exon_number 1 ; gene_id "TARS3--TM2D3^TARS3^ENSG00000185418.16"  ; gene_name TARS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149869.6"  ; havana_transcript "OTTHUMT00000313619.4"  ; hgnc_id "HGNC:24728"  ; level 2 ; orig_coord_info "chr15,101724091,101724387,-"  ; protein_id "ENSP00000338093.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TARS3--TM2D3^ENST00000335968.8"  ; transcript_name "TARS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^ENST00000326270.13"  ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
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: 
COX6CP1--COX6C	HAVANA	gene	1001	1215	.	+	.	FI_gene_label "COX6CP1^ENSG00000260318.1"  ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; exon_id "ENSE00002587981.1"  ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1"  ; havana_transcript "OTTHUMT00000421521.1"  ; hgnc_id "HGNC:2286"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,11903923,11904137,-"  ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1"  ; transcript_name "COX6CP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
COX6CP1--COX6C	HAVANA	RNA	1001	1215	.	+	.	FI_gene_label "COX6CP1^ENSG00000260318.1"  ; ID "COX6CP1--COX6C^ENST00000564972.1"  ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; exon_id "ENSE00002587981.1"  ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1"  ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1"  ; havana_transcript "OTTHUMT00000421521.1"  ; hgnc_id "HGNC:2286"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,11903923,11904137,-"  ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1"  ; transcript_name "COX6CP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B	HAVANA	RNA	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^ENST00000462729.2"  ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created: 
GGA2--WARS2-AS1	HAVANA	gene	27280	41999	.	+	.	FI_gene_label "WARS2-AS1^ENSG00000231365.6"  ; ID "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6"  ; exon_id "ENSE00001758700.1"  ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6"  ; gene_name "WARS2-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000012342.2"  ; havana_transcript "OTTHUMT00000034378.1"  ; hgnc_id "HGNC:40612"  ; level 2 ; orig_coord_info "chr1,119140730,119140793,+"  ; transcript_id "GGA2--WARS2-AS1^ENST00000413531.5"  ; transcript_name "WARS2-AS1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
GGA2--WARS2-AS1	HAVANA	RNA	27280	41999	.	+	.	FI_gene_label "WARS2-AS1^ENSG00000231365.6"  ; ID "GGA2--WARS2-AS1^ENST00000413531.5"  ; Parent "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6"  ; exon_id "ENSE00001758700.1"  ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6"  ; gene_name "WARS2-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000012342.2"  ; havana_transcript "OTTHUMT00000034378.1"  ; hgnc_id "HGNC:40612"  ; level 2 ; orig_coord_info "chr1,119140730,119140793,+"  ; transcript_id "GGA2--WARS2-AS1^ENST00000413531.5"  ; transcript_name "WARS2-AS1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
SCML2--AC095353.1	ENSEMBL	gene	23081	23210	.	+	.	FI_gene_label "AC095353.1^ENSG00000201660.1"  ; ID "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1"  ; exon_id "ENSE00001439553.1"  ; exon_number 1 ; gene_id "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1"  ; gene_name "AC095353.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chrX,5410122,5410251,+"  ; tag basic ; transcript_id "SCML2--AC095353.1^ENST00000364790.1"  ; transcript_name "AC095353.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
SCML2--AC095353.1	ENSEMBL	RNA	23081	23210	.	+	.	FI_gene_label "AC095353.1^ENSG00000201660.1"  ; ID "SCML2--AC095353.1^ENST00000364790.1"  ; Parent "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1"  ; exon_id "ENSE00001439553.1"  ; exon_number 1 ; gene_id "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1"  ; gene_name "AC095353.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chrX,5410122,5410251,+"  ; tag basic ; transcript_id "SCML2--AC095353.1^ENST00000364790.1"  ; transcript_name "AC095353.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created: 
SCML2--AC110995.1	HAVANA	gene	23081	30004	.	+	.	FI_gene_label "AC110995.1^ENSG00000236120.7"  ; ID "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7"  ; exon_id "ENSE00001766557.2"  ; exon_number 1 ; gene_id "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7"  ; gene_name "AC110995.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000021092.4"  ; havana_transcript "OTTHUMT00000055667.2"  ; level 2 ; orig_coord_info "chrX,5725930,5726326,-"  ; tag TAGENE ; transcript_id "SCML2--AC110995.1^ENST00000422914.2"  ; transcript_name "AC110995.1-202"  ; transcript_support_level 3 ; transcript_type lncRNA
SCML2--AC110995.1	HAVANA	RNA	23081	30004	.	+	.	FI_gene_label "AC110995.1^ENSG00000236120.7"  ; ID "SCML2--AC110995.1^ENST00000422914.2"  ; Parent "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7"  ; exon_id "ENSE00001766557.2"  ; exon_number 1 ; gene_id "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7"  ; gene_name "AC110995.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000021092.4"  ; havana_transcript "OTTHUMT00000055667.2"  ; level 2 ; orig_coord_info "chrX,5725930,5726326,-"  ; tag TAGENE ; transcript_id "SCML2--AC110995.1^ENST00000422914.2"  ; transcript_name "AC110995.1-202"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
SLCO1B3--SLCO1B7	HAVANA	gene	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
SLCO1B3--SLCO1B7	HAVANA	RNA	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A	HAVANA	RNA	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^ENST00000437428.3"  ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
397 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 ------------------------------
815 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 33 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