.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (RT4_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/cfcdd75fabfd5f438f3975d9bac1e5/.command.log
Size: 77.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (RT4_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/9d0a2db61e92f1d428aa3a3d184f17/fi_workdir/RT4_FFPE_RNA_0001_B23LG7FLT4_2.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/cfcdd75fabfd5f438f3975d9bac1e5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/cfcdd75fabfd5f438f3975d9bac1e5/.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: 5690
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5690
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:5690
  => 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: 
AC079781.4--ASNS	ENSEMBL	gene	4220	16952	.	+	.	FI_gene_label "ASNS^ENSG00000070669.17"  ; ID "AC079781.4--ASNS^ASNS^ENSG00000070669.17"  ; ccdsid "CCDS5652.1"  ; exon_id "ENSE00001212450.2"  ; exon_number 4 ; gene_id "AC079781.4--ASNS^ASNS^ENSG00000070669.17"  ; gene_name ASNS ; gene_type protein_coding ; havana_gene "OTTHUMG00000022892.14"  ; hgnc_id "HGNC:753"  ; level 3 ; orig_coord_info "chr7,97868908,97869156,-"  ; protein_id "ENSP00000175506.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "AC079781.4--ASNS^ENST00000175506.8"  ; transcript_name "ASNS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC079781.4--ASNS	ENSEMBL	mRNA	4220	16952	.	+	.	FI_gene_label "ASNS^ENSG00000070669.17"  ; ID "AC079781.4--ASNS^ENST00000175506.8"  ; Parent "AC079781.4--ASNS^ASNS^ENSG00000070669.17"  ; ccdsid "CCDS5652.1"  ; exon_id "ENSE00001212450.2"  ; exon_number 4 ; gene_id "AC079781.4--ASNS^ASNS^ENSG00000070669.17"  ; gene_name ASNS ; gene_type protein_coding ; havana_gene "OTTHUMG00000022892.14"  ; hgnc_id "HGNC:753"  ; level 3 ; orig_coord_info "chr7,97868908,97869156,-"  ; protein_id "ENSP00000175506.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "AC079781.4--ASNS^ENST00000175506.8"  ; transcript_name "ASNS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADGRF1--TNFRSF21	ENSEMBL	gene	10127	22869	.	+	.	FI_gene_label "ADGRF1^ENSG00000153292.16"  ; ID "ADGRF1--TNFRSF21^ADGRF1^ENSG00000153292.16"  ; exon_id "ENSE00002279638.1"  ; exon_number 1 ; gene_id "ADGRF1--TNFRSF21^ADGRF1^ENSG00000153292.16"  ; gene_name ADGRF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014795.3"  ; hgnc_id "HGNC:18990"  ; level 3 ; orig_coord_info "chr6,47018480,47018499,-"  ; protein_id "ENSP00000283297.5"  ; tag basic ; transcript_id "ADGRF1--TNFRSF21^ENST00000283297.5"  ; transcript_name "ADGRF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADGRF1--TNFRSF21	ENSEMBL	mRNA	10127	22869	.	+	.	FI_gene_label "ADGRF1^ENSG00000153292.16"  ; ID "ADGRF1--TNFRSF21^ENST00000283297.5"  ; Parent "ADGRF1--TNFRSF21^ADGRF1^ENSG00000153292.16"  ; exon_id "ENSE00002279638.1"  ; exon_number 1 ; gene_id "ADGRF1--TNFRSF21^ADGRF1^ENSG00000153292.16"  ; gene_name ADGRF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014795.3"  ; hgnc_id "HGNC:18990"  ; level 3 ; orig_coord_info "chr6,47018480,47018499,-"  ; protein_id "ENSP00000283297.5"  ; tag basic ; transcript_id "ADGRF1--TNFRSF21^ENST00000283297.5"  ; transcript_name "ADGRF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADGRF1--TNFRSF21	HAVANA	gene	28384	36978	.	+	.	FI_gene_label "TNFRSF21^ENSG00000146072.6"  ; ID "ADGRF1--TNFRSF21^TNFRSF21^ENSG00000146072.6"  ; ccdsid "CCDS4921.1"  ; exon_id "ENSE00001226615.2"  ; exon_number 1 ; gene_id "ADGRF1--TNFRSF21^TNFRSF21^ENSG00000146072.6"  ; gene_name TNFRSF21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014796.1"  ; havana_transcript "OTTHUMT00000040814.1"  ; hgnc_id "HGNC:13469"  ; level 2 ; orig_coord_info "chr6,47309416,47309511,-"  ; protein_id "ENSP00000296861.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADGRF1--TNFRSF21^ENST00000296861.2"  ; transcript_name "TNFRSF21-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADGRF1--TNFRSF21	HAVANA	mRNA	28384	36978	.	+	.	FI_gene_label "TNFRSF21^ENSG00000146072.6"  ; ID "ADGRF1--TNFRSF21^ENST00000296861.2"  ; Parent "ADGRF1--TNFRSF21^TNFRSF21^ENSG00000146072.6"  ; ccdsid "CCDS4921.1"  ; exon_id "ENSE00001226615.2"  ; exon_number 1 ; gene_id "ADGRF1--TNFRSF21^TNFRSF21^ENSG00000146072.6"  ; gene_name TNFRSF21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014796.1"  ; havana_transcript "OTTHUMT00000040814.1"  ; hgnc_id "HGNC:13469"  ; level 2 ; orig_coord_info "chr6,47309416,47309511,-"  ; protein_id "ENSP00000296861.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADGRF1--TNFRSF21^ENST00000296861.2"  ; transcript_name "TNFRSF21-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC12--SETD2	ENSEMBL	gene	1001	11603	.	+	.	FI_gene_label "CCDC12^ENSG00000160799.11"  ; ID "CCDC12--SETD2^CCDC12^ENSG00000160799.11"  ; ccdsid "CCDS63612.1"  ; exon_id "ENSE00001604390.1"  ; exon_number 2 ; gene_id "CCDC12--SETD2^CCDC12^ENSG00000160799.11"  ; gene_name CCDC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133513.5"  ; hgnc_id "HGNC:28332"  ; level 3 ; orig_coord_info "chr3,46976637,46976771,-"  ; protein_id "ENSP00000292314.2"  ; tag basic CCDS ; transcript_id "CCDC12--SETD2^ENST00000292314.6"  ; transcript_name "CCDC12-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CCDC12--SETD2	ENSEMBL	mRNA	1001	11603	.	+	.	FI_gene_label "CCDC12^ENSG00000160799.11"  ; ID "CCDC12--SETD2^ENST00000292314.6"  ; Parent "CCDC12--SETD2^CCDC12^ENSG00000160799.11"  ; ccdsid "CCDS63612.1"  ; exon_id "ENSE00001604390.1"  ; exon_number 2 ; gene_id "CCDC12--SETD2^CCDC12^ENSG00000160799.11"  ; gene_name CCDC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133513.5"  ; hgnc_id "HGNC:28332"  ; level 3 ; orig_coord_info "chr3,46976637,46976771,-"  ; protein_id "ENSP00000292314.2"  ; tag basic CCDS ; transcript_id "CCDC12--SETD2^ENST00000292314.6"  ; transcript_name "CCDC12-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CCDC12--SETD2	HAVANA	gene	17609	46907	.	+	.	FI_gene_label "SETD2^ENSG00000181555.21"  ; ID "CCDC12--SETD2^SETD2^ENSG00000181555.21"  ; exon_id "ENSE00001424129.4"  ; exon_number 1 ; gene_id "CCDC12--SETD2^SETD2^ENSG00000181555.21"  ; gene_name SETD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133514.5"  ; havana_transcript "OTTHUMT00000277105.2"  ; hgnc_id "HGNC:18420"  ; level 2 ; orig_coord_info "chr3,47120182,47124250,-"  ; protein_id "ENSP00000332415.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CCDC12--SETD2^ENST00000330022.11"  ; transcript_name "SETD2-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
CCDC12--SETD2	HAVANA	mRNA	17609	46907	.	+	.	FI_gene_label "SETD2^ENSG00000181555.21"  ; ID "CCDC12--SETD2^ENST00000330022.11"  ; Parent "CCDC12--SETD2^SETD2^ENSG00000181555.21"  ; exon_id "ENSE00001424129.4"  ; exon_number 1 ; gene_id "CCDC12--SETD2^SETD2^ENSG00000181555.21"  ; gene_name SETD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133514.5"  ; havana_transcript "OTTHUMT00000277105.2"  ; hgnc_id "HGNC:18420"  ; level 2 ; orig_coord_info "chr3,47120182,47124250,-"  ; protein_id "ENSP00000332415.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "CCDC12--SETD2^ENST00000330022.11"  ; transcript_name "SETD2-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
CCDC169--SOHLH2	HAVANA	gene	1027	13795	.	+	.	FI_gene_label "CCDC169^ENSG00000242715.8"  ; ID "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8"  ; ccdsid "CCDS45028.1"  ; exon_id "ENSE00003461130.2"  ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8"  ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4"  ; havana_transcript "OTTHUMT00000368255.2"  ; hgnc_id "HGNC:34361"  ; level 2 ; orig_coord_info "chr13,36297637,36297719,-"  ; protein_id "ENSP00000239859.7"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8"  ; transcript_name "CCDC169-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CCDC169--SOHLH2	HAVANA	mRNA	1027	13795	.	+	.	FI_gene_label "CCDC169^ENSG00000242715.8"  ; ID "CCDC169--SOHLH2^ENST00000239859.8"  ; Parent "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8"  ; ccdsid "CCDS45028.1"  ; exon_id "ENSE00003461130.2"  ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8"  ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4"  ; havana_transcript "OTTHUMT00000368255.2"  ; hgnc_id "HGNC:34361"  ; level 2 ; orig_coord_info "chr13,36297637,36297719,-"  ; protein_id "ENSP00000239859.7"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8"  ; transcript_name "CCDC169-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CCDC169--SOHLH2	HAVANA	gene	23170	30158	.	+	.	FI_gene_label "SOHLH2^ENSG00000120669.16"  ; ID "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16"  ; ccdsid "CCDS61309.1"  ; exon_id "ENSE00001482819.2"  ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16"  ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4"  ; havana_transcript "OTTHUMT00000368257.1"  ; hgnc_id "HGNC:26026"  ; level 1 ; orig_coord_info "chr13,36214479,36214526,-"  ; protein_id "ENSP00000326838.6"  ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6"  ; transcript_name "SOHLH2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC169--SOHLH2	HAVANA	mRNA	23170	30158	.	+	.	FI_gene_label "SOHLH2^ENSG00000120669.16"  ; ID "CCDC169--SOHLH2^ENST00000317764.6"  ; Parent "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16"  ; ccdsid "CCDS61309.1"  ; exon_id "ENSE00001482819.2"  ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16"  ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4"  ; havana_transcript "OTTHUMT00000368257.1"  ; hgnc_id "HGNC:26026"  ; level 1 ; orig_coord_info "chr13,36214479,36214526,-"  ; protein_id "ENSP00000326838.6"  ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6"  ; transcript_name "SOHLH2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC43--GPATCH8	HAVANA	gene	1004	7398	.	+	.	FI_gene_label "CCDC43^ENSG00000180329.14"  ; ID "CCDC43--GPATCH8^CCDC43^ENSG00000180329.14"  ; ccdsid "CCDS45704.1"  ; exon_id "ENSE00002946779.2"  ; exon_number 1 ; gene_id "CCDC43--GPATCH8^CCDC43^ENSG00000180329.14"  ; gene_name CCDC43 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181822.2"  ; havana_transcript "OTTHUMT00000457812.2"  ; hgnc_id "HGNC:26472"  ; level 2 ; orig_coord_info "chr17,44689550,44689753,-"  ; protein_id "ENSP00000323782.7"  ; tag non_canonical_U12 basic MANE_Select appris_principal_2 CCDS ; transcript_id "CCDC43--GPATCH8^ENST00000315286.13"  ; transcript_name "CCDC43-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC43--GPATCH8	HAVANA	mRNA	1004	7398	.	+	.	FI_gene_label "CCDC43^ENSG00000180329.14"  ; ID "CCDC43--GPATCH8^ENST00000315286.13"  ; Parent "CCDC43--GPATCH8^CCDC43^ENSG00000180329.14"  ; ccdsid "CCDS45704.1"  ; exon_id "ENSE00002946779.2"  ; exon_number 1 ; gene_id "CCDC43--GPATCH8^CCDC43^ENSG00000180329.14"  ; gene_name CCDC43 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181822.2"  ; havana_transcript "OTTHUMT00000457812.2"  ; hgnc_id "HGNC:26472"  ; level 2 ; orig_coord_info "chr17,44689550,44689753,-"  ; protein_id "ENSP00000323782.7"  ; tag non_canonical_U12 basic MANE_Select appris_principal_2 CCDS ; transcript_id "CCDC43--GPATCH8^ENST00000315286.13"  ; transcript_name "CCDC43-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC43--GPATCH8	HAVANA	gene	11895	27196	.	+	.	FI_gene_label "GPATCH8^ENSG00000186566.13"  ; ID "CCDC43--GPATCH8^GPATCH8^ENSG00000186566.13"  ; exon_id "ENSE00002773197.1"  ; exon_number 1 ; gene_id "CCDC43--GPATCH8^GPATCH8^ENSG00000186566.13"  ; gene_name GPATCH8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181818.5"  ; havana_transcript "OTTHUMT00000457799.2"  ; hgnc_id "HGNC:29066"  ; level 2 ; orig_coord_info "chr17,44503326,44503370,-"  ; protein_id "ENSP00000465781.1"  ; tag cds_end_NF mRNA_end_NF ; transcript_id "CCDC43--GPATCH8^ENST00000585614.1"  ; transcript_name "GPATCH8-202"  ; transcript_support_level 3 ; transcript_type protein_coding
CCDC43--GPATCH8	HAVANA	mRNA	11895	27196	.	+	.	FI_gene_label "GPATCH8^ENSG00000186566.13"  ; ID "CCDC43--GPATCH8^ENST00000585614.1"  ; Parent "CCDC43--GPATCH8^GPATCH8^ENSG00000186566.13"  ; exon_id "ENSE00002773197.1"  ; exon_number 1 ; gene_id "CCDC43--GPATCH8^GPATCH8^ENSG00000186566.13"  ; gene_name GPATCH8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181818.5"  ; havana_transcript "OTTHUMT00000457799.2"  ; hgnc_id "HGNC:29066"  ; level 2 ; orig_coord_info "chr17,44503326,44503370,-"  ; protein_id "ENSP00000465781.1"  ; tag cds_end_NF mRNA_end_NF ; transcript_id "CCDC43--GPATCH8^ENST00000585614.1"  ; transcript_name "GPATCH8-202"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
CORO7--POLR3K	HAVANA	gene	3789	26539	.	+	.	FI_gene_label "CORO7^ENSG00000262246.6"  ; ID "CORO7--POLR3K^CORO7^ENSG00000262246.6"  ; ccdsid "CCDS10513.1"  ; exon_id "ENSE00002209549.1"  ; exon_number 1 ; gene_id "CORO7--POLR3K^CORO7^ENSG00000262246.6"  ; gene_name CORO7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129465.6"  ; havana_transcript "OTTHUMT00000251628.3"  ; hgnc_id "HGNC:26161"  ; level 2 ; orig_coord_info "chr16,4416459,4416518,-"  ; protein_id "ENSP00000251166.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CORO7--POLR3K^ENST00000251166.9"  ; transcript_name "CORO7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CORO7--POLR3K	HAVANA	mRNA	3789	26539	.	+	.	FI_gene_label "CORO7^ENSG00000262246.6"  ; ID "CORO7--POLR3K^ENST00000251166.9"  ; Parent "CORO7--POLR3K^CORO7^ENSG00000262246.6"  ; ccdsid "CCDS10513.1"  ; exon_id "ENSE00002209549.1"  ; exon_number 1 ; gene_id "CORO7--POLR3K^CORO7^ENSG00000262246.6"  ; gene_name CORO7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129465.6"  ; havana_transcript "OTTHUMT00000251628.3"  ; hgnc_id "HGNC:26161"  ; level 2 ; orig_coord_info "chr16,4416459,4416518,-"  ; protein_id "ENSP00000251166.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CORO7--POLR3K^ENST00000251166.9"  ; transcript_name "CORO7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CORO7--POLR3K	HAVANA	gene	29540	33408	.	+	.	FI_gene_label "POLR3K^ENSG00000161980.6"  ; ID "CORO7--POLR3K^POLR3K^ENSG00000161980.6"  ; ccdsid "CCDS10395.1"  ; exon_id "ENSE00001321652.8"  ; exon_number 1 ; gene_id "CORO7--POLR3K^POLR3K^ENSG00000161980.6"  ; gene_name POLR3K ; gene_type protein_coding ; havana_gene "OTTHUMG00000060722.4"  ; havana_transcript "OTTHUMT00000134192.3"  ; hgnc_id "HGNC:14121"  ; level 2 ; orig_coord_info "chr16,53476,53586,-"  ; protein_id "ENSP00000293860.5"  ; tag mRNA_start_NF basic MANE_Select appris_principal_1 CCDS ; transcript_id "CORO7--POLR3K^ENST00000293860.6"  ; transcript_name "POLR3K-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CORO7--POLR3K	HAVANA	mRNA	29540	33408	.	+	.	FI_gene_label "POLR3K^ENSG00000161980.6"  ; ID "CORO7--POLR3K^ENST00000293860.6"  ; Parent "CORO7--POLR3K^POLR3K^ENSG00000161980.6"  ; ccdsid "CCDS10395.1"  ; exon_id "ENSE00001321652.8"  ; exon_number 1 ; gene_id "CORO7--POLR3K^POLR3K^ENSG00000161980.6"  ; gene_name POLR3K ; gene_type protein_coding ; havana_gene "OTTHUMG00000060722.4"  ; havana_transcript "OTTHUMT00000134192.3"  ; hgnc_id "HGNC:14121"  ; level 2 ; orig_coord_info "chr16,53476,53586,-"  ; protein_id "ENSP00000293860.5"  ; tag mRNA_start_NF basic MANE_Select appris_principal_1 CCDS ; transcript_id "CORO7--POLR3K^ENST00000293860.6"  ; transcript_name "POLR3K-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: 
FGFR3--TACC3	HAVANA	gene	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3	HAVANA	mRNA	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^ENST00000260795.8"  ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGFR3--TACC3	HAVANA	gene	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3	HAVANA	mRNA	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^ENST00000313288.9"  ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HEATR5B--STRN	HAVANA	gene	1001	40979	.	+	.	FI_gene_label "HEATR5B^ENSG00000008869.12"  ; ID "HEATR5B--STRN^HEATR5B^ENSG00000008869.12"  ; ccdsid "CCDS33181.1"  ; exon_id "ENSE00001796147.1"  ; exon_number 2 ; gene_id "HEATR5B--STRN^HEATR5B^ENSG00000008869.12"  ; gene_name HEATR5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152158.2"  ; havana_transcript "OTTHUMT00000325492.2"  ; hgnc_id "HGNC:29273"  ; level 2 ; orig_coord_info "chr2,37083289,37083414,-"  ; protein_id "ENSP00000233099.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--STRN^ENST00000233099.6"  ; transcript_name "HEATR5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HEATR5B--STRN	HAVANA	mRNA	1001	40979	.	+	.	FI_gene_label "HEATR5B^ENSG00000008869.12"  ; ID "HEATR5B--STRN^ENST00000233099.6"  ; Parent "HEATR5B--STRN^HEATR5B^ENSG00000008869.12"  ; ccdsid "CCDS33181.1"  ; exon_id "ENSE00001796147.1"  ; exon_number 2 ; gene_id "HEATR5B--STRN^HEATR5B^ENSG00000008869.12"  ; gene_name HEATR5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152158.2"  ; havana_transcript "OTTHUMT00000325492.2"  ; hgnc_id "HGNC:29273"  ; level 2 ; orig_coord_info "chr2,37083289,37083414,-"  ; protein_id "ENSP00000233099.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--STRN^ENST00000233099.6"  ; transcript_name "HEATR5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HEATR5B--STRN	HAVANA	gene	45199	75637	.	+	.	FI_gene_label "STRN^ENSG00000115808.12"  ; ID "HEATR5B--STRN^STRN^ENSG00000115808.12"  ; ccdsid "CCDS1784.1"  ; exon_id "ENSE00001140050.2"  ; exon_number 1 ; gene_id "HEATR5B--STRN^STRN^ENSG00000115808.12"  ; gene_name STRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000100959.3"  ; havana_transcript "OTTHUMT00000218568.2"  ; hgnc_id "HGNC:11424"  ; level 2 ; orig_coord_info "chr2,36966230,36966463,-"  ; protein_id "ENSP00000263918.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--STRN^ENST00000263918.9"  ; transcript_name "STRN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HEATR5B--STRN	HAVANA	mRNA	45199	75637	.	+	.	FI_gene_label "STRN^ENSG00000115808.12"  ; ID "HEATR5B--STRN^ENST00000263918.9"  ; Parent "HEATR5B--STRN^STRN^ENSG00000115808.12"  ; ccdsid "CCDS1784.1"  ; exon_id "ENSE00001140050.2"  ; exon_number 1 ; gene_id "HEATR5B--STRN^STRN^ENSG00000115808.12"  ; gene_name STRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000100959.3"  ; havana_transcript "OTTHUMT00000218568.2"  ; hgnc_id "HGNC:11424"  ; level 2 ; orig_coord_info "chr2,36966230,36966463,-"  ; protein_id "ENSP00000263918.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--STRN^ENST00000263918.9"  ; transcript_name "STRN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IFI6--ZNF146	HAVANA	gene	1035	4703	.	+	.	FI_gene_label "IFI6^ENSG00000126709.16"  ; ID "IFI6--ZNF146^IFI6^ENSG00000126709.16"  ; ccdsid "CCDS308.1"  ; exon_id "ENSE00001384799.1"  ; exon_number 2 ; gene_id "IFI6--ZNF146^IFI6^ENSG00000126709.16"  ; gene_name IFI6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003518.2"  ; havana_transcript "OTTHUMT00000009782.1"  ; hgnc_id "HGNC:4054"  ; level 2 ; orig_coord_info "chr1,27669221,27669314,-"  ; protein_id "ENSP00000342513.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IFI6--ZNF146^ENST00000339145.8"  ; transcript_name "IFI6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
IFI6--ZNF146	HAVANA	mRNA	1035	4703	.	+	.	FI_gene_label "IFI6^ENSG00000126709.16"  ; ID "IFI6--ZNF146^ENST00000339145.8"  ; Parent "IFI6--ZNF146^IFI6^ENSG00000126709.16"  ; ccdsid "CCDS308.1"  ; exon_id "ENSE00001384799.1"  ; exon_number 2 ; gene_id "IFI6--ZNF146^IFI6^ENSG00000126709.16"  ; gene_name IFI6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003518.2"  ; havana_transcript "OTTHUMT00000009782.1"  ; hgnc_id "HGNC:4054"  ; level 2 ; orig_coord_info "chr1,27669221,27669314,-"  ; protein_id "ENSP00000342513.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IFI6--ZNF146^ENST00000339145.8"  ; transcript_name "IFI6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
IFI6--ZNF146	HAVANA	gene	8208	14843	.	+	.	FI_gene_label "ZNF146^ENSG00000167635.12"  ; ID "IFI6--ZNF146^ZNF146^ENSG00000167635.12"  ; ccdsid "CCDS12492.1"  ; exon_id "ENSE00002948655.2"  ; exon_number 4 ; gene_id "IFI6--ZNF146^ZNF146^ENSG00000167635.12"  ; gene_name ZNF146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180511.1"  ; havana_transcript "OTTHUMT00000451706.1"  ; hgnc_id "HGNC:12931"  ; level 2 ; orig_coord_info "chr19,36236441,36237316,+"  ; protein_id "ENSP00000392095.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IFI6--ZNF146^ENST00000443387.3"  ; transcript_name "ZNF146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IFI6--ZNF146	HAVANA	mRNA	8208	14843	.	+	.	FI_gene_label "ZNF146^ENSG00000167635.12"  ; ID "IFI6--ZNF146^ENST00000443387.3"  ; Parent "IFI6--ZNF146^ZNF146^ENSG00000167635.12"  ; ccdsid "CCDS12492.1"  ; exon_id "ENSE00002948655.2"  ; exon_number 4 ; gene_id "IFI6--ZNF146^ZNF146^ENSG00000167635.12"  ; gene_name ZNF146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180511.1"  ; havana_transcript "OTTHUMT00000451706.1"  ; hgnc_id "HGNC:12931"  ; level 2 ; orig_coord_info "chr19,36236441,36237316,+"  ; protein_id "ENSP00000392095.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IFI6--ZNF146^ENST00000443387.3"  ; transcript_name "ZNF146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LEKR1--PAPPA2	HAVANA	gene	1827	22526	.	+	.	FI_gene_label "LEKR1^ENSG00000197980.13"  ; ID "LEKR1--PAPPA2^LEKR1^ENSG00000197980.13"  ; exon_id "ENSE00003634949.1"  ; exon_number 2 ; gene_id "LEKR1--PAPPA2^LEKR1^ENSG00000197980.13"  ; gene_name LEKR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160130.3"  ; havana_transcript "OTTHUMT00000505261.1"  ; hgnc_id "HGNC:33765"  ; level 2 ; orig_coord_info "chr3,156829330,156829377,+"  ; protein_id "ENSP00000348936.4"  ; tag not_organism_supported basic appris_principal_1 ; transcript_id "LEKR1--PAPPA2^ENST00000356539.8"  ; transcript_name "LEKR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LEKR1--PAPPA2	HAVANA	mRNA	1827	22526	.	+	.	FI_gene_label "LEKR1^ENSG00000197980.13"  ; ID "LEKR1--PAPPA2^ENST00000356539.8"  ; Parent "LEKR1--PAPPA2^LEKR1^ENSG00000197980.13"  ; exon_id "ENSE00003634949.1"  ; exon_number 2 ; gene_id "LEKR1--PAPPA2^LEKR1^ENSG00000197980.13"  ; gene_name LEKR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160130.3"  ; havana_transcript "OTTHUMT00000505261.1"  ; hgnc_id "HGNC:33765"  ; level 2 ; orig_coord_info "chr3,156829330,156829377,+"  ; protein_id "ENSP00000348936.4"  ; tag not_organism_supported basic appris_principal_1 ; transcript_id "LEKR1--PAPPA2^ENST00000356539.8"  ; transcript_name "LEKR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
LEKR1--PAPPA2	HAVANA	gene	25527	36192	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LEKR1--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LEKR1--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LEKR1--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LEKR1--PAPPA2	HAVANA	mRNA	25527	36192	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LEKR1--PAPPA2^ENST00000367661.7"  ; Parent "LEKR1--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LEKR1--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LEKR1--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC00886--PAPPA2	HAVANA	gene	10880	21545	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC00886--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC00886--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC00886--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC00886--PAPPA2	HAVANA	mRNA	10880	21545	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC00886--PAPPA2^ENST00000367661.7"  ; Parent "LINC00886--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC00886--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC00886--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC02465--PAPPA2	HAVANA	gene	41405	52070	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC02465--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC02465--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC02465--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC02465--PAPPA2	HAVANA	mRNA	41405	52070	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC02465--PAPPA2^ENST00000367661.7"  ; Parent "LINC02465--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC02465--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC02465--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC02479--PAPPA2	HAVANA	gene	6970	17635	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC02479--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC02479--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC02479--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC02479--PAPPA2	HAVANA	mRNA	6970	17635	.	+	.	FI_gene_label "PAPPA2^ENSG00000116183.11"  ; ID "LINC02479--PAPPA2^ENST00000367661.7"  ; Parent "LINC02479--PAPPA2^PAPPA2^ENSG00000116183.11"  ; ccdsid "CCDS41439.1"  ; exon_id "ENSE00001445292.1"  ; exon_number 2 ; gene_id "LINC02479--PAPPA2^PAPPA2^ENSG00000116183.11"  ; gene_name PAPPA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035025.5"  ; havana_transcript "OTTHUMT00000084811.1"  ; hgnc_id "HGNC:14615"  ; level 2 ; orig_coord_info "chr1,176556323,176557241,+"  ; protein_id "ENSP00000356633.3"  ; tag basic CCDS ; transcript_id "LINC02479--PAPPA2^ENST00000367661.7"  ; transcript_name "PAPPA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPM1--MT-RNR2	HAVANA	gene	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4"  ; havana_transcript "OTTHUMT00000252858.2"  ; hgnc_id "HGNC:7910"  ; level 2 ; orig_coord_info "chr5,171387949,171388006,+"  ; protein_id "ENSP00000296930.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPM1--MT-RNR2	HAVANA	mRNA	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--MT-RNR2^ENST00000296930.10"  ; Parent "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14"  ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4"  ; havana_transcript "OTTHUMT00000252858.2"  ; hgnc_id "HGNC:7910"  ; level 2 ; orig_coord_info "chr5,171387949,171388006,+"  ; protein_id "ENSP00000296930.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PARD3--AC044784.1	ENSEMBL	gene	1001	26610	.	+	.	FI_gene_label "PARD3^ENSG00000148498.16"  ; ID "PARD3--AC044784.1^PARD3^ENSG00000148498.16"  ; ccdsid "CCDS53516.1"  ; exon_id "ENSE00001413918.3"  ; exon_number 1 ; gene_id "PARD3--AC044784.1^PARD3^ENSG00000148498.16"  ; gene_name PARD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017948.2"  ; hgnc_id "HGNC:16051"  ; level 3 ; orig_coord_info "chr10,34814876,34814995,-"  ; protein_id "ENSP00000341844.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PARD3--AC044784.1^ENST00000340077.9"  ; transcript_name "PARD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PARD3--AC044784.1	ENSEMBL	mRNA	1001	26610	.	+	.	FI_gene_label "PARD3^ENSG00000148498.16"  ; ID "PARD3--AC044784.1^ENST00000340077.9"  ; Parent "PARD3--AC044784.1^PARD3^ENSG00000148498.16"  ; ccdsid "CCDS53516.1"  ; exon_id "ENSE00001413918.3"  ; exon_number 1 ; gene_id "PARD3--AC044784.1^PARD3^ENSG00000148498.16"  ; gene_name PARD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017948.2"  ; hgnc_id "HGNC:16051"  ; level 3 ; orig_coord_info "chr10,34814876,34814995,-"  ; protein_id "ENSP00000341844.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PARD3--AC044784.1^ENST00000340077.9"  ; transcript_name "PARD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PARD3--LINC00709	ENSEMBL	gene	1001	26610	.	+	.	FI_gene_label "PARD3^ENSG00000148498.16"  ; ID "PARD3--LINC00709^PARD3^ENSG00000148498.16"  ; ccdsid "CCDS53516.1"  ; exon_id "ENSE00001413918.3"  ; exon_number 1 ; gene_id "PARD3--LINC00709^PARD3^ENSG00000148498.16"  ; gene_name PARD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017948.2"  ; hgnc_id "HGNC:16051"  ; level 3 ; orig_coord_info "chr10,34814876,34814995,-"  ; protein_id "ENSP00000341844.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PARD3--LINC00709^ENST00000340077.9"  ; transcript_name "PARD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PARD3--LINC00709	ENSEMBL	mRNA	1001	26610	.	+	.	FI_gene_label "PARD3^ENSG00000148498.16"  ; ID "PARD3--LINC00709^ENST00000340077.9"  ; Parent "PARD3--LINC00709^PARD3^ENSG00000148498.16"  ; ccdsid "CCDS53516.1"  ; exon_id "ENSE00001413918.3"  ; exon_number 1 ; gene_id "PARD3--LINC00709^PARD3^ENSG00000148498.16"  ; gene_name PARD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017948.2"  ; hgnc_id "HGNC:16051"  ; level 3 ; orig_coord_info "chr10,34814876,34814995,-"  ; protein_id "ENSP00000341844.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PARD3--LINC00709^ENST00000340077.9"  ; transcript_name "PARD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNRNP40--NKAIN1	HAVANA	gene	1001	14008	.	+	.	FI_gene_label "SNRNP40^ENSG00000060688.13"  ; ID "SNRNP40--NKAIN1^SNRNP40^ENSG00000060688.13"  ; ccdsid "CCDS340.1"  ; exon_id "ENSE00001830257.2"  ; exon_number 1 ; gene_id "SNRNP40--NKAIN1^SNRNP40^ENSG00000060688.13"  ; gene_name SNRNP40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003790.3"  ; havana_transcript "OTTHUMT00000010657.3"  ; hgnc_id "HGNC:30857"  ; level 2 ; orig_coord_info "chr1,31296611,31296751,-"  ; protein_id "ENSP00000263694.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNRNP40--NKAIN1^ENST00000263694.9"  ; transcript_name "SNRNP40-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SNRNP40--NKAIN1	HAVANA	mRNA	1001	14008	.	+	.	FI_gene_label "SNRNP40^ENSG00000060688.13"  ; ID "SNRNP40--NKAIN1^ENST00000263694.9"  ; Parent "SNRNP40--NKAIN1^SNRNP40^ENSG00000060688.13"  ; ccdsid "CCDS340.1"  ; exon_id "ENSE00001830257.2"  ; exon_number 1 ; gene_id "SNRNP40--NKAIN1^SNRNP40^ENSG00000060688.13"  ; gene_name SNRNP40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003790.3"  ; havana_transcript "OTTHUMT00000010657.3"  ; hgnc_id "HGNC:30857"  ; level 2 ; orig_coord_info "chr1,31296611,31296751,-"  ; protein_id "ENSP00000263694.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNRNP40--NKAIN1^ENST00000263694.9"  ; transcript_name "SNRNP40-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNRNP40--NKAIN1	HAVANA	gene	17009	26063	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "SNRNP40--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "SNRNP40--NKAIN1^NKAIN1^ENSG00000084628.10"  ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5"  ; havana_transcript "OTTHUMT00000010655.3"  ; hgnc_id "HGNC:25743"  ; level 2 ; orig_coord_info "chr1,31239494,31239547,-"  ; protein_id "ENSP00000362841.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNRNP40--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
SNRNP40--NKAIN1	HAVANA	mRNA	17009	26063	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "SNRNP40--NKAIN1^ENST00000373736.7"  ; Parent "SNRNP40--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "SNRNP40--NKAIN1^NKAIN1^ENSG00000084628.10"  ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5"  ; havana_transcript "OTTHUMT00000010655.3"  ; hgnc_id "HGNC:25743"  ; level 2 ; orig_coord_info "chr1,31239494,31239547,-"  ; protein_id "ENSP00000362841.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNRNP40--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
STIM1--OR51M1	HAVANA	gene	2176	30043	.	+	.	FI_gene_label "STIM1^ENSG00000167323.12"  ; ID "STIM1--OR51M1^STIM1^ENSG00000167323.12"  ; ccdsid "CCDS7749.1"  ; exon_id "ENSE00001211661.4"  ; exon_number 1 ; gene_id "STIM1--OR51M1^STIM1^ENSG00000167323.12"  ; gene_name STIM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133360.4"  ; havana_transcript "OTTHUMT00000257196.1"  ; hgnc_id "HGNC:11386"  ; level 2 ; orig_coord_info "chr11,3856271,3856409,+"  ; protein_id "ENSP00000300737.4"  ; tag basic appris_principal_2 CCDS ; transcript_id "STIM1--OR51M1^ENST00000300737.8"  ; transcript_name "STIM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STIM1--OR51M1	HAVANA	mRNA	2176	30043	.	+	.	FI_gene_label "STIM1^ENSG00000167323.12"  ; ID "STIM1--OR51M1^ENST00000300737.8"  ; Parent "STIM1--OR51M1^STIM1^ENSG00000167323.12"  ; ccdsid "CCDS7749.1"  ; exon_id "ENSE00001211661.4"  ; exon_number 1 ; gene_id "STIM1--OR51M1^STIM1^ENSG00000167323.12"  ; gene_name STIM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133360.4"  ; havana_transcript "OTTHUMT00000257196.1"  ; hgnc_id "HGNC:11386"  ; level 2 ; orig_coord_info "chr11,3856271,3856409,+"  ; protein_id "ENSP00000300737.4"  ; tag basic appris_principal_2 CCDS ; transcript_id "STIM1--OR51M1^ENST00000300737.8"  ; transcript_name "STIM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STIM1--OR51M1	ENSEMBL	gene	35257	36314	.	+	.	FI_gene_label "OR51M1^ENSG00000184698.5"  ; ID "STIM1--OR51M1^OR51M1^ENSG00000184698.5"  ; ccdsid "CCDS53596.1"  ; exon_id "ENSE00001299316.5"  ; exon_number 1 ; gene_id "STIM1--OR51M1^OR51M1^ENSG00000184698.5"  ; gene_name OR51M1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000066680.3"  ; hgnc_id "HGNC:14847"  ; level 3 ; orig_coord_info "chr11,5389399,5390376,+"  ; protein_id "ENSP00000333196.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "STIM1--OR51M1^ENST00000328611.5"  ; transcript_name "OR51M1-201"  ; transcript_support_level NA ; transcript_type protein_coding
STIM1--OR51M1	ENSEMBL	mRNA	35257	36314	.	+	.	FI_gene_label "OR51M1^ENSG00000184698.5"  ; ID "STIM1--OR51M1^ENST00000328611.5"  ; Parent "STIM1--OR51M1^OR51M1^ENSG00000184698.5"  ; ccdsid "CCDS53596.1"  ; exon_id "ENSE00001299316.5"  ; exon_number 1 ; gene_id "STIM1--OR51M1^OR51M1^ENSG00000184698.5"  ; gene_name OR51M1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000066680.3"  ; hgnc_id "HGNC:14847"  ; level 3 ; orig_coord_info "chr11,5389399,5390376,+"  ; protein_id "ENSP00000333196.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "STIM1--OR51M1^ENST00000328611.5"  ; transcript_name "OR51M1-201"  ; transcript_support_level NA ; 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: 
TBC1D8--RFX8	HAVANA	gene	5989	27663	.	+	.	FI_gene_label "TBC1D8^ENSG00000204634.13"  ; ID "TBC1D8--RFX8^TBC1D8^ENSG00000204634.13"  ; ccdsid "CCDS46375.1"  ; exon_id "ENSE00002112114.1"  ; exon_number 1 ; gene_id "TBC1D8--RFX8^TBC1D8^ENSG00000204634.13"  ; gene_name TBC1D8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153040.2"  ; havana_transcript "OTTHUMT00000376092.1"  ; hgnc_id "HGNC:17791"  ; level 2 ; orig_coord_info "chr2,101151127,101151253,-"  ; protein_id "ENSP00000366036.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "TBC1D8--RFX8^ENST00000376840.8"  ; transcript_name "TBC1D8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TBC1D8--RFX8	HAVANA	mRNA	5989	27663	.	+	.	FI_gene_label "TBC1D8^ENSG00000204634.13"  ; ID "TBC1D8--RFX8^ENST00000376840.8"  ; Parent "TBC1D8--RFX8^TBC1D8^ENSG00000204634.13"  ; ccdsid "CCDS46375.1"  ; exon_id "ENSE00002112114.1"  ; exon_number 1 ; gene_id "TBC1D8--RFX8^TBC1D8^ENSG00000204634.13"  ; gene_name TBC1D8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153040.2"  ; havana_transcript "OTTHUMT00000376092.1"  ; hgnc_id "HGNC:17791"  ; level 2 ; orig_coord_info "chr2,101151127,101151253,-"  ; protein_id "ENSP00000366036.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "TBC1D8--RFX8^ENST00000376840.8"  ; transcript_name "TBC1D8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TBC1D8--RFX8	HAVANA	gene	31053	49032	.	+	.	FI_gene_label "RFX8^ENSG00000196460.14"  ; ID "TBC1D8--RFX8^RFX8^ENSG00000196460.14"  ; ccdsid "CCDS46376.1"  ; exon_id "ENSE00003679552.1"  ; exon_number 2 ; gene_id "TBC1D8--RFX8^RFX8^ENSG00000196460.14"  ; gene_name RFX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130693.7"  ; havana_transcript "OTTHUMT00000339800.3"  ; hgnc_id "HGNC:37253"  ; level 2 ; orig_coord_info "chr2,101466777,101466848,-"  ; protein_id "ENSP00000401536.1"  ; tag basic MANE_Select CCDS ; transcript_id "TBC1D8--RFX8^ENST00000428343.6"  ; transcript_name "RFX8-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TBC1D8--RFX8	HAVANA	mRNA	31053	49032	.	+	.	FI_gene_label "RFX8^ENSG00000196460.14"  ; ID "TBC1D8--RFX8^ENST00000428343.6"  ; Parent "TBC1D8--RFX8^RFX8^ENSG00000196460.14"  ; ccdsid "CCDS46376.1"  ; exon_id "ENSE00003679552.1"  ; exon_number 2 ; gene_id "TBC1D8--RFX8^RFX8^ENSG00000196460.14"  ; gene_name RFX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130693.7"  ; havana_transcript "OTTHUMT00000339800.3"  ; hgnc_id "HGNC:37253"  ; level 2 ; orig_coord_info "chr2,101466777,101466848,-"  ; protein_id "ENSP00000401536.1"  ; tag basic MANE_Select CCDS ; transcript_id "TBC1D8--RFX8^ENST00000428343.6"  ; transcript_name "RFX8-201"  ; transcript_support_level 2 ; 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: 
TMED7--TICAM2	HAVANA	gene	11056	15867	.	+	.	FI_gene_label "TICAM2^ENSG00000243414.6"  ; ID "TMED7--TICAM2^TICAM2^ENSG00000243414.6"  ; ccdsid "CCDS4119.1"  ; exon_id "ENSE00001741902.2"  ; exon_number 2 ; gene_id "TMED7--TICAM2^TICAM2^ENSG00000243414.6"  ; gene_name TICAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162905.2"  ; havana_transcript "OTTHUMT00000338755.1"  ; hgnc_id "HGNC:21354"  ; level 2 ; orig_coord_info "chr5,115580552,115581256,-"  ; protein_id "ENSP00000415139.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000427199.3"  ; transcript_name "TICAM2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMED7--TICAM2	HAVANA	mRNA	11056	15867	.	+	.	FI_gene_label "TICAM2^ENSG00000243414.6"  ; ID "TMED7--TICAM2^ENST00000427199.3"  ; Parent "TMED7--TICAM2^TICAM2^ENSG00000243414.6"  ; ccdsid "CCDS4119.1"  ; exon_id "ENSE00001741902.2"  ; exon_number 2 ; gene_id "TMED7--TICAM2^TICAM2^ENSG00000243414.6"  ; gene_name TICAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162905.2"  ; havana_transcript "OTTHUMT00000338755.1"  ; hgnc_id "HGNC:21354"  ; level 2 ; orig_coord_info "chr5,115580552,115581256,-"  ; protein_id "ENSP00000415139.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000427199.3"  ; transcript_name "TICAM2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMED7--TICAM2	HAVANA	gene	2138	8055	.	+	.	FI_gene_label "TMED7^ENSG00000134970.14"  ; ID "TMED7--TICAM2^TMED7^ENSG00000134970.14"  ; ccdsid "CCDS4120.1"  ; exon_id "ENSE00002252373.2"  ; exon_number 1 ; gene_id "TMED7--TICAM2^TMED7^ENSG00000134970.14"  ; gene_name TMED7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132013.8"  ; havana_transcript "OTTHUMT00000254990.5"  ; hgnc_id "HGNC:24253"  ; level 2 ; orig_coord_info "chr5,115625601,115625792,-"  ; protein_id "ENSP00000405926.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000456936.4"  ; transcript_name "TMED7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMED7--TICAM2	HAVANA	mRNA	2138	8055	.	+	.	FI_gene_label "TMED7^ENSG00000134970.14"  ; ID "TMED7--TICAM2^ENST00000456936.4"  ; Parent "TMED7--TICAM2^TMED7^ENSG00000134970.14"  ; ccdsid "CCDS4120.1"  ; exon_id "ENSE00002252373.2"  ; exon_number 1 ; gene_id "TMED7--TICAM2^TMED7^ENSG00000134970.14"  ; gene_name TMED7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132013.8"  ; havana_transcript "OTTHUMT00000254990.5"  ; hgnc_id "HGNC:24253"  ; level 2 ; orig_coord_info "chr5,115625601,115625792,-"  ; protein_id "ENSP00000405926.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000456936.4"  ; transcript_name "TMED7-201"  ; 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: 
UBE2Q2P2--ZDHHC14	HAVANA	gene	19215	25988	.	+	.	FI_gene_label "ZDHHC14^ENSG00000175048.17"  ; ID "UBE2Q2P2--ZDHHC14^ZDHHC14^ENSG00000175048.17"  ; exon_id "ENSE00001624516.1"  ; exon_number 1 ; gene_id "UBE2Q2P2--ZDHHC14^ZDHHC14^ENSG00000175048.17"  ; gene_name ZDHHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015896.7"  ; havana_transcript "OTTHUMT00000042843.5"  ; hgnc_id "HGNC:20341"  ; level 2 ; orig_coord_info "chr6,157593009,157593146,+"  ; protein_id "ENSP00000345721.7"  ; tag not_organism_supported mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "UBE2Q2P2--ZDHHC14^ENST00000340347.7"  ; transcript_name "ZDHHC14-201"  ; transcript_support_level 5 ; transcript_type protein_coding
UBE2Q2P2--ZDHHC14	HAVANA	mRNA	19215	25988	.	+	.	FI_gene_label "ZDHHC14^ENSG00000175048.17"  ; ID "UBE2Q2P2--ZDHHC14^ENST00000340347.7"  ; Parent "UBE2Q2P2--ZDHHC14^ZDHHC14^ENSG00000175048.17"  ; exon_id "ENSE00001624516.1"  ; exon_number 1 ; gene_id "UBE2Q2P2--ZDHHC14^ZDHHC14^ENSG00000175048.17"  ; gene_name ZDHHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015896.7"  ; havana_transcript "OTTHUMT00000042843.5"  ; hgnc_id "HGNC:20341"  ; level 2 ; orig_coord_info "chr6,157593009,157593146,+"  ; protein_id "ENSP00000345721.7"  ; tag not_organism_supported mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "UBE2Q2P2--ZDHHC14^ENST00000340347.7"  ; transcript_name "ZDHHC14-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
AC079781.4--ASNS	HAVANA	gene	1001	1219	.	+	.	FI_gene_label "AC079781.4^ENSG00000284627.1"  ; ID "AC079781.4--ASNS^AC079781.4^ENSG00000284627.1"  ; exon_id "ENSE00003813582.1"  ; exon_number 1 ; gene_id "AC079781.4--ASNS^AC079781.4^ENSG00000284627.1"  ; gene_name "AC079781.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192224.1"  ; havana_transcript "OTTHUMT00000492944.1"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr7,97928082,97928300,-"  ; tag non_submitted_evidence pseudo_consens basic ; transcript_id "AC079781.4--ASNS^ENST00000641908.1"  ; transcript_name "AC079781.4-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC079781.4--ASNS	HAVANA	RNA	1001	1219	.	+	.	FI_gene_label "AC079781.4^ENSG00000284627.1"  ; ID "AC079781.4--ASNS^ENST00000641908.1"  ; Parent "AC079781.4--ASNS^AC079781.4^ENSG00000284627.1"  ; exon_id "ENSE00003813582.1"  ; exon_number 1 ; gene_id "AC079781.4--ASNS^AC079781.4^ENSG00000284627.1"  ; gene_name "AC079781.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192224.1"  ; havana_transcript "OTTHUMT00000492944.1"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr7,97928082,97928300,-"  ; tag non_submitted_evidence pseudo_consens basic ; transcript_id "AC079781.4--ASNS^ENST00000641908.1"  ; transcript_name "AC079781.4-201"  ; transcript_type transcribed_unprocessed_pseudogene
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: 
LINC00886--PAPPA2	HAVANA	gene	1029	7876	.	+	.	FI_gene_label "LINC00886^ENSG00000240875.6"  ; ID "LINC00886--PAPPA2^LINC00886^ENSG00000240875.6"  ; exon_id "ENSE00001874578.1"  ; exon_number 1 ; gene_id "LINC00886--PAPPA2^LINC00886^ENSG00000240875.6"  ; gene_name LINC00886 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158647.5"  ; havana_transcript "OTTHUMT00000351622.1"  ; hgnc_id "HGNC:48572"  ; level 2 ; orig_coord_info "chr3,156816887,156817034,-"  ; tag basic ; transcript_id "LINC00886--PAPPA2^ENST00000472943.5"  ; transcript_name "LINC00886-201"  ; transcript_support_level 2 ; transcript_type lncRNA
LINC00886--PAPPA2	HAVANA	RNA	1029	7876	.	+	.	FI_gene_label "LINC00886^ENSG00000240875.6"  ; ID "LINC00886--PAPPA2^ENST00000472943.5"  ; Parent "LINC00886--PAPPA2^LINC00886^ENSG00000240875.6"  ; exon_id "ENSE00001874578.1"  ; exon_number 1 ; gene_id "LINC00886--PAPPA2^LINC00886^ENSG00000240875.6"  ; gene_name LINC00886 ; gene_type lncRNA ; havana_gene "OTTHUMG00000158647.5"  ; havana_transcript "OTTHUMT00000351622.1"  ; hgnc_id "HGNC:48572"  ; level 2 ; orig_coord_info "chr3,156816887,156817034,-"  ; tag basic ; transcript_id "LINC00886--PAPPA2^ENST00000472943.5"  ; transcript_name "LINC00886-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
LINC02465--PAPPA2	HAVANA	gene	16896	28793	.	+	.	FI_gene_label "LINC02465^ENSG00000249618.6"  ; ID "LINC02465--PAPPA2^LINC02465^ENSG00000249618.6"  ; exon_id "ENSE00002042516.1"  ; exon_number 1 ; gene_id "LINC02465--PAPPA2^LINC02465^ENSG00000249618.6"  ; gene_name LINC02465 ; gene_type lncRNA ; havana_gene "OTTHUMG00000161197.25"  ; havana_transcript "OTTHUMT00000364130.1"  ; hgnc_id "HGNC:53403"  ; level 2 ; orig_coord_info "chr4,129837361,129837425,+"  ; transcript_id "LINC02465--PAPPA2^ENST00000507099.1"  ; transcript_name "LINC02465-201"  ; transcript_support_level 4 ; transcript_type lncRNA
LINC02465--PAPPA2	HAVANA	RNA	16896	28793	.	+	.	FI_gene_label "LINC02465^ENSG00000249618.6"  ; ID "LINC02465--PAPPA2^ENST00000507099.1"  ; Parent "LINC02465--PAPPA2^LINC02465^ENSG00000249618.6"  ; exon_id "ENSE00002042516.1"  ; exon_number 1 ; gene_id "LINC02465--PAPPA2^LINC02465^ENSG00000249618.6"  ; gene_name LINC02465 ; gene_type lncRNA ; havana_gene "OTTHUMG00000161197.25"  ; havana_transcript "OTTHUMT00000364130.1"  ; hgnc_id "HGNC:53403"  ; level 2 ; orig_coord_info "chr4,129837361,129837425,+"  ; transcript_id "LINC02465--PAPPA2^ENST00000507099.1"  ; transcript_name "LINC02465-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
LINC02479--PAPPA2	HAVANA	gene	1001	2630	.	+	.	FI_gene_label "LINC02479^ENSG00000251326.2"  ; ID "LINC02479--PAPPA2^LINC02479^ENSG00000251326.2"  ; exon_id "ENSE00002059150.1"  ; exon_number 1 ; gene_id "LINC02479--PAPPA2^LINC02479^ENSG00000251326.2"  ; gene_name LINC02479 ; gene_type lncRNA ; havana_gene "OTTHUMG00000161766.2"  ; havana_transcript "OTTHUMT00000366028.1"  ; hgnc_id "HGNC:53453"  ; level 2 ; orig_coord_info "chr4,130376229,130376559,+"  ; transcript_id "LINC02479--PAPPA2^ENST00000508942.1"  ; transcript_name "LINC02479-201"  ; transcript_support_level 3 ; transcript_type lncRNA
LINC02479--PAPPA2	HAVANA	RNA	1001	2630	.	+	.	FI_gene_label "LINC02479^ENSG00000251326.2"  ; ID "LINC02479--PAPPA2^ENST00000508942.1"  ; Parent "LINC02479--PAPPA2^LINC02479^ENSG00000251326.2"  ; exon_id "ENSE00002059150.1"  ; exon_number 1 ; gene_id "LINC02479--PAPPA2^LINC02479^ENSG00000251326.2"  ; gene_name LINC02479 ; gene_type lncRNA ; havana_gene "OTTHUMG00000161766.2"  ; havana_transcript "OTTHUMT00000366028.1"  ; hgnc_id "HGNC:53453"  ; level 2 ; orig_coord_info "chr4,130376229,130376559,+"  ; transcript_id "LINC02479--PAPPA2^ENST00000508942.1"  ; transcript_name "LINC02479-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
NPM1--MT-RNR2	ENSEMBL	gene	18634	20192	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
NPM1--MT-RNR2	ENSEMBL	RNA	18634	20192	.	+	.	FI_gene_label "MT-RNR2^ENSG00000210082.2"  ; ID "NPM1--MT-RNR2^ENST00000387347.2"  ; Parent "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; exon_id "ENSE00001544497.2"  ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2"  ; gene_name "MT-RNR2"  ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471"  ; level 3 ; orig_coord_info "chrM,1671,3229,+"  ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2"  ; transcript_name "MT-RNR2-201"  ; transcript_support_level NA ; transcript_type Mt_rRNA
L1 and L2 created: 
PARD3--AC044784.1	HAVANA	gene	37221	38897	.	+	.	FI_gene_label "AC044784.1^ENSG00000223808.1"  ; ID "PARD3--AC044784.1^AC044784.1^ENSG00000223808.1"  ; exon_id "ENSE00001666537.1"  ; exon_number 1 ; gene_id "PARD3--AC044784.1^AC044784.1^ENSG00000223808.1"  ; gene_name "AC044784.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017651.1"  ; havana_transcript "OTTHUMT00000046734.1"  ; level 2 ; orig_coord_info "chr10,8970125,8970272,+"  ; tag basic ; transcript_id "PARD3--AC044784.1^ENST00000456526.1"  ; transcript_name "AC044784.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
PARD3--AC044784.1	HAVANA	RNA	37221	38897	.	+	.	FI_gene_label "AC044784.1^ENSG00000223808.1"  ; ID "PARD3--AC044784.1^ENST00000456526.1"  ; Parent "PARD3--AC044784.1^AC044784.1^ENSG00000223808.1"  ; exon_id "ENSE00001666537.1"  ; exon_number 1 ; gene_id "PARD3--AC044784.1^AC044784.1^ENSG00000223808.1"  ; gene_name "AC044784.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017651.1"  ; havana_transcript "OTTHUMT00000046734.1"  ; level 2 ; orig_coord_info "chr10,8970125,8970272,+"  ; tag basic ; transcript_id "PARD3--AC044784.1^ENST00000456526.1"  ; transcript_name "AC044784.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PARD3--LINC00709	HAVANA	gene	37221	38714	.	+	.	FI_gene_label "LINC00709^ENSG00000230014.1"  ; ID "PARD3--LINC00709^LINC00709^ENSG00000230014.1"  ; exon_id "ENSE00001608895.1"  ; exon_number 1 ; gene_id "PARD3--LINC00709^LINC00709^ENSG00000230014.1"  ; gene_name LINC00709 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017652.1"  ; havana_transcript "OTTHUMT00000046735.1"  ; hgnc_id "HGNC:44700"  ; level 2 ; orig_coord_info "chr10,9275833,9275860,+"  ; tag basic ; transcript_id "PARD3--LINC00709^ENST00000458168.1"  ; transcript_name "LINC00709-201"  ; transcript_support_level 2 ; transcript_type lncRNA
PARD3--LINC00709	HAVANA	RNA	37221	38714	.	+	.	FI_gene_label "LINC00709^ENSG00000230014.1"  ; ID "PARD3--LINC00709^ENST00000458168.1"  ; Parent "PARD3--LINC00709^LINC00709^ENSG00000230014.1"  ; exon_id "ENSE00001608895.1"  ; exon_number 1 ; gene_id "PARD3--LINC00709^LINC00709^ENSG00000230014.1"  ; gene_name LINC00709 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017652.1"  ; havana_transcript "OTTHUMT00000046735.1"  ; hgnc_id "HGNC:44700"  ; level 2 ; orig_coord_info "chr10,9275833,9275860,+"  ; tag basic ; transcript_id "PARD3--LINC00709^ENST00000458168.1"  ; transcript_name "LINC00709-201"  ; transcript_support_level 2 ; transcript_type lncRNA
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
L1 and L2 created: 
UBE2Q2P2--ZDHHC14	HAVANA	gene	9027	11999	.	+	.	FI_gene_label "UBE2Q2P2^ENSG00000259429.5"  ; ID "UBE2Q2P2--ZDHHC14^UBE2Q2P2^ENSG00000259429.5"  ; exon_id "ENSE00003731023.1"  ; exon_number 1 ; gene_id "UBE2Q2P2--ZDHHC14^UBE2Q2P2^ENSG00000259429.5"  ; gene_name UBE2Q2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000172604.3"  ; havana_transcript "OTTHUMT00000419282.2"  ; hgnc_id "HGNC:37440"  ; level 2 ; orig_coord_info "chr15,82414787,82414804,+"  ; transcript_id "UBE2Q2P2--ZDHHC14^ENST00000558542.2"  ; transcript_name "UBE2Q2P2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
UBE2Q2P2--ZDHHC14	HAVANA	RNA	9027	11999	.	+	.	FI_gene_label "UBE2Q2P2^ENSG00000259429.5"  ; ID "UBE2Q2P2--ZDHHC14^ENST00000558542.2"  ; Parent "UBE2Q2P2--ZDHHC14^UBE2Q2P2^ENSG00000259429.5"  ; exon_id "ENSE00003731023.1"  ; exon_number 1 ; gene_id "UBE2Q2P2--ZDHHC14^UBE2Q2P2^ENSG00000259429.5"  ; gene_name UBE2Q2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000172604.3"  ; havana_transcript "OTTHUMT00000419282.2"  ; hgnc_id "HGNC:37440"  ; level 2 ; orig_coord_info "chr15,82414787,82414804,+"  ; transcript_id "UBE2Q2P2--ZDHHC14^ENST00000558542.2"  ; transcript_name "UBE2Q2P2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
441 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 1 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 ------------------------------
801 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 37 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