.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-09b6a3-R1_A23WJ53LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/6db67db6c22a14d251a5cb12b9fbf1/.command.out
Size: 60.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-09b6a3-R1_A23WJ53LT4_1)
Attempt
Content

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 8359
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 8359
=> 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:8359
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
ATP6V1C1--ZNF280D	HAVANA	gene	21516	52404	.	+	.	FI_gene_label "ZNF280D^ENSG00000137871.21"  ; ID "ATP6V1C1--ZNF280D^ZNF280D^ENSG00000137871.21"  ; ccdsid "CCDS32245.1"  ; exon_id "ENSE00001414286.2"  ; exon_number 3 ; gene_id "ATP6V1C1--ZNF280D^ZNF280D^ENSG00000137871.21"  ; gene_name ZNF280D ; gene_type protein_coding ; havana_gene "OTTHUMG00000172509.7"  ; havana_transcript "OTTHUMT00000418891.2"  ; hgnc_id "HGNC:25953"  ; level 2 ; orig_coord_info "chr15,56707082,56707109,-"  ; protein_id "ENSP00000267807.7"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ATP6V1C1--ZNF280D^ENST00000267807.12"  ; transcript_name "ZNF280D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP6V1C1--ZNF280D	HAVANA	mRNA	21516	52404	.	+	.	FI_gene_label "ZNF280D^ENSG00000137871.21"  ; ID "ATP6V1C1--ZNF280D^ENST00000267807.12"  ; Parent "ATP6V1C1--ZNF280D^ZNF280D^ENSG00000137871.21"  ; ccdsid "CCDS32245.1"  ; exon_id "ENSE00001414286.2"  ; exon_number 3 ; gene_id "ATP6V1C1--ZNF280D^ZNF280D^ENSG00000137871.21"  ; gene_name ZNF280D ; gene_type protein_coding ; havana_gene "OTTHUMG00000172509.7"  ; havana_transcript "OTTHUMT00000418891.2"  ; hgnc_id "HGNC:25953"  ; level 2 ; orig_coord_info "chr15,56707082,56707109,-"  ; protein_id "ENSP00000267807.7"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ATP6V1C1--ZNF280D^ENST00000267807.12"  ; transcript_name "ZNF280D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATP6V1C1--ZNF280D	HAVANA	gene	1001	17938	.	+	.	FI_gene_label "ATP6V1C1^ENSG00000155097.12"  ; ID "ATP6V1C1--ZNF280D^ATP6V1C1^ENSG00000155097.12"  ; ccdsid "CCDS6296.1"  ; exon_id "ENSE00001019178.6"  ; exon_number 2 ; gene_id "ATP6V1C1--ZNF280D^ATP6V1C1^ENSG00000155097.12"  ; gene_name ATP6V1C1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164761.2"  ; havana_transcript "OTTHUMT00000380101.1"  ; hgnc_id "HGNC:856"  ; level 2 ; orig_coord_info "chr8,103040837,103040968,+"  ; protein_id "ENSP00000379203.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "ATP6V1C1--ZNF280D^ENST00000395862.7"  ; transcript_name "ATP6V1C1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP6V1C1--ZNF280D	HAVANA	mRNA	1001	17938	.	+	.	FI_gene_label "ATP6V1C1^ENSG00000155097.12"  ; ID "ATP6V1C1--ZNF280D^ENST00000395862.7"  ; Parent "ATP6V1C1--ZNF280D^ATP6V1C1^ENSG00000155097.12"  ; ccdsid "CCDS6296.1"  ; exon_id "ENSE00001019178.6"  ; exon_number 2 ; gene_id "ATP6V1C1--ZNF280D^ATP6V1C1^ENSG00000155097.12"  ; gene_name ATP6V1C1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164761.2"  ; havana_transcript "OTTHUMT00000380101.1"  ; hgnc_id "HGNC:856"  ; level 2 ; orig_coord_info "chr8,103040837,103040968,+"  ; protein_id "ENSP00000379203.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "ATP6V1C1--ZNF280D^ENST00000395862.7"  ; transcript_name "ATP6V1C1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CEP85--CATSPER4	HAVANA	gene	1003	17373	.	+	.	FI_gene_label "CEP85^ENSG00000130695.16"  ; ID "CEP85--CATSPER4^CEP85^ENSG00000130695.16"  ; ccdsid "CCDS277.1"  ; exon_id "ENSE00002185613.1"  ; exon_number 2 ; gene_id "CEP85--CATSPER4^CEP85^ENSG00000130695.16"  ; gene_name CEP85 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003380.6"  ; havana_transcript "OTTHUMT00000009492.2"  ; hgnc_id "HGNC:25309"  ; level 2 ; orig_coord_info "chr1,26239784,26239838,+"  ; protein_id "ENSP00000252992.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "CEP85--CATSPER4^ENST00000252992.8"  ; transcript_name "CEP85-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CEP85--CATSPER4	HAVANA	mRNA	1003	17373	.	+	.	FI_gene_label "CEP85^ENSG00000130695.16"  ; ID "CEP85--CATSPER4^ENST00000252992.8"  ; Parent "CEP85--CATSPER4^CEP85^ENSG00000130695.16"  ; ccdsid "CCDS277.1"  ; exon_id "ENSE00002185613.1"  ; exon_number 2 ; gene_id "CEP85--CATSPER4^CEP85^ENSG00000130695.16"  ; gene_name CEP85 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003380.6"  ; havana_transcript "OTTHUMT00000009492.2"  ; hgnc_id "HGNC:25309"  ; level 2 ; orig_coord_info "chr1,26239784,26239838,+"  ; protein_id "ENSP00000252992.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "CEP85--CATSPER4^ENST00000252992.8"  ; transcript_name "CEP85-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CEP85--CATSPER4	HAVANA	gene	20374	26799	.	+	.	FI_gene_label "CATSPER4^ENSG00000188782.9"  ; ID "CEP85--CATSPER4^CATSPER4^ENSG00000188782.9"  ; exon_id "ENSE00001755599.2"  ; exon_number 1 ; gene_id "CEP85--CATSPER4^CATSPER4^ENSG00000188782.9"  ; gene_name CATSPER4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003383.4"  ; havana_transcript "OTTHUMT00000381673.2"  ; hgnc_id "HGNC:23220"  ; level 2 ; orig_coord_info "chr1,26190628,26190840,+"  ; protein_id "ENSP00000341006.2"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "CEP85--CATSPER4^ENST00000338855.6"  ; transcript_name "CATSPER4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CEP85--CATSPER4	HAVANA	mRNA	20374	26799	.	+	.	FI_gene_label "CATSPER4^ENSG00000188782.9"  ; ID "CEP85--CATSPER4^ENST00000338855.6"  ; Parent "CEP85--CATSPER4^CATSPER4^ENSG00000188782.9"  ; exon_id "ENSE00001755599.2"  ; exon_number 1 ; gene_id "CEP85--CATSPER4^CATSPER4^ENSG00000188782.9"  ; gene_name CATSPER4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003383.4"  ; havana_transcript "OTTHUMT00000381673.2"  ; hgnc_id "HGNC:23220"  ; level 2 ; orig_coord_info "chr1,26190628,26190840,+"  ; protein_id "ENSP00000341006.2"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "CEP85--CATSPER4^ENST00000338855.6"  ; transcript_name "CATSPER4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
DOCK1--AZIN1	HAVANA	gene	1001	58387	.	+	.	FI_gene_label "DOCK1^ENSG00000150760.13"  ; ID "DOCK1--AZIN1^DOCK1^ENSG00000150760.13"  ; ccdsid "CCDS73222.1"  ; exon_id "ENSE00001885401.1"  ; exon_number 1 ; gene_id "DOCK1--AZIN1^DOCK1^ENSG00000150760.13"  ; gene_name DOCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019249.4"  ; havana_transcript "OTTHUMT00000050979.2"  ; hgnc_id "HGNC:2987"  ; level 2 ; orig_coord_info "chr10,126905518,126905563,+"  ; protein_id "ENSP00000280333.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "DOCK1--AZIN1^ENST00000280333.9"  ; transcript_name "DOCK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DOCK1--AZIN1	HAVANA	mRNA	1001	58387	.	+	.	FI_gene_label "DOCK1^ENSG00000150760.13"  ; ID "DOCK1--AZIN1^ENST00000280333.9"  ; Parent "DOCK1--AZIN1^DOCK1^ENSG00000150760.13"  ; ccdsid "CCDS73222.1"  ; exon_id "ENSE00001885401.1"  ; exon_number 1 ; gene_id "DOCK1--AZIN1^DOCK1^ENSG00000150760.13"  ; gene_name DOCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019249.4"  ; havana_transcript "OTTHUMT00000050979.2"  ; hgnc_id "HGNC:2987"  ; level 2 ; orig_coord_info "chr10,126905518,126905563,+"  ; protein_id "ENSP00000280333.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "DOCK1--AZIN1^ENST00000280333.9"  ; transcript_name "DOCK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DOCK1--AZIN1	HAVANA	gene	64846	81228	.	+	.	FI_gene_label "AZIN1^ENSG00000155096.14"  ; ID "DOCK1--AZIN1^AZIN1^ENSG00000155096.14"  ; ccdsid "CCDS6295.1"  ; exon_id "ENSE00003694945.1"  ; exon_number 3 ; gene_id "DOCK1--AZIN1^AZIN1^ENSG00000155096.14"  ; gene_name AZIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164766.9"  ; havana_transcript "OTTHUMT00000380133.2"  ; hgnc_id "HGNC:16432"  ; level 2 ; orig_coord_info "chr8,102843551,102843652,-"  ; protein_id "ENSP00000337180.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOCK1--AZIN1^ENST00000337198.10"  ; transcript_name "AZIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DOCK1--AZIN1	HAVANA	mRNA	64846	81228	.	+	.	FI_gene_label "AZIN1^ENSG00000155096.14"  ; ID "DOCK1--AZIN1^ENST00000337198.10"  ; Parent "DOCK1--AZIN1^AZIN1^ENSG00000155096.14"  ; ccdsid "CCDS6295.1"  ; exon_id "ENSE00003694945.1"  ; exon_number 3 ; gene_id "DOCK1--AZIN1^AZIN1^ENSG00000155096.14"  ; gene_name AZIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164766.9"  ; havana_transcript "OTTHUMT00000380133.2"  ; hgnc_id "HGNC:16432"  ; level 2 ; orig_coord_info "chr8,102843551,102843652,-"  ; protein_id "ENSP00000337180.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOCK1--AZIN1^ENST00000337198.10"  ; transcript_name "AZIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DUT--ANXA2	HAVANA	gene	1419	9093	.	+	.	FI_gene_label "DUT^ENSG00000128951.14"  ; ID "DUT--ANXA2^DUT^ENSG00000128951.14"  ; ccdsid "CCDS32231.1"  ; exon_id "ENSE00001487133.3"  ; exon_number 1 ; gene_id "DUT--ANXA2^DUT^ENSG00000128951.14"  ; gene_name DUT ; gene_type protein_coding ; havana_gene "OTTHUMG00000172155.4"  ; havana_transcript "OTTHUMT00000417142.3"  ; hgnc_id "HGNC:3078"  ; level 2 ; orig_coord_info "chr15,48331516,48331795,+"  ; protein_id "ENSP00000370376.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "DUT--ANXA2^ENST00000331200.8"  ; transcript_name "DUT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DUT--ANXA2	HAVANA	mRNA	1419	9093	.	+	.	FI_gene_label "DUT^ENSG00000128951.14"  ; ID "DUT--ANXA2^ENST00000331200.8"  ; Parent "DUT--ANXA2^DUT^ENSG00000128951.14"  ; ccdsid "CCDS32231.1"  ; exon_id "ENSE00001487133.3"  ; exon_number 1 ; gene_id "DUT--ANXA2^DUT^ENSG00000128951.14"  ; gene_name DUT ; gene_type protein_coding ; havana_gene "OTTHUMG00000172155.4"  ; havana_transcript "OTTHUMT00000417142.3"  ; hgnc_id "HGNC:3078"  ; level 2 ; orig_coord_info "chr15,48331516,48331795,+"  ; protein_id "ENSP00000370376.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "DUT--ANXA2^ENST00000331200.8"  ; transcript_name "DUT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DUT--ANXA2	HAVANA	gene	13966	42891	.	+	.	FI_gene_label "ANXA2^ENSG00000182718.18"  ; ID "DUT--ANXA2^ANXA2^ENSG00000182718.18"  ; ccdsid "CCDS32256.1"  ; exon_id "ENSE00001383920.3"  ; exon_number 1 ; gene_id "DUT--ANXA2^ANXA2^ENSG00000182718.18"  ; gene_name ANXA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132763.5"  ; havana_transcript "OTTHUMT00000416470.1"  ; hgnc_id "HGNC:537"  ; level 2 ; orig_coord_info "chr15,60397871,60397913,-"  ; protein_id "ENSP00000346032.3"  ; tag basic CCDS ; transcript_id "DUT--ANXA2^ENST00000332680.8"  ; transcript_name "ANXA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DUT--ANXA2	HAVANA	mRNA	13966	42891	.	+	.	FI_gene_label "ANXA2^ENSG00000182718.18"  ; ID "DUT--ANXA2^ENST00000332680.8"  ; Parent "DUT--ANXA2^ANXA2^ENSG00000182718.18"  ; ccdsid "CCDS32256.1"  ; exon_id "ENSE00001383920.3"  ; exon_number 1 ; gene_id "DUT--ANXA2^ANXA2^ENSG00000182718.18"  ; gene_name ANXA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132763.5"  ; havana_transcript "OTTHUMT00000416470.1"  ; hgnc_id "HGNC:537"  ; level 2 ; orig_coord_info "chr15,60397871,60397913,-"  ; protein_id "ENSP00000346032.3"  ; tag basic CCDS ; transcript_id "DUT--ANXA2^ENST00000332680.8"  ; transcript_name "ANXA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GRID1--ADK	HAVANA	gene	25528	47020	.	+	.	FI_gene_label "ADK^ENSG00000156110.15"  ; ID "GRID1--ADK^ADK^ENSG00000156110.15"  ; exon_id "ENSE00001248887.4"  ; exon_number 1 ; gene_id "GRID1--ADK^ADK^ENSG00000156110.15"  ; gene_name ADK ; gene_type protein_coding ; havana_gene "OTTHUMG00000018506.4"  ; havana_transcript "OTTHUMT00000529318.1"  ; hgnc_id "HGNC:257"  ; level 2 ; orig_coord_info "chr10,74151279,74151343,+"  ; protein_id "ENSP00000286621.3"  ; tag RNA_Seq_supported_only basic ; transcript_id "GRID1--ADK^ENST00000286621.7"  ; transcript_name "ADK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GRID1--ADK	HAVANA	mRNA	25528	47020	.	+	.	FI_gene_label "ADK^ENSG00000156110.15"  ; ID "GRID1--ADK^ENST00000286621.7"  ; Parent "GRID1--ADK^ADK^ENSG00000156110.15"  ; exon_id "ENSE00001248887.4"  ; exon_number 1 ; gene_id "GRID1--ADK^ADK^ENSG00000156110.15"  ; gene_name ADK ; gene_type protein_coding ; havana_gene "OTTHUMG00000018506.4"  ; havana_transcript "OTTHUMT00000529318.1"  ; hgnc_id "HGNC:257"  ; level 2 ; orig_coord_info "chr10,74151279,74151343,+"  ; protein_id "ENSP00000286621.3"  ; tag RNA_Seq_supported_only basic ; transcript_id "GRID1--ADK^ENST00000286621.7"  ; transcript_name "ADK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GRID1--ADK	HAVANA	gene	1001	22505	.	+	.	FI_gene_label "GRID1^ENSG00000182771.19"  ; ID "GRID1--ADK^GRID1^ENSG00000182771.19"  ; ccdsid "CCDS31236.1"  ; exon_id "ENSE00001328131.3"  ; exon_number 1 ; gene_id "GRID1--ADK^GRID1^ENSG00000182771.19"  ; gene_name GRID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018650.7"  ; havana_transcript "OTTHUMT00000049148.4"  ; hgnc_id "HGNC:4575"  ; level 2 ; orig_coord_info "chr10,86366314,86366392,-"  ; protein_id "ENSP00000330148.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRID1--ADK^ENST00000327946.12"  ; transcript_name "GRID1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
GRID1--ADK	HAVANA	mRNA	1001	22505	.	+	.	FI_gene_label "GRID1^ENSG00000182771.19"  ; ID "GRID1--ADK^ENST00000327946.12"  ; Parent "GRID1--ADK^GRID1^ENSG00000182771.19"  ; ccdsid "CCDS31236.1"  ; exon_id "ENSE00001328131.3"  ; exon_number 1 ; gene_id "GRID1--ADK^GRID1^ENSG00000182771.19"  ; gene_name GRID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018650.7"  ; havana_transcript "OTTHUMT00000049148.4"  ; hgnc_id "HGNC:4575"  ; level 2 ; orig_coord_info "chr10,86366314,86366392,-"  ; protein_id "ENSP00000330148.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRID1--ADK^ENST00000327946.12"  ; transcript_name "GRID1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
KAT6B--RPA2P2	HAVANA	gene	2674	47560	.	+	.	FI_gene_label "KAT6B^ENSG00000156650.14"  ; ID "KAT6B--RPA2P2^KAT6B^ENSG00000156650.14"  ; ccdsid "CCDS7345.1"  ; exon_id "ENSE00001167134.1"  ; exon_number 3 ; gene_id "KAT6B--RPA2P2^KAT6B^ENSG00000156650.14"  ; gene_name KAT6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000018509.9"  ; havana_transcript "OTTHUMT00000048771.3"  ; hgnc_id "HGNC:17582"  ; level 2 ; orig_coord_info "chr10,74842858,74843478,+"  ; protein_id "ENSP00000287239.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KAT6B--RPA2P2^ENST00000287239.10"  ; transcript_name "KAT6B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KAT6B--RPA2P2	HAVANA	mRNA	2674	47560	.	+	.	FI_gene_label "KAT6B^ENSG00000156650.14"  ; ID "KAT6B--RPA2P2^ENST00000287239.10"  ; Parent "KAT6B--RPA2P2^KAT6B^ENSG00000156650.14"  ; ccdsid "CCDS7345.1"  ; exon_id "ENSE00001167134.1"  ; exon_number 3 ; gene_id "KAT6B--RPA2P2^KAT6B^ENSG00000156650.14"  ; gene_name KAT6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000018509.9"  ; havana_transcript "OTTHUMT00000048771.3"  ; hgnc_id "HGNC:17582"  ; level 2 ; orig_coord_info "chr10,74842858,74843478,+"  ; protein_id "ENSP00000287239.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KAT6B--RPA2P2^ENST00000287239.10"  ; transcript_name "KAT6B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KAT6B--WARS2P1	HAVANA	gene	2674	47560	.	+	.	FI_gene_label "KAT6B^ENSG00000156650.14"  ; ID "KAT6B--WARS2P1^KAT6B^ENSG00000156650.14"  ; ccdsid "CCDS7345.1"  ; exon_id "ENSE00001167134.1"  ; exon_number 3 ; gene_id "KAT6B--WARS2P1^KAT6B^ENSG00000156650.14"  ; gene_name KAT6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000018509.9"  ; havana_transcript "OTTHUMT00000048771.3"  ; hgnc_id "HGNC:17582"  ; level 2 ; orig_coord_info "chr10,74842858,74843478,+"  ; protein_id "ENSP00000287239.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KAT6B--WARS2P1^ENST00000287239.10"  ; transcript_name "KAT6B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KAT6B--WARS2P1	HAVANA	mRNA	2674	47560	.	+	.	FI_gene_label "KAT6B^ENSG00000156650.14"  ; ID "KAT6B--WARS2P1^ENST00000287239.10"  ; Parent "KAT6B--WARS2P1^KAT6B^ENSG00000156650.14"  ; ccdsid "CCDS7345.1"  ; exon_id "ENSE00001167134.1"  ; exon_number 3 ; gene_id "KAT6B--WARS2P1^KAT6B^ENSG00000156650.14"  ; gene_name KAT6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000018509.9"  ; havana_transcript "OTTHUMT00000048771.3"  ; hgnc_id "HGNC:17582"  ; level 2 ; orig_coord_info "chr10,74842858,74843478,+"  ; protein_id "ENSP00000287239.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KAT6B--WARS2P1^ENST00000287239.10"  ; transcript_name "KAT6B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRP5--OR4A9P	HAVANA	gene	1001	30833	.	+	.	FI_gene_label "LRP5^ENSG00000162337.12"  ; ID "LRP5--OR4A9P^LRP5^ENSG00000162337.12"  ; ccdsid "CCDS8181.1"  ; exon_id "ENSE00001413096.5"  ; exon_number 1 ; gene_id "LRP5--OR4A9P^LRP5^ENSG00000162337.12"  ; gene_name LRP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167570.2"  ; havana_transcript "OTTHUMT00000395088.2"  ; hgnc_id "HGNC:6697"  ; level 2 ; orig_coord_info "chr11,68312715,68312805,+"  ; protein_id "ENSP00000294304.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP5--OR4A9P^ENST00000294304.12"  ; transcript_name "LRP5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LRP5--OR4A9P	HAVANA	mRNA	1001	30833	.	+	.	FI_gene_label "LRP5^ENSG00000162337.12"  ; ID "LRP5--OR4A9P^ENST00000294304.12"  ; Parent "LRP5--OR4A9P^LRP5^ENSG00000162337.12"  ; ccdsid "CCDS8181.1"  ; exon_id "ENSE00001413096.5"  ; exon_number 1 ; gene_id "LRP5--OR4A9P^LRP5^ENSG00000162337.12"  ; gene_name LRP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167570.2"  ; havana_transcript "OTTHUMT00000395088.2"  ; hgnc_id "HGNC:6697"  ; level 2 ; orig_coord_info "chr11,68312715,68312805,+"  ; protein_id "ENSP00000294304.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP5--OR4A9P^ENST00000294304.12"  ; transcript_name "LRP5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRP5--OR4X7P	HAVANA	gene	1001	30833	.	+	.	FI_gene_label "LRP5^ENSG00000162337.12"  ; ID "LRP5--OR4X7P^LRP5^ENSG00000162337.12"  ; ccdsid "CCDS8181.1"  ; exon_id "ENSE00001413096.5"  ; exon_number 1 ; gene_id "LRP5--OR4X7P^LRP5^ENSG00000162337.12"  ; gene_name LRP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167570.2"  ; havana_transcript "OTTHUMT00000395088.2"  ; hgnc_id "HGNC:6697"  ; level 2 ; orig_coord_info "chr11,68312715,68312805,+"  ; protein_id "ENSP00000294304.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP5--OR4X7P^ENST00000294304.12"  ; transcript_name "LRP5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LRP5--OR4X7P	HAVANA	mRNA	1001	30833	.	+	.	FI_gene_label "LRP5^ENSG00000162337.12"  ; ID "LRP5--OR4X7P^ENST00000294304.12"  ; Parent "LRP5--OR4X7P^LRP5^ENSG00000162337.12"  ; ccdsid "CCDS8181.1"  ; exon_id "ENSE00001413096.5"  ; exon_number 1 ; gene_id "LRP5--OR4X7P^LRP5^ENSG00000162337.12"  ; gene_name LRP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167570.2"  ; havana_transcript "OTTHUMT00000395088.2"  ; hgnc_id "HGNC:6697"  ; level 2 ; orig_coord_info "chr11,68312715,68312805,+"  ; protein_id "ENSP00000294304.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP5--OR4X7P^ENST00000294304.12"  ; transcript_name "LRP5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LY6K--TSNARE1	HAVANA	gene	1001	6017	.	+	.	FI_gene_label "LY6K^ENSG00000160886.13"  ; ID "LY6K--TSNARE1^LY6K^ENSG00000160886.13"  ; ccdsid "CCDS6385.2"  ; exon_id "ENSE00002094746.1"  ; exon_number 1 ; gene_id "LY6K--TSNARE1^LY6K^ENSG00000160886.13"  ; gene_name LY6K ; gene_type protein_coding ; havana_gene "OTTHUMG00000164720.3"  ; havana_transcript "OTTHUMT00000379893.2"  ; hgnc_id "HGNC:24225"  ; level 2 ; orig_coord_info "chr8,142700528,142700630,+"  ; protein_id "ENSP00000292430.6"  ; tag upstream_ATG basic MANE_Select appris_principal_2 CCDS ; transcript_id "LY6K--TSNARE1^ENST00000292430.10"  ; transcript_name "LY6K-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LY6K--TSNARE1	HAVANA	mRNA	1001	6017	.	+	.	FI_gene_label "LY6K^ENSG00000160886.13"  ; ID "LY6K--TSNARE1^ENST00000292430.10"  ; Parent "LY6K--TSNARE1^LY6K^ENSG00000160886.13"  ; ccdsid "CCDS6385.2"  ; exon_id "ENSE00002094746.1"  ; exon_number 1 ; gene_id "LY6K--TSNARE1^LY6K^ENSG00000160886.13"  ; gene_name LY6K ; gene_type protein_coding ; havana_gene "OTTHUMG00000164720.3"  ; havana_transcript "OTTHUMT00000379893.2"  ; hgnc_id "HGNC:24225"  ; level 2 ; orig_coord_info "chr8,142700528,142700630,+"  ; protein_id "ENSP00000292430.6"  ; tag upstream_ATG basic MANE_Select appris_principal_2 CCDS ; transcript_id "LY6K--TSNARE1^ENST00000292430.10"  ; transcript_name "LY6K-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LY6K--TSNARE1	ENSEMBL	gene	9018	29915	.	+	.	FI_gene_label "TSNARE1^ENSG00000171045.16"  ; ID "LY6K--TSNARE1^TSNARE1^ENSG00000171045.16"  ; ccdsid "CCDS87630.1"  ; exon_id "ENSE00003464885.1"  ; exon_number 2 ; gene_id "LY6K--TSNARE1^TSNARE1^ENSG00000171045.16"  ; gene_name TSNARE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164867.7"  ; hgnc_id "HGNC:26437"  ; level 3 ; orig_coord_info "chr8,142354637,142354724,-"  ; protein_id "ENSP00000303437.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "LY6K--TSNARE1^ENST00000307180.4"  ; transcript_name "TSNARE1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LY6K--TSNARE1	ENSEMBL	mRNA	9018	29915	.	+	.	FI_gene_label "TSNARE1^ENSG00000171045.16"  ; ID "LY6K--TSNARE1^ENST00000307180.4"  ; Parent "LY6K--TSNARE1^TSNARE1^ENSG00000171045.16"  ; ccdsid "CCDS87630.1"  ; exon_id "ENSE00003464885.1"  ; exon_number 2 ; gene_id "LY6K--TSNARE1^TSNARE1^ENSG00000171045.16"  ; gene_name TSNARE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164867.7"  ; hgnc_id "HGNC:26437"  ; level 3 ; orig_coord_info "chr8,142354637,142354724,-"  ; protein_id "ENSP00000303437.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "LY6K--TSNARE1^ENST00000307180.4"  ; transcript_name "TSNARE1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MROH1--AC105118.1	ENSEMBL	gene	3988	38249	.	+	.	FI_gene_label "MROH1^ENSG00000179832.17"  ; ID "MROH1--AC105118.1^MROH1^ENSG00000179832.17"  ; ccdsid "CCDS47938.1"  ; exon_id "ENSE00002236754.1"  ; exon_number 1 ; gene_id "MROH1--AC105118.1^MROH1^ENSG00000179832.17"  ; gene_name MROH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165781.1"  ; hgnc_id "HGNC:26958"  ; level 3 ; orig_coord_info "chr8,144163827,144163848,+"  ; protein_id "ENSP00000321737.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "MROH1--AC105118.1^ENST00000326134.9"  ; transcript_name "MROH1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MROH1--AC105118.1	ENSEMBL	mRNA	3988	38249	.	+	.	FI_gene_label "MROH1^ENSG00000179832.17"  ; ID "MROH1--AC105118.1^ENST00000326134.9"  ; Parent "MROH1--AC105118.1^MROH1^ENSG00000179832.17"  ; ccdsid "CCDS47938.1"  ; exon_id "ENSE00002236754.1"  ; exon_number 1 ; gene_id "MROH1--AC105118.1^MROH1^ENSG00000179832.17"  ; gene_name MROH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165781.1"  ; hgnc_id "HGNC:26958"  ; level 3 ; orig_coord_info "chr8,144163827,144163848,+"  ; protein_id "ENSP00000321737.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "MROH1--AC105118.1^ENST00000326134.9"  ; transcript_name "MROH1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NEO1--CSMD3	HAVANA	gene	1754	36482	.	+	.	FI_gene_label "NEO1^ENSG00000067141.17"  ; ID "NEO1--CSMD3^NEO1^ENSG00000067141.17"  ; ccdsid "CCDS10247.1"  ; exon_id "ENSE00003841280.1"  ; exon_number 1 ; gene_id "NEO1--CSMD3^NEO1^ENSG00000067141.17"  ; gene_name NEO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133509.8"  ; havana_transcript "OTTHUMT00000504367.2"  ; hgnc_id "HGNC:7754"  ; level 2 ; orig_coord_info "chr15,73052676,73052805,+"  ; protein_id "ENSP00000261908.6"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "NEO1--CSMD3^ENST00000261908.11"  ; transcript_name "NEO1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NEO1--CSMD3	HAVANA	mRNA	1754	36482	.	+	.	FI_gene_label "NEO1^ENSG00000067141.17"  ; ID "NEO1--CSMD3^ENST00000261908.11"  ; Parent "NEO1--CSMD3^NEO1^ENSG00000067141.17"  ; ccdsid "CCDS10247.1"  ; exon_id "ENSE00003841280.1"  ; exon_number 1 ; gene_id "NEO1--CSMD3^NEO1^ENSG00000067141.17"  ; gene_name NEO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133509.8"  ; havana_transcript "OTTHUMT00000504367.2"  ; hgnc_id "HGNC:7754"  ; level 2 ; orig_coord_info "chr15,73052676,73052805,+"  ; protein_id "ENSP00000261908.6"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "NEO1--CSMD3^ENST00000261908.11"  ; transcript_name "NEO1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NEO1--CSMD3	HAVANA	gene	39483	129404	.	+	.	FI_gene_label "CSMD3^ENSG00000164796.18"  ; ID "NEO1--CSMD3^CSMD3^ENSG00000164796.18"  ; ccdsid "CCDS6315.1"  ; exon_id "ENSE00001850376.2"  ; exon_number 1 ; gene_id "NEO1--CSMD3^CSMD3^ENSG00000164796.18"  ; gene_name CSMD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157027.5"  ; havana_transcript "OTTHUMT00000347141.2"  ; hgnc_id "HGNC:19291"  ; level 2 ; orig_coord_info "chr8,113436677,113436854,-"  ; protein_id "ENSP00000297405.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NEO1--CSMD3^ENST00000297405.10"  ; transcript_name "CSMD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NEO1--CSMD3	HAVANA	mRNA	39483	129404	.	+	.	FI_gene_label "CSMD3^ENSG00000164796.18"  ; ID "NEO1--CSMD3^ENST00000297405.10"  ; Parent "NEO1--CSMD3^CSMD3^ENSG00000164796.18"  ; ccdsid "CCDS6315.1"  ; exon_id "ENSE00001850376.2"  ; exon_number 1 ; gene_id "NEO1--CSMD3^CSMD3^ENSG00000164796.18"  ; gene_name CSMD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157027.5"  ; havana_transcript "OTTHUMT00000347141.2"  ; hgnc_id "HGNC:19291"  ; level 2 ; orig_coord_info "chr8,113436677,113436854,-"  ; protein_id "ENSP00000297405.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NEO1--CSMD3^ENST00000297405.10"  ; transcript_name "CSMD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAPSS2--BLNK	HAVANA	gene	18677	40387	.	+	.	FI_gene_label "BLNK^ENSG00000095585.17"  ; ID "PAPSS2--BLNK^BLNK^ENSG00000095585.17"  ; ccdsid "CCDS7446.1"  ; exon_id "ENSE00000000178.2"  ; exon_number 1 ; gene_id "PAPSS2--BLNK^BLNK^ENSG00000095585.17"  ; gene_name BLNK ; gene_type protein_coding ; havana_gene "OTTHUMG00000018827.3"  ; havana_transcript "OTTHUMT00000049593.1"  ; hgnc_id "HGNC:14211"  ; level 2 ; orig_coord_info "chr10,96271352,96271398,-"  ; protein_id "ENSP00000224337.6"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "PAPSS2--BLNK^ENST00000224337.10"  ; transcript_name "BLNK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAPSS2--BLNK	HAVANA	mRNA	18677	40387	.	+	.	FI_gene_label "BLNK^ENSG00000095585.17"  ; ID "PAPSS2--BLNK^ENST00000224337.10"  ; Parent "PAPSS2--BLNK^BLNK^ENSG00000095585.17"  ; ccdsid "CCDS7446.1"  ; exon_id "ENSE00000000178.2"  ; exon_number 1 ; gene_id "PAPSS2--BLNK^BLNK^ENSG00000095585.17"  ; gene_name BLNK ; gene_type protein_coding ; havana_gene "OTTHUMG00000018827.3"  ; havana_transcript "OTTHUMT00000049593.1"  ; hgnc_id "HGNC:14211"  ; level 2 ; orig_coord_info "chr10,96271352,96271398,-"  ; protein_id "ENSP00000224337.6"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "PAPSS2--BLNK^ENST00000224337.10"  ; transcript_name "BLNK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAPSS2--BLNK	HAVANA	gene	1001	15658	.	+	.	FI_gene_label "PAPSS2^ENSG00000198682.13"  ; ID "PAPSS2--BLNK^PAPSS2^ENSG00000198682.13"  ; ccdsid "CCDS7385.1"  ; exon_id "ENSE00001937461.1"  ; exon_number 1 ; gene_id "PAPSS2--BLNK^PAPSS2^ENSG00000198682.13"  ; gene_name PAPSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018683.3"  ; havana_transcript "OTTHUMT00000049229.1"  ; hgnc_id "HGNC:8604"  ; level 2 ; orig_coord_info "chr10,87659982,87660008,+"  ; protein_id "ENSP00000354436.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "PAPSS2--BLNK^ENST00000361175.8"  ; transcript_name "PAPSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAPSS2--BLNK	HAVANA	mRNA	1001	15658	.	+	.	FI_gene_label "PAPSS2^ENSG00000198682.13"  ; ID "PAPSS2--BLNK^ENST00000361175.8"  ; Parent "PAPSS2--BLNK^PAPSS2^ENSG00000198682.13"  ; ccdsid "CCDS7385.1"  ; exon_id "ENSE00001937461.1"  ; exon_number 1 ; gene_id "PAPSS2--BLNK^PAPSS2^ENSG00000198682.13"  ; gene_name PAPSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018683.3"  ; havana_transcript "OTTHUMT00000049229.1"  ; hgnc_id "HGNC:8604"  ; level 2 ; orig_coord_info "chr10,87659982,87660008,+"  ; protein_id "ENSP00000354436.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "PAPSS2--BLNK^ENST00000361175.8"  ; transcript_name "PAPSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PVT1--COLEC10	HAVANA	gene	82659	91084	.	+	.	FI_gene_label "COLEC10^ENSG00000184374.3"  ; ID "PVT1--COLEC10^COLEC10^ENSG00000184374.3"  ; ccdsid "CCDS6327.1"  ; exon_id "ENSE00001309494.5"  ; exon_number 1 ; gene_id "PVT1--COLEC10^COLEC10^ENSG00000184374.3"  ; gene_name COLEC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164971.2"  ; havana_transcript "OTTHUMT00000381225.2"  ; hgnc_id "HGNC:2220"  ; level 2 ; orig_coord_info "chr8,119067282,119067429,+"  ; protein_id "ENSP00000332723.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PVT1--COLEC10^ENST00000332843.3"  ; transcript_name "COLEC10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PVT1--COLEC10	HAVANA	mRNA	82659	91084	.	+	.	FI_gene_label "COLEC10^ENSG00000184374.3"  ; ID "PVT1--COLEC10^ENST00000332843.3"  ; Parent "PVT1--COLEC10^COLEC10^ENSG00000184374.3"  ; ccdsid "CCDS6327.1"  ; exon_id "ENSE00001309494.5"  ; exon_number 1 ; gene_id "PVT1--COLEC10^COLEC10^ENSG00000184374.3"  ; gene_name COLEC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164971.2"  ; havana_transcript "OTTHUMT00000381225.2"  ; hgnc_id "HGNC:2220"  ; level 2 ; orig_coord_info "chr8,119067282,119067429,+"  ; protein_id "ENSP00000332723.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PVT1--COLEC10^ENST00000332843.3"  ; transcript_name "COLEC10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STK3--PPP1R16A	HAVANA	gene	45884	53534	.	+	.	FI_gene_label "PPP1R16A^ENSG00000160972.9"  ; ID "STK3--PPP1R16A^PPP1R16A^ENSG00000160972.9"  ; ccdsid "CCDS6429.1"  ; exon_id "ENSE00001473528.2"  ; exon_number 2 ; gene_id "STK3--PPP1R16A^PPP1R16A^ENSG00000160972.9"  ; gene_name PPP1R16A ; gene_type protein_coding ; havana_gene "OTTHUMG00000165173.5"  ; havana_transcript "OTTHUMT00000382459.1"  ; hgnc_id "HGNC:14941"  ; level 2 ; orig_coord_info "chr8,144497195,144497453,+"  ; protein_id "ENSP00000292539.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "STK3--PPP1R16A^ENST00000292539.8"  ; transcript_name "PPP1R16A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
STK3--PPP1R16A	HAVANA	mRNA	45884	53534	.	+	.	FI_gene_label "PPP1R16A^ENSG00000160972.9"  ; ID "STK3--PPP1R16A^ENST00000292539.8"  ; Parent "STK3--PPP1R16A^PPP1R16A^ENSG00000160972.9"  ; ccdsid "CCDS6429.1"  ; exon_id "ENSE00001473528.2"  ; exon_number 2 ; gene_id "STK3--PPP1R16A^PPP1R16A^ENSG00000160972.9"  ; gene_name PPP1R16A ; gene_type protein_coding ; havana_gene "OTTHUMG00000165173.5"  ; havana_transcript "OTTHUMT00000382459.1"  ; hgnc_id "HGNC:14941"  ; level 2 ; orig_coord_info "chr8,144497195,144497453,+"  ; protein_id "ENSP00000292539.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "STK3--PPP1R16A^ENST00000292539.8"  ; transcript_name "PPP1R16A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
STK3--PPP1R16A	HAVANA	gene	10954	32531	.	+	.	FI_gene_label "STK3^ENSG00000104375.17"  ; ID "STK3--PPP1R16A^STK3^ENSG00000104375.17"  ; ccdsid "CCDS47900.1"  ; exon_id "ENSE00001478384.5"  ; exon_number 1 ; gene_id "STK3--PPP1R16A^STK3^ENSG00000104375.17"  ; gene_name STK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164651.10"  ; havana_transcript "OTTHUMT00000379635.3"  ; hgnc_id "HGNC:11406"  ; level 2 ; orig_coord_info "chr8,98825515,98825540,-"  ; protein_id "ENSP00000390500.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STK3--PPP1R16A^ENST00000419617.7"  ; transcript_name "STK3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STK3--PPP1R16A	HAVANA	mRNA	10954	32531	.	+	.	FI_gene_label "STK3^ENSG00000104375.17"  ; ID "STK3--PPP1R16A^ENST00000419617.7"  ; Parent "STK3--PPP1R16A^STK3^ENSG00000104375.17"  ; ccdsid "CCDS47900.1"  ; exon_id "ENSE00001478384.5"  ; exon_number 1 ; gene_id "STK3--PPP1R16A^STK3^ENSG00000104375.17"  ; gene_name STK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164651.10"  ; havana_transcript "OTTHUMT00000379635.3"  ; hgnc_id "HGNC:11406"  ; level 2 ; orig_coord_info "chr8,98825515,98825540,-"  ; protein_id "ENSP00000390500.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STK3--PPP1R16A^ENST00000419617.7"  ; transcript_name "STK3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TCF7L2--RNU7-165P	HAVANA	gene	15542	23732	.	+	.	FI_gene_label "TCF7L2^ENSG00000148737.17"  ; ID "TCF7L2--RNU7-165P^TCF7L2^ENSG00000148737.17"  ; exon_id "ENSE00001738678.1"  ; exon_number 1 ; gene_id "TCF7L2--RNU7-165P^TCF7L2^ENSG00000148737.17"  ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11"  ; havana_transcript "OTTHUMT00000050420.2"  ; hgnc_id "HGNC:11641"  ; level 2 ; orig_coord_info "chr10,113146072,113146097,+"  ; protein_id "ENSP00000277945.7"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TCF7L2--RNU7-165P^ENST00000277945.11"  ; transcript_name "TCF7L2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TCF7L2--RNU7-165P	HAVANA	mRNA	15542	23732	.	+	.	FI_gene_label "TCF7L2^ENSG00000148737.17"  ; ID "TCF7L2--RNU7-165P^ENST00000277945.11"  ; Parent "TCF7L2--RNU7-165P^TCF7L2^ENSG00000148737.17"  ; exon_id "ENSE00001738678.1"  ; exon_number 1 ; gene_id "TCF7L2--RNU7-165P^TCF7L2^ENSG00000148737.17"  ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11"  ; havana_transcript "OTTHUMT00000050420.2"  ; hgnc_id "HGNC:11641"  ; level 2 ; orig_coord_info "chr10,113146072,113146097,+"  ; protein_id "ENSP00000277945.7"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TCF7L2--RNU7-165P^ENST00000277945.11"  ; transcript_name "TCF7L2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
THSD4--AC103993.1	ENSEMBL	gene	10375	35733	.	+	.	FI_gene_label "THSD4^ENSG00000187720.14"  ; ID "THSD4--AC103993.1^THSD4^ENSG00000187720.14"  ; exon_id "ENSE00003748996.1"  ; exon_number 1 ; gene_id "THSD4--AC103993.1^THSD4^ENSG00000187720.14"  ; gene_name THSD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133389.7"  ; hgnc_id "HGNC:25835"  ; level 3 ; orig_coord_info "chr15,71547410,71547481,+"  ; protein_id "ENSP00000261862.7"  ; tag basic ; transcript_id "THSD4--AC103993.1^ENST00000261862.7"  ; transcript_name "THSD4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
THSD4--AC103993.1	ENSEMBL	mRNA	10375	35733	.	+	.	FI_gene_label "THSD4^ENSG00000187720.14"  ; ID "THSD4--AC103993.1^ENST00000261862.7"  ; Parent "THSD4--AC103993.1^THSD4^ENSG00000187720.14"  ; exon_id "ENSE00003748996.1"  ; exon_number 1 ; gene_id "THSD4--AC103993.1^THSD4^ENSG00000187720.14"  ; gene_name THSD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133389.7"  ; hgnc_id "HGNC:25835"  ; level 3 ; orig_coord_info "chr15,71547410,71547481,+"  ; protein_id "ENSP00000261862.7"  ; tag basic ; transcript_id "THSD4--AC103993.1^ENST00000261862.7"  ; transcript_name "THSD4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TRPS1--CSMD3	HAVANA	gene	3960	20612	.	+	.	FI_gene_label "TRPS1^ENSG00000104447.13"  ; ID "TRPS1--CSMD3^TRPS1^ENSG00000104447.13"  ; ccdsid "CCDS83316.1"  ; exon_id "ENSE00003549754.1"  ; exon_number 2 ; gene_id "TRPS1--CSMD3^TRPS1^ENSG00000104447.13"  ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6"  ; havana_transcript "OTTHUMT00000286436.3"  ; hgnc_id "HGNC:12340"  ; level 2 ; orig_coord_info "chr8,115619132,115620058,-"  ; protein_id "ENSP00000220888.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "TRPS1--CSMD3^ENST00000220888.9"  ; transcript_name "TRPS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRPS1--CSMD3	HAVANA	mRNA	3960	20612	.	+	.	FI_gene_label "TRPS1^ENSG00000104447.13"  ; ID "TRPS1--CSMD3^ENST00000220888.9"  ; Parent "TRPS1--CSMD3^TRPS1^ENSG00000104447.13"  ; ccdsid "CCDS83316.1"  ; exon_id "ENSE00003549754.1"  ; exon_number 2 ; gene_id "TRPS1--CSMD3^TRPS1^ENSG00000104447.13"  ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6"  ; havana_transcript "OTTHUMT00000286436.3"  ; hgnc_id "HGNC:12340"  ; level 2 ; orig_coord_info "chr8,115619132,115620058,-"  ; protein_id "ENSP00000220888.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "TRPS1--CSMD3^ENST00000220888.9"  ; transcript_name "TRPS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRPS1--CSMD3	HAVANA	gene	27666	117587	.	+	.	FI_gene_label "CSMD3^ENSG00000164796.18"  ; ID "TRPS1--CSMD3^CSMD3^ENSG00000164796.18"  ; ccdsid "CCDS6315.1"  ; exon_id "ENSE00001850376.2"  ; exon_number 1 ; gene_id "TRPS1--CSMD3^CSMD3^ENSG00000164796.18"  ; gene_name CSMD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157027.5"  ; havana_transcript "OTTHUMT00000347141.2"  ; hgnc_id "HGNC:19291"  ; level 2 ; orig_coord_info "chr8,113436677,113436854,-"  ; protein_id "ENSP00000297405.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPS1--CSMD3^ENST00000297405.10"  ; transcript_name "CSMD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRPS1--CSMD3	HAVANA	mRNA	27666	117587	.	+	.	FI_gene_label "CSMD3^ENSG00000164796.18"  ; ID "TRPS1--CSMD3^ENST00000297405.10"  ; Parent "TRPS1--CSMD3^CSMD3^ENSG00000164796.18"  ; ccdsid "CCDS6315.1"  ; exon_id "ENSE00001850376.2"  ; exon_number 1 ; gene_id "TRPS1--CSMD3^CSMD3^ENSG00000164796.18"  ; gene_name CSMD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157027.5"  ; havana_transcript "OTTHUMT00000347141.2"  ; hgnc_id "HGNC:19291"  ; level 2 ; orig_coord_info "chr8,113436677,113436854,-"  ; protein_id "ENSP00000297405.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPS1--CSMD3^ENST00000297405.10"  ; transcript_name "CSMD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRPS1--EBAG9	HAVANA	gene	3960	20612	.	+	.	FI_gene_label "TRPS1^ENSG00000104447.13"  ; ID "TRPS1--EBAG9^TRPS1^ENSG00000104447.13"  ; ccdsid "CCDS83316.1"  ; exon_id "ENSE00003549754.1"  ; exon_number 2 ; gene_id "TRPS1--EBAG9^TRPS1^ENSG00000104447.13"  ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6"  ; havana_transcript "OTTHUMT00000286436.3"  ; hgnc_id "HGNC:12340"  ; level 2 ; orig_coord_info "chr8,115619132,115620058,-"  ; protein_id "ENSP00000220888.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "TRPS1--EBAG9^ENST00000220888.9"  ; transcript_name "TRPS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRPS1--EBAG9	HAVANA	mRNA	3960	20612	.	+	.	FI_gene_label "TRPS1^ENSG00000104447.13"  ; ID "TRPS1--EBAG9^ENST00000220888.9"  ; Parent "TRPS1--EBAG9^TRPS1^ENSG00000104447.13"  ; ccdsid "CCDS83316.1"  ; exon_id "ENSE00003549754.1"  ; exon_number 2 ; gene_id "TRPS1--EBAG9^TRPS1^ENSG00000104447.13"  ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6"  ; havana_transcript "OTTHUMT00000286436.3"  ; hgnc_id "HGNC:12340"  ; level 2 ; orig_coord_info "chr8,115619132,115620058,-"  ; protein_id "ENSP00000220888.5"  ; tag basic appris_alternative_1 CCDS ; transcript_id "TRPS1--EBAG9^ENST00000220888.9"  ; transcript_name "TRPS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRPS1--EBAG9	HAVANA	gene	28128	39041	.	+	.	FI_gene_label "EBAG9^ENSG00000147654.15"  ; ID "TRPS1--EBAG9^EBAG9^ENSG00000147654.15"  ; ccdsid "CCDS6313.1"  ; exon_id "ENSE00003501492.1"  ; exon_number 2 ; gene_id "TRPS1--EBAG9^EBAG9^ENSG00000147654.15"  ; gene_name EBAG9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165346.4"  ; havana_transcript "OTTHUMT00000383536.2"  ; hgnc_id "HGNC:3123"  ; level 2 ; orig_coord_info "chr8,109550825,109550907,+"  ; protein_id "ENSP00000337675.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPS1--EBAG9^ENST00000337573.10"  ; transcript_name "EBAG9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRPS1--EBAG9	HAVANA	mRNA	28128	39041	.	+	.	FI_gene_label "EBAG9^ENSG00000147654.15"  ; ID "TRPS1--EBAG9^ENST00000337573.10"  ; Parent "TRPS1--EBAG9^EBAG9^ENSG00000147654.15"  ; ccdsid "CCDS6313.1"  ; exon_id "ENSE00003501492.1"  ; exon_number 2 ; gene_id "TRPS1--EBAG9^EBAG9^ENSG00000147654.15"  ; gene_name EBAG9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165346.4"  ; havana_transcript "OTTHUMT00000383536.2"  ; hgnc_id "HGNC:3123"  ; level 2 ; orig_coord_info "chr8,109550825,109550907,+"  ; protein_id "ENSP00000337675.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPS1--EBAG9^ENST00000337573.10"  ; transcript_name "EBAG9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZHX2--COL14A1	ENSEMBL	gene	40724	68387	.	+	.	FI_gene_label "COL14A1^ENSG00000187955.12"  ; ID "ZHX2--COL14A1^COL14A1^ENSG00000187955.12"  ; exon_id "ENSE00003734994.1"  ; exon_number 5 ; gene_id "ZHX2--COL14A1^COL14A1^ENSG00000187955.12"  ; gene_name COL14A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149877.5"  ; hgnc_id "HGNC:2191"  ; level 3 ; orig_coord_info "chr8,120270074,120270100,+"  ; protein_id "ENSP00000247781.4"  ; tag basic ; transcript_id "ZHX2--COL14A1^ENST00000247781.4"  ; transcript_name "COL14A1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ZHX2--COL14A1	ENSEMBL	mRNA	40724	68387	.	+	.	FI_gene_label "COL14A1^ENSG00000187955.12"  ; ID "ZHX2--COL14A1^ENST00000247781.4"  ; Parent "ZHX2--COL14A1^COL14A1^ENSG00000187955.12"  ; exon_id "ENSE00003734994.1"  ; exon_number 5 ; gene_id "ZHX2--COL14A1^COL14A1^ENSG00000187955.12"  ; gene_name COL14A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149877.5"  ; hgnc_id "HGNC:2191"  ; level 3 ; orig_coord_info "chr8,120270074,120270100,+"  ; protein_id "ENSP00000247781.4"  ; tag basic ; transcript_id "ZHX2--COL14A1^ENST00000247781.4"  ; transcript_name "COL14A1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ZHX2--COL14A1	HAVANA	gene	1001	8453	.	+	.	FI_gene_label "ZHX2^ENSG00000178764.8"  ; ID "ZHX2--COL14A1^ZHX2^ENSG00000178764.8"  ; ccdsid "CCDS6336.1"  ; exon_id "ENSE00001252625.2"  ; exon_number 3 ; gene_id "ZHX2--COL14A1^ZHX2^ENSG00000178764.8"  ; gene_name ZHX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165077.7"  ; havana_transcript "OTTHUMT00000381709.3"  ; hgnc_id "HGNC:18513"  ; level 2 ; orig_coord_info "chr8,122951511,122954021,+"  ; protein_id "ENSP00000314709.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZHX2--COL14A1^ENST00000314393.6"  ; transcript_name "ZHX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZHX2--COL14A1	HAVANA	mRNA	1001	8453	.	+	.	FI_gene_label "ZHX2^ENSG00000178764.8"  ; ID "ZHX2--COL14A1^ENST00000314393.6"  ; Parent "ZHX2--COL14A1^ZHX2^ENSG00000178764.8"  ; ccdsid "CCDS6336.1"  ; exon_id "ENSE00001252625.2"  ; exon_number 3 ; gene_id "ZHX2--COL14A1^ZHX2^ENSG00000178764.8"  ; gene_name ZHX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165077.7"  ; havana_transcript "OTTHUMT00000381709.3"  ; hgnc_id "HGNC:18513"  ; level 2 ; orig_coord_info "chr8,122951511,122954021,+"  ; protein_id "ENSP00000314709.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZHX2--COL14A1^ENST00000314393.6"  ; transcript_name "ZHX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KAT6B--RPA2P2	HAVANA	gene	50561	51356	.	+	.	FI_gene_label "RPA2P2^ENSG00000226466.2"  ; ID "KAT6B--RPA2P2^RPA2P2^ENSG00000226466.2"  ; exon_id "ENSE00001753092.1"  ; exon_number 1 ; gene_id "KAT6B--RPA2P2^RPA2P2^ENSG00000226466.2"  ; gene_name RPA2P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000018623.1"  ; havana_transcript "OTTHUMT00000049100.1"  ; hgnc_id "HGNC:45117"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,81136540,81137335,-"  ; tag pseudo_consens basic ; transcript_id "KAT6B--RPA2P2^ENST00000419698.1"  ; transcript_name "RPA2P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
KAT6B--RPA2P2	HAVANA	RNA	50561	51356	.	+	.	FI_gene_label "RPA2P2^ENSG00000226466.2"  ; ID "KAT6B--RPA2P2^ENST00000419698.1"  ; Parent "KAT6B--RPA2P2^RPA2P2^ENSG00000226466.2"  ; exon_id "ENSE00001753092.1"  ; exon_number 1 ; gene_id "KAT6B--RPA2P2^RPA2P2^ENSG00000226466.2"  ; gene_name RPA2P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000018623.1"  ; havana_transcript "OTTHUMT00000049100.1"  ; hgnc_id "HGNC:45117"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,81136540,81137335,-"  ; tag pseudo_consens basic ; transcript_id "KAT6B--RPA2P2^ENST00000419698.1"  ; transcript_name "RPA2P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
KAT6B--WARS2P1	HAVANA	gene	50561	51097	.	+	.	FI_gene_label "WARS2P1^ENSG00000227209.1"  ; ID "KAT6B--WARS2P1^WARS2P1^ENSG00000227209.1"  ; exon_id "ENSE00001794592.1"  ; exon_number 1 ; gene_id "KAT6B--WARS2P1^WARS2P1^ENSG00000227209.1"  ; gene_name WARS2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000018622.1"  ; havana_transcript "OTTHUMT00000049099.1"  ; hgnc_id "HGNC:45116"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,80940665,80941201,-"  ; tag pseudo_consens basic ; transcript_id "KAT6B--WARS2P1^ENST00000429678.1"  ; transcript_name "WARS2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
KAT6B--WARS2P1	HAVANA	RNA	50561	51097	.	+	.	FI_gene_label "WARS2P1^ENSG00000227209.1"  ; ID "KAT6B--WARS2P1^ENST00000429678.1"  ; Parent "KAT6B--WARS2P1^WARS2P1^ENSG00000227209.1"  ; exon_id "ENSE00001794592.1"  ; exon_number 1 ; gene_id "KAT6B--WARS2P1^WARS2P1^ENSG00000227209.1"  ; gene_name WARS2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000018622.1"  ; havana_transcript "OTTHUMT00000049099.1"  ; hgnc_id "HGNC:45116"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr10,80940665,80941201,-"  ; tag pseudo_consens basic ; transcript_id "KAT6B--WARS2P1^ENST00000429678.1"  ; transcript_name "WARS2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
LRP5--OR4A9P	HAVANA	gene	33834	34777	.	+	.	FI_gene_label "OR4A9P^ENSG00000254891.1"  ; ID "LRP5--OR4A9P^OR4A9P^ENSG00000254891.1"  ; exon_id "ENSE00002163690.1"  ; exon_number 1 ; gene_id "LRP5--OR4A9P^OR4A9P^ENSG00000254891.1"  ; gene_name OR4A9P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166712.1"  ; havana_transcript "OTTHUMT00000391162.1"  ; hgnc_id "HGNC:15166"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr11,55388529,55389472,+"  ; tag basic ; transcript_id "LRP5--OR4A9P^ENST00000526326.1"  ; transcript_name "OR4A9P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
LRP5--OR4A9P	HAVANA	RNA	33834	34777	.	+	.	FI_gene_label "OR4A9P^ENSG00000254891.1"  ; ID "LRP5--OR4A9P^ENST00000526326.1"  ; Parent "LRP5--OR4A9P^OR4A9P^ENSG00000254891.1"  ; exon_id "ENSE00002163690.1"  ; exon_number 1 ; gene_id "LRP5--OR4A9P^OR4A9P^ENSG00000254891.1"  ; gene_name OR4A9P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166712.1"  ; havana_transcript "OTTHUMT00000391162.1"  ; hgnc_id "HGNC:15166"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr11,55388529,55389472,+"  ; tag basic ; transcript_id "LRP5--OR4A9P^ENST00000526326.1"  ; transcript_name "OR4A9P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
LRP5--OR4X7P	HAVANA	gene	33834	34025	.	+	.	FI_gene_label "OR4X7P^ENSG00000255077.1"  ; ID "LRP5--OR4X7P^OR4X7P^ENSG00000255077.1"  ; exon_id "ENSE00002153517.1"  ; exon_number 1 ; gene_id "LRP5--OR4X7P^OR4X7P^ENSG00000255077.1"  ; gene_name OR4X7P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166777.1"  ; havana_transcript "OTTHUMT00000391440.1"  ; hgnc_id "HGNC:31277"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr11,55411526,55411717,+"  ; tag basic ; transcript_id "LRP5--OR4X7P^ENST00000526939.1"  ; transcript_name "OR4X7P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
LRP5--OR4X7P	HAVANA	RNA	33834	34025	.	+	.	FI_gene_label "OR4X7P^ENSG00000255077.1"  ; ID "LRP5--OR4X7P^ENST00000526939.1"  ; Parent "LRP5--OR4X7P^OR4X7P^ENSG00000255077.1"  ; exon_id "ENSE00002153517.1"  ; exon_number 1 ; gene_id "LRP5--OR4X7P^OR4X7P^ENSG00000255077.1"  ; gene_name OR4X7P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166777.1"  ; havana_transcript "OTTHUMT00000391440.1"  ; hgnc_id "HGNC:31277"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr11,55411526,55411717,+"  ; tag basic ; transcript_id "LRP5--OR4X7P^ENST00000526939.1"  ; transcript_name "OR4X7P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
MROH1--AC105118.1	HAVANA	gene	41250	43128	.	+	.	FI_gene_label "AC105118.1^ENSG00000253931.1"  ; ID "MROH1--AC105118.1^AC105118.1^ENSG00000253931.1"  ; exon_id "ENSE00002102743.1"  ; exon_number 1 ; gene_id "MROH1--AC105118.1^AC105118.1^ENSG00000253931.1"  ; gene_name "AC105118.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165016.1"  ; havana_transcript "OTTHUMT00000381459.1"  ; level 1 ; orig_coord_info "chr8,143412749,143412856,+"  ; tag basic exp_conf ; transcript_id "MROH1--AC105118.1^ENST00000523002.1"  ; transcript_name "AC105118.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
MROH1--AC105118.1	HAVANA	RNA	41250	43128	.	+	.	FI_gene_label "AC105118.1^ENSG00000253931.1"  ; ID "MROH1--AC105118.1^ENST00000523002.1"  ; Parent "MROH1--AC105118.1^AC105118.1^ENSG00000253931.1"  ; exon_id "ENSE00002102743.1"  ; exon_number 1 ; gene_id "MROH1--AC105118.1^AC105118.1^ENSG00000253931.1"  ; gene_name "AC105118.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165016.1"  ; havana_transcript "OTTHUMT00000381459.1"  ; level 1 ; orig_coord_info "chr8,143412749,143412856,+"  ; tag basic exp_conf ; transcript_id "MROH1--AC105118.1^ENST00000523002.1"  ; transcript_name "AC105118.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PVT1--COLEC10	HAVANA	gene	1010	23032	.	+	.	FI_gene_label "PVT1^ENSG00000249859.12"  ; ID "PVT1--COLEC10^PVT1^ENSG00000249859.12"  ; exon_id "ENSE00003880231.1"  ; exon_number 1 ; gene_id "PVT1--COLEC10^PVT1^ENSG00000249859.12"  ; gene_name PVT1 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164871.168"  ; havana_transcript "OTTHUMT00000514270.1"  ; hgnc_id "HGNC:9709"  ; level 2 ; orig_coord_info "chr8,127794535,127794734,+"  ; tag TAGENE ; transcript_id "PVT1--COLEC10^ENST00000504719.7"  ; transcript_name "PVT1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
PVT1--COLEC10	HAVANA	RNA	1010	23032	.	+	.	FI_gene_label "PVT1^ENSG00000249859.12"  ; ID "PVT1--COLEC10^ENST00000504719.7"  ; Parent "PVT1--COLEC10^PVT1^ENSG00000249859.12"  ; exon_id "ENSE00003880231.1"  ; exon_number 1 ; gene_id "PVT1--COLEC10^PVT1^ENSG00000249859.12"  ; gene_name PVT1 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164871.168"  ; havana_transcript "OTTHUMT00000514270.1"  ; hgnc_id "HGNC:9709"  ; level 2 ; orig_coord_info "chr8,127794535,127794734,+"  ; tag TAGENE ; transcript_id "PVT1--COLEC10^ENST00000504719.7"  ; transcript_name "PVT1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
TCF7L2--RNU7-165P	ENSEMBL	gene	28779	28838	.	+	.	FI_gene_label "RNU7-165P^ENSG00000238380.1"  ; ID "TCF7L2--RNU7-165P^RNU7-165P^ENSG00000238380.1"  ; exon_id "ENSE00001807990.1"  ; exon_number 1 ; gene_id "TCF7L2--RNU7-165P^RNU7-165P^ENSG00000238380.1"  ; gene_name "RNU7-165P"  ; gene_type snRNA ; hgnc_id "HGNC:45699"  ; level 3 ; orig_coord_info "chr10,113353425,113353484,+"  ; tag basic ; transcript_id "TCF7L2--RNU7-165P^ENST00000458864.1"  ; transcript_name "RNU7-165P-201"  ; transcript_support_level NA ; transcript_type snRNA
TCF7L2--RNU7-165P	ENSEMBL	RNA	28779	28838	.	+	.	FI_gene_label "RNU7-165P^ENSG00000238380.1"  ; ID "TCF7L2--RNU7-165P^ENST00000458864.1"  ; Parent "TCF7L2--RNU7-165P^RNU7-165P^ENSG00000238380.1"  ; exon_id "ENSE00001807990.1"  ; exon_number 1 ; gene_id "TCF7L2--RNU7-165P^RNU7-165P^ENSG00000238380.1"  ; gene_name "RNU7-165P"  ; gene_type snRNA ; hgnc_id "HGNC:45699"  ; level 3 ; orig_coord_info "chr10,113353425,113353484,+"  ; tag basic ; transcript_id "TCF7L2--RNU7-165P^ENST00000458864.1"  ; transcript_name "RNU7-165P-201"  ; transcript_support_level NA ; transcript_type snRNA
L1 and L2 created: 
THSD4--AC103993.1	HAVANA	gene	39967	41421	.	+	.	FI_gene_label "AC103993.1^ENSG00000253207.3"  ; ID "THSD4--AC103993.1^AC103993.1^ENSG00000253207.3"  ; exon_id "ENSE00002112593.1"  ; exon_number 1 ; gene_id "THSD4--AC103993.1^AC103993.1^ENSG00000253207.3"  ; gene_name "AC103993.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000164895.3"  ; havana_transcript "OTTHUMT00000380838.2"  ; level 2 ; orig_coord_info "chr8,113615504,113615688,+"  ; transcript_id "THSD4--AC103993.1^ENST00000518558.2"  ; transcript_name "AC103993.1-202"  ; transcript_support_level 2 ; transcript_type lncRNA
THSD4--AC103993.1	HAVANA	RNA	39967	41421	.	+	.	FI_gene_label "AC103993.1^ENSG00000253207.3"  ; ID "THSD4--AC103993.1^ENST00000518558.2"  ; Parent "THSD4--AC103993.1^AC103993.1^ENSG00000253207.3"  ; exon_id "ENSE00002112593.1"  ; exon_number 1 ; gene_id "THSD4--AC103993.1^AC103993.1^ENSG00000253207.3"  ; gene_name "AC103993.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000164895.3"  ; havana_transcript "OTTHUMT00000380838.2"  ; level 2 ; orig_coord_info "chr8,113615504,113615688,+"  ; transcript_id "THSD4--AC103993.1^ENST00000518558.2"  ; transcript_name "AC103993.1-202"  ; transcript_support_level 2 ; transcript_type lncRNA
583 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------

------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------

------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 1 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
836 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 24 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