.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cTi-T1-TRNA-1_B23WHTKLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/46e3f68552e475bbccf61fd70bca03/.command.out
Size: 57.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cTi-T1-TRNA-1_B23WHTKLT4_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: 3375
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3375
=> 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:3375
  => 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: 
AC020637.1--TMEM243	HAVANA	gene	12778	19800	.	+	.	FI_gene_label "TMEM243^ENSG00000135185.12"  ; ID "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12"  ; ccdsid "CCDS5602.1"  ; exon_id "ENSE00001207780.5"  ; exon_number 1 ; gene_id "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12"  ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8"  ; havana_transcript "OTTHUMT00000253377.4"  ; hgnc_id "HGNC:21707"  ; level 2 ; orig_coord_info "chr7,87219426,87219503,-"  ; protein_id "ENSP00000257637.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC020637.1--TMEM243^ENST00000257637.8"  ; transcript_name "TMEM243-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC020637.1--TMEM243	HAVANA	mRNA	12778	19800	.	+	.	FI_gene_label "TMEM243^ENSG00000135185.12"  ; ID "AC020637.1--TMEM243^ENST00000257637.8"  ; Parent "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12"  ; ccdsid "CCDS5602.1"  ; exon_id "ENSE00001207780.5"  ; exon_number 1 ; gene_id "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12"  ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8"  ; havana_transcript "OTTHUMT00000253377.4"  ; hgnc_id "HGNC:21707"  ; level 2 ; orig_coord_info "chr7,87219426,87219503,-"  ; protein_id "ENSP00000257637.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC020637.1--TMEM243^ENST00000257637.8"  ; transcript_name "TMEM243-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC083805.1--EEF1AKMT3	HAVANA	gene	14982	19922	.	+	.	FI_gene_label "EEF1AKMT3^ENSG00000123427.17"  ; ID "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17"  ; ccdsid "CCDS8957.1"  ; exon_id "ENSE00002301479.2"  ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17"  ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2"  ; havana_transcript "OTTHUMT00000409268.2"  ; hgnc_id "HGNC:24936"  ; level 2 ; orig_coord_info "chr12,57772725,57772901,+"  ; protein_id "ENSP00000300209.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000300209.13"  ; transcript_name "EEF1AKMT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC083805.1--EEF1AKMT3	HAVANA	mRNA	14982	19922	.	+	.	FI_gene_label "EEF1AKMT3^ENSG00000123427.17"  ; ID "AC083805.1--EEF1AKMT3^ENST00000300209.13"  ; Parent "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17"  ; ccdsid "CCDS8957.1"  ; exon_id "ENSE00002301479.2"  ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17"  ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2"  ; havana_transcript "OTTHUMT00000409268.2"  ; hgnc_id "HGNC:24936"  ; level 2 ; orig_coord_info "chr12,57772725,57772901,+"  ; protein_id "ENSP00000300209.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000300209.13"  ; transcript_name "EEF1AKMT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC083805.1--TSFM	HAVANA	gene	13875	20936	.	+	.	FI_gene_label "TSFM^ENSG00000123297.20"  ; ID "AC083805.1--TSFM^TSFM^ENSG00000123297.20"  ; ccdsid "CCDS53809.1"  ; exon_id "ENSE00001479920.3"  ; exon_number 1 ; gene_id "AC083805.1--TSFM^TSFM^ENSG00000123297.20"  ; gene_name TSFM ; gene_type protein_coding ; havana_gene "OTTHUMG00000153042.13"  ; havana_transcript "OTTHUMT00000329193.1"  ; hgnc_id "HGNC:12367"  ; level 2 ; orig_coord_info "chr12,57782802,57782858,+"  ; protein_id "ENSP00000313877.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AC083805.1--TSFM^ENST00000323833.12"  ; transcript_name "TSFM-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC083805.1--TSFM	HAVANA	mRNA	13875	20936	.	+	.	FI_gene_label "TSFM^ENSG00000123297.20"  ; ID "AC083805.1--TSFM^ENST00000323833.12"  ; Parent "AC083805.1--TSFM^TSFM^ENSG00000123297.20"  ; ccdsid "CCDS53809.1"  ; exon_id "ENSE00001479920.3"  ; exon_number 1 ; gene_id "AC083805.1--TSFM^TSFM^ENSG00000123297.20"  ; gene_name TSFM ; gene_type protein_coding ; havana_gene "OTTHUMG00000153042.13"  ; havana_transcript "OTTHUMT00000329193.1"  ; hgnc_id "HGNC:12367"  ; level 2 ; orig_coord_info "chr12,57782802,57782858,+"  ; protein_id "ENSP00000313877.8"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AC083805.1--TSFM^ENST00000323833.12"  ; transcript_name "TSFM-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC093890.1--SOS2	HAVANA	gene	4541	33009	.	+	.	FI_gene_label "SOS2^ENSG00000100485.12"  ; ID "AC093890.1--SOS2^SOS2^ENSG00000100485.12"  ; ccdsid "CCDS9697.1"  ; exon_id "ENSE00002525812.2"  ; exon_number 1 ; gene_id "AC093890.1--SOS2^SOS2^ENSG00000100485.12"  ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5"  ; havana_transcript "OTTHUMT00000276878.4"  ; hgnc_id "HGNC:11188"  ; level 2 ; orig_coord_info "chr14,50231197,50231283,-"  ; protein_id "ENSP00000216373.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC093890.1--SOS2^ENST00000216373.10"  ; transcript_name "SOS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC093890.1--SOS2	HAVANA	mRNA	4541	33009	.	+	.	FI_gene_label "SOS2^ENSG00000100485.12"  ; ID "AC093890.1--SOS2^ENST00000216373.10"  ; Parent "AC093890.1--SOS2^SOS2^ENSG00000100485.12"  ; ccdsid "CCDS9697.1"  ; exon_id "ENSE00002525812.2"  ; exon_number 1 ; gene_id "AC093890.1--SOS2^SOS2^ENSG00000100485.12"  ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5"  ; havana_transcript "OTTHUMT00000276878.4"  ; hgnc_id "HGNC:11188"  ; level 2 ; orig_coord_info "chr14,50231197,50231283,-"  ; protein_id "ENSP00000216373.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC093890.1--SOS2^ENST00000216373.10"  ; transcript_name "SOS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCNY--AL353600.1	ENSEMBL	gene	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--AL353600.1^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--AL353600.1^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--AL353600.1^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCNY--AL353600.1	ENSEMBL	mRNA	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--AL353600.1^ENST00000265375.13"  ; Parent "CCNY--AL353600.1^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--AL353600.1^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--AL353600.1^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCNY--AL353600.2	ENSEMBL	gene	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--AL353600.2^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--AL353600.2^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--AL353600.2^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCNY--AL353600.2	ENSEMBL	mRNA	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--AL353600.2^ENST00000265375.13"  ; Parent "CCNY--AL353600.2^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--AL353600.2^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--AL353600.2^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCNY--NRP1	HAVANA	gene	27174	58914	.	+	.	FI_gene_label "NRP1^ENSG00000099250.18"  ; ID "CCNY--NRP1^NRP1^ENSG00000099250.18"  ; ccdsid "CCDS7177.1"  ; exon_id "ENSE00001465117.2"  ; exon_number 2 ; gene_id "CCNY--NRP1^NRP1^ENSG00000099250.18"  ; gene_name NRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019343.8"  ; havana_transcript "OTTHUMT00000051203.2"  ; hgnc_id "HGNC:8004"  ; level 2 ; orig_coord_info "chr10,33334310,33334382,-"  ; protein_id "ENSP00000265371.3"  ; tag alternative_5_UTR basic appris_principal_3 CCDS ; transcript_id "CCNY--NRP1^ENST00000265371.8"  ; transcript_name "NRP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CCNY--NRP1	HAVANA	mRNA	27174	58914	.	+	.	FI_gene_label "NRP1^ENSG00000099250.18"  ; ID "CCNY--NRP1^ENST00000265371.8"  ; Parent "CCNY--NRP1^NRP1^ENSG00000099250.18"  ; ccdsid "CCDS7177.1"  ; exon_id "ENSE00001465117.2"  ; exon_number 2 ; gene_id "CCNY--NRP1^NRP1^ENSG00000099250.18"  ; gene_name NRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019343.8"  ; havana_transcript "OTTHUMT00000051203.2"  ; hgnc_id "HGNC:8004"  ; level 2 ; orig_coord_info "chr10,33334310,33334382,-"  ; protein_id "ENSP00000265371.3"  ; tag alternative_5_UTR basic appris_principal_3 CCDS ; transcript_id "CCNY--NRP1^ENST00000265371.8"  ; transcript_name "NRP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CCNY--NRP1	ENSEMBL	gene	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--NRP1^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--NRP1^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--NRP1^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCNY--NRP1	ENSEMBL	mRNA	7867	24173	.	+	.	FI_gene_label "CCNY^ENSG00000108100.18"  ; ID "CCNY--NRP1^ENST00000265375.13"  ; Parent "CCNY--NRP1^CCNY^ENSG00000108100.18"  ; ccdsid "CCDS7190.1"  ; exon_id "ENSE00003652968.1"  ; exon_number 3 ; gene_id "CCNY--NRP1^CCNY^ENSG00000108100.18"  ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5"  ; hgnc_id "HGNC:23354"  ; level 3 ; orig_coord_info "chr10,35483412,35483478,+"  ; protein_id "ENSP00000265375.9"  ; tag basic CCDS ; transcript_id "CCNY--NRP1^ENST00000265375.13"  ; transcript_name "CCNY-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EEF1AKMT3--CTDSP2	HAVANA	gene	2123	7063	.	+	.	FI_gene_label "EEF1AKMT3^ENSG00000123427.17"  ; ID "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17"  ; ccdsid "CCDS8957.1"  ; exon_id "ENSE00002301479.2"  ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17"  ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2"  ; havana_transcript "OTTHUMT00000409268.2"  ; hgnc_id "HGNC:24936"  ; level 2 ; orig_coord_info "chr12,57772725,57772901,+"  ; protein_id "ENSP00000300209.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000300209.13"  ; transcript_name "EEF1AKMT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EEF1AKMT3--CTDSP2	HAVANA	mRNA	2123	7063	.	+	.	FI_gene_label "EEF1AKMT3^ENSG00000123427.17"  ; ID "EEF1AKMT3--CTDSP2^ENST00000300209.13"  ; Parent "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17"  ; ccdsid "CCDS8957.1"  ; exon_id "ENSE00002301479.2"  ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17"  ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2"  ; havana_transcript "OTTHUMT00000409268.2"  ; hgnc_id "HGNC:24936"  ; level 2 ; orig_coord_info "chr12,57772725,57772901,+"  ; protein_id "ENSP00000300209.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000300209.13"  ; transcript_name "EEF1AKMT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EEF1AKMT3--CTDSP2	HAVANA	gene	10064	20364	.	+	.	FI_gene_label "CTDSP2^ENSG00000175215.11"  ; ID "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11"  ; ccdsid "CCDS41801.1"  ; exon_id "ENSE00001377388.4"  ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11"  ; gene_name CTDSP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170483.3"  ; havana_transcript "OTTHUMT00000409353.2"  ; hgnc_id "HGNC:17077"  ; level 2 ; orig_coord_info "chr12,57846372,57846435,-"  ; protein_id "ENSP00000381148.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000398073.7"  ; transcript_name "CTDSP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EEF1AKMT3--CTDSP2	HAVANA	mRNA	10064	20364	.	+	.	FI_gene_label "CTDSP2^ENSG00000175215.11"  ; ID "EEF1AKMT3--CTDSP2^ENST00000398073.7"  ; Parent "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11"  ; ccdsid "CCDS41801.1"  ; exon_id "ENSE00001377388.4"  ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11"  ; gene_name CTDSP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170483.3"  ; havana_transcript "OTTHUMT00000409353.2"  ; hgnc_id "HGNC:17077"  ; level 2 ; orig_coord_info "chr12,57846372,57846435,-"  ; protein_id "ENSP00000381148.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000398073.7"  ; transcript_name "CTDSP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^ENST00000240618.11"  ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^ENST00000309384.2"  ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MRPS35--TMTC1	HAVANA	gene	1011	10930	.	+	.	FI_gene_label "MRPS35^ENSG00000061794.13"  ; ID "MRPS35--TMTC1^MRPS35^ENSG00000061794.13"  ; ccdsid "CCDS8714.1"  ; exon_id "ENSE00001008074.3"  ; exon_number 1 ; gene_id "MRPS35--TMTC1^MRPS35^ENSG00000061794.13"  ; gene_name MRPS35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169215.2"  ; havana_transcript "OTTHUMT00000402897.2"  ; hgnc_id "HGNC:16635"  ; level 2 ; orig_coord_info "chr12,27710844,27710955,+"  ; protein_id "ENSP00000081029.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS35--TMTC1^ENST00000081029.8"  ; transcript_name "MRPS35-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MRPS35--TMTC1	HAVANA	mRNA	1011	10930	.	+	.	FI_gene_label "MRPS35^ENSG00000061794.13"  ; ID "MRPS35--TMTC1^ENST00000081029.8"  ; Parent "MRPS35--TMTC1^MRPS35^ENSG00000061794.13"  ; ccdsid "CCDS8714.1"  ; exon_id "ENSE00001008074.3"  ; exon_number 1 ; gene_id "MRPS35--TMTC1^MRPS35^ENSG00000061794.13"  ; gene_name MRPS35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169215.2"  ; havana_transcript "OTTHUMT00000402897.2"  ; hgnc_id "HGNC:16635"  ; level 2 ; orig_coord_info "chr12,27710844,27710955,+"  ; protein_id "ENSP00000081029.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS35--TMTC1^ENST00000081029.8"  ; transcript_name "MRPS35-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MRPS35--TMTC1	HAVANA	gene	13931	51649	.	+	.	FI_gene_label "TMTC1^ENSG00000133687.16"  ; ID "MRPS35--TMTC1^TMTC1^ENSG00000133687.16"  ; ccdsid "CCDS8718.1"  ; exon_id "ENSE00003646738.1"  ; exon_number 2 ; gene_id "MRPS35--TMTC1^TMTC1^ENSG00000133687.16"  ; gene_name TMTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169324.2"  ; havana_transcript "OTTHUMT00000403503.1"  ; hgnc_id "HGNC:24099"  ; level 2 ; orig_coord_info "chr12,29767898,29768053,-"  ; protein_id "ENSP00000256062.5"  ; tag basic CCDS ; transcript_id "MRPS35--TMTC1^ENST00000256062.9"  ; transcript_name "TMTC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MRPS35--TMTC1	HAVANA	mRNA	13931	51649	.	+	.	FI_gene_label "TMTC1^ENSG00000133687.16"  ; ID "MRPS35--TMTC1^ENST00000256062.9"  ; Parent "MRPS35--TMTC1^TMTC1^ENSG00000133687.16"  ; ccdsid "CCDS8718.1"  ; exon_id "ENSE00003646738.1"  ; exon_number 2 ; gene_id "MRPS35--TMTC1^TMTC1^ENSG00000133687.16"  ; gene_name TMTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169324.2"  ; havana_transcript "OTTHUMT00000403503.1"  ; hgnc_id "HGNC:24099"  ; level 2 ; orig_coord_info "chr12,29767898,29768053,-"  ; protein_id "ENSP00000256062.5"  ; tag basic CCDS ; transcript_id "MRPS35--TMTC1^ENST00000256062.9"  ; transcript_name "TMTC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP2R3B--TMLHE	HAVANA	gene	22666	34361	.	+	.	FI_gene_label "TMLHE^ENSG00000185973.12"  ; ID "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12"  ; ccdsid "CCDS14768.1"  ; exon_id "ENSE00003660615.1"  ; exon_number 2 ; gene_id "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12"  ; gene_name TMLHE ; gene_type protein_coding ; havana_gene "OTTHUMG00000022674.3"  ; havana_transcript "OTTHUMT00000058817.2"  ; hgnc_id "HGNC:18308"  ; level 2 ; orig_coord_info "chrX,155545096,155545276,-"  ; protein_id "ENSP00000335261.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP2R3B--TMLHE^ENST00000334398.8"  ; transcript_name "TMLHE-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPP2R3B--TMLHE	HAVANA	mRNA	22666	34361	.	+	.	FI_gene_label "TMLHE^ENSG00000185973.12"  ; ID "PPP2R3B--TMLHE^ENST00000334398.8"  ; Parent "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12"  ; ccdsid "CCDS14768.1"  ; exon_id "ENSE00003660615.1"  ; exon_number 2 ; gene_id "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12"  ; gene_name TMLHE ; gene_type protein_coding ; havana_gene "OTTHUMG00000022674.3"  ; havana_transcript "OTTHUMT00000058817.2"  ; hgnc_id "HGNC:18308"  ; level 2 ; orig_coord_info "chrX,155545096,155545276,-"  ; protein_id "ENSP00000335261.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP2R3B--TMLHE^ENST00000334398.8"  ; transcript_name "TMLHE-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP2R3B--TMLHE	HAVANA	gene	2589	6257	.	+	.	FI_gene_label "PPP2R3B^ENSG00000167393.18"  ; ID "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18"  ; exon_id "ENSE00001489321.3"  ; exon_number 1 ; gene_id "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18"  ; gene_name PPP2R3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000021052.4"  ; havana_transcript "OTTHUMT00000055578.3"  ; hgnc_id "HGNC:13417"  ; level 2 ; orig_coord_info "chrX,373532,373771,-"  ; protein_id "ENSP00000371038.4"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PPP2R3B--TMLHE^ENST00000381625.9"  ; transcript_name "PPP2R3B-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PPP2R3B--TMLHE	HAVANA	mRNA	2589	6257	.	+	.	FI_gene_label "PPP2R3B^ENSG00000167393.18"  ; ID "PPP2R3B--TMLHE^ENST00000381625.9"  ; Parent "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18"  ; exon_id "ENSE00001489321.3"  ; exon_number 1 ; gene_id "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18"  ; gene_name PPP2R3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000021052.4"  ; havana_transcript "OTTHUMT00000055578.3"  ; hgnc_id "HGNC:13417"  ; level 2 ; orig_coord_info "chrX,373532,373771,-"  ; protein_id "ENSP00000371038.4"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "PPP2R3B--TMLHE^ENST00000381625.9"  ; transcript_name "PPP2R3B-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RAP1B--SRGAP1	HAVANA	gene	1045	26964	.	+	.	FI_gene_label "RAP1B^ENSG00000127314.18"  ; ID "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18"  ; ccdsid "CCDS8984.1"  ; exon_id "ENSE00003505440.1"  ; exon_number 2 ; gene_id "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18"  ; gene_name RAP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133660.8"  ; havana_transcript "OTTHUMT00000257821.5"  ; hgnc_id "HGNC:9857"  ; level 2 ; orig_coord_info "chr12,68648725,68648781,+"  ; protein_id "ENSP00000250559.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000250559.14"  ; transcript_name "RAP1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAP1B--SRGAP1	HAVANA	mRNA	1045	26964	.	+	.	FI_gene_label "RAP1B^ENSG00000127314.18"  ; ID "RAP1B--SRGAP1^ENST00000250559.14"  ; Parent "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18"  ; ccdsid "CCDS8984.1"  ; exon_id "ENSE00003505440.1"  ; exon_number 2 ; gene_id "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18"  ; gene_name RAP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133660.8"  ; havana_transcript "OTTHUMT00000257821.5"  ; hgnc_id "HGNC:9857"  ; level 2 ; orig_coord_info "chr12,68648725,68648781,+"  ; protein_id "ENSP00000250559.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000250559.14"  ; transcript_name "RAP1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAP1B--SRGAP1	HAVANA	gene	29965	75316	.	+	.	FI_gene_label "SRGAP1^ENSG00000196935.9"  ; ID "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9"  ; ccdsid "CCDS8967.1"  ; exon_id "ENSE00002278180.2"  ; exon_number 1 ; gene_id "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9"  ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3"  ; havana_transcript "OTTHUMT00000400896.3"  ; hgnc_id "HGNC:17382"  ; level 2 ; orig_coord_info "chr12,63844817,63844883,+"  ; protein_id "ENSP00000347198.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000355086.8"  ; transcript_name "SRGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAP1B--SRGAP1	HAVANA	mRNA	29965	75316	.	+	.	FI_gene_label "SRGAP1^ENSG00000196935.9"  ; ID "RAP1B--SRGAP1^ENST00000355086.8"  ; Parent "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9"  ; ccdsid "CCDS8967.1"  ; exon_id "ENSE00002278180.2"  ; exon_number 1 ; gene_id "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9"  ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3"  ; havana_transcript "OTTHUMT00000400896.3"  ; hgnc_id "HGNC:17382"  ; level 2 ; orig_coord_info "chr12,63844817,63844883,+"  ; protein_id "ENSP00000347198.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000355086.8"  ; transcript_name "SRGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SAV1--SOS2	HAVANA	gene	14032	42500	.	+	.	FI_gene_label "SOS2^ENSG00000100485.12"  ; ID "SAV1--SOS2^SOS2^ENSG00000100485.12"  ; ccdsid "CCDS9697.1"  ; exon_id "ENSE00002525812.2"  ; exon_number 1 ; gene_id "SAV1--SOS2^SOS2^ENSG00000100485.12"  ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5"  ; havana_transcript "OTTHUMT00000276878.4"  ; hgnc_id "HGNC:11188"  ; level 2 ; orig_coord_info "chr14,50231197,50231283,-"  ; protein_id "ENSP00000216373.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000216373.10"  ; transcript_name "SOS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SAV1--SOS2	HAVANA	mRNA	14032	42500	.	+	.	FI_gene_label "SOS2^ENSG00000100485.12"  ; ID "SAV1--SOS2^ENST00000216373.10"  ; Parent "SAV1--SOS2^SOS2^ENSG00000100485.12"  ; ccdsid "CCDS9697.1"  ; exon_id "ENSE00002525812.2"  ; exon_number 1 ; gene_id "SAV1--SOS2^SOS2^ENSG00000100485.12"  ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5"  ; havana_transcript "OTTHUMT00000276878.4"  ; hgnc_id "HGNC:11188"  ; level 2 ; orig_coord_info "chr14,50231197,50231283,-"  ; protein_id "ENSP00000216373.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000216373.10"  ; transcript_name "SOS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SAV1--SOS2	HAVANA	gene	1001	9509	.	+	.	FI_gene_label "SAV1^ENSG00000151748.15"  ; ID "SAV1--SOS2^SAV1^ENSG00000151748.15"  ; ccdsid "CCDS9701.1"  ; exon_id "ENSE00001246829.5"  ; exon_number 1 ; gene_id "SAV1--SOS2^SAV1^ENSG00000151748.15"  ; gene_name SAV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140293.8"  ; havana_transcript "OTTHUMT00000276879.2"  ; hgnc_id "HGNC:17795"  ; level 2 ; orig_coord_info "chr14,50667874,50667967,-"  ; protein_id "ENSP00000324729.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000324679.5"  ; transcript_name "SAV1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SAV1--SOS2	HAVANA	mRNA	1001	9509	.	+	.	FI_gene_label "SAV1^ENSG00000151748.15"  ; ID "SAV1--SOS2^ENST00000324679.5"  ; Parent "SAV1--SOS2^SAV1^ENSG00000151748.15"  ; ccdsid "CCDS9701.1"  ; exon_id "ENSE00001246829.5"  ; exon_number 1 ; gene_id "SAV1--SOS2^SAV1^ENSG00000151748.15"  ; gene_name SAV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140293.8"  ; havana_transcript "OTTHUMT00000276879.2"  ; hgnc_id "HGNC:17795"  ; level 2 ; orig_coord_info "chr14,50667874,50667967,-"  ; protein_id "ENSP00000324729.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000324679.5"  ; transcript_name "SAV1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRGAP1--GRIP1	HAVANA	gene	1001	46352	.	+	.	FI_gene_label "SRGAP1^ENSG00000196935.9"  ; ID "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9"  ; ccdsid "CCDS8967.1"  ; exon_id "ENSE00002278180.2"  ; exon_number 1 ; gene_id "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9"  ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3"  ; havana_transcript "OTTHUMT00000400896.3"  ; hgnc_id "HGNC:17382"  ; level 2 ; orig_coord_info "chr12,63844817,63844883,+"  ; protein_id "ENSP00000347198.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRGAP1--GRIP1^ENST00000355086.8"  ; transcript_name "SRGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SRGAP1--GRIP1	HAVANA	mRNA	1001	46352	.	+	.	FI_gene_label "SRGAP1^ENSG00000196935.9"  ; ID "SRGAP1--GRIP1^ENST00000355086.8"  ; Parent "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9"  ; ccdsid "CCDS8967.1"  ; exon_id "ENSE00002278180.2"  ; exon_number 1 ; gene_id "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9"  ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3"  ; havana_transcript "OTTHUMT00000400896.3"  ; hgnc_id "HGNC:17382"  ; level 2 ; orig_coord_info "chr12,63844817,63844883,+"  ; protein_id "ENSP00000347198.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRGAP1--GRIP1^ENST00000355086.8"  ; transcript_name "SRGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRGAP1--GRIP1	HAVANA	gene	52869	85366	.	+	.	FI_gene_label "GRIP1^ENSG00000155974.13"  ; ID "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13"  ; exon_id "ENSE00003912333.1"  ; exon_number 1 ; gene_id "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13"  ; gene_name GRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169019.7"  ; hgnc_id "HGNC:18708"  ; level 2 ; orig_coord_info "chr12,66678850,66678904,-"  ; protein_id "ENSP00000352780.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 ; transcript_id "SRGAP1--GRIP1^ENST00000359742.9"  ; transcript_name "GRIP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SRGAP1--GRIP1	HAVANA	mRNA	52869	85366	.	+	.	FI_gene_label "GRIP1^ENSG00000155974.13"  ; ID "SRGAP1--GRIP1^ENST00000359742.9"  ; Parent "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13"  ; exon_id "ENSE00003912333.1"  ; exon_number 1 ; gene_id "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13"  ; gene_name GRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169019.7"  ; hgnc_id "HGNC:18708"  ; level 2 ; orig_coord_info "chr12,66678850,66678904,-"  ; protein_id "ENSP00000352780.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 ; transcript_id "SRGAP1--GRIP1^ENST00000359742.9"  ; transcript_name "GRIP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TMEM243--AC020637.1	HAVANA	gene	1856	8878	.	+	.	FI_gene_label "TMEM243^ENSG00000135185.12"  ; ID "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12"  ; ccdsid "CCDS5602.1"  ; exon_id "ENSE00001207780.5"  ; exon_number 1 ; gene_id "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12"  ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8"  ; havana_transcript "OTTHUMT00000253377.4"  ; hgnc_id "HGNC:21707"  ; level 2 ; orig_coord_info "chr7,87219426,87219503,-"  ; protein_id "ENSP00000257637.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM243--AC020637.1^ENST00000257637.8"  ; transcript_name "TMEM243-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMEM243--AC020637.1	HAVANA	mRNA	1856	8878	.	+	.	FI_gene_label "TMEM243^ENSG00000135185.12"  ; ID "TMEM243--AC020637.1^ENST00000257637.8"  ; Parent "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12"  ; ccdsid "CCDS5602.1"  ; exon_id "ENSE00001207780.5"  ; exon_number 1 ; gene_id "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12"  ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8"  ; havana_transcript "OTTHUMT00000253377.4"  ; hgnc_id "HGNC:21707"  ; level 2 ; orig_coord_info "chr7,87219426,87219503,-"  ; protein_id "ENSP00000257637.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM243--AC020637.1^ENST00000257637.8"  ; transcript_name "TMEM243-201"  ; 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: 
TYW1--VKORC1L1	HAVANA	gene	2339	20501	.	+	.	FI_gene_label "TYW1^ENSG00000198874.13"  ; ID "TYW1--VKORC1L1^TYW1^ENSG00000198874.13"  ; ccdsid "CCDS5538.1"  ; exon_id "ENSE00001947681.2"  ; exon_number 1 ; gene_id "TYW1--VKORC1L1^TYW1^ENSG00000198874.13"  ; gene_name TYW1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129723.5"  ; havana_transcript "OTTHUMT00000251932.3"  ; hgnc_id "HGNC:25598"  ; level 2 ; orig_coord_info "chr7,66996979,66996982,+"  ; protein_id "ENSP00000352645.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000359626.10"  ; transcript_name "TYW1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TYW1--VKORC1L1	HAVANA	mRNA	2339	20501	.	+	.	FI_gene_label "TYW1^ENSG00000198874.13"  ; ID "TYW1--VKORC1L1^ENST00000359626.10"  ; Parent "TYW1--VKORC1L1^TYW1^ENSG00000198874.13"  ; ccdsid "CCDS5538.1"  ; exon_id "ENSE00001947681.2"  ; exon_number 1 ; gene_id "TYW1--VKORC1L1^TYW1^ENSG00000198874.13"  ; gene_name TYW1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129723.5"  ; havana_transcript "OTTHUMT00000251932.3"  ; hgnc_id "HGNC:25598"  ; level 2 ; orig_coord_info "chr7,66996979,66996982,+"  ; protein_id "ENSP00000352645.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000359626.10"  ; transcript_name "TYW1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TYW1--VKORC1L1	HAVANA	gene	23507	31593	.	+	.	FI_gene_label "VKORC1L1^ENSG00000196715.7"  ; ID "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7"  ; ccdsid "CCDS5529.1"  ; exon_id "ENSE00003846291.1"  ; exon_number 1 ; gene_id "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7"  ; gene_name VKORC1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129449.5"  ; havana_transcript "OTTHUMT00000251612.5"  ; hgnc_id "HGNC:21492"  ; level 2 ; orig_coord_info "chr7,65873372,65873565,+"  ; protein_id "ENSP00000353998.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000360768.5"  ; transcript_name "VKORC1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TYW1--VKORC1L1	HAVANA	mRNA	23507	31593	.	+	.	FI_gene_label "VKORC1L1^ENSG00000196715.7"  ; ID "TYW1--VKORC1L1^ENST00000360768.5"  ; Parent "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7"  ; ccdsid "CCDS5529.1"  ; exon_id "ENSE00003846291.1"  ; exon_number 1 ; gene_id "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7"  ; gene_name VKORC1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129449.5"  ; havana_transcript "OTTHUMT00000251612.5"  ; hgnc_id "HGNC:21492"  ; level 2 ; orig_coord_info "chr7,65873372,65873565,+"  ; protein_id "ENSP00000353998.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000360768.5"  ; transcript_name "VKORC1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
VGLL4--ATG7	HAVANA	gene	4453	29477	.	+	.	FI_gene_label "VGLL4^ENSG00000144560.15"  ; ID "VGLL4--ATG7^VGLL4^ENSG00000144560.15"  ; ccdsid "CCDS2606.1"  ; exon_id "ENSE00003614736.1"  ; exon_number 2 ; gene_id "VGLL4--ATG7^VGLL4^ENSG00000144560.15"  ; gene_name VGLL4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129739.21"  ; havana_transcript "OTTHUMT00000251950.2"  ; hgnc_id "HGNC:28966"  ; level 2 ; orig_coord_info "chr3,11702971,11703034,-"  ; protein_id "ENSP00000273038.3"  ; tag basic CCDS ; transcript_id "VGLL4--ATG7^ENST00000273038.7"  ; transcript_name "VGLL4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
VGLL4--ATG7	HAVANA	mRNA	4453	29477	.	+	.	FI_gene_label "VGLL4^ENSG00000144560.15"  ; ID "VGLL4--ATG7^ENST00000273038.7"  ; Parent "VGLL4--ATG7^VGLL4^ENSG00000144560.15"  ; ccdsid "CCDS2606.1"  ; exon_id "ENSE00003614736.1"  ; exon_number 2 ; gene_id "VGLL4--ATG7^VGLL4^ENSG00000144560.15"  ; gene_name VGLL4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129739.21"  ; havana_transcript "OTTHUMT00000251950.2"  ; hgnc_id "HGNC:28966"  ; level 2 ; orig_coord_info "chr3,11702971,11703034,-"  ; protein_id "ENSP00000273038.3"  ; tag basic CCDS ; transcript_id "VGLL4--ATG7^ENST00000273038.7"  ; transcript_name "VGLL4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
VGLL4--ATG7	HAVANA	gene	32586	67624	.	+	.	FI_gene_label "ATG7^ENSG00000197548.12"  ; ID "VGLL4--ATG7^ATG7^ENSG00000197548.12"  ; ccdsid "CCDS2605.1"  ; exon_id "ENSE00003638636.1"  ; exon_number 2 ; gene_id "VGLL4--ATG7^ATG7^ENSG00000197548.12"  ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21"  ; havana_transcript "OTTHUMT00000251951.3"  ; hgnc_id "HGNC:16935"  ; level 2 ; orig_coord_info "chr3,11298696,11298855,+"  ; protein_id "ENSP00000346437.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "VGLL4--ATG7^ENST00000354449.7"  ; transcript_name "ATG7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
VGLL4--ATG7	HAVANA	mRNA	32586	67624	.	+	.	FI_gene_label "ATG7^ENSG00000197548.12"  ; ID "VGLL4--ATG7^ENST00000354449.7"  ; Parent "VGLL4--ATG7^ATG7^ENSG00000197548.12"  ; ccdsid "CCDS2605.1"  ; exon_id "ENSE00003638636.1"  ; exon_number 2 ; gene_id "VGLL4--ATG7^ATG7^ENSG00000197548.12"  ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21"  ; havana_transcript "OTTHUMT00000251951.3"  ; hgnc_id "HGNC:16935"  ; level 2 ; orig_coord_info "chr3,11298696,11298855,+"  ; protein_id "ENSP00000346437.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "VGLL4--ATG7^ENST00000354449.7"  ; transcript_name "ATG7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC020637.1--TMEM243	HAVANA	gene	1001	8922	.	+	.	FI_gene_label "AC020637.1^ENSG00000258231.5"  ; ID "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5"  ; exon_id "ENSE00002337014.1"  ; exon_number 1 ; gene_id "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5"  ; gene_name "AC020637.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2"  ; havana_transcript "OTTHUMT00000406685.1"  ; level 1 ; orig_coord_info "chr12,58544124,58544179,+"  ; tag basic exp_conf ; transcript_id "AC020637.1--TMEM243^ENST00000546977.5"  ; transcript_name "AC020637.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
AC020637.1--TMEM243	HAVANA	RNA	1001	8922	.	+	.	FI_gene_label "AC020637.1^ENSG00000258231.5"  ; ID "AC020637.1--TMEM243^ENST00000546977.5"  ; Parent "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5"  ; exon_id "ENSE00002337014.1"  ; exon_number 1 ; gene_id "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5"  ; gene_name "AC020637.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2"  ; havana_transcript "OTTHUMT00000406685.1"  ; level 1 ; orig_coord_info "chr12,58544124,58544179,+"  ; tag basic exp_conf ; transcript_id "AC020637.1--TMEM243^ENST00000546977.5"  ; transcript_name "AC020637.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
AC083805.1--EEF1AKMT3	HAVANA	gene	1001	10858	.	+	.	FI_gene_label "AC083805.1^ENSG00000245651.3"  ; ID "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3"  ; exon_id "ENSE00001961223.2"  ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3"  ; gene_name "AC083805.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11"  ; havana_transcript "OTTHUMT00000409363.1"  ; level 2 ; orig_coord_info "chr12,57893740,57896482,-"  ; tag basic ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000499481.2"  ; transcript_name "AC083805.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
AC083805.1--EEF1AKMT3	HAVANA	RNA	1001	10858	.	+	.	FI_gene_label "AC083805.1^ENSG00000245651.3"  ; ID "AC083805.1--EEF1AKMT3^ENST00000499481.2"  ; Parent "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3"  ; exon_id "ENSE00001961223.2"  ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3"  ; gene_name "AC083805.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11"  ; havana_transcript "OTTHUMT00000409363.1"  ; level 2 ; orig_coord_info "chr12,57893740,57896482,-"  ; tag basic ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000499481.2"  ; transcript_name "AC083805.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
AC083805.1--TSFM	HAVANA	gene	1001	10858	.	+	.	FI_gene_label "AC083805.1^ENSG00000245651.3"  ; ID "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3"  ; exon_id "ENSE00001961223.2"  ; exon_number 1 ; gene_id "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3"  ; gene_name "AC083805.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11"  ; havana_transcript "OTTHUMT00000409363.1"  ; level 2 ; orig_coord_info "chr12,57893740,57896482,-"  ; tag basic ; transcript_id "AC083805.1--TSFM^ENST00000499481.2"  ; transcript_name "AC083805.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
AC083805.1--TSFM	HAVANA	RNA	1001	10858	.	+	.	FI_gene_label "AC083805.1^ENSG00000245651.3"  ; ID "AC083805.1--TSFM^ENST00000499481.2"  ; Parent "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3"  ; exon_id "ENSE00001961223.2"  ; exon_number 1 ; gene_id "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3"  ; gene_name "AC083805.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11"  ; havana_transcript "OTTHUMT00000409363.1"  ; level 2 ; orig_coord_info "chr12,57893740,57896482,-"  ; tag basic ; transcript_id "AC083805.1--TSFM^ENST00000499481.2"  ; transcript_name "AC083805.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
AC093890.1--SOS2	HAVANA	gene	1001	1540	.	+	.	FI_gene_label "AC093890.1^ENSG00000249741.2"  ; ID "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2"  ; exon_id "ENSE00002087602.2"  ; exon_number 1 ; gene_id "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2"  ; gene_name "AC093890.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161401.2"  ; havana_transcript "OTTHUMT00000364779.2"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr4,143911514,143912053,-"  ; tag pseudo_consens basic ; transcript_id "AC093890.1--SOS2^ENST00000502554.2"  ; transcript_name "AC093890.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
AC093890.1--SOS2	HAVANA	RNA	1001	1540	.	+	.	FI_gene_label "AC093890.1^ENSG00000249741.2"  ; ID "AC093890.1--SOS2^ENST00000502554.2"  ; Parent "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2"  ; exon_id "ENSE00002087602.2"  ; exon_number 1 ; gene_id "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2"  ; gene_name "AC093890.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161401.2"  ; havana_transcript "OTTHUMT00000364779.2"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr4,143911514,143912053,-"  ; tag pseudo_consens basic ; transcript_id "AC093890.1--SOS2^ENST00000502554.2"  ; transcript_name "AC093890.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
CCNY--AL353600.1	HAVANA	gene	27174	27424	.	+	.	FI_gene_label "AL353600.1^ENSG00000273012.1"  ; ID "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1"  ; exon_id "ENSE00003710377.1"  ; exon_number 1 ; gene_id "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1"  ; gene_name "AL353600.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186206.1"  ; havana_transcript "OTTHUMT00000472416.1"  ; level 2 ; orig_coord_info "chr10,33341655,33341905,+"  ; tag basic ; transcript_id "CCNY--AL353600.1^ENST00000608148.1"  ; transcript_name "AL353600.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
CCNY--AL353600.1	HAVANA	RNA	27174	27424	.	+	.	FI_gene_label "AL353600.1^ENSG00000273012.1"  ; ID "CCNY--AL353600.1^ENST00000608148.1"  ; Parent "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1"  ; exon_id "ENSE00003710377.1"  ; exon_number 1 ; gene_id "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1"  ; gene_name "AL353600.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186206.1"  ; havana_transcript "OTTHUMT00000472416.1"  ; level 2 ; orig_coord_info "chr10,33341655,33341905,+"  ; tag basic ; transcript_id "CCNY--AL353600.1^ENST00000608148.1"  ; transcript_name "AL353600.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created: 
CCNY--AL353600.2	HAVANA	gene	27174	30614	.	+	.	FI_gene_label "AL353600.2^ENSG00000287278.1"  ; ID "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1"  ; exon_id "ENSE00003868179.1"  ; exon_number 1 ; gene_id "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1"  ; gene_name "AL353600.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194969.1"  ; havana_transcript "OTTHUMT00000523464.1"  ; level 2 ; orig_coord_info "chr10,33384891,33385325,+"  ; tag basic TAGENE ; transcript_id "CCNY--AL353600.2^ENST00000654047.1"  ; transcript_name "AL353600.2-201"  ; transcript_type lncRNA
CCNY--AL353600.2	HAVANA	RNA	27174	30614	.	+	.	FI_gene_label "AL353600.2^ENSG00000287278.1"  ; ID "CCNY--AL353600.2^ENST00000654047.1"  ; Parent "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1"  ; exon_id "ENSE00003868179.1"  ; exon_number 1 ; gene_id "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1"  ; gene_name "AL353600.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194969.1"  ; havana_transcript "OTTHUMT00000523464.1"  ; level 2 ; orig_coord_info "chr10,33384891,33385325,+"  ; tag basic TAGENE ; transcript_id "CCNY--AL353600.2^ENST00000654047.1"  ; transcript_name "AL353600.2-201"  ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
TMEM243--AC020637.1	HAVANA	gene	11879	19800	.	+	.	FI_gene_label "AC020637.1^ENSG00000258231.5"  ; ID "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5"  ; exon_id "ENSE00002337014.1"  ; exon_number 1 ; gene_id "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5"  ; gene_name "AC020637.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2"  ; havana_transcript "OTTHUMT00000406685.1"  ; level 1 ; orig_coord_info "chr12,58544124,58544179,+"  ; tag basic exp_conf ; transcript_id "TMEM243--AC020637.1^ENST00000546977.5"  ; transcript_name "AC020637.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TMEM243--AC020637.1	HAVANA	RNA	11879	19800	.	+	.	FI_gene_label "AC020637.1^ENSG00000258231.5"  ; ID "TMEM243--AC020637.1^ENST00000546977.5"  ; Parent "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5"  ; exon_id "ENSE00002337014.1"  ; exon_number 1 ; gene_id "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5"  ; gene_name "AC020637.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2"  ; havana_transcript "OTTHUMT00000406685.1"  ; level 1 ; orig_coord_info "chr12,58544124,58544179,+"  ; tag basic exp_conf ; transcript_id "TMEM243--AC020637.1^ENST00000546977.5"  ; transcript_name "AC020637.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
313 cases fixed where L3 features have parent feature(s) missing
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--------------------------- 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 ------------------------------
532 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 0 second) ------                   


GFF3 file parsed