.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-184b05-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b1f5fb5d81b2ab46cc668b114de399/.command.log
Size: 77.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-184b05-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/50b62780288ca327d96e45869a9c83/fi_workdir/aih-tih-sc-184b05-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b1f5fb5d81b2ab46cc668b114de399/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b1f5fb5d81b2ab46cc668b114de399/.command.run
==> STAGING COMPLETE (3 inputs)

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: 5562
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5562
=> 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:5562
  => 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: 
AC026336.1--PIWIL1	HAVANA	gene	4352	24217	.	+	.	FI_gene_label "PIWIL1^ENSG00000125207.7"  ; ID "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7"  ; ccdsid "CCDS9268.1"  ; exon_id "ENSE00001002623.3"  ; exon_number 2 ; gene_id "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7"  ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3"  ; havana_transcript "OTTHUMT00000399510.1"  ; hgnc_id "HGNC:9007"  ; level 2 ; orig_coord_info "chr12,130342592,130342669,+"  ; protein_id "ENSP00000245255.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026336.1--PIWIL1^ENST00000245255.7"  ; transcript_name "PIWIL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC026336.1--PIWIL1	HAVANA	mRNA	4352	24217	.	+	.	FI_gene_label "PIWIL1^ENSG00000125207.7"  ; ID "AC026336.1--PIWIL1^ENST00000245255.7"  ; Parent "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7"  ; ccdsid "CCDS9268.1"  ; exon_id "ENSE00001002623.3"  ; exon_number 2 ; gene_id "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7"  ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3"  ; havana_transcript "OTTHUMT00000399510.1"  ; hgnc_id "HGNC:9007"  ; level 2 ; orig_coord_info "chr12,130342592,130342669,+"  ; protein_id "ENSP00000245255.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026336.1--PIWIL1^ENST00000245255.7"  ; transcript_name "PIWIL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ACTBP6--ACTB	HAVANA	gene	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ACTBP6--ACTB	HAVANA	mRNA	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ENST00000414620.1"  ; Parent "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
AGAP12P--FRMPD2	HAVANA	gene	13554	48555	.	+	.	FI_gene_label "FRMPD2^ENSG00000170324.21"  ; ID "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21"  ; ccdsid "CCDS81460.1"  ; exon_id "ENSE00001390154.1"  ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21"  ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7"  ; havana_transcript "OTTHUMT00000277029.1"  ; hgnc_id "HGNC:28572"  ; level 2 ; orig_coord_info "chr10,48251566,48251710,-"  ; protein_id "ENSP00000307079.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3"  ; transcript_name "FRMPD2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AGAP12P--FRMPD2	HAVANA	mRNA	13554	48555	.	+	.	FI_gene_label "FRMPD2^ENSG00000170324.21"  ; ID "AGAP12P--FRMPD2^ENST00000305531.3"  ; Parent "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21"  ; ccdsid "CCDS81460.1"  ; exon_id "ENSE00001390154.1"  ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21"  ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7"  ; havana_transcript "OTTHUMT00000277029.1"  ; hgnc_id "HGNC:28572"  ; level 2 ; orig_coord_info "chr10,48251566,48251710,-"  ; protein_id "ENSP00000307079.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3"  ; transcript_name "FRMPD2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
BICD1--ITPR2	HAVANA	gene	26282	32017	.	+	.	FI_gene_label "ITPR2^ENSG00000123104.12"  ; ID "BICD1--ITPR2^ITPR2^ENSG00000123104.12"  ; exon_id "ENSE00002282656.1"  ; exon_number 1 ; gene_id "BICD1--ITPR2^ITPR2^ENSG00000123104.12"  ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5"  ; havana_transcript "OTTHUMT00000402735.1"  ; hgnc_id "HGNC:6181"  ; level 2 ; orig_coord_info "chr12,26832690,26832781,-"  ; protein_id "ENSP00000242737.5"  ; tag basic ; transcript_id "BICD1--ITPR2^ENST00000242737.5"  ; transcript_name "ITPR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BICD1--ITPR2	HAVANA	mRNA	26282	32017	.	+	.	FI_gene_label "ITPR2^ENSG00000123104.12"  ; ID "BICD1--ITPR2^ENST00000242737.5"  ; Parent "BICD1--ITPR2^ITPR2^ENSG00000123104.12"  ; exon_id "ENSE00002282656.1"  ; exon_number 1 ; gene_id "BICD1--ITPR2^ITPR2^ENSG00000123104.12"  ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5"  ; havana_transcript "OTTHUMT00000402735.1"  ; hgnc_id "HGNC:6181"  ; level 2 ; orig_coord_info "chr12,26832690,26832781,-"  ; protein_id "ENSP00000242737.5"  ; tag basic ; transcript_id "BICD1--ITPR2^ENST00000242737.5"  ; transcript_name "ITPR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BICD1--ITPR2	HAVANA	gene	1418	17158	.	+	.	FI_gene_label "BICD1^ENSG00000151746.15"  ; ID "BICD1--ITPR2^BICD1^ENSG00000151746.15"  ; ccdsid "CCDS86290.1"  ; exon_id "ENSE00001269108.5"  ; exon_number 1 ; gene_id "BICD1--ITPR2^BICD1^ENSG00000151746.15"  ; gene_name BICD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169307.6"  ; havana_transcript "OTTHUMT00000403381.1"  ; hgnc_id "HGNC:1049"  ; level 2 ; orig_coord_info "chr12,32107332,32107544,+"  ; protein_id "ENSP00000379107.3"  ; tag CCDS ; transcript_id "BICD1--ITPR2^ENST00000395758.3"  ; transcript_name "BICD1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
BICD1--ITPR2	HAVANA	mRNA	1418	17158	.	+	.	FI_gene_label "BICD1^ENSG00000151746.15"  ; ID "BICD1--ITPR2^ENST00000395758.3"  ; Parent "BICD1--ITPR2^BICD1^ENSG00000151746.15"  ; ccdsid "CCDS86290.1"  ; exon_id "ENSE00001269108.5"  ; exon_number 1 ; gene_id "BICD1--ITPR2^BICD1^ENSG00000151746.15"  ; gene_name BICD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169307.6"  ; havana_transcript "OTTHUMT00000403381.1"  ; hgnc_id "HGNC:1049"  ; level 2 ; orig_coord_info "chr12,32107332,32107544,+"  ; protein_id "ENSP00000379107.3"  ; tag CCDS ; transcript_id "BICD1--ITPR2^ENST00000395758.3"  ; transcript_name "BICD1-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGD4--PIK3C2G	HAVANA	gene	3702	28028	.	+	.	FI_gene_label "FGD4^ENSG00000139132.15"  ; ID "FGD4--PIK3C2G^FGD4^ENSG00000139132.15"  ; exon_id "ENSE00003586205.1"  ; exon_number 3 ; gene_id "FGD4--PIK3C2G^FGD4^ENSG00000139132.15"  ; gene_name FGD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137374.7"  ; havana_transcript "OTTHUMT00000268019.2"  ; hgnc_id "HGNC:19125"  ; level 2 ; orig_coord_info "chr12,32576358,32576449,+"  ; protein_id "ENSP00000379089.1"  ; transcript_id "FGD4--PIK3C2G^ENST00000395740.5"  ; transcript_name "FGD4-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGD4--PIK3C2G	HAVANA	mRNA	3702	28028	.	+	.	FI_gene_label "FGD4^ENSG00000139132.15"  ; ID "FGD4--PIK3C2G^ENST00000395740.5"  ; Parent "FGD4--PIK3C2G^FGD4^ENSG00000139132.15"  ; exon_id "ENSE00003586205.1"  ; exon_number 3 ; gene_id "FGD4--PIK3C2G^FGD4^ENSG00000139132.15"  ; gene_name FGD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137374.7"  ; havana_transcript "OTTHUMT00000268019.2"  ; hgnc_id "HGNC:19125"  ; level 2 ; orig_coord_info "chr12,32576358,32576449,+"  ; protein_id "ENSP00000379089.1"  ; transcript_id "FGD4--PIK3C2G^ENST00000395740.5"  ; transcript_name "FGD4-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGD4--PIK3C2G	HAVANA	gene	40383	79838	.	+	.	FI_gene_label "PIK3C2G^ENSG00000139144.11"  ; ID "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11"  ; ccdsid "CCDS44839.1"  ; exon_id "ENSE00001121910.3"  ; exon_number 2 ; gene_id "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11"  ; gene_name PIK3C2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000168841.7"  ; havana_transcript "OTTHUMT00000401316.4"  ; hgnc_id "HGNC:8973"  ; level 2 ; orig_coord_info "chr12,18282082,18282759,+"  ; protein_id "ENSP00000404845.1"  ; tag basic CCDS ; transcript_id "FGD4--PIK3C2G^ENST00000433979.6"  ; transcript_name "PIK3C2G-201"  ; transcript_support_level 5 ; transcript_type protein_coding
FGD4--PIK3C2G	HAVANA	mRNA	40383	79838	.	+	.	FI_gene_label "PIK3C2G^ENSG00000139144.11"  ; ID "FGD4--PIK3C2G^ENST00000433979.6"  ; Parent "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11"  ; ccdsid "CCDS44839.1"  ; exon_id "ENSE00001121910.3"  ; exon_number 2 ; gene_id "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11"  ; gene_name PIK3C2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000168841.7"  ; havana_transcript "OTTHUMT00000401316.4"  ; hgnc_id "HGNC:8973"  ; level 2 ; orig_coord_info "chr12,18282082,18282759,+"  ; protein_id "ENSP00000404845.1"  ; tag basic CCDS ; transcript_id "FGD4--PIK3C2G^ENST00000433979.6"  ; transcript_name "PIK3C2G-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
FZD10--PIWIL1	ENSEMBL	gene	1001	4281	.	+	.	FI_gene_label "FZD10^ENSG00000111432.4"  ; ID "FZD10--PIWIL1^FZD10^ENSG00000111432.4"  ; ccdsid "CCDS9267.1"  ; exon_id "ENSE00002290283.1"  ; exon_number 1 ; gene_id "FZD10--PIWIL1^FZD10^ENSG00000111432.4"  ; gene_name FZD10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168380.3"  ; hgnc_id "HGNC:4039"  ; level 3 ; orig_coord_info "chr12,130162943,130164685,+"  ; protein_id "ENSP00000229030.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000229030.4"  ; transcript_name "FZD10-201"  ; transcript_support_level NA ; transcript_type protein_coding
FZD10--PIWIL1	ENSEMBL	mRNA	1001	4281	.	+	.	FI_gene_label "FZD10^ENSG00000111432.4"  ; ID "FZD10--PIWIL1^ENST00000229030.4"  ; Parent "FZD10--PIWIL1^FZD10^ENSG00000111432.4"  ; ccdsid "CCDS9267.1"  ; exon_id "ENSE00002290283.1"  ; exon_number 1 ; gene_id "FZD10--PIWIL1^FZD10^ENSG00000111432.4"  ; gene_name FZD10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168380.3"  ; hgnc_id "HGNC:4039"  ; level 3 ; orig_coord_info "chr12,130162943,130164685,+"  ; protein_id "ENSP00000229030.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000229030.4"  ; transcript_name "FZD10-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
FZD10--PIWIL1	HAVANA	gene	7283	27148	.	+	.	FI_gene_label "PIWIL1^ENSG00000125207.7"  ; ID "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7"  ; ccdsid "CCDS9268.1"  ; exon_id "ENSE00001002623.3"  ; exon_number 2 ; gene_id "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7"  ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3"  ; havana_transcript "OTTHUMT00000399510.1"  ; hgnc_id "HGNC:9007"  ; level 2 ; orig_coord_info "chr12,130342592,130342669,+"  ; protein_id "ENSP00000245255.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000245255.7"  ; transcript_name "PIWIL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FZD10--PIWIL1	HAVANA	mRNA	7283	27148	.	+	.	FI_gene_label "PIWIL1^ENSG00000125207.7"  ; ID "FZD10--PIWIL1^ENST00000245255.7"  ; Parent "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7"  ; ccdsid "CCDS9268.1"  ; exon_id "ENSE00001002623.3"  ; exon_number 2 ; gene_id "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7"  ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3"  ; havana_transcript "OTTHUMT00000399510.1"  ; hgnc_id "HGNC:9007"  ; level 2 ; orig_coord_info "chr12,130342592,130342669,+"  ; protein_id "ENSP00000245255.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000245255.7"  ; transcript_name "PIWIL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GTF2F2--CBY2	HAVANA	gene	16609	20258	.	+	.	FI_gene_label "CBY2^ENSG00000174015.10"  ; ID "GTF2F2--CBY2^CBY2^ENSG00000174015.10"  ; ccdsid "CCDS9399.1"  ; exon_id "ENSE00002150255.1"  ; exon_number 1 ; gene_id "GTF2F2--CBY2^CBY2^ENSG00000174015.10"  ; gene_name CBY2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016861.5"  ; havana_transcript "OTTHUMT00000044786.3"  ; hgnc_id "HGNC:30720"  ; level 2 ; orig_coord_info "chr13,45702391,45702465,+"  ; protein_id "ENSP00000309189.1"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000310521.6"  ; transcript_name "CBY2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTF2F2--CBY2	HAVANA	mRNA	16609	20258	.	+	.	FI_gene_label "CBY2^ENSG00000174015.10"  ; ID "GTF2F2--CBY2^ENST00000310521.6"  ; Parent "GTF2F2--CBY2^CBY2^ENSG00000174015.10"  ; ccdsid "CCDS9399.1"  ; exon_id "ENSE00002150255.1"  ; exon_number 1 ; gene_id "GTF2F2--CBY2^CBY2^ENSG00000174015.10"  ; gene_name CBY2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016861.5"  ; havana_transcript "OTTHUMT00000044786.3"  ; hgnc_id "HGNC:30720"  ; level 2 ; orig_coord_info "chr13,45702391,45702465,+"  ; protein_id "ENSP00000309189.1"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000310521.6"  ; transcript_name "CBY2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GTF2F2--CBY2	HAVANA	gene	1001	13608	.	+	.	FI_gene_label "GTF2F2^ENSG00000188342.12"  ; ID "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12"  ; ccdsid "CCDS9395.1"  ; exon_id "ENSE00001479865.5"  ; exon_number 1 ; gene_id "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12"  ; gene_name GTF2F2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016849.5"  ; havana_transcript "OTTHUMT00000044767.5"  ; hgnc_id "HGNC:4653"  ; level 2 ; orig_coord_info "chr13,45120656,45120721,+"  ; protein_id "ENSP00000340823.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000340473.8"  ; transcript_name "GTF2F2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTF2F2--CBY2	HAVANA	mRNA	1001	13608	.	+	.	FI_gene_label "GTF2F2^ENSG00000188342.12"  ; ID "GTF2F2--CBY2^ENST00000340473.8"  ; Parent "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12"  ; ccdsid "CCDS9395.1"  ; exon_id "ENSE00001479865.5"  ; exon_number 1 ; gene_id "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12"  ; gene_name GTF2F2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016849.5"  ; havana_transcript "OTTHUMT00000044767.5"  ; hgnc_id "HGNC:4653"  ; level 2 ; orig_coord_info "chr13,45120656,45120721,+"  ; protein_id "ENSP00000340823.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000340473.8"  ; transcript_name "GTF2F2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ITPR2--AC048344.1	HAVANA	gene	1414	7149	.	+	.	FI_gene_label "ITPR2^ENSG00000123104.12"  ; ID "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12"  ; exon_id "ENSE00002282656.1"  ; exon_number 1 ; gene_id "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12"  ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5"  ; havana_transcript "OTTHUMT00000402735.1"  ; hgnc_id "HGNC:6181"  ; level 2 ; orig_coord_info "chr12,26832690,26832781,-"  ; protein_id "ENSP00000242737.5"  ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000242737.5"  ; transcript_name "ITPR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITPR2--AC048344.1	HAVANA	mRNA	1414	7149	.	+	.	FI_gene_label "ITPR2^ENSG00000123104.12"  ; ID "ITPR2--AC048344.1^ENST00000242737.5"  ; Parent "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12"  ; exon_id "ENSE00002282656.1"  ; exon_number 1 ; gene_id "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12"  ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5"  ; havana_transcript "OTTHUMT00000402735.1"  ; hgnc_id "HGNC:6181"  ; level 2 ; orig_coord_info "chr12,26832690,26832781,-"  ; protein_id "ENSP00000242737.5"  ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000242737.5"  ; transcript_name "ITPR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPM1--VPS72	HAVANA	gene	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--VPS72^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--VPS72^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--VPS72^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPM1--VPS72	HAVANA	mRNA	1734	14723	.	+	.	FI_gene_label "NPM1^ENSG00000181163.14"  ; ID "NPM1--VPS72^ENST00000296930.10"  ; Parent "NPM1--VPS72^NPM1^ENSG00000181163.14"  ; ccdsid "CCDS4376.1"  ; exon_id "ENSE00003906984.1"  ; exon_number 1 ; gene_id "NPM1--VPS72^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--VPS72^ENST00000296930.10"  ; transcript_name "NPM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPM1--VPS72	HAVANA	gene	19732	25191	.	+	.	FI_gene_label "VPS72^ENSG00000163159.14"  ; ID "NPM1--VPS72^VPS72^ENSG00000163159.14"  ; ccdsid "CCDS59201.1"  ; exon_id "ENSE00001932993.1"  ; exon_number 1 ; gene_id "NPM1--VPS72^VPS72^ENSG00000163159.14"  ; gene_name VPS72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012345.10"  ; havana_transcript "OTTHUMT00000034394.3"  ; hgnc_id "HGNC:11644"  ; level 1 ; orig_coord_info "chr1,151190005,151190121,-"  ; protein_id "ENSP00000346464.4"  ; tag mRNA_start_NF exp_conf CCDS ; transcript_id "NPM1--VPS72^ENST00000354473.4"  ; transcript_name "VPS72-201"  ; transcript_support_level 3 ; transcript_type protein_coding
NPM1--VPS72	HAVANA	mRNA	19732	25191	.	+	.	FI_gene_label "VPS72^ENSG00000163159.14"  ; ID "NPM1--VPS72^ENST00000354473.4"  ; Parent "NPM1--VPS72^VPS72^ENSG00000163159.14"  ; ccdsid "CCDS59201.1"  ; exon_id "ENSE00001932993.1"  ; exon_number 1 ; gene_id "NPM1--VPS72^VPS72^ENSG00000163159.14"  ; gene_name VPS72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012345.10"  ; havana_transcript "OTTHUMT00000034394.3"  ; hgnc_id "HGNC:11644"  ; level 1 ; orig_coord_info "chr1,151190005,151190121,-"  ; protein_id "ENSP00000346464.4"  ; tag mRNA_start_NF exp_conf CCDS ; transcript_id "NPM1--VPS72^ENST00000354473.4"  ; transcript_name "VPS72-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
PCDHB14--PCDHB15	HAVANA	gene	8418	12388	.	+	.	FI_gene_label "PCDHB15^ENSG00000113248.6"  ; ID "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6"  ; ccdsid "CCDS4257.1"  ; exon_id "ENSE00000766437.10"  ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6"  ; gene_name PCDHB15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129609.6"  ; havana_transcript "OTTHUMT00000251804.5"  ; hgnc_id "HGNC:8686"  ; level 2 ; orig_coord_info "chr5,141245579,141247939,+"  ; protein_id "ENSP00000231173.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000231173.6"  ; transcript_name "PCDHB15-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHB14--PCDHB15	HAVANA	mRNA	8418	12388	.	+	.	FI_gene_label "PCDHB15^ENSG00000113248.6"  ; ID "PCDHB14--PCDHB15^ENST00000231173.6"  ; Parent "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6"  ; ccdsid "CCDS4257.1"  ; exon_id "ENSE00000766437.10"  ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6"  ; gene_name PCDHB15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129609.6"  ; havana_transcript "OTTHUMT00000251804.5"  ; hgnc_id "HGNC:8686"  ; level 2 ; orig_coord_info "chr5,141245579,141247939,+"  ; protein_id "ENSP00000231173.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000231173.6"  ; transcript_name "PCDHB15-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHB14--PCDHB15	HAVANA	gene	1001	5417	.	+	.	FI_gene_label "PCDHB14^ENSG00000120327.7"  ; ID "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7"  ; ccdsid "CCDS4256.1"  ; exon_id "ENSE00001430609.6"  ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7"  ; gene_name PCDHB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129619.4"  ; havana_transcript "OTTHUMT00000251814.3"  ; hgnc_id "HGNC:8685"  ; level 2 ; orig_coord_info "chr5,141223506,141225899,+"  ; protein_id "ENSP00000239449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000239449.7"  ; transcript_name "PCDHB14-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHB14--PCDHB15	HAVANA	mRNA	1001	5417	.	+	.	FI_gene_label "PCDHB14^ENSG00000120327.7"  ; ID "PCDHB14--PCDHB15^ENST00000239449.7"  ; Parent "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7"  ; ccdsid "CCDS4256.1"  ; exon_id "ENSE00001430609.6"  ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7"  ; gene_name PCDHB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129619.4"  ; havana_transcript "OTTHUMT00000251814.3"  ; hgnc_id "HGNC:8685"  ; level 2 ; orig_coord_info "chr5,141223506,141225899,+"  ; protein_id "ENSP00000239449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000239449.7"  ; transcript_name "PCDHB14-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PDXDC2P--NPIPB3	HAVANA	gene	27345	37259	.	+	.	FI_gene_label "NPIPB3^ENSG00000169246.16"  ; ID "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16"  ; exon_id "ENSE00003561690.1"  ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16"  ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5"  ; havana_transcript "OTTHUMT00000400432.2"  ; hgnc_id "HGNC:28989"  ; level 2 ; orig_coord_info "chr16,21424979,21425003,-"  ; protein_id "ENSP00000413141.2"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6"  ; transcript_name "NPIPB3-201"  ; transcript_support_level 3 ; transcript_type protein_coding
PDXDC2P--NPIPB3	HAVANA	mRNA	27345	37259	.	+	.	FI_gene_label "NPIPB3^ENSG00000169246.16"  ; ID "PDXDC2P--NPIPB3^ENST00000419180.6"  ; Parent "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16"  ; exon_id "ENSE00003561690.1"  ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16"  ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5"  ; havana_transcript "OTTHUMT00000400432.2"  ; hgnc_id "HGNC:28989"  ; level 2 ; orig_coord_info "chr16,21424979,21425003,-"  ; protein_id "ENSP00000413141.2"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6"  ; transcript_name "NPIPB3-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
PRPF40B--DERA	HAVANA	gene	10252	22842	.	+	.	FI_gene_label "PRPF40B^ENSG00000110844.14"  ; ID "PRPF40B--DERA^PRPF40B^ENSG00000110844.14"  ; exon_id "ENSE00003759647.1"  ; exon_number 2 ; gene_id "PRPF40B--DERA^PRPF40B^ENSG00000110844.14"  ; gene_name PRPF40B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169568.7"  ; havana_transcript "OTTHUMT00000404847.1"  ; hgnc_id "HGNC:25031"  ; level 2 ; orig_coord_info "chr12,49631401,49631544,+"  ; protein_id "ENSP00000261897.1"  ; tag basic appris_alternative_2 ; transcript_id "PRPF40B--DERA^ENST00000261897.5"  ; transcript_name "PRPF40B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRPF40B--DERA	HAVANA	mRNA	10252	22842	.	+	.	FI_gene_label "PRPF40B^ENSG00000110844.14"  ; ID "PRPF40B--DERA^ENST00000261897.5"  ; Parent "PRPF40B--DERA^PRPF40B^ENSG00000110844.14"  ; exon_id "ENSE00003759647.1"  ; exon_number 2 ; gene_id "PRPF40B--DERA^PRPF40B^ENSG00000110844.14"  ; gene_name PRPF40B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169568.7"  ; havana_transcript "OTTHUMT00000404847.1"  ; hgnc_id "HGNC:25031"  ; level 2 ; orig_coord_info "chr12,49631401,49631544,+"  ; protein_id "ENSP00000261897.1"  ; tag basic appris_alternative_2 ; transcript_id "PRPF40B--DERA^ENST00000261897.5"  ; transcript_name "PRPF40B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRPF40B--DERA	HAVANA	gene	25873	39428	.	+	.	FI_gene_label "DERA^ENSG00000023697.13"  ; ID "PRPF40B--DERA^DERA^ENSG00000023697.13"  ; ccdsid "CCDS44838.1"  ; exon_id "ENSE00002203313.2"  ; exon_number 1 ; gene_id "PRPF40B--DERA^DERA^ENSG00000023697.13"  ; gene_name DERA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165537.4"  ; havana_transcript "OTTHUMT00000384731.3"  ; hgnc_id "HGNC:24269"  ; level 2 ; orig_coord_info "chr12,15911384,15911414,+"  ; protein_id "ENSP00000416583.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF40B--DERA^ENST00000428559.7"  ; transcript_name "DERA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRPF40B--DERA	HAVANA	mRNA	25873	39428	.	+	.	FI_gene_label "DERA^ENSG00000023697.13"  ; ID "PRPF40B--DERA^ENST00000428559.7"  ; Parent "PRPF40B--DERA^DERA^ENSG00000023697.13"  ; ccdsid "CCDS44838.1"  ; exon_id "ENSE00002203313.2"  ; exon_number 1 ; gene_id "PRPF40B--DERA^DERA^ENSG00000023697.13"  ; gene_name DERA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165537.4"  ; havana_transcript "OTTHUMT00000384731.3"  ; hgnc_id "HGNC:24269"  ; level 2 ; orig_coord_info "chr12,15911384,15911414,+"  ; protein_id "ENSP00000416583.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF40B--DERA^ENST00000428559.7"  ; transcript_name "DERA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RMND5B--AC026403.1	HAVANA	gene	1019	15232	.	+	.	FI_gene_label "RMND5B^ENSG00000145916.19"  ; ID "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19"  ; ccdsid "CCDS4431.1"  ; exon_id "ENSE00003577478.1"  ; exon_number 3 ; gene_id "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19"  ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4"  ; havana_transcript "OTTHUMT00000253483.2"  ; hgnc_id "HGNC:26181"  ; level 2 ; orig_coord_info "chr5,178138120,178138258,+"  ; protein_id "ENSP00000320623.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC026403.1^ENST00000313386.9"  ; transcript_name "RMND5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RMND5B--AC026403.1	HAVANA	mRNA	1019	15232	.	+	.	FI_gene_label "RMND5B^ENSG00000145916.19"  ; ID "RMND5B--AC026403.1^ENST00000313386.9"  ; Parent "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19"  ; ccdsid "CCDS4431.1"  ; exon_id "ENSE00003577478.1"  ; exon_number 3 ; gene_id "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19"  ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4"  ; havana_transcript "OTTHUMT00000253483.2"  ; hgnc_id "HGNC:26181"  ; level 2 ; orig_coord_info "chr5,178138120,178138258,+"  ; protein_id "ENSP00000320623.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC026403.1^ENST00000313386.9"  ; transcript_name "RMND5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RMND5B--AC114321.1	HAVANA	gene	1019	15232	.	+	.	FI_gene_label "RMND5B^ENSG00000145916.19"  ; ID "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19"  ; ccdsid "CCDS4431.1"  ; exon_id "ENSE00003577478.1"  ; exon_number 3 ; gene_id "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19"  ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4"  ; havana_transcript "OTTHUMT00000253483.2"  ; hgnc_id "HGNC:26181"  ; level 2 ; orig_coord_info "chr5,178138120,178138258,+"  ; protein_id "ENSP00000320623.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC114321.1^ENST00000313386.9"  ; transcript_name "RMND5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RMND5B--AC114321.1	HAVANA	mRNA	1019	15232	.	+	.	FI_gene_label "RMND5B^ENSG00000145916.19"  ; ID "RMND5B--AC114321.1^ENST00000313386.9"  ; Parent "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19"  ; ccdsid "CCDS4431.1"  ; exon_id "ENSE00003577478.1"  ; exon_number 3 ; gene_id "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19"  ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4"  ; havana_transcript "OTTHUMT00000253483.2"  ; hgnc_id "HGNC:26181"  ; level 2 ; orig_coord_info "chr5,178138120,178138258,+"  ; protein_id "ENSP00000320623.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC114321.1^ENST00000313386.9"  ; transcript_name "RMND5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SELENBP1--FABP6-AS1	HAVANA	gene	1003	8052	.	+	.	FI_gene_label "SELENBP1^ENSG00000143416.21"  ; ID "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21"  ; ccdsid "CCDS995.1"  ; exon_id "ENSE00003513345.1"  ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21"  ; gene_name SELENBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012498.26"  ; havana_transcript "OTTHUMT00000034904.5"  ; hgnc_id "HGNC:10719"  ; level 2 ; orig_coord_info "chr1,151372638,151372641,-"  ; protein_id "ENSP00000357861.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENBP1--FABP6-AS1^ENST00000368868.10"  ; transcript_name "SELENBP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SELENBP1--FABP6-AS1	HAVANA	mRNA	1003	8052	.	+	.	FI_gene_label "SELENBP1^ENSG00000143416.21"  ; ID "SELENBP1--FABP6-AS1^ENST00000368868.10"  ; Parent "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21"  ; ccdsid "CCDS995.1"  ; exon_id "ENSE00003513345.1"  ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21"  ; gene_name SELENBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012498.26"  ; havana_transcript "OTTHUMT00000034904.5"  ; hgnc_id "HGNC:10719"  ; level 2 ; orig_coord_info "chr1,151372638,151372641,-"  ; protein_id "ENSP00000357861.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENBP1--FABP6-AS1^ENST00000368868.10"  ; transcript_name "SELENBP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STAG1--COPB2	HAVANA	gene	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--COPB2^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--COPB2^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--COPB2^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STAG1--COPB2	HAVANA	mRNA	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--COPB2^ENST00000236698.9"  ; Parent "STAG1--COPB2^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--COPB2^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--COPB2^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STAG1--COPB2	HAVANA	gene	45108	70759	.	+	.	FI_gene_label "COPB2^ENSG00000184432.11"  ; ID "STAG1--COPB2^COPB2^ENSG00000184432.11"  ; ccdsid "CCDS3108.1"  ; exon_id "ENSE00002035761.2"  ; exon_number 1 ; gene_id "STAG1--COPB2^COPB2^ENSG00000184432.11"  ; gene_name COPB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159959.5"  ; havana_transcript "OTTHUMT00000358495.3"  ; hgnc_id "HGNC:2232"  ; level 2 ; orig_coord_info "chr3,139389548,139389550,-"  ; protein_id "ENSP00000329419.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STAG1--COPB2^ENST00000333188.10"  ; transcript_name "COPB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STAG1--COPB2	HAVANA	mRNA	45108	70759	.	+	.	FI_gene_label "COPB2^ENSG00000184432.11"  ; ID "STAG1--COPB2^ENST00000333188.10"  ; Parent "STAG1--COPB2^COPB2^ENSG00000184432.11"  ; ccdsid "CCDS3108.1"  ; exon_id "ENSE00002035761.2"  ; exon_number 1 ; gene_id "STAG1--COPB2^COPB2^ENSG00000184432.11"  ; gene_name COPB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159959.5"  ; havana_transcript "OTTHUMT00000358495.3"  ; hgnc_id "HGNC:2232"  ; level 2 ; orig_coord_info "chr3,139389548,139389550,-"  ; protein_id "ENSP00000329419.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STAG1--COPB2^ENST00000333188.10"  ; transcript_name "COPB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--BET1L	HAVANA	gene	40092	44550	.	+	.	FI_gene_label "BET1L^ENSG00000177951.17"  ; ID "TLK2--BET1L^BET1L^ENSG00000177951.17"  ; ccdsid "CCDS7689.1"  ; exon_id "ENSE00001955579.1"  ; exon_number 1 ; gene_id "TLK2--BET1L^BET1L^ENSG00000177951.17"  ; gene_name BET1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000119071.4"  ; havana_transcript "OTTHUMT00000239284.1"  ; hgnc_id "HGNC:19348"  ; level 2 ; orig_coord_info "chr11,207303,207321,-"  ; protein_id "ENSP00000339093.7"  ; tag basic CCDS ; transcript_id "TLK2--BET1L^ENST00000325147.13"  ; transcript_name "BET1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--BET1L	HAVANA	mRNA	40092	44550	.	+	.	FI_gene_label "BET1L^ENSG00000177951.17"  ; ID "TLK2--BET1L^ENST00000325147.13"  ; Parent "TLK2--BET1L^BET1L^ENSG00000177951.17"  ; ccdsid "CCDS7689.1"  ; exon_id "ENSE00001955579.1"  ; exon_number 1 ; gene_id "TLK2--BET1L^BET1L^ENSG00000177951.17"  ; gene_name BET1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000119071.4"  ; havana_transcript "OTTHUMT00000239284.1"  ; hgnc_id "HGNC:19348"  ; level 2 ; orig_coord_info "chr11,207303,207321,-"  ; protein_id "ENSP00000339093.7"  ; tag basic CCDS ; transcript_id "TLK2--BET1L^ENST00000325147.13"  ; transcript_name "BET1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--BET1L	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--BET1L^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--BET1L^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--BET1L^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--BET1L	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--BET1L^ENST00000326270.13"  ; Parent "TLK2--BET1L^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--BET1L^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--BET1L^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRPV5--AC245427.1	HAVANA	gene	1001	12415	.	+	.	FI_gene_label "TRPV5^ENSG00000127412.7"  ; ID "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7"  ; ccdsid "CCDS5875.1"  ; exon_id "ENSE00001047561.2"  ; exon_number 1 ; gene_id "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7"  ; gene_name TRPV5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157157.5"  ; havana_transcript "OTTHUMT00000347660.3"  ; hgnc_id "HGNC:3145"  ; level 2 ; orig_coord_info "chr7,142933332,142933459,-"  ; protein_id "ENSP00000265310.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPV5--AC245427.1^ENST00000265310.6"  ; transcript_name "TRPV5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRPV5--AC245427.1	HAVANA	mRNA	1001	12415	.	+	.	FI_gene_label "TRPV5^ENSG00000127412.7"  ; ID "TRPV5--AC245427.1^ENST00000265310.6"  ; Parent "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7"  ; ccdsid "CCDS5875.1"  ; exon_id "ENSE00001047561.2"  ; exon_number 1 ; gene_id "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7"  ; gene_name TRPV5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157157.5"  ; havana_transcript "OTTHUMT00000347660.3"  ; hgnc_id "HGNC:3145"  ; level 2 ; orig_coord_info "chr7,142933332,142933459,-"  ; protein_id "ENSP00000265310.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPV5--AC245427.1^ENST00000265310.6"  ; transcript_name "TRPV5-201"  ; 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: 
ZFAT--AC084116.2	HAVANA	gene	1019	29713	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC084116.2^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFAT--AC084116.2	HAVANA	mRNA	1019	29713	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "ZFAT--AC084116.2^ENST00000377838.8"  ; Parent "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC084116.2^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZFAT--AC087667.1	HAVANA	gene	1019	29713	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC087667.1^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFAT--AC087667.1	HAVANA	mRNA	1019	29713	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "ZFAT--AC087667.1^ENST00000377838.8"  ; Parent "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC087667.1^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC004923.1--AC127526.2	HAVANA	gene	7777	10354	.	+	.	FI_gene_label "AC127526.2^ENSG00000255367.3"  ; ID "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3"  ; exon_id "ENSE00002167014.1"  ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3"  ; gene_name "AC127526.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166987.2"  ; havana_transcript "OTTHUMT00000392274.1"  ; level 1 ; orig_coord_info "chr11,3571935,3571987,-"  ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000526533.1"  ; transcript_name "AC127526.2-202"  ; transcript_support_level 4 ; transcript_type lncRNA
AC004923.1--AC127526.2	HAVANA	RNA	7777	10354	.	+	.	FI_gene_label "AC127526.2^ENSG00000255367.3"  ; ID "AC004923.1--AC127526.2^ENST00000526533.1"  ; Parent "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3"  ; exon_id "ENSE00002167014.1"  ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3"  ; gene_name "AC127526.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166987.2"  ; havana_transcript "OTTHUMT00000392274.1"  ; level 1 ; orig_coord_info "chr11,3571935,3571987,-"  ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000526533.1"  ; transcript_name "AC127526.2-202"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
AC004923.1--AC127526.2	HAVANA	gene	1001	4776	.	+	.	FI_gene_label "AC004923.1^ENSG00000254610.3"  ; ID "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3"  ; exon_id "ENSE00003779619.1"  ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3"  ; gene_name "AC004923.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167303.4"  ; havana_transcript "OTTHUMT00000394105.2"  ; level 1 ; orig_coord_info "chr11,67955482,67955802,-"  ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000527543.2"  ; transcript_name "AC004923.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
AC004923.1--AC127526.2	HAVANA	RNA	1001	4776	.	+	.	FI_gene_label "AC004923.1^ENSG00000254610.3"  ; ID "AC004923.1--AC127526.2^ENST00000527543.2"  ; Parent "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3"  ; exon_id "ENSE00003779619.1"  ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3"  ; gene_name "AC004923.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167303.4"  ; havana_transcript "OTTHUMT00000394105.2"  ; level 1 ; orig_coord_info "chr11,67955482,67955802,-"  ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000527543.2"  ; transcript_name "AC004923.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
AC026336.1--PIWIL1	HAVANA	gene	1001	1351	.	+	.	FI_gene_label "AC026336.1^ENSG00000242963.1"  ; ID "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1"  ; exon_id "ENSE00001847789.1"  ; exon_number 1 ; gene_id "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1"  ; gene_name "AC026336.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157836.1"  ; havana_transcript "OTTHUMT00000349760.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr12,130216807,130217157,-"  ; tag pseudo_consens basic ; transcript_id "AC026336.1--PIWIL1^ENST00000466577.1"  ; transcript_name "AC026336.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
AC026336.1--PIWIL1	HAVANA	RNA	1001	1351	.	+	.	FI_gene_label "AC026336.1^ENSG00000242963.1"  ; ID "AC026336.1--PIWIL1^ENST00000466577.1"  ; Parent "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1"  ; exon_id "ENSE00001847789.1"  ; exon_number 1 ; gene_id "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1"  ; gene_name "AC026336.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157836.1"  ; havana_transcript "OTTHUMT00000349760.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr12,130216807,130217157,-"  ; tag pseudo_consens basic ; transcript_id "AC026336.1--PIWIL1^ENST00000466577.1"  ; transcript_name "AC026336.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
ACTBP6--ACTB	HAVANA	gene	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ACTBP6--ACTB	HAVANA	RNA	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ENST00000520036.1"  ; Parent "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
AGAP12P--FRMPD2	HAVANA	gene	1042	9399	.	+	.	FI_gene_label "AGAP12P^ENSG00000265018.6"  ; ID "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6"  ; exon_id "ENSE00002718806.2"  ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6"  ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4"  ; havana_transcript "OTTHUMT00000047912.4"  ; hgnc_id "HGNC:23661"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48031376,48031599,-"  ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6"  ; transcript_name "AGAP12P-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AGAP12P--FRMPD2	HAVANA	RNA	1042	9399	.	+	.	FI_gene_label "AGAP12P^ENSG00000265018.6"  ; ID "AGAP12P--FRMPD2^ENST00000585227.6"  ; Parent "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6"  ; exon_id "ENSE00002718806.2"  ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6"  ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4"  ; havana_transcript "OTTHUMT00000047912.4"  ; hgnc_id "HGNC:23661"  ; level 1 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48031376,48031599,-"  ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6"  ; transcript_name "AGAP12P-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AP006294.2--ENPP7P3	HAVANA	gene	4210	4450	.	+	.	FI_gene_label "ENPP7P3^ENSG00000248618.1"  ; ID "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1"  ; exon_id "ENSE00002066185.1"  ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1"  ; gene_name ENPP7P3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000159714.4"  ; havana_transcript "OTTHUMT00000357026.3"  ; hgnc_id "HGNC:48686"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr3,130167790,130168030,-"  ; tag basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000509123.1"  ; transcript_name "ENPP7P3-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
AP006294.2--ENPP7P3	HAVANA	RNA	4210	4450	.	+	.	FI_gene_label "ENPP7P3^ENSG00000248618.1"  ; ID "AP006294.2--ENPP7P3^ENST00000509123.1"  ; Parent "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1"  ; exon_id "ENSE00002066185.1"  ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1"  ; gene_name ENPP7P3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000159714.4"  ; havana_transcript "OTTHUMT00000357026.3"  ; hgnc_id "HGNC:48686"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr3,130167790,130168030,-"  ; tag basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000509123.1"  ; transcript_name "ENPP7P3-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
AP006294.2--ENPP7P3	HAVANA	gene	1001	1209	.	+	.	FI_gene_label "AP006294.2^ENSG00000284639.1"  ; ID "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1"  ; exon_id "ENSE00003812576.1"  ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1"  ; gene_name "AP006294.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1"  ; havana_transcript "OTTHUMT00000492980.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3580927,3581135,-"  ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000641667.1"  ; transcript_name "AP006294.2-201"  ; transcript_type transcribed_unprocessed_pseudogene
AP006294.2--ENPP7P3	HAVANA	RNA	1001	1209	.	+	.	FI_gene_label "AP006294.2^ENSG00000284639.1"  ; ID "AP006294.2--ENPP7P3^ENST00000641667.1"  ; Parent "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1"  ; exon_id "ENSE00003812576.1"  ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1"  ; gene_name "AP006294.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1"  ; havana_transcript "OTTHUMT00000492980.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3580927,3581135,-"  ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000641667.1"  ; transcript_name "AP006294.2-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AP006294.2--LINC00665	HAVANA	gene	4246	18758	.	+	.	FI_gene_label "LINC00665^ENSG00000232677.9"  ; ID "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9"  ; exon_id "ENSE00003882974.1"  ; exon_number 1 ; gene_id "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9"  ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6"  ; havana_transcript "OTTHUMT00000109548.1"  ; hgnc_id "HGNC:44323"  ; level 1 ; orig_coord_info "chr19,36331447,36331734,-"  ; tag exp_conf ; transcript_id "AP006294.2--LINC00665^ENST00000412740.7"  ; transcript_name "LINC00665-201"  ; transcript_support_level 3 ; transcript_type lncRNA
AP006294.2--LINC00665	HAVANA	RNA	4246	18758	.	+	.	FI_gene_label "LINC00665^ENSG00000232677.9"  ; ID "AP006294.2--LINC00665^ENST00000412740.7"  ; Parent "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9"  ; exon_id "ENSE00003882974.1"  ; exon_number 1 ; gene_id "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9"  ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6"  ; havana_transcript "OTTHUMT00000109548.1"  ; hgnc_id "HGNC:44323"  ; level 1 ; orig_coord_info "chr19,36331447,36331734,-"  ; tag exp_conf ; transcript_id "AP006294.2--LINC00665^ENST00000412740.7"  ; transcript_name "LINC00665-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
AP006294.2--LINC00665	HAVANA	gene	1001	1209	.	+	.	FI_gene_label "AP006294.2^ENSG00000284639.1"  ; ID "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1"  ; exon_id "ENSE00003812576.1"  ; exon_number 1 ; gene_id "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1"  ; gene_name "AP006294.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1"  ; havana_transcript "OTTHUMT00000492980.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3580927,3581135,-"  ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--LINC00665^ENST00000641667.1"  ; transcript_name "AP006294.2-201"  ; transcript_type transcribed_unprocessed_pseudogene
AP006294.2--LINC00665	HAVANA	RNA	1001	1209	.	+	.	FI_gene_label "AP006294.2^ENSG00000284639.1"  ; ID "AP006294.2--LINC00665^ENST00000641667.1"  ; Parent "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1"  ; exon_id "ENSE00003812576.1"  ; exon_number 1 ; gene_id "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1"  ; gene_name "AP006294.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1"  ; havana_transcript "OTTHUMT00000492980.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3580927,3581135,-"  ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--LINC00665^ENST00000641667.1"  ; transcript_name "AP006294.2-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
ITPR2--AC048344.1	HAVANA	gene	70020	71811	.	+	.	FI_gene_label "AC048344.1^ENSG00000257530.1"  ; ID "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1"  ; exon_id "ENSE00002386363.1"  ; exon_number 1 ; gene_id "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1"  ; gene_name "AC048344.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169306.1"  ; havana_transcript "OTTHUMT00000403378.1"  ; level 2 ; orig_coord_info "chr12,32107394,32107528,-"  ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000551974.1"  ; transcript_name "AC048344.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
ITPR2--AC048344.1	HAVANA	RNA	70020	71811	.	+	.	FI_gene_label "AC048344.1^ENSG00000257530.1"  ; ID "ITPR2--AC048344.1^ENST00000551974.1"  ; Parent "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1"  ; exon_id "ENSE00002386363.1"  ; exon_number 1 ; gene_id "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1"  ; gene_name "AC048344.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169306.1"  ; havana_transcript "OTTHUMT00000403378.1"  ; level 2 ; orig_coord_info "chr12,32107394,32107528,-"  ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000551974.1"  ; transcript_name "AC048344.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
PDXDC2P--NPIPB3	HAVANA	gene	1161	3891	.	+	.	FI_gene_label "PDXDC2P^ENSG00000255185.6"  ; ID "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6"  ; exon_id "ENSE00002159321.1"  ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6"  ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2"  ; havana_transcript "OTTHUMT00000395272.1"  ; hgnc_id "HGNC:27559"  ; level 2 ; orig_coord_info "chr16,70065756,70065785,-"  ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1"  ; transcript_name "PDXDC2P-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
PDXDC2P--NPIPB3	HAVANA	RNA	1161	3891	.	+	.	FI_gene_label "PDXDC2P^ENSG00000255185.6"  ; ID "PDXDC2P--NPIPB3^ENST00000525173.1"  ; Parent "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6"  ; exon_id "ENSE00002159321.1"  ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6"  ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2"  ; havana_transcript "OTTHUMT00000395272.1"  ; hgnc_id "HGNC:27559"  ; level 2 ; orig_coord_info "chr16,70065756,70065785,-"  ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1"  ; transcript_name "PDXDC2P-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
RMND5B--AC026403.1	HAVANA	gene	18233	18527	.	+	.	FI_gene_label "AC026403.1^ENSG00000229119.3"  ; ID "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3"  ; exon_id "ENSE00002132375.1"  ; exon_number 1 ; gene_id "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3"  ; gene_name "AC026403.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162895.1"  ; havana_transcript "OTTHUMT00000370958.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,166382305,166382599,+"  ; tag pseudo_consens basic ; transcript_id "RMND5B--AC026403.1^ENST00000518938.1"  ; transcript_name "AC026403.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
RMND5B--AC026403.1	HAVANA	RNA	18233	18527	.	+	.	FI_gene_label "AC026403.1^ENSG00000229119.3"  ; ID "RMND5B--AC026403.1^ENST00000518938.1"  ; Parent "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3"  ; exon_id "ENSE00002132375.1"  ; exon_number 1 ; gene_id "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3"  ; gene_name "AC026403.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162895.1"  ; havana_transcript "OTTHUMT00000370958.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,166382305,166382599,+"  ; tag pseudo_consens basic ; transcript_id "RMND5B--AC026403.1^ENST00000518938.1"  ; transcript_name "AC026403.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
RMND5B--AC114321.1	HAVANA	gene	18233	20765	.	+	.	FI_gene_label "AC114321.1^ENSG00000254171.1"  ; ID "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1"  ; exon_id "ENSE00002130197.1"  ; exon_number 1 ; gene_id "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1"  ; gene_name "AC114321.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163917.1"  ; havana_transcript "OTTHUMT00000376394.1"  ; level 1 ; orig_coord_info "chr5,166128498,166128650,+"  ; tag basic exp_conf ; transcript_id "RMND5B--AC114321.1^ENST00000520075.1"  ; transcript_name "AC114321.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
RMND5B--AC114321.1	HAVANA	RNA	18233	20765	.	+	.	FI_gene_label "AC114321.1^ENSG00000254171.1"  ; ID "RMND5B--AC114321.1^ENST00000520075.1"  ; Parent "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1"  ; exon_id "ENSE00002130197.1"  ; exon_number 1 ; gene_id "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1"  ; gene_name "AC114321.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163917.1"  ; havana_transcript "OTTHUMT00000376394.1"  ; level 1 ; orig_coord_info "chr5,166128498,166128650,+"  ; tag basic exp_conf ; transcript_id "RMND5B--AC114321.1^ENST00000520075.1"  ; transcript_name "AC114321.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
SELENBP1--FABP6-AS1	HAVANA	gene	11053	14738	.	+	.	FI_gene_label "FABP6-AS1^ENSG00000247699.2"  ; ID "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2"  ; exon_id "ENSE00001637490.2"  ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2"  ; gene_name "FABP6-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163565.1"  ; havana_transcript "OTTHUMT00000374243.1"  ; hgnc_id "HGNC:40226"  ; level 2 ; orig_coord_info "chr5,160204722,160204826,-"  ; tag basic ; transcript_id "SELENBP1--FABP6-AS1^ENST00000501818.1"  ; transcript_name "FABP6-AS1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
SELENBP1--FABP6-AS1	HAVANA	RNA	11053	14738	.	+	.	FI_gene_label "FABP6-AS1^ENSG00000247699.2"  ; ID "SELENBP1--FABP6-AS1^ENST00000501818.1"  ; Parent "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2"  ; exon_id "ENSE00001637490.2"  ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2"  ; gene_name "FABP6-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163565.1"  ; havana_transcript "OTTHUMT00000374243.1"  ; hgnc_id "HGNC:40226"  ; level 2 ; orig_coord_info "chr5,160204722,160204826,-"  ; tag basic ; transcript_id "SELENBP1--FABP6-AS1^ENST00000501818.1"  ; transcript_name "FABP6-AS1-201"  ; transcript_support_level 2 ; 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: 
TRPV5--AC245427.1	HAVANA	gene	15416	16678	.	+	.	FI_gene_label "AC245427.1^ENSG00000224970.2"  ; ID "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2"  ; exon_id "ENSE00001646161.1"  ; exon_number 1 ; gene_id "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2"  ; gene_name "AC245427.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000157156.2"  ; havana_transcript "OTTHUMT00000347659.2"  ; level 1 ; orig_coord_info "chr7,142875836,142875934,+"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported 3_nested_supported_extension basic exp_conf ; transcript_id "TRPV5--AC245427.1^ENST00000438839.2"  ; transcript_name "AC245427.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
TRPV5--AC245427.1	HAVANA	RNA	15416	16678	.	+	.	FI_gene_label "AC245427.1^ENSG00000224970.2"  ; ID "TRPV5--AC245427.1^ENST00000438839.2"  ; Parent "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2"  ; exon_id "ENSE00001646161.1"  ; exon_number 1 ; gene_id "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2"  ; gene_name "AC245427.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000157156.2"  ; havana_transcript "OTTHUMT00000347659.2"  ; level 1 ; orig_coord_info "chr7,142875836,142875934,+"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported 3_nested_supported_extension basic exp_conf ; transcript_id "TRPV5--AC245427.1^ENST00000438839.2"  ; transcript_name "AC245427.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
ZFAT--AC084116.2	HAVANA	gene	32714	35128	.	+	.	FI_gene_label "AC084116.2^ENSG00000253427.1"  ; ID "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1"  ; exon_id "ENSE00002122040.1"  ; exon_number 1 ; gene_id "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1"  ; gene_name "AC084116.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165031.1"  ; havana_transcript "OTTHUMT00000381484.1"  ; level 2 ; orig_coord_info "chr8,126474189,126474287,+"  ; tag basic ; transcript_id "ZFAT--AC084116.2^ENST00000520171.1"  ; transcript_name "AC084116.2-201"  ; transcript_support_level 4 ; transcript_type lncRNA
ZFAT--AC084116.2	HAVANA	RNA	32714	35128	.	+	.	FI_gene_label "AC084116.2^ENSG00000253427.1"  ; ID "ZFAT--AC084116.2^ENST00000520171.1"  ; Parent "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1"  ; exon_id "ENSE00002122040.1"  ; exon_number 1 ; gene_id "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1"  ; gene_name "AC084116.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165031.1"  ; havana_transcript "OTTHUMT00000381484.1"  ; level 2 ; orig_coord_info "chr8,126474189,126474287,+"  ; tag basic ; transcript_id "ZFAT--AC084116.2^ENST00000520171.1"  ; transcript_name "AC084116.2-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
ZFAT--AC087667.1	HAVANA	gene	32714	36100	.	+	.	FI_gene_label "AC087667.1^ENSG00000244791.3"  ; ID "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3"  ; exon_id "ENSE00003879284.1"  ; exon_number 1 ; gene_id "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3"  ; gene_name "AC087667.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165030.4"  ; havana_transcript "OTTHUMT00000381483.2"  ; level 2 ; orig_coord_info "chr8,126325454,126325557,+"  ; tag basic TAGENE ; transcript_id "ZFAT--AC087667.1^ENST00000500180.3"  ; transcript_name "AC087667.1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
ZFAT--AC087667.1	HAVANA	RNA	32714	36100	.	+	.	FI_gene_label "AC087667.1^ENSG00000244791.3"  ; ID "ZFAT--AC087667.1^ENST00000500180.3"  ; Parent "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3"  ; exon_id "ENSE00003879284.1"  ; exon_number 1 ; gene_id "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3"  ; gene_name "AC087667.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000165030.4"  ; havana_transcript "OTTHUMT00000381483.2"  ; level 2 ; orig_coord_info "chr8,126325454,126325557,+"  ; tag basic TAGENE ; transcript_id "ZFAT--AC087667.1^ENST00000500180.3"  ; transcript_name "AC087667.1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
434 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------

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

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

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

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

----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
1001 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 30 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 0 second) ------                   


GFF3 file parsed