.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00588_B23MVV7LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/3aab01c32fa9a4ab2c0bb35903fc88/.command.out
Size: 68.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00588_B23MVV7LT4_1)
Attempt
Content

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 5189
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5189
=> 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:5189
  => 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: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCSER1--DMP1	HAVANA	gene	41502	47846	.	+	.	FI_gene_label "DMP1^ENSG00000152592.14"  ; ID "CCSER1--DMP1^DMP1^ENSG00000152592.14"  ; ccdsid "CCDS43249.1"  ; exon_id "ENSE00001374293.2"  ; exon_number 2 ; gene_id "CCSER1--DMP1^DMP1^ENSG00000152592.14"  ; gene_name DMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130598.3"  ; havana_transcript "OTTHUMT00000361347.1"  ; hgnc_id "HGNC:2932"  ; level 2 ; orig_coord_info "chr4,87656493,87656546,+"  ; protein_id "ENSP00000282479.6"  ; tag basic CCDS ; transcript_id "CCSER1--DMP1^ENST00000282479.7"  ; transcript_name "DMP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCSER1--DMP1	HAVANA	mRNA	41502	47846	.	+	.	FI_gene_label "DMP1^ENSG00000152592.14"  ; ID "CCSER1--DMP1^ENST00000282479.7"  ; Parent "CCSER1--DMP1^DMP1^ENSG00000152592.14"  ; ccdsid "CCDS43249.1"  ; exon_id "ENSE00001374293.2"  ; exon_number 2 ; gene_id "CCSER1--DMP1^DMP1^ENSG00000152592.14"  ; gene_name DMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130598.3"  ; havana_transcript "OTTHUMT00000361347.1"  ; hgnc_id "HGNC:2932"  ; level 2 ; orig_coord_info "chr4,87656493,87656546,+"  ; protein_id "ENSP00000282479.6"  ; tag basic CCDS ; transcript_id "CCSER1--DMP1^ENST00000282479.7"  ; transcript_name "DMP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCSER1--DMP1	HAVANA	gene	2298	21760	.	+	.	FI_gene_label "CCSER1^ENSG00000184305.15"  ; ID "CCSER1--DMP1^CCSER1^ENSG00000184305.15"  ; ccdsid "CCDS47100.1"  ; exon_id "ENSE00001292028.3"  ; exon_number 2 ; gene_id "CCSER1--DMP1^CCSER1^ENSG00000184305.15"  ; gene_name CCSER1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160950.6"  ; havana_transcript "OTTHUMT00000363336.1"  ; hgnc_id "HGNC:29349"  ; level 2 ; orig_coord_info "chr4,90308285,90309608,+"  ; protein_id "ENSP00000389283.2"  ; tag basic CCDS ; transcript_id "CCSER1--DMP1^ENST00000432775.6"  ; transcript_name "CCSER1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCSER1--DMP1	HAVANA	mRNA	2298	21760	.	+	.	FI_gene_label "CCSER1^ENSG00000184305.15"  ; ID "CCSER1--DMP1^ENST00000432775.6"  ; Parent "CCSER1--DMP1^CCSER1^ENSG00000184305.15"  ; ccdsid "CCDS47100.1"  ; exon_id "ENSE00001292028.3"  ; exon_number 2 ; gene_id "CCSER1--DMP1^CCSER1^ENSG00000184305.15"  ; gene_name CCSER1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160950.6"  ; havana_transcript "OTTHUMT00000363336.1"  ; hgnc_id "HGNC:29349"  ; level 2 ; orig_coord_info "chr4,90308285,90309608,+"  ; protein_id "ENSP00000389283.2"  ; tag basic CCDS ; transcript_id "CCSER1--DMP1^ENST00000432775.6"  ; transcript_name "CCSER1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ERBB2--SRCIN1	HAVANA	gene	5981	25761	.	+	.	FI_gene_label "ERBB2^ENSG00000141736.14"  ; ID "ERBB2--SRCIN1^ERBB2^ENSG00000141736.14"  ; ccdsid "CCDS32642.1"  ; exon_id "ENSE00003909903.1"  ; exon_number 1 ; gene_id "ERBB2--SRCIN1^ERBB2^ENSG00000141736.14"  ; gene_name ERBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179300.3"  ; havana_transcript "OTTHUMT00000445621.2"  ; hgnc_id "HGNC:3430"  ; level 2 ; orig_coord_info "chr17,39700239,39700311,+"  ; protein_id "ENSP00000269571.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERBB2--SRCIN1^ENST00000269571.10"  ; transcript_name "ERBB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ERBB2--SRCIN1	HAVANA	mRNA	5981	25761	.	+	.	FI_gene_label "ERBB2^ENSG00000141736.14"  ; ID "ERBB2--SRCIN1^ENST00000269571.10"  ; Parent "ERBB2--SRCIN1^ERBB2^ENSG00000141736.14"  ; ccdsid "CCDS32642.1"  ; exon_id "ENSE00003909903.1"  ; exon_number 1 ; gene_id "ERBB2--SRCIN1^ERBB2^ENSG00000141736.14"  ; gene_name ERBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179300.3"  ; havana_transcript "OTTHUMT00000445621.2"  ; hgnc_id "HGNC:3430"  ; level 2 ; orig_coord_info "chr17,39700239,39700311,+"  ; protein_id "ENSP00000269571.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERBB2--SRCIN1^ENST00000269571.10"  ; transcript_name "ERBB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ERBB2--SRCIN1	HAVANA	gene	31439	39542	.	+	.	FI_gene_label "SRCIN1^ENSG00000277363.5"  ; ID "ERBB2--SRCIN1^SRCIN1^ENSG00000277363.5"  ; exon_id "ENSE00003740142.1"  ; exon_number 1 ; gene_id "ERBB2--SRCIN1^SRCIN1^ENSG00000277363.5"  ; gene_name SRCIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188493.4"  ; havana_transcript "OTTHUMT00000477426.2"  ; hgnc_id "HGNC:29506"  ; level 2 ; orig_coord_info "chr17,38604479,38604602,-"  ; protein_id "ENSP00000478342.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "ERBB2--SRCIN1^ENST00000612431.1"  ; transcript_name "SRCIN1-211"  ; transcript_support_level 1 ; transcript_type protein_coding
ERBB2--SRCIN1	HAVANA	mRNA	31439	39542	.	+	.	FI_gene_label "SRCIN1^ENSG00000277363.5"  ; ID "ERBB2--SRCIN1^ENST00000612431.1"  ; Parent "ERBB2--SRCIN1^SRCIN1^ENSG00000277363.5"  ; exon_id "ENSE00003740142.1"  ; exon_number 1 ; gene_id "ERBB2--SRCIN1^SRCIN1^ENSG00000277363.5"  ; gene_name SRCIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188493.4"  ; havana_transcript "OTTHUMT00000477426.2"  ; hgnc_id "HGNC:29506"  ; level 2 ; orig_coord_info "chr17,38604479,38604602,-"  ; protein_id "ENSP00000478342.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "ERBB2--SRCIN1^ENST00000612431.1"  ; transcript_name "SRCIN1-211"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXL20--IKZF3	HAVANA	gene	1898	26528	.	+	.	FI_gene_label "FBXL20^ENSG00000108306.13"  ; ID "FBXL20--IKZF3^FBXL20^ENSG00000108306.13"  ; ccdsid "CCDS32640.1"  ; exon_id "ENSE00002727680.2"  ; exon_number 1 ; gene_id "FBXL20--IKZF3^FBXL20^ENSG00000108306.13"  ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9"  ; havana_transcript "OTTHUMT00000444315.4"  ; hgnc_id "HGNC:24679"  ; level 2 ; orig_coord_info "chr17,39401361,39401402,-"  ; protein_id "ENSP00000264658.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--IKZF3^ENST00000264658.11"  ; transcript_name "FBXL20-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXL20--IKZF3	HAVANA	mRNA	1898	26528	.	+	.	FI_gene_label "FBXL20^ENSG00000108306.13"  ; ID "FBXL20--IKZF3^ENST00000264658.11"  ; Parent "FBXL20--IKZF3^FBXL20^ENSG00000108306.13"  ; ccdsid "CCDS32640.1"  ; exon_id "ENSE00002727680.2"  ; exon_number 1 ; gene_id "FBXL20--IKZF3^FBXL20^ENSG00000108306.13"  ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9"  ; havana_transcript "OTTHUMT00000444315.4"  ; hgnc_id "HGNC:24679"  ; level 2 ; orig_coord_info "chr17,39401361,39401402,-"  ; protein_id "ENSP00000264658.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--IKZF3^ENST00000264658.11"  ; transcript_name "FBXL20-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXL20--IKZF3	HAVANA	gene	29653	39208	.	+	.	FI_gene_label "IKZF3^ENSG00000161405.17"  ; ID "FBXL20--IKZF3^IKZF3^ENSG00000161405.17"  ; exon_id "ENSE00002692875.1"  ; exon_number 1 ; gene_id "FBXL20--IKZF3^IKZF3^ENSG00000161405.17"  ; gene_name IKZF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133250.5"  ; havana_transcript "OTTHUMT00000257011.2"  ; hgnc_id "HGNC:13178"  ; level 2 ; orig_coord_info "chr17,39864120,39864126,-"  ; protein_id "ENSP00000462791.1"  ; transcript_id "FBXL20--IKZF3^ENST00000293068.9"  ; transcript_name "IKZF3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FBXL20--IKZF3	HAVANA	mRNA	29653	39208	.	+	.	FI_gene_label "IKZF3^ENSG00000161405.17"  ; ID "FBXL20--IKZF3^ENST00000293068.9"  ; Parent "FBXL20--IKZF3^IKZF3^ENSG00000161405.17"  ; exon_id "ENSE00002692875.1"  ; exon_number 1 ; gene_id "FBXL20--IKZF3^IKZF3^ENSG00000161405.17"  ; gene_name IKZF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133250.5"  ; havana_transcript "OTTHUMT00000257011.2"  ; hgnc_id "HGNC:13178"  ; level 2 ; orig_coord_info "chr17,39864120,39864126,-"  ; protein_id "ENSP00000462791.1"  ; transcript_id "FBXL20--IKZF3^ENST00000293068.9"  ; transcript_name "IKZF3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
KIF2A--LINC02229	HAVANA	gene	1090	25759	.	+	.	FI_gene_label "KIF2A^ENSG00000068796.19"  ; ID "KIF2A--LINC02229^KIF2A^ENSG00000068796.19"  ; exon_id "ENSE00003473057.1"  ; exon_number 3 ; gene_id "KIF2A--LINC02229^KIF2A^ENSG00000068796.19"  ; gene_name KIF2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000097755.9"  ; havana_transcript "OTTHUMT00000214988.2"  ; hgnc_id "HGNC:6318"  ; level 1 ; orig_coord_info "chr5,62347147,62347224,+"  ; protein_id "ENSP00000370493.3"  ; tag upstream_ATG basic exp_conf ; transcript_id "KIF2A--LINC02229^ENST00000381103.7"  ; transcript_name "KIF2A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIF2A--LINC02229	HAVANA	mRNA	1090	25759	.	+	.	FI_gene_label "KIF2A^ENSG00000068796.19"  ; ID "KIF2A--LINC02229^ENST00000381103.7"  ; Parent "KIF2A--LINC02229^KIF2A^ENSG00000068796.19"  ; exon_id "ENSE00003473057.1"  ; exon_number 3 ; gene_id "KIF2A--LINC02229^KIF2A^ENSG00000068796.19"  ; gene_name KIF2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000097755.9"  ; havana_transcript "OTTHUMT00000214988.2"  ; hgnc_id "HGNC:6318"  ; level 1 ; orig_coord_info "chr5,62347147,62347224,+"  ; protein_id "ENSP00000370493.3"  ; tag upstream_ATG basic exp_conf ; transcript_id "KIF2A--LINC02229^ENST00000381103.7"  ; transcript_name "KIF2A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LZTS2--FFAR4	HAVANA	gene	3746	11815	.	+	.	FI_gene_label "LZTS2^ENSG00000107816.17"  ; ID "LZTS2--FFAR4^LZTS2^ENSG00000107816.17"  ; ccdsid "CCDS7507.1"  ; exon_id "ENSE00001452101.1"  ; exon_number 1 ; gene_id "LZTS2--FFAR4^LZTS2^ENSG00000107816.17"  ; gene_name LZTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018914.4"  ; havana_transcript "OTTHUMT00000049872.1"  ; hgnc_id "HGNC:29381"  ; level 2 ; orig_coord_info "chr10,101002539,101002946,+"  ; protein_id "ENSP00000359240.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "LZTS2--FFAR4^ENST00000370220.1"  ; transcript_name "LZTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LZTS2--FFAR4	HAVANA	mRNA	3746	11815	.	+	.	FI_gene_label "LZTS2^ENSG00000107816.17"  ; ID "LZTS2--FFAR4^ENST00000370220.1"  ; Parent "LZTS2--FFAR4^LZTS2^ENSG00000107816.17"  ; ccdsid "CCDS7507.1"  ; exon_id "ENSE00001452101.1"  ; exon_number 1 ; gene_id "LZTS2--FFAR4^LZTS2^ENSG00000107816.17"  ; gene_name LZTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018914.4"  ; havana_transcript "OTTHUMT00000049872.1"  ; hgnc_id "HGNC:29381"  ; level 2 ; orig_coord_info "chr10,101002539,101002946,+"  ; protein_id "ENSP00000359240.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "LZTS2--FFAR4^ENST00000370220.1"  ; transcript_name "LZTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LZTS2--FFAR4	HAVANA	gene	14816	21468	.	+	.	FI_gene_label "FFAR4^ENSG00000186188.11"  ; ID "LZTS2--FFAR4^FFAR4^ENSG00000186188.11"  ; ccdsid "CCDS55720.1"  ; exon_id "ENSE00003902173.1"  ; exon_number 1 ; gene_id "LZTS2--FFAR4^FFAR4^ENSG00000186188.11"  ; gene_name FFAR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034409.2"  ; havana_transcript "OTTHUMT00000083178.1"  ; hgnc_id "HGNC:19061"  ; level 2 ; orig_coord_info "chr10,93566721,93567287,+"  ; protein_id "ENSP00000360536.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LZTS2--FFAR4^ENST00000371481.9"  ; transcript_name "FFAR4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LZTS2--FFAR4	HAVANA	mRNA	14816	21468	.	+	.	FI_gene_label "FFAR4^ENSG00000186188.11"  ; ID "LZTS2--FFAR4^ENST00000371481.9"  ; Parent "LZTS2--FFAR4^FFAR4^ENSG00000186188.11"  ; ccdsid "CCDS55720.1"  ; exon_id "ENSE00003902173.1"  ; exon_number 1 ; gene_id "LZTS2--FFAR4^FFAR4^ENSG00000186188.11"  ; gene_name FFAR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034409.2"  ; havana_transcript "OTTHUMT00000083178.1"  ; hgnc_id "HGNC:19061"  ; level 2 ; orig_coord_info "chr10,93566721,93567287,+"  ; protein_id "ENSP00000360536.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LZTS2--FFAR4^ENST00000371481.9"  ; transcript_name "FFAR4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAGI3--AL357055.2	HAVANA	gene	1001	31109	.	+	.	FI_gene_label "MAGI3^ENSG00000081026.19"  ; ID "MAGI3--AL357055.2^MAGI3^ENSG00000081026.19"  ; ccdsid "CCDS44196.1"  ; exon_id "ENSE00001940018.2"  ; exon_number 1 ; gene_id "MAGI3--AL357055.2^MAGI3^ENSG00000081026.19"  ; gene_name MAGI3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011737.4"  ; havana_transcript "OTTHUMT00000032429.2"  ; hgnc_id "HGNC:29647"  ; level 1 ; orig_coord_info "chr1,113391034,113391349,+"  ; protein_id "ENSP00000304604.9"  ; tag basic MANE_Select exp_conf CCDS ; transcript_id "MAGI3--AL357055.2^ENST00000307546.14"  ; transcript_name "MAGI3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MAGI3--AL357055.2	HAVANA	mRNA	1001	31109	.	+	.	FI_gene_label "MAGI3^ENSG00000081026.19"  ; ID "MAGI3--AL357055.2^ENST00000307546.14"  ; Parent "MAGI3--AL357055.2^MAGI3^ENSG00000081026.19"  ; ccdsid "CCDS44196.1"  ; exon_id "ENSE00001940018.2"  ; exon_number 1 ; gene_id "MAGI3--AL357055.2^MAGI3^ENSG00000081026.19"  ; gene_name MAGI3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011737.4"  ; havana_transcript "OTTHUMT00000032429.2"  ; hgnc_id "HGNC:29647"  ; level 1 ; orig_coord_info "chr1,113391034,113391349,+"  ; protein_id "ENSP00000304604.9"  ; tag basic MANE_Select exp_conf CCDS ; transcript_id "MAGI3--AL357055.2^ENST00000307546.14"  ; transcript_name "MAGI3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NEBL--PLXDC2	HAVANA	gene	25843	63335	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "NEBL--PLXDC2^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "NEBL--PLXDC2^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "NEBL--PLXDC2^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; transcript_support_level 1 ; transcript_type protein_coding
NEBL--PLXDC2	HAVANA	mRNA	25843	63335	.	+	.	FI_gene_label "NEBL^ENSG00000078114.19"  ; ID "NEBL--PLXDC2^ENST00000377122.9"  ; Parent "NEBL--PLXDC2^NEBL^ENSG00000078114.19"  ; ccdsid "CCDS7134.1"  ; exon_id "ENSE00001376454.2"  ; exon_number 1 ; gene_id "NEBL--PLXDC2^NEBL^ENSG00000078114.19"  ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5"  ; havana_transcript "OTTHUMT00000047113.1"  ; hgnc_id "HGNC:16932"  ; level 2 ; orig_coord_info "chr10,20897125,20897205,-"  ; protein_id "ENSP00000366326.4"  ; tag basic MANE_Select CCDS ; transcript_id "NEBL--PLXDC2^ENST00000377122.9"  ; transcript_name "NEBL-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NEBL--PLXDC2	HAVANA	gene	66336	82636	.	+	.	FI_gene_label "PLXDC2^ENSG00000120594.17"  ; ID "NEBL--PLXDC2^PLXDC2^ENSG00000120594.17"  ; ccdsid "CCDS60497.1"  ; exon_id "ENSE00003265815.1"  ; exon_number 1 ; gene_id "NEBL--PLXDC2^PLXDC2^ENSG00000120594.17"  ; gene_name PLXDC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017781.6"  ; havana_transcript "OTTHUMT00000047102.1"  ; hgnc_id "HGNC:21013"  ; level 2 ; orig_coord_info "chr10,19817080,19817191,+"  ; protein_id "ENSP00000366450.3"  ; tag basic CCDS ; transcript_id "NEBL--PLXDC2^ENST00000377242.7"  ; transcript_name "PLXDC2-202"  ; transcript_support_level 1 ; transcript_type protein_coding
NEBL--PLXDC2	HAVANA	mRNA	66336	82636	.	+	.	FI_gene_label "PLXDC2^ENSG00000120594.17"  ; ID "NEBL--PLXDC2^ENST00000377242.7"  ; Parent "NEBL--PLXDC2^PLXDC2^ENSG00000120594.17"  ; ccdsid "CCDS60497.1"  ; exon_id "ENSE00003265815.1"  ; exon_number 1 ; gene_id "NEBL--PLXDC2^PLXDC2^ENSG00000120594.17"  ; gene_name PLXDC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017781.6"  ; havana_transcript "OTTHUMT00000047102.1"  ; hgnc_id "HGNC:21013"  ; level 2 ; orig_coord_info "chr10,19817080,19817191,+"  ; protein_id "ENSP00000366450.3"  ; tag basic CCDS ; transcript_id "NEBL--PLXDC2^ENST00000377242.7"  ; transcript_name "PLXDC2-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^ENST00000616325.1"  ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; 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: 
PCGF2--ERBB2	HAVANA	gene	18444	38224	.	+	.	FI_gene_label "ERBB2^ENSG00000141736.14"  ; ID "PCGF2--ERBB2^ERBB2^ENSG00000141736.14"  ; ccdsid "CCDS32642.1"  ; exon_id "ENSE00003909903.1"  ; exon_number 1 ; gene_id "PCGF2--ERBB2^ERBB2^ENSG00000141736.14"  ; gene_name ERBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179300.3"  ; havana_transcript "OTTHUMT00000445621.2"  ; hgnc_id "HGNC:3430"  ; level 2 ; orig_coord_info "chr17,39700239,39700311,+"  ; protein_id "ENSP00000269571.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCGF2--ERBB2^ENST00000269571.10"  ; transcript_name "ERBB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCGF2--ERBB2	HAVANA	mRNA	18444	38224	.	+	.	FI_gene_label "ERBB2^ENSG00000141736.14"  ; ID "PCGF2--ERBB2^ENST00000269571.10"  ; Parent "PCGF2--ERBB2^ERBB2^ENSG00000141736.14"  ; ccdsid "CCDS32642.1"  ; exon_id "ENSE00003909903.1"  ; exon_number 1 ; gene_id "PCGF2--ERBB2^ERBB2^ENSG00000141736.14"  ; gene_name ERBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179300.3"  ; havana_transcript "OTTHUMT00000445621.2"  ; hgnc_id "HGNC:3430"  ; level 2 ; orig_coord_info "chr17,39700239,39700311,+"  ; protein_id "ENSP00000269571.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCGF2--ERBB2^ENST00000269571.10"  ; transcript_name "ERBB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCGF2--ERBB2	HAVANA	gene	8765	10461	.	+	.	FI_gene_label "PCGF2^ENSG00000277258.5"  ; ID "PCGF2--ERBB2^PCGF2^ENSG00000277258.5"  ; exon_id "ENSE00003739135.1"  ; exon_number 1 ; gene_id "PCGF2--ERBB2^PCGF2^ENSG00000277258.5"  ; gene_name PCGF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188501.3"  ; havana_transcript "OTTHUMT00000477448.1"  ; hgnc_id "HGNC:12929"  ; level 2 ; orig_coord_info "chr17,38735492,38735596,-"  ; protein_id "ENSP00000483741.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "PCGF2--ERBB2^ENST00000610747.1"  ; transcript_name "PCGF2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PCGF2--ERBB2	HAVANA	mRNA	8765	10461	.	+	.	FI_gene_label "PCGF2^ENSG00000277258.5"  ; ID "PCGF2--ERBB2^ENST00000610747.1"  ; Parent "PCGF2--ERBB2^PCGF2^ENSG00000277258.5"  ; exon_id "ENSE00003739135.1"  ; exon_number 1 ; gene_id "PCGF2--ERBB2^PCGF2^ENSG00000277258.5"  ; gene_name PCGF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188501.3"  ; havana_transcript "OTTHUMT00000477448.1"  ; hgnc_id "HGNC:12929"  ; level 2 ; orig_coord_info "chr17,38735492,38735596,-"  ; protein_id "ENSP00000483741.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "PCGF2--ERBB2^ENST00000610747.1"  ; transcript_name "PCGF2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PLXDC1--ACACA	HAVANA	gene	3724	30794	.	+	.	FI_gene_label "PLXDC1^ENSG00000161381.14"  ; ID "PLXDC1--ACACA^PLXDC1^ENSG00000161381.14"  ; ccdsid "CCDS11333.1"  ; exon_id "ENSE00002721375.2"  ; exon_number 1 ; gene_id "PLXDC1--ACACA^PLXDC1^ENSG00000161381.14"  ; gene_name PLXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133183.15"  ; havana_transcript "OTTHUMT00000256892.3"  ; hgnc_id "HGNC:20945"  ; level 2 ; orig_coord_info "chr17,39151362,39151437,-"  ; protein_id "ENSP00000323927.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PLXDC1--ACACA^ENST00000315392.9"  ; transcript_name "PLXDC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLXDC1--ACACA	HAVANA	mRNA	3724	30794	.	+	.	FI_gene_label "PLXDC1^ENSG00000161381.14"  ; ID "PLXDC1--ACACA^ENST00000315392.9"  ; Parent "PLXDC1--ACACA^PLXDC1^ENSG00000161381.14"  ; ccdsid "CCDS11333.1"  ; exon_id "ENSE00002721375.2"  ; exon_number 1 ; gene_id "PLXDC1--ACACA^PLXDC1^ENSG00000161381.14"  ; gene_name PLXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133183.15"  ; havana_transcript "OTTHUMT00000256892.3"  ; hgnc_id "HGNC:20945"  ; level 2 ; orig_coord_info "chr17,39151362,39151437,-"  ; protein_id "ENSP00000323927.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PLXDC1--ACACA^ENST00000315392.9"  ; transcript_name "PLXDC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PLXDC1--ACACA	HAVANA	gene	39097	45987	.	+	.	FI_gene_label "ACACA^ENSG00000278540.5"  ; ID "PLXDC1--ACACA^ACACA^ENSG00000278540.5"  ; exon_id "ENSE00003745454.1"  ; exon_number 3 ; gene_id "PLXDC1--ACACA^ACACA^ENSG00000278540.5"  ; gene_name ACACA ; gene_type protein_coding ; havana_gene "OTTHUMG00000188463.3"  ; havana_transcript "OTTHUMT00000477332.2"  ; hgnc_id "HGNC:84"  ; level 2 ; orig_coord_info "chr17,37330173,37330399,-"  ; protein_id "ENSP00000484948.1"  ; transcript_id "PLXDC1--ACACA^ENST00000612007.1"  ; transcript_name "ACACA-224"  ; transcript_support_level 5 ; transcript_type non_stop_decay
PLXDC1--ACACA	HAVANA	mRNA	39097	45987	.	+	.	FI_gene_label "ACACA^ENSG00000278540.5"  ; ID "PLXDC1--ACACA^ENST00000612007.1"  ; Parent "PLXDC1--ACACA^ACACA^ENSG00000278540.5"  ; exon_id "ENSE00003745454.1"  ; exon_number 3 ; gene_id "PLXDC1--ACACA^ACACA^ENSG00000278540.5"  ; gene_name ACACA ; gene_type protein_coding ; havana_gene "OTTHUMG00000188463.3"  ; havana_transcript "OTTHUMT00000477332.2"  ; hgnc_id "HGNC:84"  ; level 2 ; orig_coord_info "chr17,37330173,37330399,-"  ; protein_id "ENSP00000484948.1"  ; transcript_id "PLXDC1--ACACA^ENST00000612007.1"  ; transcript_name "ACACA-224"  ; transcript_support_level 5 ; transcript_type non_stop_decay
L1 and L2 created: 
PRKCH--MDGA2	HAVANA	gene	5549	39248	.	+	.	FI_gene_label "PRKCH^ENSG00000027075.15"  ; ID "PRKCH--MDGA2^PRKCH^ENSG00000027075.15"  ; ccdsid "CCDS9752.1"  ; exon_id "ENSE00001313856.7"  ; exon_number 1 ; gene_id "PRKCH--MDGA2^PRKCH^ENSG00000027075.15"  ; gene_name PRKCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000152341.7"  ; havana_transcript "OTTHUMT00000276974.3"  ; hgnc_id "HGNC:9403"  ; level 2 ; orig_coord_info "chr14,61322102,61322464,+"  ; protein_id "ENSP00000329127.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "PRKCH--MDGA2^ENST00000332981.10"  ; transcript_name "PRKCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRKCH--MDGA2	HAVANA	mRNA	5549	39248	.	+	.	FI_gene_label "PRKCH^ENSG00000027075.15"  ; ID "PRKCH--MDGA2^ENST00000332981.10"  ; Parent "PRKCH--MDGA2^PRKCH^ENSG00000027075.15"  ; ccdsid "CCDS9752.1"  ; exon_id "ENSE00001313856.7"  ; exon_number 1 ; gene_id "PRKCH--MDGA2^PRKCH^ENSG00000027075.15"  ; gene_name PRKCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000152341.7"  ; havana_transcript "OTTHUMT00000276974.3"  ; hgnc_id "HGNC:9403"  ; level 2 ; orig_coord_info "chr14,61322102,61322464,+"  ; protein_id "ENSP00000329127.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "PRKCH--MDGA2^ENST00000332981.10"  ; transcript_name "PRKCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRKCH--MDGA2	HAVANA	gene	45641	71247	.	+	.	FI_gene_label "MDGA2^ENSG00000139915.21"  ; ID "PRKCH--MDGA2^MDGA2^ENSG00000139915.21"  ; ccdsid "CCDS41948.1"  ; exon_id "ENSE00003481168.1"  ; exon_number 5 ; gene_id "PRKCH--MDGA2^MDGA2^ENSG00000139915.21"  ; gene_name MDGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000029429.13"  ; havana_transcript "OTTHUMT00000277084.2"  ; hgnc_id "HGNC:19835"  ; level 2 ; orig_coord_info "chr14,47131714,47131744,-"  ; protein_id "ENSP00000349925.3"  ; tag basic CCDS ; transcript_id "PRKCH--MDGA2^ENST00000357362.7"  ; transcript_name "MDGA2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PRKCH--MDGA2	HAVANA	mRNA	45641	71247	.	+	.	FI_gene_label "MDGA2^ENSG00000139915.21"  ; ID "PRKCH--MDGA2^ENST00000357362.7"  ; Parent "PRKCH--MDGA2^MDGA2^ENSG00000139915.21"  ; ccdsid "CCDS41948.1"  ; exon_id "ENSE00003481168.1"  ; exon_number 5 ; gene_id "PRKCH--MDGA2^MDGA2^ENSG00000139915.21"  ; gene_name MDGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000029429.13"  ; havana_transcript "OTTHUMT00000277084.2"  ; hgnc_id "HGNC:19835"  ; level 2 ; orig_coord_info "chr14,47131714,47131744,-"  ; protein_id "ENSP00000349925.3"  ; tag basic CCDS ; transcript_id "PRKCH--MDGA2^ENST00000357362.7"  ; transcript_name "MDGA2-201"  ; transcript_support_level 5 ; 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: 
SUFU--HIF1AN	HAVANA	gene	23822	41737	.	+	.	FI_gene_label "HIF1AN^ENSG00000166135.14"  ; ID "SUFU--HIF1AN^HIF1AN^ENSG00000166135.14"  ; ccdsid "CCDS7498.1"  ; exon_id "ENSE00001695622.4"  ; exon_number 1 ; gene_id "SUFU--HIF1AN^HIF1AN^ENSG00000166135.14"  ; gene_name HIF1AN ; gene_type protein_coding ; havana_gene "OTTHUMG00000018911.7"  ; havana_transcript "OTTHUMT00000049865.6"  ; hgnc_id "HGNC:17113"  ; level 2 ; orig_coord_info "chr10,100535959,100536135,+"  ; protein_id "ENSP00000299163.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUFU--HIF1AN^ENST00000299163.7"  ; transcript_name "HIF1AN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SUFU--HIF1AN	HAVANA	mRNA	23822	41737	.	+	.	FI_gene_label "HIF1AN^ENSG00000166135.14"  ; ID "SUFU--HIF1AN^ENST00000299163.7"  ; Parent "SUFU--HIF1AN^HIF1AN^ENSG00000166135.14"  ; ccdsid "CCDS7498.1"  ; exon_id "ENSE00001695622.4"  ; exon_number 1 ; gene_id "SUFU--HIF1AN^HIF1AN^ENSG00000166135.14"  ; gene_name HIF1AN ; gene_type protein_coding ; havana_gene "OTTHUMG00000018911.7"  ; havana_transcript "OTTHUMT00000049865.6"  ; hgnc_id "HGNC:17113"  ; level 2 ; orig_coord_info "chr10,100535959,100536135,+"  ; protein_id "ENSP00000299163.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUFU--HIF1AN^ENST00000299163.7"  ; transcript_name "HIF1AN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUFU--HIF1AN	HAVANA	gene	1036	13929	.	+	.	FI_gene_label "SUFU^ENSG00000107882.12"  ; ID "SUFU--HIF1AN^SUFU^ENSG00000107882.12"  ; ccdsid "CCDS53571.1"  ; exon_id "ENSE00001451217.1"  ; exon_number 1 ; gene_id "SUFU--HIF1AN^SUFU^ENSG00000107882.12"  ; gene_name SUFU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018966.4"  ; havana_transcript "OTTHUMT00000050092.2"  ; hgnc_id "HGNC:16466"  ; level 2 ; orig_coord_info "chr10,102504153,102504334,+"  ; protein_id "ENSP00000358915.2"  ; tag basic CCDS ; transcript_id "SUFU--HIF1AN^ENST00000369899.6"  ; transcript_name "SUFU-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SUFU--HIF1AN	HAVANA	mRNA	1036	13929	.	+	.	FI_gene_label "SUFU^ENSG00000107882.12"  ; ID "SUFU--HIF1AN^ENST00000369899.6"  ; Parent "SUFU--HIF1AN^SUFU^ENSG00000107882.12"  ; ccdsid "CCDS53571.1"  ; exon_id "ENSE00001451217.1"  ; exon_number 1 ; gene_id "SUFU--HIF1AN^SUFU^ENSG00000107882.12"  ; gene_name SUFU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018966.4"  ; havana_transcript "OTTHUMT00000050092.2"  ; hgnc_id "HGNC:16466"  ; level 2 ; orig_coord_info "chr10,102504153,102504334,+"  ; protein_id "ENSP00000358915.2"  ; tag basic CCDS ; transcript_id "SUFU--HIF1AN^ENST00000369899.6"  ; transcript_name "SUFU-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TOGARAM1--PLEKHD1	HAVANA	gene	33880	47639	.	+	.	FI_gene_label "PLEKHD1^ENSG00000175985.10"  ; ID "TOGARAM1--PLEKHD1^PLEKHD1^ENSG00000175985.10"  ; ccdsid "CCDS53903.1"  ; exon_id "ENSE00001721640.3"  ; exon_number 1 ; gene_id "TOGARAM1--PLEKHD1^PLEKHD1^ENSG00000175985.10"  ; gene_name PLEKHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171233.4"  ; havana_transcript "OTTHUMT00000412451.4"  ; hgnc_id "HGNC:20148"  ; level 2 ; orig_coord_info "chr14,69484966,69485114,+"  ; protein_id "ENSP00000317175.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOGARAM1--PLEKHD1^ENST00000322564.9"  ; transcript_name "PLEKHD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TOGARAM1--PLEKHD1	HAVANA	mRNA	33880	47639	.	+	.	FI_gene_label "PLEKHD1^ENSG00000175985.10"  ; ID "TOGARAM1--PLEKHD1^ENST00000322564.9"  ; Parent "TOGARAM1--PLEKHD1^PLEKHD1^ENSG00000175985.10"  ; ccdsid "CCDS53903.1"  ; exon_id "ENSE00001721640.3"  ; exon_number 1 ; gene_id "TOGARAM1--PLEKHD1^PLEKHD1^ENSG00000175985.10"  ; gene_name PLEKHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171233.4"  ; havana_transcript "OTTHUMT00000412451.4"  ; hgnc_id "HGNC:20148"  ; level 2 ; orig_coord_info "chr14,69484966,69485114,+"  ; protein_id "ENSP00000317175.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOGARAM1--PLEKHD1^ENST00000322564.9"  ; transcript_name "PLEKHD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TOGARAM1--PLEKHD1	HAVANA	gene	1001	30843	.	+	.	FI_gene_label "TOGARAM1^ENSG00000198718.13"  ; ID "TOGARAM1--PLEKHD1^TOGARAM1^ENSG00000198718.13"  ; ccdsid "CCDS76676.1"  ; exon_id "ENSE00001491322.2"  ; exon_number 1 ; gene_id "TOGARAM1--PLEKHD1^TOGARAM1^ENSG00000198718.13"  ; gene_name TOGARAM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140264.4"  ; havana_transcript "OTTHUMT00000276792.2"  ; hgnc_id "HGNC:19959"  ; level 2 ; orig_coord_info "chr14,44962422,44964467,+"  ; protein_id "ENSP00000354917.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOGARAM1--PLEKHD1^ENST00000361462.7"  ; transcript_name "TOGARAM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TOGARAM1--PLEKHD1	HAVANA	mRNA	1001	30843	.	+	.	FI_gene_label "TOGARAM1^ENSG00000198718.13"  ; ID "TOGARAM1--PLEKHD1^ENST00000361462.7"  ; Parent "TOGARAM1--PLEKHD1^TOGARAM1^ENSG00000198718.13"  ; ccdsid "CCDS76676.1"  ; exon_id "ENSE00001491322.2"  ; exon_number 1 ; gene_id "TOGARAM1--PLEKHD1^TOGARAM1^ENSG00000198718.13"  ; gene_name TOGARAM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140264.4"  ; havana_transcript "OTTHUMT00000276792.2"  ; hgnc_id "HGNC:19959"  ; level 2 ; orig_coord_info "chr14,44962422,44964467,+"  ; protein_id "ENSP00000354917.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOGARAM1--PLEKHD1^ENST00000361462.7"  ; transcript_name "TOGARAM1-201"  ; 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: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
KIF2A--LINC02229	HAVANA	gene	33402	36057	.	+	.	FI_gene_label "LINC02229^ENSG00000250313.3"  ; ID "KIF2A--LINC02229^LINC02229^ENSG00000250313.3"  ; exon_id "ENSE00002044732.2"  ; exon_number 1 ; gene_id "KIF2A--LINC02229^LINC02229^ENSG00000250313.3"  ; gene_name LINC02229 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162359.3"  ; havana_transcript "OTTHUMT00000368628.3"  ; hgnc_id "HGNC:53098"  ; level 1 ; orig_coord_info "chr5,66511557,66511644,-"  ; tag basic TAGENE exp_conf ; transcript_id "KIF2A--LINC02229^ENST00000508486.3"  ; transcript_name "LINC02229-201"  ; transcript_support_level 3 ; transcript_type lncRNA
KIF2A--LINC02229	HAVANA	RNA	33402	36057	.	+	.	FI_gene_label "LINC02229^ENSG00000250313.3"  ; ID "KIF2A--LINC02229^ENST00000508486.3"  ; Parent "KIF2A--LINC02229^LINC02229^ENSG00000250313.3"  ; exon_id "ENSE00002044732.2"  ; exon_number 1 ; gene_id "KIF2A--LINC02229^LINC02229^ENSG00000250313.3"  ; gene_name LINC02229 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162359.3"  ; havana_transcript "OTTHUMT00000368628.3"  ; hgnc_id "HGNC:53098"  ; level 1 ; orig_coord_info "chr5,66511557,66511644,-"  ; tag basic TAGENE exp_conf ; transcript_id "KIF2A--LINC02229^ENST00000508486.3"  ; transcript_name "LINC02229-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
MAGI3--AL357055.2	HAVANA	gene	34110	34543	.	+	.	FI_gene_label "AL357055.2^ENSG00000236887.1"  ; ID "MAGI3--AL357055.2^AL357055.2^ENSG00000236887.1"  ; exon_id "ENSE00001601740.1"  ; exon_number 1 ; gene_id "MAGI3--AL357055.2^AL357055.2^ENSG00000236887.1"  ; gene_name "AL357055.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000012185.1"  ; havana_transcript "OTTHUMT00000033695.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,113198825,113199258,+"  ; tag pseudo_consens basic ; transcript_id "MAGI3--AL357055.2^ENST00000412567.1"  ; transcript_name "AL357055.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MAGI3--AL357055.2	HAVANA	RNA	34110	34543	.	+	.	FI_gene_label "AL357055.2^ENSG00000236887.1"  ; ID "MAGI3--AL357055.2^ENST00000412567.1"  ; Parent "MAGI3--AL357055.2^AL357055.2^ENSG00000236887.1"  ; exon_id "ENSE00001601740.1"  ; exon_number 1 ; gene_id "MAGI3--AL357055.2^AL357055.2^ENSG00000236887.1"  ; gene_name "AL357055.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000012185.1"  ; havana_transcript "OTTHUMT00000033695.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,113198825,113199258,+"  ; tag pseudo_consens basic ; transcript_id "MAGI3--AL357055.2^ENST00000412567.1"  ; transcript_name "AL357055.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
370 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 ------------------------------
694 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 1 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 31 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