.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/507ccfd2696b6f8fae4bd77ec9b95d/.command.log
Size: 60.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/531693ac1c4f68cdaf856c4e1cbeb4/fi_workdir/BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/507ccfd2696b6f8fae4bd77ec9b95d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/507ccfd2696b6f8fae4bd77ec9b95d/.command.run
==> STAGING COMPLETE (3 inputs)

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 3582
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3582
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:3582
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 1 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
AC092070.2--MAN2B1	HAVANA	gene	12061	27290	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "AC092070.2--MAN2B1^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092070.2--MAN2B1	HAVANA	mRNA	12061	27290	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "AC092070.2--MAN2B1^ENST00000221363.8"  ; Parent "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "AC092070.2--MAN2B1^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C22orf39--MYO18B-AS1	HAVANA	gene	1001	5839	.	+	.	FI_gene_label "C22orf39^ENSG00000242259.9"  ; ID "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9"  ; exon_id "ENSE00003708298.2"  ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9"  ; gene_name C22orf39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150137.4"  ; havana_transcript "OTTHUMT00000316494.3"  ; hgnc_id "HGNC:27012"  ; level 2 ; orig_coord_info "chr22,19447665,19447688,-"  ; protein_id "ENSP00000382474.5"  ; tag CAGE_supported_TSS upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "C22orf39--MYO18B-AS1^ENST00000399562.9"  ; transcript_name "C22orf39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
C22orf39--MYO18B-AS1	HAVANA	mRNA	1001	5839	.	+	.	FI_gene_label "C22orf39^ENSG00000242259.9"  ; ID "C22orf39--MYO18B-AS1^ENST00000399562.9"  ; Parent "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9"  ; exon_id "ENSE00003708298.2"  ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9"  ; gene_name C22orf39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150137.4"  ; havana_transcript "OTTHUMT00000316494.3"  ; hgnc_id "HGNC:27012"  ; level 2 ; orig_coord_info "chr22,19447665,19447688,-"  ; protein_id "ENSP00000382474.5"  ; tag CAGE_supported_TSS upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "C22orf39--MYO18B-AS1^ENST00000399562.9"  ; transcript_name "C22orf39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DOK7--MICB	HAVANA	gene	17080	22456	.	+	.	FI_gene_label "MICB^ENSG00000204516.10"  ; ID "DOK7--MICB^MICB^ENSG00000204516.10"  ; ccdsid "CCDS43449.1"  ; exon_id "ENSE00001842955.2"  ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10"  ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4"  ; havana_transcript "OTTHUMT00000076102.4"  ; hgnc_id "HGNC:7091"  ; level 2 ; orig_coord_info "chr6,31498194,31498263,+"  ; protein_id "ENSP00000252229.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7"  ; transcript_name "MICB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB	HAVANA	mRNA	17080	22456	.	+	.	FI_gene_label "MICB^ENSG00000204516.10"  ; ID "DOK7--MICB^ENST00000252229.7"  ; Parent "DOK7--MICB^MICB^ENSG00000204516.10"  ; ccdsid "CCDS43449.1"  ; exon_id "ENSE00001842955.2"  ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10"  ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4"  ; havana_transcript "OTTHUMT00000076102.4"  ; hgnc_id "HGNC:7091"  ; level 2 ; orig_coord_info "chr6,31498194,31498263,+"  ; protein_id "ENSP00000252229.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7"  ; transcript_name "MICB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DOK7--MICB	HAVANA	gene	1001	9638	.	+	.	FI_gene_label "DOK7^ENSG00000175920.18"  ; ID "DOK7--MICB^DOK7^ENSG00000175920.18"  ; ccdsid "CCDS3370.2"  ; exon_id "ENSE00003845135.1"  ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18"  ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8"  ; havana_transcript "OTTHUMT00000313538.2"  ; hgnc_id "HGNC:26594"  ; level 2 ; orig_coord_info "chr4,3463376,3463429,+"  ; protein_id "ENSP00000344432.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6"  ; transcript_name "DOK7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB	HAVANA	mRNA	1001	9638	.	+	.	FI_gene_label "DOK7^ENSG00000175920.18"  ; ID "DOK7--MICB^ENST00000340083.6"  ; Parent "DOK7--MICB^DOK7^ENSG00000175920.18"  ; ccdsid "CCDS3370.2"  ; exon_id "ENSE00003845135.1"  ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18"  ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8"  ; havana_transcript "OTTHUMT00000313538.2"  ; hgnc_id "HGNC:26594"  ; level 2 ; orig_coord_info "chr4,3463376,3463429,+"  ; protein_id "ENSP00000344432.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6"  ; transcript_name "DOK7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EXOC2--EPHA5-AS1	HAVANA	gene	1001	32550	.	+	.	FI_gene_label "EXOC2^ENSG00000112685.14"  ; ID "EXOC2--EPHA5-AS1^EXOC2^ENSG00000112685.14"  ; ccdsid "CCDS34327.1"  ; exon_id "ENSE00000679928.3"  ; exon_number 2 ; gene_id "EXOC2--EPHA5-AS1^EXOC2^ENSG00000112685.14"  ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4"  ; havana_transcript "OTTHUMT00000039627.2"  ; hgnc_id "HGNC:24968"  ; level 2 ; orig_coord_info "chr6,637701,637818,-"  ; protein_id "ENSP00000230449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5-AS1^ENST00000230449.9"  ; transcript_name "EXOC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5-AS1	HAVANA	mRNA	1001	32550	.	+	.	FI_gene_label "EXOC2^ENSG00000112685.14"  ; ID "EXOC2--EPHA5-AS1^ENST00000230449.9"  ; Parent "EXOC2--EPHA5-AS1^EXOC2^ENSG00000112685.14"  ; ccdsid "CCDS34327.1"  ; exon_id "ENSE00000679928.3"  ; exon_number 2 ; gene_id "EXOC2--EPHA5-AS1^EXOC2^ENSG00000112685.14"  ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4"  ; havana_transcript "OTTHUMT00000039627.2"  ; hgnc_id "HGNC:24968"  ; level 2 ; orig_coord_info "chr6,637701,637818,-"  ; protein_id "ENSP00000230449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5-AS1^ENST00000230449.9"  ; transcript_name "EXOC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EXOC2--EPHA5	HAVANA	gene	1001	32550	.	+	.	FI_gene_label "EXOC2^ENSG00000112685.14"  ; ID "EXOC2--EPHA5^EXOC2^ENSG00000112685.14"  ; ccdsid "CCDS34327.1"  ; exon_id "ENSE00000679928.3"  ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14"  ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4"  ; havana_transcript "OTTHUMT00000039627.2"  ; hgnc_id "HGNC:24968"  ; level 2 ; orig_coord_info "chr6,637701,637818,-"  ; protein_id "ENSP00000230449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9"  ; transcript_name "EXOC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5	HAVANA	mRNA	1001	32550	.	+	.	FI_gene_label "EXOC2^ENSG00000112685.14"  ; ID "EXOC2--EPHA5^ENST00000230449.9"  ; Parent "EXOC2--EPHA5^EXOC2^ENSG00000112685.14"  ; ccdsid "CCDS34327.1"  ; exon_id "ENSE00000679928.3"  ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14"  ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4"  ; havana_transcript "OTTHUMT00000039627.2"  ; hgnc_id "HGNC:24968"  ; level 2 ; orig_coord_info "chr6,637701,637818,-"  ; protein_id "ENSP00000230449.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9"  ; transcript_name "EXOC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EXOC2--EPHA5	HAVANA	gene	35703	62112	.	+	.	FI_gene_label "EPHA5^ENSG00000145242.14"  ; ID "EXOC2--EPHA5^EPHA5^ENSG00000145242.14"  ; ccdsid "CCDS3513.1"  ; exon_id "ENSE00001816165.1"  ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14"  ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4"  ; havana_transcript "OTTHUMT00000251388.2"  ; hgnc_id "HGNC:3389"  ; level 2 ; orig_coord_info "chr4,65669562,65669742,-"  ; protein_id "ENSP00000273854.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7"  ; transcript_name "EPHA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5	HAVANA	mRNA	35703	62112	.	+	.	FI_gene_label "EPHA5^ENSG00000145242.14"  ; ID "EXOC2--EPHA5^ENST00000273854.7"  ; Parent "EXOC2--EPHA5^EPHA5^ENSG00000145242.14"  ; ccdsid "CCDS3513.1"  ; exon_id "ENSE00001816165.1"  ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14"  ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4"  ; havana_transcript "OTTHUMT00000251388.2"  ; hgnc_id "HGNC:3389"  ; level 2 ; orig_coord_info "chr4,65669562,65669742,-"  ; protein_id "ENSP00000273854.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7"  ; transcript_name "EPHA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GTPBP2--AL008627.1	ENSEMBL	gene	2477	9348	.	+	.	FI_gene_label "GTPBP2^ENSG00000172432.19"  ; ID "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19"  ; ccdsid "CCDS69124.1"  ; exon_id "ENSE00003534858.1"  ; exon_number 3 ; gene_id "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19"  ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13"  ; hgnc_id "HGNC:4670"  ; level 3 ; orig_coord_info "chr6,43626226,43626359,-"  ; protein_id "ENSP00000304893.7"  ; tag basic CCDS ; transcript_id "GTPBP2--AL008627.1^ENST00000307114.11"  ; transcript_name "GTPBP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
GTPBP2--AL008627.1	ENSEMBL	mRNA	2477	9348	.	+	.	FI_gene_label "GTPBP2^ENSG00000172432.19"  ; ID "GTPBP2--AL008627.1^ENST00000307114.11"  ; Parent "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19"  ; ccdsid "CCDS69124.1"  ; exon_id "ENSE00003534858.1"  ; exon_number 3 ; gene_id "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19"  ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13"  ; hgnc_id "HGNC:4670"  ; level 3 ; orig_coord_info "chr6,43626226,43626359,-"  ; protein_id "ENSP00000304893.7"  ; tag basic CCDS ; transcript_id "GTPBP2--AL008627.1^ENST00000307114.11"  ; transcript_name "GTPBP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GTPBP2--MBOAT1	ENSEMBL	gene	2477	9348	.	+	.	FI_gene_label "GTPBP2^ENSG00000172432.19"  ; ID "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19"  ; ccdsid "CCDS69124.1"  ; exon_id "ENSE00003534858.1"  ; exon_number 3 ; gene_id "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19"  ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13"  ; hgnc_id "HGNC:4670"  ; level 3 ; orig_coord_info "chr6,43626226,43626359,-"  ; protein_id "ENSP00000304893.7"  ; tag basic CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000307114.11"  ; transcript_name "GTPBP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
GTPBP2--MBOAT1	ENSEMBL	mRNA	2477	9348	.	+	.	FI_gene_label "GTPBP2^ENSG00000172432.19"  ; ID "GTPBP2--MBOAT1^ENST00000307114.11"  ; Parent "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19"  ; ccdsid "CCDS69124.1"  ; exon_id "ENSE00003534858.1"  ; exon_number 3 ; gene_id "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19"  ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13"  ; hgnc_id "HGNC:4670"  ; level 3 ; orig_coord_info "chr6,43626226,43626359,-"  ; protein_id "ENSP00000304893.7"  ; tag basic CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000307114.11"  ; transcript_name "GTPBP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GTPBP2--MBOAT1	HAVANA	gene	13779	30103	.	+	.	FI_gene_label "MBOAT1^ENSG00000172197.11"  ; ID "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11"  ; ccdsid "CCDS34346.1"  ; exon_id "ENSE00001299453.6"  ; exon_number 1 ; gene_id "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11"  ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2"  ; havana_transcript "OTTHUMT00000039980.2"  ; hgnc_id "HGNC:21579"  ; level 2 ; orig_coord_info "chr6,20212136,20212234,-"  ; protein_id "ENSP00000324944.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000324607.8"  ; transcript_name "MBOAT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTPBP2--MBOAT1	HAVANA	mRNA	13779	30103	.	+	.	FI_gene_label "MBOAT1^ENSG00000172197.11"  ; ID "GTPBP2--MBOAT1^ENST00000324607.8"  ; Parent "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11"  ; ccdsid "CCDS34346.1"  ; exon_id "ENSE00001299453.6"  ; exon_number 1 ; gene_id "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11"  ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2"  ; havana_transcript "OTTHUMT00000039980.2"  ; hgnc_id "HGNC:21579"  ; level 2 ; orig_coord_info "chr6,20212136,20212234,-"  ; protein_id "ENSP00000324944.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000324607.8"  ; transcript_name "MBOAT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GUSBP13--NAIP	ENSEMBL	gene	10656	31835	.	+	.	FI_gene_label "NAIP^ENSG00000249437.8"  ; ID "GUSBP13--NAIP^NAIP^ENSG00000249437.8"  ; ccdsid "CCDS4009.1"  ; exon_id "ENSE00002284906.1"  ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8"  ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7"  ; hgnc_id "HGNC:7634"  ; level 3 ; orig_coord_info "chr5,71012348,71012915,-"  ; protein_id "ENSP00000443944.1"  ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8"  ; transcript_name "NAIP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GUSBP13--NAIP	ENSEMBL	mRNA	10656	31835	.	+	.	FI_gene_label "NAIP^ENSG00000249437.8"  ; ID "GUSBP13--NAIP^ENST00000194097.8"  ; Parent "GUSBP13--NAIP^NAIP^ENSG00000249437.8"  ; ccdsid "CCDS4009.1"  ; exon_id "ENSE00002284906.1"  ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8"  ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7"  ; hgnc_id "HGNC:7634"  ; level 3 ; orig_coord_info "chr5,71012348,71012915,-"  ; protein_id "ENSP00000443944.1"  ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8"  ; transcript_name "NAIP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HIRA--MYO18B-AS1	HAVANA	gene	2074	28792	.	+	.	FI_gene_label "HIRA^ENSG00000100084.14"  ; ID "HIRA--MYO18B-AS1^HIRA^ENSG00000100084.14"  ; ccdsid "CCDS13759.1"  ; exon_id "ENSE00001933986.1"  ; exon_number 1 ; gene_id "HIRA--MYO18B-AS1^HIRA^ENSG00000100084.14"  ; gene_name HIRA ; gene_type protein_coding ; havana_gene "OTTHUMG00000150134.5"  ; havana_transcript "OTTHUMT00000316488.2"  ; hgnc_id "HGNC:4916"  ; level 2 ; orig_coord_info "chr22,19431440,19431476,-"  ; protein_id "ENSP00000263208.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HIRA--MYO18B-AS1^ENST00000263208.5"  ; transcript_name "HIRA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HIRA--MYO18B-AS1	HAVANA	mRNA	2074	28792	.	+	.	FI_gene_label "HIRA^ENSG00000100084.14"  ; ID "HIRA--MYO18B-AS1^ENST00000263208.5"  ; Parent "HIRA--MYO18B-AS1^HIRA^ENSG00000100084.14"  ; ccdsid "CCDS13759.1"  ; exon_id "ENSE00001933986.1"  ; exon_number 1 ; gene_id "HIRA--MYO18B-AS1^HIRA^ENSG00000100084.14"  ; gene_name HIRA ; gene_type protein_coding ; havana_gene "OTTHUMG00000150134.5"  ; havana_transcript "OTTHUMT00000316488.2"  ; hgnc_id "HGNC:4916"  ; level 2 ; orig_coord_info "chr22,19431440,19431476,-"  ; protein_id "ENSP00000263208.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HIRA--MYO18B-AS1^ENST00000263208.5"  ; transcript_name "HIRA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MSI2--CLTC	HAVANA	gene	57253	91788	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "MSI2--CLTC^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "MSI2--CLTC^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--CLTC	HAVANA	mRNA	57253	91788	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "MSI2--CLTC^ENST00000269122.8"  ; Parent "MSI2--CLTC^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "MSI2--CLTC^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MSI2--CLTC	HAVANA	gene	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--CLTC^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--CLTC^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--CLTC	HAVANA	mRNA	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--CLTC^ENST00000284073.7"  ; Parent "MSI2--CLTC^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--CLTC^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NARS2--GAB2	HAVANA	gene	1011	17072	.	+	.	FI_gene_label "NARS2^ENSG00000137513.10"  ; ID "NARS2--GAB2^NARS2^ENSG00000137513.10"  ; ccdsid "CCDS8261.1"  ; exon_id "ENSE00001151727.6"  ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10"  ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4"  ; havana_transcript "OTTHUMT00000391138.3"  ; hgnc_id "HGNC:26274"  ; level 2 ; orig_coord_info "chr11,78574348,78574488,-"  ; protein_id "ENSP00000281038.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10"  ; transcript_name "NARS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2	HAVANA	mRNA	1011	17072	.	+	.	FI_gene_label "NARS2^ENSG00000137513.10"  ; ID "NARS2--GAB2^ENST00000281038.10"  ; Parent "NARS2--GAB2^NARS2^ENSG00000137513.10"  ; ccdsid "CCDS8261.1"  ; exon_id "ENSE00001151727.6"  ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10"  ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4"  ; havana_transcript "OTTHUMT00000391138.3"  ; hgnc_id "HGNC:26274"  ; level 2 ; orig_coord_info "chr11,78574348,78574488,-"  ; protein_id "ENSP00000281038.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10"  ; transcript_name "NARS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NARS2--GAB2	HAVANA	gene	22864	39485	.	+	.	FI_gene_label "GAB2^ENSG00000033327.13"  ; ID "NARS2--GAB2^GAB2^ENSG00000033327.13"  ; ccdsid "CCDS8260.1"  ; exon_id "ENSE00003464974.1"  ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13"  ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3"  ; havana_transcript "OTTHUMT00000391084.1"  ; hgnc_id "HGNC:14458"  ; level 2 ; orig_coord_info "chr11,78280601,78280862,-"  ; protein_id "ENSP00000343959.2"  ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6"  ; transcript_name "GAB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2	HAVANA	mRNA	22864	39485	.	+	.	FI_gene_label "GAB2^ENSG00000033327.13"  ; ID "NARS2--GAB2^ENST00000340149.6"  ; Parent "NARS2--GAB2^GAB2^ENSG00000033327.13"  ; ccdsid "CCDS8260.1"  ; exon_id "ENSE00003464974.1"  ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13"  ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3"  ; havana_transcript "OTTHUMT00000391084.1"  ; hgnc_id "HGNC:14458"  ; level 2 ; orig_coord_info "chr11,78280601,78280862,-"  ; protein_id "ENSP00000343959.2"  ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6"  ; transcript_name "GAB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RIC1--FMNL1	HAVANA	gene	1001	25077	.	+	.	FI_gene_label "RIC1^ENSG00000107036.12"  ; ID "RIC1--FMNL1^RIC1^ENSG00000107036.12"  ; ccdsid "CCDS47949.2"  ; exon_id "ENSE00001626901.2"  ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12"  ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5"  ; havana_transcript "OTTHUMT00000051635.3"  ; hgnc_id "HGNC:17686"  ; level 2 ; orig_coord_info "chr9,5629310,5629453,+"  ; protein_id "ENSP00000251879.6"  ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10"  ; transcript_name "RIC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RIC1--FMNL1	HAVANA	mRNA	1001	25077	.	+	.	FI_gene_label "RIC1^ENSG00000107036.12"  ; ID "RIC1--FMNL1^ENST00000251879.10"  ; Parent "RIC1--FMNL1^RIC1^ENSG00000107036.12"  ; ccdsid "CCDS47949.2"  ; exon_id "ENSE00001626901.2"  ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12"  ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5"  ; havana_transcript "OTTHUMT00000051635.3"  ; hgnc_id "HGNC:17686"  ; level 2 ; orig_coord_info "chr9,5629310,5629453,+"  ; protein_id "ENSP00000251879.6"  ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10"  ; transcript_name "RIC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RIC1--FMNL1	ENSEMBL	gene	34309	51145	.	+	.	FI_gene_label "FMNL1^ENSG00000184922.14"  ; ID "RIC1--FMNL1^FMNL1^ENSG00000184922.14"  ; exon_id "ENSE00001337921.3"  ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14"  ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5"  ; hgnc_id "HGNC:1212"  ; level 3 ; orig_coord_info "chr17,45222125,45222187,+"  ; protein_id "ENSP00000327442.4"  ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7"  ; transcript_name "FMNL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
RIC1--FMNL1	ENSEMBL	mRNA	34309	51145	.	+	.	FI_gene_label "FMNL1^ENSG00000184922.14"  ; ID "RIC1--FMNL1^ENST00000328118.7"  ; Parent "RIC1--FMNL1^FMNL1^ENSG00000184922.14"  ; exon_id "ENSE00001337921.3"  ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14"  ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5"  ; hgnc_id "HGNC:1212"  ; level 3 ; orig_coord_info "chr17,45222125,45222187,+"  ; protein_id "ENSP00000327442.4"  ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7"  ; transcript_name "FMNL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
SHMT2--RACGAP1	HAVANA	gene	11765	30952	.	+	.	FI_gene_label "RACGAP1^ENSG00000161800.13"  ; ID "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13"  ; ccdsid "CCDS8795.1"  ; exon_id "ENSE00003599562.1"  ; exon_number 2 ; gene_id "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13"  ; gene_name RACGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169811.7"  ; havana_transcript "OTTHUMT00000405998.3"  ; hgnc_id "HGNC:9804"  ; level 2 ; orig_coord_info "chr12,50016631,50016715,-"  ; protein_id "ENSP00000309871.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000312377.10"  ; transcript_name "RACGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SHMT2--RACGAP1	HAVANA	mRNA	11765	30952	.	+	.	FI_gene_label "RACGAP1^ENSG00000161800.13"  ; ID "SHMT2--RACGAP1^ENST00000312377.10"  ; Parent "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13"  ; ccdsid "CCDS8795.1"  ; exon_id "ENSE00003599562.1"  ; exon_number 2 ; gene_id "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13"  ; gene_name RACGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169811.7"  ; havana_transcript "OTTHUMT00000405998.3"  ; hgnc_id "HGNC:9804"  ; level 2 ; orig_coord_info "chr12,50016631,50016715,-"  ; protein_id "ENSP00000309871.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000312377.10"  ; transcript_name "RACGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SHMT2--RACGAP1	HAVANA	gene	1139	6363	.	+	.	FI_gene_label "SHMT2^ENSG00000182199.11"  ; ID "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11"  ; ccdsid "CCDS8934.1"  ; exon_id "ENSE00003673873.1"  ; exon_number 1 ; gene_id "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11"  ; gene_name SHMT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171246.15"  ; havana_transcript "OTTHUMT00000412525.3"  ; hgnc_id "HGNC:10852"  ; level 2 ; orig_coord_info "chr12,57229779,57229811,+"  ; protein_id "ENSP00000333667.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000328923.8"  ; transcript_name "SHMT2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SHMT2--RACGAP1	HAVANA	mRNA	1139	6363	.	+	.	FI_gene_label "SHMT2^ENSG00000182199.11"  ; ID "SHMT2--RACGAP1^ENST00000328923.8"  ; Parent "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11"  ; ccdsid "CCDS8934.1"  ; exon_id "ENSE00003673873.1"  ; exon_number 1 ; gene_id "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11"  ; gene_name SHMT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171246.15"  ; havana_transcript "OTTHUMT00000412525.3"  ; hgnc_id "HGNC:10852"  ; level 2 ; orig_coord_info "chr12,57229779,57229811,+"  ; protein_id "ENSP00000333667.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000328923.8"  ; transcript_name "SHMT2-201"  ; 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: 
ZNF525--AC007786.2	HAVANA	gene	1015	11888	.	+	.	FI_gene_label "ZNF525^ENSG00000203326.12"  ; ID "ZNF525--AC007786.2^ZNF525^ENSG00000203326.12"  ; ccdsid "CCDS86803.1"  ; exon_id "ENSE00003635523.1"  ; exon_number 3 ; gene_id "ZNF525--AC007786.2^ZNF525^ENSG00000203326.12"  ; gene_name ZNF525 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158277.5"  ; havana_transcript "OTTHUMT00000350551.4"  ; hgnc_id "HGNC:29423"  ; level 2 ; orig_coord_info "chr19,53375863,53375896,+"  ; protein_id "ENSP00000419136.1"  ; tag basic CCDS ; transcript_id "ZNF525--AC007786.2^ENST00000467003.1"  ; transcript_name "ZNF525-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ZNF525--AC007786.2	HAVANA	mRNA	1015	11888	.	+	.	FI_gene_label "ZNF525^ENSG00000203326.12"  ; ID "ZNF525--AC007786.2^ENST00000467003.1"  ; Parent "ZNF525--AC007786.2^ZNF525^ENSG00000203326.12"  ; ccdsid "CCDS86803.1"  ; exon_id "ENSE00003635523.1"  ; exon_number 3 ; gene_id "ZNF525--AC007786.2^ZNF525^ENSG00000203326.12"  ; gene_name ZNF525 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158277.5"  ; havana_transcript "OTTHUMT00000350551.4"  ; hgnc_id "HGNC:29423"  ; level 2 ; orig_coord_info "chr19,53375863,53375896,+"  ; protein_id "ENSP00000419136.1"  ; tag basic CCDS ; transcript_id "ZNF525--AC007786.2^ENST00000467003.1"  ; transcript_name "ZNF525-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
ZNF525--AC007786.3	HAVANA	gene	1015	11888	.	+	.	FI_gene_label "ZNF525^ENSG00000203326.12"  ; ID "ZNF525--AC007786.3^ZNF525^ENSG00000203326.12"  ; ccdsid "CCDS86803.1"  ; exon_id "ENSE00003635523.1"  ; exon_number 3 ; gene_id "ZNF525--AC007786.3^ZNF525^ENSG00000203326.12"  ; gene_name ZNF525 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158277.5"  ; havana_transcript "OTTHUMT00000350551.4"  ; hgnc_id "HGNC:29423"  ; level 2 ; orig_coord_info "chr19,53375863,53375896,+"  ; protein_id "ENSP00000419136.1"  ; tag basic CCDS ; transcript_id "ZNF525--AC007786.3^ENST00000467003.1"  ; transcript_name "ZNF525-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ZNF525--AC007786.3	HAVANA	mRNA	1015	11888	.	+	.	FI_gene_label "ZNF525^ENSG00000203326.12"  ; ID "ZNF525--AC007786.3^ENST00000467003.1"  ; Parent "ZNF525--AC007786.3^ZNF525^ENSG00000203326.12"  ; ccdsid "CCDS86803.1"  ; exon_id "ENSE00003635523.1"  ; exon_number 3 ; gene_id "ZNF525--AC007786.3^ZNF525^ENSG00000203326.12"  ; gene_name ZNF525 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158277.5"  ; havana_transcript "OTTHUMT00000350551.4"  ; hgnc_id "HGNC:29423"  ; level 2 ; orig_coord_info "chr19,53375863,53375896,+"  ; protein_id "ENSP00000419136.1"  ; tag basic CCDS ; transcript_id "ZNF525--AC007786.3^ENST00000467003.1"  ; transcript_name "ZNF525-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
ZSCAN22--WWC3	HAVANA	gene	1001	7654	.	+	.	FI_gene_label "ZSCAN22^ENSG00000182318.6"  ; ID "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6"  ; ccdsid "CCDS12975.1"  ; exon_id "ENSE00001333334.1"  ; exon_number 2 ; gene_id "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6"  ; gene_name ZSCAN22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183463.2"  ; havana_transcript "OTTHUMT00000466765.2"  ; hgnc_id "HGNC:4929"  ; level 2 ; orig_coord_info "chr19,58334803,58335205,+"  ; protein_id "ENSP00000332433.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000329665.5"  ; transcript_name "ZSCAN22-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZSCAN22--WWC3	HAVANA	mRNA	1001	7654	.	+	.	FI_gene_label "ZSCAN22^ENSG00000182318.6"  ; ID "ZSCAN22--WWC3^ENST00000329665.5"  ; Parent "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6"  ; ccdsid "CCDS12975.1"  ; exon_id "ENSE00001333334.1"  ; exon_number 2 ; gene_id "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6"  ; gene_name ZSCAN22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183463.2"  ; havana_transcript "OTTHUMT00000466765.2"  ; hgnc_id "HGNC:4929"  ; level 2 ; orig_coord_info "chr19,58334803,58335205,+"  ; protein_id "ENSP00000332433.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000329665.5"  ; transcript_name "ZSCAN22-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZSCAN22--WWC3	HAVANA	gene	10655	38629	.	+	.	FI_gene_label "WWC3^ENSG00000047644.19"  ; ID "ZSCAN22--WWC3^WWC3^ENSG00000047644.19"  ; ccdsid "CCDS14136.1"  ; exon_id "ENSE00001486696.1"  ; exon_number 2 ; gene_id "ZSCAN22--WWC3^WWC3^ENSG00000047644.19"  ; gene_name WWC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021123.1"  ; havana_transcript "OTTHUMT00000055725.1"  ; hgnc_id "HGNC:29237"  ; level 2 ; orig_coord_info "chrX,10063539,10063554,+"  ; protein_id "ENSP00000370242.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000380861.9"  ; transcript_name "WWC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZSCAN22--WWC3	HAVANA	mRNA	10655	38629	.	+	.	FI_gene_label "WWC3^ENSG00000047644.19"  ; ID "ZSCAN22--WWC3^ENST00000380861.9"  ; Parent "ZSCAN22--WWC3^WWC3^ENSG00000047644.19"  ; ccdsid "CCDS14136.1"  ; exon_id "ENSE00001486696.1"  ; exon_number 2 ; gene_id "ZSCAN22--WWC3^WWC3^ENSG00000047644.19"  ; gene_name WWC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021123.1"  ; havana_transcript "OTTHUMT00000055725.1"  ; hgnc_id "HGNC:29237"  ; level 2 ; orig_coord_info "chrX,10063539,10063554,+"  ; protein_id "ENSP00000370242.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000380861.9"  ; transcript_name "WWC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC092070.2--MAN2B1	HAVANA	gene	1001	5545	.	+	.	FI_gene_label "AC092070.2^ENSG00000269001.2"  ; ID "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2"  ; exon_id "ENSE00003144051.1"  ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2"  ; gene_name "AC092070.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182887.2"  ; havana_transcript "OTTHUMT00000464185.1"  ; level 2 ; orig_coord_info "chr19,53197111,53197262,+"  ; tag basic ; transcript_id "AC092070.2--MAN2B1^ENST00000597550.5"  ; transcript_name "AC092070.2-201"  ; transcript_support_level 4 ; transcript_type processed_transcript
AC092070.2--MAN2B1	HAVANA	RNA	1001	5545	.	+	.	FI_gene_label "AC092070.2^ENSG00000269001.2"  ; ID "AC092070.2--MAN2B1^ENST00000597550.5"  ; Parent "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2"  ; exon_id "ENSE00003144051.1"  ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2"  ; gene_name "AC092070.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182887.2"  ; havana_transcript "OTTHUMT00000464185.1"  ; level 2 ; orig_coord_info "chr19,53197111,53197262,+"  ; tag basic ; transcript_id "AC092070.2--MAN2B1^ENST00000597550.5"  ; transcript_name "AC092070.2-201"  ; transcript_support_level 4 ; transcript_type processed_transcript
L1 and L2 created: 
C22orf39--MYO18B-AS1	HAVANA	gene	33040	44724	.	+	.	FI_gene_label "MYO18B-AS1^ENSG00000231933.7"  ; ID "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; exon_id "ENSE00003705478.1"  ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; gene_name "MYO18B-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4"  ; havana_transcript "OTTHUMT00000461522.3"  ; hgnc_id "HGNC:40831"  ; level 1 ; orig_coord_info "chr22,25900825,25901042,-"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "C22orf39--MYO18B-AS1^ENST00000453457.7"  ; transcript_name "MYO18B-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
C22orf39--MYO18B-AS1	HAVANA	RNA	33040	44724	.	+	.	FI_gene_label "MYO18B-AS1^ENSG00000231933.7"  ; ID "C22orf39--MYO18B-AS1^ENST00000453457.7"  ; Parent "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; exon_id "ENSE00003705478.1"  ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; gene_name "MYO18B-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4"  ; havana_transcript "OTTHUMT00000461522.3"  ; hgnc_id "HGNC:40831"  ; level 1 ; orig_coord_info "chr22,25900825,25901042,-"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "C22orf39--MYO18B-AS1^ENST00000453457.7"  ; transcript_name "MYO18B-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
EXOC2--EPHA5-AS1	HAVANA	gene	36199	40808	.	+	.	FI_gene_label "EPHA5-AS1^ENSG00000250846.6"  ; ID "EXOC2--EPHA5-AS1^EPHA5-AS1^ENSG00000250846.6"  ; exon_id "ENSE00002042971.1"  ; exon_number 1 ; gene_id "EXOC2--EPHA5-AS1^EPHA5-AS1^ENSG00000250846.6"  ; gene_name "EPHA5-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000161982.1"  ; havana_transcript "OTTHUMT00000361853.1"  ; hgnc_id "HGNC:50602"  ; level 2 ; orig_coord_info "chr4,65670609,65670673,+"  ; transcript_id "EXOC2--EPHA5-AS1^ENST00000507117.1"  ; transcript_name "EPHA5-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
EXOC2--EPHA5-AS1	HAVANA	RNA	36199	40808	.	+	.	FI_gene_label "EPHA5-AS1^ENSG00000250846.6"  ; ID "EXOC2--EPHA5-AS1^ENST00000507117.1"  ; Parent "EXOC2--EPHA5-AS1^EPHA5-AS1^ENSG00000250846.6"  ; exon_id "ENSE00002042971.1"  ; exon_number 1 ; gene_id "EXOC2--EPHA5-AS1^EPHA5-AS1^ENSG00000250846.6"  ; gene_name "EPHA5-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000161982.1"  ; havana_transcript "OTTHUMT00000361853.1"  ; hgnc_id "HGNC:50602"  ; level 2 ; orig_coord_info "chr4,65670609,65670673,+"  ; transcript_id "EXOC2--EPHA5-AS1^ENST00000507117.1"  ; transcript_name "EPHA5-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
GTPBP2--AL008627.1	HAVANA	gene	13779	14264	.	+	.	FI_gene_label "AL008627.1^ENSG00000229700.1"  ; ID "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1"  ; exon_id "ENSE00001629587.1"  ; exon_number 1 ; gene_id "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1"  ; gene_name "AL008627.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016195.1"  ; havana_transcript "OTTHUMT00000043482.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr6,20042455,20042940,-"  ; tag pseudo_consens basic ; transcript_id "GTPBP2--AL008627.1^ENST00000446953.1"  ; transcript_name "AL008627.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
GTPBP2--AL008627.1	HAVANA	RNA	13779	14264	.	+	.	FI_gene_label "AL008627.1^ENSG00000229700.1"  ; ID "GTPBP2--AL008627.1^ENST00000446953.1"  ; Parent "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1"  ; exon_id "ENSE00001629587.1"  ; exon_number 1 ; gene_id "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1"  ; gene_name "AL008627.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016195.1"  ; havana_transcript "OTTHUMT00000043482.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr6,20042455,20042940,-"  ; tag pseudo_consens basic ; transcript_id "GTPBP2--AL008627.1^ENST00000446953.1"  ; transcript_name "AL008627.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
GUSBP13--NAIP	HAVANA	gene	1001	5633	.	+	.	FI_gene_label "GUSBP13^ENSG00000198237.8"  ; ID "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8"  ; exon_id "ENSE00002091111.1"  ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8"  ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1"  ; havana_transcript "OTTHUMT00000379319.1"  ; hgnc_id "HGNC:54495"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr5,69875271,69875319,+"  ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2"  ; transcript_name "GUSBP13-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GUSBP13--NAIP	HAVANA	RNA	1001	5633	.	+	.	FI_gene_label "GUSBP13^ENSG00000198237.8"  ; ID "GUSBP13--NAIP^ENST00000506490.2"  ; Parent "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8"  ; exon_id "ENSE00002091111.1"  ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8"  ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1"  ; havana_transcript "OTTHUMT00000379319.1"  ; hgnc_id "HGNC:54495"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr5,69875271,69875319,+"  ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2"  ; transcript_name "GUSBP13-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
HIRA--MYO18B-AS1	HAVANA	gene	33080	44764	.	+	.	FI_gene_label "MYO18B-AS1^ENSG00000231933.7"  ; ID "HIRA--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; exon_id "ENSE00003705478.1"  ; exon_number 1 ; gene_id "HIRA--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; gene_name "MYO18B-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4"  ; havana_transcript "OTTHUMT00000461522.3"  ; hgnc_id "HGNC:40831"  ; level 1 ; orig_coord_info "chr22,25900825,25901042,-"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "HIRA--MYO18B-AS1^ENST00000453457.7"  ; transcript_name "MYO18B-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
HIRA--MYO18B-AS1	HAVANA	RNA	33080	44764	.	+	.	FI_gene_label "MYO18B-AS1^ENSG00000231933.7"  ; ID "HIRA--MYO18B-AS1^ENST00000453457.7"  ; Parent "HIRA--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; exon_id "ENSE00003705478.1"  ; exon_number 1 ; gene_id "HIRA--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7"  ; gene_name "MYO18B-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4"  ; havana_transcript "OTTHUMT00000461522.3"  ; hgnc_id "HGNC:40831"  ; level 1 ; orig_coord_info "chr22,25900825,25901042,-"  ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "HIRA--MYO18B-AS1^ENST00000453457.7"  ; transcript_name "MYO18B-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
ZNF525--AC007786.2	HAVANA	gene	16239	17041	.	+	.	FI_gene_label "AC007786.2^ENSG00000276251.1"  ; ID "ZNF525--AC007786.2^AC007786.2^ENSG00000276251.1"  ; exon_id "ENSE00003747336.1"  ; exon_number 1 ; gene_id "ZNF525--AC007786.2^AC007786.2^ENSG00000276251.1"  ; gene_name "AC007786.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186711.1"  ; havana_transcript "OTTHUMT00000473658.1"  ; level 2 ; orig_coord_info "chr19,29220864,29221666,+"  ; tag basic ; transcript_id "ZNF525--AC007786.2^ENST00000618791.1"  ; transcript_name "AC007786.2-201"  ; transcript_support_level NA ; transcript_type lncRNA
ZNF525--AC007786.2	HAVANA	RNA	16239	17041	.	+	.	FI_gene_label "AC007786.2^ENSG00000276251.1"  ; ID "ZNF525--AC007786.2^ENST00000618791.1"  ; Parent "ZNF525--AC007786.2^AC007786.2^ENSG00000276251.1"  ; exon_id "ENSE00003747336.1"  ; exon_number 1 ; gene_id "ZNF525--AC007786.2^AC007786.2^ENSG00000276251.1"  ; gene_name "AC007786.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186711.1"  ; havana_transcript "OTTHUMT00000473658.1"  ; level 2 ; orig_coord_info "chr19,29220864,29221666,+"  ; tag basic ; transcript_id "ZNF525--AC007786.2^ENST00000618791.1"  ; transcript_name "AC007786.2-201"  ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created: 
ZNF525--AC007786.3	HAVANA	gene	16239	16834	.	+	.	FI_gene_label "AC007786.3^ENSG00000276631.1"  ; ID "ZNF525--AC007786.3^AC007786.3^ENSG00000276631.1"  ; exon_id "ENSE00003726915.1"  ; exon_number 1 ; gene_id "ZNF525--AC007786.3^AC007786.3^ENSG00000276631.1"  ; gene_name "AC007786.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186712.1"  ; havana_transcript "OTTHUMT00000473659.1"  ; level 2 ; orig_coord_info "chr19,29222542,29223137,+"  ; tag basic ; transcript_id "ZNF525--AC007786.3^ENST00000615154.1"  ; transcript_name "AC007786.3-201"  ; transcript_support_level NA ; transcript_type lncRNA
ZNF525--AC007786.3	HAVANA	RNA	16239	16834	.	+	.	FI_gene_label "AC007786.3^ENSG00000276631.1"  ; ID "ZNF525--AC007786.3^ENST00000615154.1"  ; Parent "ZNF525--AC007786.3^AC007786.3^ENSG00000276631.1"  ; exon_id "ENSE00003726915.1"  ; exon_number 1 ; gene_id "ZNF525--AC007786.3^AC007786.3^ENSG00000276631.1"  ; gene_name "AC007786.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186712.1"  ; havana_transcript "OTTHUMT00000473659.1"  ; level 2 ; orig_coord_info "chr19,29222542,29223137,+"  ; tag basic ; transcript_id "ZNF525--AC007786.3^ENST00000615154.1"  ; transcript_name "AC007786.3-201"  ; transcript_support_level NA ; transcript_type lncRNA
337 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 ------------------------------
525 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 29 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