.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (RGB_RLP_lowDV_1ststrand_42C_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/d8ca3046496d9e8064a98f0da2ba18/.command.log
Size: 63.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (RGB_RLP_lowDV_1ststrand_42C_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/0372e0cd418f9c24844f1a603fc5c6/fi_workdir/RGB_RLP_lowDV_1ststrand_42C_2.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/d8ca3046496d9e8064a98f0da2ba18/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/d8ca3046496d9e8064a98f0da2ba18/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
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                          ------ 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: 4097
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4097
=> 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:4097
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
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: 
ASPH--LINC02842	HAVANA	gene	1045	33265	.	+	.	FI_gene_label "ASPH^ENSG00000198363.18"  ; ID "ASPH--LINC02842^ASPH^ENSG00000198363.18"  ; ccdsid "CCDS43742.1"  ; exon_id "ENSE00002130497.1"  ; exon_number 1 ; gene_id "ASPH--LINC02842^ASPH^ENSG00000198363.18"  ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13"  ; havana_transcript "OTTHUMT00000378511.2"  ; hgnc_id "HGNC:757"  ; level 2 ; orig_coord_info "chr8,61714269,61714371,-"  ; protein_id "ENSP00000348841.5"  ; tag basic CCDS ; transcript_id "ASPH--LINC02842^ENST00000356457.9"  ; transcript_name "ASPH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ASPH--LINC02842	HAVANA	mRNA	1045	33265	.	+	.	FI_gene_label "ASPH^ENSG00000198363.18"  ; ID "ASPH--LINC02842^ENST00000356457.9"  ; Parent "ASPH--LINC02842^ASPH^ENSG00000198363.18"  ; ccdsid "CCDS43742.1"  ; exon_id "ENSE00002130497.1"  ; exon_number 1 ; gene_id "ASPH--LINC02842^ASPH^ENSG00000198363.18"  ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13"  ; havana_transcript "OTTHUMT00000378511.2"  ; hgnc_id "HGNC:757"  ; level 2 ; orig_coord_info "chr8,61714269,61714371,-"  ; protein_id "ENSP00000348841.5"  ; tag basic CCDS ; transcript_id "ASPH--LINC02842^ENST00000356457.9"  ; transcript_name "ASPH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATP11A--AL359649.1	ENSEMBL	gene	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--AL359649.1^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--AL359649.1	ENSEMBL	mRNA	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--AL359649.1^ENST00000375630.6"  ; Parent "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--AL359649.1^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ATP11A--LINC00354	ENSEMBL	gene	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--LINC00354^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--LINC00354^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--LINC00354^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--LINC00354	ENSEMBL	mRNA	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--LINC00354^ENST00000375630.6"  ; Parent "ATP11A--LINC00354^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--LINC00354^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--LINC00354^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ATP11A--MCF2L	HAVANA	gene	94647	104280	.	+	.	FI_gene_label "MCF2L^ENSG00000126217.21"  ; ID "ATP11A--MCF2L^MCF2L^ENSG00000126217.21"  ; exon_id "ENSE00001643016.1"  ; exon_number 1 ; gene_id "ATP11A--MCF2L^MCF2L^ENSG00000126217.21"  ; gene_name MCF2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000017377.18"  ; havana_transcript "OTTHUMT00000339076.1"  ; hgnc_id "HGNC:14576"  ; level 2 ; orig_coord_info "chr13,113087350,113087456,+"  ; protein_id "ENSP00000261963.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ATP11A--MCF2L^ENST00000261963.11"  ; transcript_name "MCF2L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP11A--MCF2L	HAVANA	mRNA	94647	104280	.	+	.	FI_gene_label "MCF2L^ENSG00000126217.21"  ; ID "ATP11A--MCF2L^ENST00000261963.11"  ; Parent "ATP11A--MCF2L^MCF2L^ENSG00000126217.21"  ; exon_id "ENSE00001643016.1"  ; exon_number 1 ; gene_id "ATP11A--MCF2L^MCF2L^ENSG00000126217.21"  ; gene_name MCF2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000017377.18"  ; havana_transcript "OTTHUMT00000339076.1"  ; hgnc_id "HGNC:14576"  ; level 2 ; orig_coord_info "chr13,113087350,113087456,+"  ; protein_id "ENSP00000261963.7"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ATP11A--MCF2L^ENST00000261963.11"  ; transcript_name "MCF2L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATP11A--MCF2L	ENSEMBL	gene	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--MCF2L^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--MCF2L^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--MCF2L^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--MCF2L	ENSEMBL	mRNA	1001	44637	.	+	.	FI_gene_label "ATP11A^ENSG00000068650.18"  ; ID "ATP11A--MCF2L^ENST00000375630.6"  ; Parent "ATP11A--MCF2L^ATP11A^ENSG00000068650.18"  ; exon_id "ENSE00001740661.1"  ; exon_number 1 ; gene_id "ATP11A--MCF2L^ATP11A^ENSG00000068650.18"  ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10"  ; hgnc_id "HGNC:13552"  ; level 3 ; orig_coord_info "chr13,112690417,112690455,+"  ; protein_id "ENSP00000364781.2"  ; tag basic appris_alternative_2 ; transcript_id "ATP11A--MCF2L^ENST00000375630.6"  ; transcript_name "ATP11A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CAB39--ARFIP1	HAVANA	gene	1001	15013	.	+	.	FI_gene_label "CAB39^ENSG00000135932.11"  ; ID "CAB39--ARFIP1^CAB39^ENSG00000135932.11"  ; ccdsid "CCDS2478.1"  ; exon_id "ENSE00001174710.1"  ; exon_number 2 ; gene_id "CAB39--ARFIP1^CAB39^ENSG00000135932.11"  ; gene_name CAB39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133220.4"  ; havana_transcript "OTTHUMT00000256955.3"  ; hgnc_id "HGNC:20292"  ; level 2 ; orig_coord_info "chr2,230760002,230760115,+"  ; protein_id "ENSP00000258418.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000258418.10"  ; transcript_name "CAB39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CAB39--ARFIP1	HAVANA	mRNA	1001	15013	.	+	.	FI_gene_label "CAB39^ENSG00000135932.11"  ; ID "CAB39--ARFIP1^ENST00000258418.10"  ; Parent "CAB39--ARFIP1^CAB39^ENSG00000135932.11"  ; ccdsid "CCDS2478.1"  ; exon_id "ENSE00001174710.1"  ; exon_number 2 ; gene_id "CAB39--ARFIP1^CAB39^ENSG00000135932.11"  ; gene_name CAB39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133220.4"  ; havana_transcript "OTTHUMT00000256955.3"  ; hgnc_id "HGNC:20292"  ; level 2 ; orig_coord_info "chr2,230760002,230760115,+"  ; protein_id "ENSP00000258418.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000258418.10"  ; transcript_name "CAB39-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CAB39--ARFIP1	HAVANA	gene	18031	33854	.	+	.	FI_gene_label "ARFIP1^ENSG00000164144.16"  ; ID "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16"  ; ccdsid "CCDS34080.1"  ; exon_id "ENSE00003895784.1"  ; exon_number 2 ; gene_id "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16"  ; gene_name ARFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161468.3"  ; havana_transcript "OTTHUMT00000504379.2"  ; hgnc_id "HGNC:21496"  ; level 2 ; orig_coord_info "chr4,152829634,152829726,+"  ; protein_id "ENSP00000296557.4"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_4 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000353617.7"  ; transcript_name "ARFIP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CAB39--ARFIP1	HAVANA	mRNA	18031	33854	.	+	.	FI_gene_label "ARFIP1^ENSG00000164144.16"  ; ID "CAB39--ARFIP1^ENST00000353617.7"  ; Parent "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16"  ; ccdsid "CCDS34080.1"  ; exon_id "ENSE00003895784.1"  ; exon_number 2 ; gene_id "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16"  ; gene_name ARFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161468.3"  ; havana_transcript "OTTHUMT00000504379.2"  ; hgnc_id "HGNC:21496"  ; level 2 ; orig_coord_info "chr4,152829634,152829726,+"  ; protein_id "ENSP00000296557.4"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_4 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000353617.7"  ; transcript_name "ARFIP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
LHFPL5--CLPSL1	HAVANA	gene	3397	10913	.	+	.	FI_gene_label "LHFPL5^ENSG00000197753.11"  ; ID "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; ccdsid "CCDS4812.1"  ; exon_id "ENSE00003831190.2"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; gene_name LHFPL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014584.6"  ; havana_transcript "OTTHUMT00000040323.4"  ; hgnc_id "HGNC:21253"  ; level 2 ; orig_coord_info "chr6,35805671,35806082,+"  ; protein_id "ENSP00000353346.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000360215.3"  ; transcript_name "LHFPL5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LHFPL5--CLPSL1	HAVANA	mRNA	3397	10913	.	+	.	FI_gene_label "LHFPL5^ENSG00000197753.11"  ; ID "LHFPL5--CLPSL1^ENST00000360215.3"  ; Parent "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; ccdsid "CCDS4812.1"  ; exon_id "ENSE00003831190.2"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^LHFPL5^ENSG00000197753.11"  ; gene_name LHFPL5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014584.6"  ; havana_transcript "OTTHUMT00000040323.4"  ; hgnc_id "HGNC:21253"  ; level 2 ; orig_coord_info "chr6,35805671,35806082,+"  ; protein_id "ENSP00000353346.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000360215.3"  ; transcript_name "LHFPL5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LHFPL5--CLPSL1	HAVANA	gene	20636	22979	.	+	.	FI_gene_label "CLPSL1^ENSG00000204140.10"  ; ID "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; ccdsid "CCDS43456.1"  ; exon_id "ENSE00001569343.4"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; gene_name CLPSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014582.3"  ; havana_transcript "OTTHUMT00000040317.3"  ; hgnc_id "HGNC:21251"  ; level 2 ; orig_coord_info "chr6,35781111,35781209,+"  ; protein_id "ENSP00000362968.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000373861.6"  ; transcript_name "CLPSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LHFPL5--CLPSL1	HAVANA	mRNA	20636	22979	.	+	.	FI_gene_label "CLPSL1^ENSG00000204140.10"  ; ID "LHFPL5--CLPSL1^ENST00000373861.6"  ; Parent "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; ccdsid "CCDS43456.1"  ; exon_id "ENSE00001569343.4"  ; exon_number 1 ; gene_id "LHFPL5--CLPSL1^CLPSL1^ENSG00000204140.10"  ; gene_name CLPSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014582.3"  ; havana_transcript "OTTHUMT00000040317.3"  ; hgnc_id "HGNC:21251"  ; level 2 ; orig_coord_info "chr6,35781111,35781209,+"  ; protein_id "ENSP00000362968.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LHFPL5--CLPSL1^ENST00000373861.6"  ; transcript_name "CLPSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MACROD1--AC128677.1	HAVANA	gene	1001	10888	.	+	.	FI_gene_label "MACROD1^ENSG00000133315.12"  ; ID "MACROD1--AC128677.1^MACROD1^ENSG00000133315.12"  ; ccdsid "CCDS8056.1"  ; exon_id "ENSE00002299420.2"  ; exon_number 1 ; gene_id "MACROD1--AC128677.1^MACROD1^ENSG00000133315.12"  ; gene_name MACROD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167843.3"  ; havana_transcript "OTTHUMT00000396570.2"  ; hgnc_id "HGNC:29598"  ; level 2 ; orig_coord_info "chr11,64165697,64165994,-"  ; protein_id "ENSP00000255681.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MACROD1--AC128677.1^ENST00000255681.7"  ; transcript_name "MACROD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MACROD1--AC128677.1	HAVANA	mRNA	1001	10888	.	+	.	FI_gene_label "MACROD1^ENSG00000133315.12"  ; ID "MACROD1--AC128677.1^ENST00000255681.7"  ; Parent "MACROD1--AC128677.1^MACROD1^ENSG00000133315.12"  ; ccdsid "CCDS8056.1"  ; exon_id "ENSE00002299420.2"  ; exon_number 1 ; gene_id "MACROD1--AC128677.1^MACROD1^ENSG00000133315.12"  ; gene_name MACROD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167843.3"  ; havana_transcript "OTTHUMT00000396570.2"  ; hgnc_id "HGNC:29598"  ; level 2 ; orig_coord_info "chr11,64165697,64165994,-"  ; protein_id "ENSP00000255681.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MACROD1--AC128677.1^ENST00000255681.7"  ; transcript_name "MACROD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MACROD1--CHEK2P3	HAVANA	gene	1001	10888	.	+	.	FI_gene_label "MACROD1^ENSG00000133315.12"  ; ID "MACROD1--CHEK2P3^MACROD1^ENSG00000133315.12"  ; ccdsid "CCDS8056.1"  ; exon_id "ENSE00002299420.2"  ; exon_number 1 ; gene_id "MACROD1--CHEK2P3^MACROD1^ENSG00000133315.12"  ; gene_name MACROD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167843.3"  ; havana_transcript "OTTHUMT00000396570.2"  ; hgnc_id "HGNC:29598"  ; level 2 ; orig_coord_info "chr11,64165697,64165994,-"  ; protein_id "ENSP00000255681.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MACROD1--CHEK2P3^ENST00000255681.7"  ; transcript_name "MACROD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MACROD1--CHEK2P3	HAVANA	mRNA	1001	10888	.	+	.	FI_gene_label "MACROD1^ENSG00000133315.12"  ; ID "MACROD1--CHEK2P3^ENST00000255681.7"  ; Parent "MACROD1--CHEK2P3^MACROD1^ENSG00000133315.12"  ; ccdsid "CCDS8056.1"  ; exon_id "ENSE00002299420.2"  ; exon_number 1 ; gene_id "MACROD1--CHEK2P3^MACROD1^ENSG00000133315.12"  ; gene_name MACROD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167843.3"  ; havana_transcript "OTTHUMT00000396570.2"  ; hgnc_id "HGNC:29598"  ; level 2 ; orig_coord_info "chr11,64165697,64165994,-"  ; protein_id "ENSP00000255681.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MACROD1--CHEK2P3^ENST00000255681.7"  ; transcript_name "MACROD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MCU--TSPAN15	HAVANA	gene	1013	19124	.	+	.	FI_gene_label "MCU^ENSG00000156026.14"  ; ID "MCU--TSPAN15^MCU^ENSG00000156026.14"  ; ccdsid "CCDS59218.1"  ; exon_id "ENSE00001855279.1"  ; exon_number 1 ; gene_id "MCU--TSPAN15^MCU^ENSG00000156026.14"  ; gene_name MCU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018443.3"  ; havana_transcript "OTTHUMT00000048593.1"  ; hgnc_id "HGNC:23526"  ; level 2 ; orig_coord_info "chr10,72692152,72692301,+"  ; protein_id "ENSP00000349680.6"  ; tag basic CCDS ; transcript_id "MCU--TSPAN15^ENST00000357157.10"  ; transcript_name "MCU-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MCU--TSPAN15	HAVANA	mRNA	1013	19124	.	+	.	FI_gene_label "MCU^ENSG00000156026.14"  ; ID "MCU--TSPAN15^ENST00000357157.10"  ; Parent "MCU--TSPAN15^MCU^ENSG00000156026.14"  ; ccdsid "CCDS59218.1"  ; exon_id "ENSE00001855279.1"  ; exon_number 1 ; gene_id "MCU--TSPAN15^MCU^ENSG00000156026.14"  ; gene_name MCU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018443.3"  ; havana_transcript "OTTHUMT00000048593.1"  ; hgnc_id "HGNC:23526"  ; level 2 ; orig_coord_info "chr10,72692152,72692301,+"  ; protein_id "ENSP00000349680.6"  ; tag basic CCDS ; transcript_id "MCU--TSPAN15^ENST00000357157.10"  ; transcript_name "MCU-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MCU--TSPAN15	HAVANA	gene	22125	31433	.	+	.	FI_gene_label "TSPAN15^ENSG00000099282.10"  ; ID "MCU--TSPAN15^TSPAN15^ENSG00000099282.10"  ; ccdsid "CCDS7294.1"  ; exon_id "ENSE00001886704.2"  ; exon_number 1 ; gene_id "MCU--TSPAN15^TSPAN15^ENSG00000099282.10"  ; gene_name TSPAN15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018381.4"  ; havana_transcript "OTTHUMT00000048444.2"  ; hgnc_id "HGNC:23298"  ; level 2 ; orig_coord_info "chr10,69451595,69451690,+"  ; protein_id "ENSP00000362387.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MCU--TSPAN15^ENST00000373290.7"  ; transcript_name "TSPAN15-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MCU--TSPAN15	HAVANA	mRNA	22125	31433	.	+	.	FI_gene_label "TSPAN15^ENSG00000099282.10"  ; ID "MCU--TSPAN15^ENST00000373290.7"  ; Parent "MCU--TSPAN15^TSPAN15^ENSG00000099282.10"  ; ccdsid "CCDS7294.1"  ; exon_id "ENSE00001886704.2"  ; exon_number 1 ; gene_id "MCU--TSPAN15^TSPAN15^ENSG00000099282.10"  ; gene_name TSPAN15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018381.4"  ; havana_transcript "OTTHUMT00000048444.2"  ; hgnc_id "HGNC:23298"  ; level 2 ; orig_coord_info "chr10,69451595,69451690,+"  ; protein_id "ENSP00000362387.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MCU--TSPAN15^ENST00000373290.7"  ; transcript_name "TSPAN15-201"  ; 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: 
PCDHA6--PCDHA13	HAVANA	gene	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHA13	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^ENST00000378126.4"  ; Parent "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
SMIM14--CECR2	ENSEMBL	gene	18633	42307	.	+	.	FI_gene_label "CECR2^ENSG00000099954.18"  ; ID "SMIM14--CECR2^CECR2^ENSG00000099954.18"  ; exon_id "ENSE00003472152.1"  ; exon_number 4 ; gene_id "SMIM14--CECR2^CECR2^ENSG00000099954.18"  ; gene_name CECR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150072.9"  ; hgnc_id "HGNC:1840"  ; level 3 ; orig_coord_info "chr22,17499494,17499549,+"  ; protein_id "ENSP00000262608.10"  ; tag basic appris_alternative_2 ; transcript_id "SMIM14--CECR2^ENST00000262608.12"  ; transcript_name "CECR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SMIM14--CECR2	ENSEMBL	mRNA	18633	42307	.	+	.	FI_gene_label "CECR2^ENSG00000099954.18"  ; ID "SMIM14--CECR2^ENST00000262608.12"  ; Parent "SMIM14--CECR2^CECR2^ENSG00000099954.18"  ; exon_id "ENSE00003472152.1"  ; exon_number 4 ; gene_id "SMIM14--CECR2^CECR2^ENSG00000099954.18"  ; gene_name CECR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150072.9"  ; hgnc_id "HGNC:1840"  ; level 3 ; orig_coord_info "chr22,17499494,17499549,+"  ; protein_id "ENSP00000262608.10"  ; tag basic appris_alternative_2 ; transcript_id "SMIM14--CECR2^ENST00000262608.12"  ; transcript_name "CECR2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SMIM14--CECR2	HAVANA	gene	1038	14035	.	+	.	FI_gene_label "SMIM14^ENSG00000163683.12"  ; ID "SMIM14--CECR2^SMIM14^ENSG00000163683.12"  ; ccdsid "CCDS3456.1"  ; exon_id "ENSE00001123004.1"  ; exon_number 2 ; gene_id "SMIM14--CECR2^SMIM14^ENSG00000163683.12"  ; gene_name SMIM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128581.8"  ; havana_transcript "OTTHUMT00000250434.5"  ; hgnc_id "HGNC:27321"  ; level 1 ; orig_coord_info "chr4,39605071,39605145,-"  ; protein_id "ENSP00000295958.4"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "SMIM14--CECR2^ENST00000295958.10"  ; transcript_name "SMIM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SMIM14--CECR2	HAVANA	mRNA	1038	14035	.	+	.	FI_gene_label "SMIM14^ENSG00000163683.12"  ; ID "SMIM14--CECR2^ENST00000295958.10"  ; Parent "SMIM14--CECR2^SMIM14^ENSG00000163683.12"  ; ccdsid "CCDS3456.1"  ; exon_id "ENSE00001123004.1"  ; exon_number 2 ; gene_id "SMIM14--CECR2^SMIM14^ENSG00000163683.12"  ; gene_name SMIM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128581.8"  ; havana_transcript "OTTHUMT00000250434.5"  ; hgnc_id "HGNC:27321"  ; level 1 ; orig_coord_info "chr4,39605071,39605145,-"  ; protein_id "ENSP00000295958.4"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "SMIM14--CECR2^ENST00000295958.10"  ; transcript_name "SMIM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SREBF1--NCOR1	ENSEMBL	gene	1001	12895	.	+	.	FI_gene_label "SREBF1^ENSG00000072310.17"  ; ID "SREBF1--NCOR1^SREBF1^ENSG00000072310.17"  ; ccdsid "CCDS11189.1"  ; exon_id "ENSE00003873048.1"  ; exon_number 1 ; gene_id "SREBF1--NCOR1^SREBF1^ENSG00000072310.17"  ; gene_name SREBF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059313.9"  ; hgnc_id "HGNC:11289"  ; level 3 ; orig_coord_info "chr17,17836727,17836817,-"  ; protein_id "ENSP00000261646.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000261646.10"  ; transcript_name "SREBF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SREBF1--NCOR1	ENSEMBL	mRNA	1001	12895	.	+	.	FI_gene_label "SREBF1^ENSG00000072310.17"  ; ID "SREBF1--NCOR1^ENST00000261646.10"  ; Parent "SREBF1--NCOR1^SREBF1^ENSG00000072310.17"  ; ccdsid "CCDS11189.1"  ; exon_id "ENSE00003873048.1"  ; exon_number 1 ; gene_id "SREBF1--NCOR1^SREBF1^ENSG00000072310.17"  ; gene_name SREBF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059313.9"  ; hgnc_id "HGNC:11289"  ; level 3 ; orig_coord_info "chr17,17836727,17836817,-"  ; protein_id "ENSP00000261646.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000261646.10"  ; transcript_name "SREBF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SREBF1--NCOR1	HAVANA	gene	18731	74680	.	+	.	FI_gene_label "NCOR1^ENSG00000141027.21"  ; ID "SREBF1--NCOR1^NCOR1^ENSG00000141027.21"  ; ccdsid "CCDS11175.1"  ; exon_id "ENSE00003656730.1"  ; exon_number 2 ; gene_id "SREBF1--NCOR1^NCOR1^ENSG00000141027.21"  ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12"  ; havana_transcript "OTTHUMT00000131751.6"  ; hgnc_id "HGNC:7672"  ; level 2 ; orig_coord_info "chr17,16194462,16194569,-"  ; protein_id "ENSP00000268712.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000268712.8"  ; transcript_name "NCOR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SREBF1--NCOR1	HAVANA	mRNA	18731	74680	.	+	.	FI_gene_label "NCOR1^ENSG00000141027.21"  ; ID "SREBF1--NCOR1^ENST00000268712.8"  ; Parent "SREBF1--NCOR1^NCOR1^ENSG00000141027.21"  ; ccdsid "CCDS11175.1"  ; exon_id "ENSE00003656730.1"  ; exon_number 2 ; gene_id "SREBF1--NCOR1^NCOR1^ENSG00000141027.21"  ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12"  ; havana_transcript "OTTHUMT00000131751.6"  ; hgnc_id "HGNC:7672"  ; level 2 ; orig_coord_info "chr17,16194462,16194569,-"  ; protein_id "ENSP00000268712.2"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000268712.8"  ; transcript_name "NCOR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRGAP2B--SEC22B3P	HAVANA	gene	1001	17112	.	+	.	FI_gene_label "SRGAP2B^ENSG00000196369.11"  ; ID "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11"  ; exon_id "ENSE00001848190.1"  ; exon_number 2 ; gene_id "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11"  ; gene_name SRGAP2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000041442.8"  ; havana_transcript "OTTHUMT00000099258.6"  ; hgnc_id "HGNC:35237"  ; level 2 ; orig_coord_info "chr1,145092835,145092901,-"  ; protein_id "ENSP00000477776.1"  ; tag basic appris_alternative_2 ; transcript_id "SRGAP2B--SEC22B3P^ENST00000612199.4"  ; transcript_name "SRGAP2B-204"  ; transcript_support_level 1 ; transcript_type protein_coding
SRGAP2B--SEC22B3P	HAVANA	mRNA	1001	17112	.	+	.	FI_gene_label "SRGAP2B^ENSG00000196369.11"  ; ID "SRGAP2B--SEC22B3P^ENST00000612199.4"  ; Parent "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11"  ; exon_id "ENSE00001848190.1"  ; exon_number 2 ; gene_id "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11"  ; gene_name SRGAP2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000041442.8"  ; havana_transcript "OTTHUMT00000099258.6"  ; hgnc_id "HGNC:35237"  ; level 2 ; orig_coord_info "chr1,145092835,145092901,-"  ; protein_id "ENSP00000477776.1"  ; tag basic appris_alternative_2 ; transcript_id "SRGAP2B--SEC22B3P^ENST00000612199.4"  ; transcript_name "SRGAP2B-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUZ12P1--AFMID	HAVANA	gene	20691	30890	.	+	.	FI_gene_label "AFMID^ENSG00000183077.15"  ; ID "SUZ12P1--AFMID^AFMID^ENSG00000183077.15"  ; ccdsid "CCDS45801.1"  ; exon_id "ENSE00003668375.1"  ; exon_number 1 ; gene_id "SUZ12P1--AFMID^AFMID^ENSG00000183077.15"  ; gene_name AFMID ; gene_type protein_coding ; havana_gene "OTTHUMG00000153957.4"  ; havana_transcript "OTTHUMT00000333203.1"  ; hgnc_id "HGNC:20910"  ; level 2 ; orig_coord_info "chr17,78187371,78187433,+"  ; protein_id "ENSP00000328938.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUZ12P1--AFMID^ENST00000327898.9"  ; transcript_name "AFMID-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SUZ12P1--AFMID	HAVANA	mRNA	20691	30890	.	+	.	FI_gene_label "AFMID^ENSG00000183077.15"  ; ID "SUZ12P1--AFMID^ENST00000327898.9"  ; Parent "SUZ12P1--AFMID^AFMID^ENSG00000183077.15"  ; ccdsid "CCDS45801.1"  ; exon_id "ENSE00003668375.1"  ; exon_number 1 ; gene_id "SUZ12P1--AFMID^AFMID^ENSG00000183077.15"  ; gene_name AFMID ; gene_type protein_coding ; havana_gene "OTTHUMG00000153957.4"  ; havana_transcript "OTTHUMT00000333203.1"  ; hgnc_id "HGNC:20910"  ; level 2 ; orig_coord_info "chr17,78187371,78187433,+"  ; protein_id "ENSP00000328938.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUZ12P1--AFMID^ENST00000327898.9"  ; transcript_name "AFMID-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: 
ASPH--LINC02842	HAVANA	gene	58793	62237	.	+	.	FI_gene_label "LINC02842^ENSG00000254119.5"  ; ID "ASPH--LINC02842^LINC02842^ENSG00000254119.5"  ; exon_id "ENSE00002098747.1"  ; exon_number 1 ; gene_id "ASPH--LINC02842^LINC02842^ENSG00000254119.5"  ; gene_name LINC02842 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164339.3"  ; havana_transcript "OTTHUMT00000378340.1"  ; hgnc_id "HGNC:54378"  ; level 2 ; orig_coord_info "chr8,61834917,61834996,+"  ; tag basic ; transcript_id "ASPH--LINC02842^ENST00000517953.5"  ; transcript_name "LINC02842-201"  ; transcript_support_level 3 ; transcript_type lncRNA
ASPH--LINC02842	HAVANA	RNA	58793	62237	.	+	.	FI_gene_label "LINC02842^ENSG00000254119.5"  ; ID "ASPH--LINC02842^ENST00000517953.5"  ; Parent "ASPH--LINC02842^LINC02842^ENSG00000254119.5"  ; exon_id "ENSE00002098747.1"  ; exon_number 1 ; gene_id "ASPH--LINC02842^LINC02842^ENSG00000254119.5"  ; gene_name LINC02842 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164339.3"  ; havana_transcript "OTTHUMT00000378340.1"  ; hgnc_id "HGNC:54378"  ; level 2 ; orig_coord_info "chr8,61834917,61834996,+"  ; tag basic ; transcript_id "ASPH--LINC02842^ENST00000517953.5"  ; transcript_name "LINC02842-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
ATP11A--AL359649.1	HAVANA	gene	47728	52767	.	+	.	FI_gene_label "AL359649.1^ENSG00000204398.5"  ; ID "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5"  ; exon_id "ENSE00001468102.1"  ; exon_number 1 ; gene_id "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5"  ; gene_name "AL359649.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017360.3"  ; havana_transcript "OTTHUMT00000045814.2"  ; level 2 ; orig_coord_info "chr13,111588291,111588344,+"  ; tag basic ; transcript_id "ATP11A--AL359649.1^ENST00000375713.1"  ; transcript_name "AL359649.1-202"  ; transcript_support_level 5 ; transcript_type lncRNA
ATP11A--AL359649.1	HAVANA	RNA	47728	52767	.	+	.	FI_gene_label "AL359649.1^ENSG00000204398.5"  ; ID "ATP11A--AL359649.1^ENST00000375713.1"  ; Parent "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5"  ; exon_id "ENSE00001468102.1"  ; exon_number 1 ; gene_id "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5"  ; gene_name "AL359649.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017360.3"  ; havana_transcript "OTTHUMT00000045814.2"  ; level 2 ; orig_coord_info "chr13,111588291,111588344,+"  ; tag basic ; transcript_id "ATP11A--AL359649.1^ENST00000375713.1"  ; transcript_name "AL359649.1-202"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
ATP11A--LINC00354	HAVANA	gene	51573	52521	.	+	.	FI_gene_label "LINC00354^ENSG00000226903.2"  ; ID "ATP11A--LINC00354^LINC00354^ENSG00000226903.2"  ; exon_id "ENSE00001724879.1"  ; exon_number 1 ; gene_id "ATP11A--LINC00354^LINC00354^ENSG00000226903.2"  ; gene_name LINC00354 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017361.10"  ; havana_transcript "OTTHUMT00000045815.1"  ; hgnc_id "HGNC:42672"  ; level 2 ; orig_coord_info "chr13,111899988,111900083,+"  ; transcript_id "ATP11A--LINC00354^ENST00000412119.1"  ; transcript_name "LINC00354-201"  ; transcript_support_level 5 ; transcript_type lncRNA
ATP11A--LINC00354	HAVANA	RNA	51573	52521	.	+	.	FI_gene_label "LINC00354^ENSG00000226903.2"  ; ID "ATP11A--LINC00354^ENST00000412119.1"  ; Parent "ATP11A--LINC00354^LINC00354^ENSG00000226903.2"  ; exon_id "ENSE00001724879.1"  ; exon_number 1 ; gene_id "ATP11A--LINC00354^LINC00354^ENSG00000226903.2"  ; gene_name LINC00354 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017361.10"  ; havana_transcript "OTTHUMT00000045815.1"  ; hgnc_id "HGNC:42672"  ; level 2 ; orig_coord_info "chr13,111899988,111900083,+"  ; transcript_id "ATP11A--LINC00354^ENST00000412119.1"  ; transcript_name "LINC00354-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
MACROD1--AC128677.1	HAVANA	gene	13889	14330	.	+	.	FI_gene_label "AC128677.1^ENSG00000235147.1"  ; ID "MACROD1--AC128677.1^AC128677.1^ENSG00000235147.1"  ; exon_id "ENSE00001686012.1"  ; exon_number 1 ; gene_id "MACROD1--AC128677.1^AC128677.1^ENSG00000235147.1"  ; gene_name "AC128677.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000155084.1"  ; havana_transcript "OTTHUMT00000338376.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr2,92006680,92007121,-"  ; tag basic ; transcript_id "MACROD1--AC128677.1^ENST00000436016.1"  ; transcript_name "AC128677.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MACROD1--AC128677.1	HAVANA	RNA	13889	14330	.	+	.	FI_gene_label "AC128677.1^ENSG00000235147.1"  ; ID "MACROD1--AC128677.1^ENST00000436016.1"  ; Parent "MACROD1--AC128677.1^AC128677.1^ENSG00000235147.1"  ; exon_id "ENSE00001686012.1"  ; exon_number 1 ; gene_id "MACROD1--AC128677.1^AC128677.1^ENSG00000235147.1"  ; gene_name "AC128677.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000155084.1"  ; havana_transcript "OTTHUMT00000338376.1"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr2,92006680,92007121,-"  ; tag basic ; transcript_id "MACROD1--AC128677.1^ENST00000436016.1"  ; transcript_name "AC128677.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
MACROD1--CHEK2P3	HAVANA	gene	13889	16136	.	+	.	FI_gene_label "CHEK2P3^ENSG00000234898.1"  ; ID "MACROD1--CHEK2P3^CHEK2P3^ENSG00000234898.1"  ; exon_id "ENSE00001592921.1"  ; exon_number 1 ; gene_id "MACROD1--CHEK2P3^CHEK2P3^ENSG00000234898.1"  ; gene_name CHEK2P3 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155087.1"  ; havana_transcript "OTTHUMT00000338379.1"  ; hgnc_id "HGNC:43579"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr2,91957436,91957524,+"  ; tag basic ; transcript_id "MACROD1--CHEK2P3^ENST00000416118.1"  ; transcript_name "CHEK2P3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
MACROD1--CHEK2P3	HAVANA	RNA	13889	16136	.	+	.	FI_gene_label "CHEK2P3^ENSG00000234898.1"  ; ID "MACROD1--CHEK2P3^ENST00000416118.1"  ; Parent "MACROD1--CHEK2P3^CHEK2P3^ENSG00000234898.1"  ; exon_id "ENSE00001592921.1"  ; exon_number 1 ; gene_id "MACROD1--CHEK2P3^CHEK2P3^ENSG00000234898.1"  ; gene_name CHEK2P3 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155087.1"  ; havana_transcript "OTTHUMT00000338379.1"  ; hgnc_id "HGNC:43579"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr2,91957436,91957524,+"  ; tag basic ; transcript_id "MACROD1--CHEK2P3^ENST00000416118.1"  ; transcript_name "CHEK2P3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
SRGAP2B--SEC22B3P	HAVANA	gene	20113	23688	.	+	.	FI_gene_label "SEC22B3P^ENSG00000275140.1"  ; ID "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; exon_id "ENSE00003747856.1"  ; exon_number 1 ; gene_id "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1"  ; havana_transcript "OTTHUMT00000477871.1"  ; hgnc_id "HGNC:53891"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr1,148784482,148784594,-"  ; tag basic ; transcript_id "SRGAP2B--SEC22B3P^ENST00000616023.1"  ; transcript_name "SEC22B3P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
SRGAP2B--SEC22B3P	HAVANA	RNA	20113	23688	.	+	.	FI_gene_label "SEC22B3P^ENSG00000275140.1"  ; ID "SRGAP2B--SEC22B3P^ENST00000616023.1"  ; Parent "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; exon_id "ENSE00003747856.1"  ; exon_number 1 ; gene_id "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1"  ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1"  ; havana_transcript "OTTHUMT00000477871.1"  ; hgnc_id "HGNC:53891"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr1,148784482,148784594,-"  ; tag basic ; transcript_id "SRGAP2B--SEC22B3P^ENST00000616023.1"  ; transcript_name "SEC22B3P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
SUZ12P1--AFMID	HAVANA	gene	2514	7684	.	+	.	FI_gene_label "SUZ12P1^ENSG00000264538.6"  ; ID "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6"  ; exon_id "ENSE00002690561.1"  ; exon_number 1 ; gene_id "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6"  ; gene_name SUZ12P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000178989.2"  ; havana_transcript "OTTHUMT00000444258.1"  ; hgnc_id "HGNC:32421"  ; level 2 ; orig_coord_info "chr17,30731706,30732123,+"  ; transcript_id "SUZ12P1--AFMID^ENST00000497969.6"  ; transcript_name "SUZ12P1-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
SUZ12P1--AFMID	HAVANA	RNA	2514	7684	.	+	.	FI_gene_label "SUZ12P1^ENSG00000264538.6"  ; ID "SUZ12P1--AFMID^ENST00000497969.6"  ; Parent "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6"  ; exon_id "ENSE00002690561.1"  ; exon_number 1 ; gene_id "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6"  ; gene_name SUZ12P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000178989.2"  ; havana_transcript "OTTHUMT00000444258.1"  ; hgnc_id "HGNC:32421"  ; level 2 ; orig_coord_info "chr17,30731706,30732123,+"  ; transcript_id "SUZ12P1--AFMID^ENST00000497969.6"  ; transcript_name "SUZ12P1-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
346 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 ------------------------------
429 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 23 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