.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-01eb49-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2bce0a1fb9ee224540f727d98e995d/.command.log
Size: 59.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-01eb49-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/7d3b7b5942f6076b959672014e6035/fi_workdir/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2bce0a1fb9ee224540f727d98e995d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2bce0a1fb9ee224540f727d98e995d/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 4155
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4155
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:4155
  => 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: 
AC015712.1--KLK9	HAVANA	gene	9982	13429	.	+	.	FI_gene_label "KLK9^ENSG00000213022.6"  ; ID "AC015712.1--KLK9^KLK9^ENSG00000213022.6"  ; exon_id "ENSE00001320748.5"  ; exon_number 1 ; gene_id "AC015712.1--KLK9^KLK9^ENSG00000213022.6"  ; gene_name KLK9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183087.5"  ; havana_transcript "OTTHUMT00000465036.3"  ; hgnc_id "HGNC:6370"  ; level 2 ; orig_coord_info "chr19,51009505,51009547,-"  ; protein_id "ENSP00000443289.1"  ; transcript_id "AC015712.1--KLK9^ENST00000544410.1"  ; transcript_name "KLK9-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
AC015712.1--KLK9	HAVANA	mRNA	9982	13429	.	+	.	FI_gene_label "KLK9^ENSG00000213022.6"  ; ID "AC015712.1--KLK9^ENST00000544410.1"  ; Parent "AC015712.1--KLK9^KLK9^ENSG00000213022.6"  ; exon_id "ENSE00001320748.5"  ; exon_number 1 ; gene_id "AC015712.1--KLK9^KLK9^ENSG00000213022.6"  ; gene_name KLK9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183087.5"  ; havana_transcript "OTTHUMT00000465036.3"  ; hgnc_id "HGNC:6370"  ; level 2 ; orig_coord_info "chr19,51009505,51009547,-"  ; protein_id "ENSP00000443289.1"  ; transcript_id "AC015712.1--KLK9^ENST00000544410.1"  ; transcript_name "KLK9-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
AC015911.9--SLFN12L	HAVANA	gene	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L	HAVANA	mRNA	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^ENST00000260908.12"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ACIN1--HOMEZ	HAVANA	gene	1001	23157	.	+	.	FI_gene_label "ACIN1^ENSG00000100813.14"  ; ID "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14"  ; ccdsid "CCDS9587.1"  ; exon_id "ENSE00001031625.1"  ; exon_number 1 ; gene_id "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14"  ; gene_name ACIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028716.8"  ; havana_transcript "OTTHUMT00000071707.3"  ; hgnc_id "HGNC:17066"  ; level 2 ; orig_coord_info "chr14,23094975,23095286,-"  ; protein_id "ENSP00000262710.1"  ; tag basic appris_principal_4 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000262710.5"  ; transcript_name "ACIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ACIN1--HOMEZ	HAVANA	mRNA	1001	23157	.	+	.	FI_gene_label "ACIN1^ENSG00000100813.14"  ; ID "ACIN1--HOMEZ^ENST00000262710.5"  ; Parent "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14"  ; ccdsid "CCDS9587.1"  ; exon_id "ENSE00001031625.1"  ; exon_number 1 ; gene_id "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14"  ; gene_name ACIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028716.8"  ; havana_transcript "OTTHUMT00000071707.3"  ; hgnc_id "HGNC:17066"  ; level 2 ; orig_coord_info "chr14,23094975,23095286,-"  ; protein_id "ENSP00000262710.1"  ; tag basic appris_principal_4 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000262710.5"  ; transcript_name "ACIN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ACIN1--HOMEZ	HAVANA	gene	26161	33068	.	+	.	FI_gene_label "HOMEZ^ENSG00000215271.9"  ; ID "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9"  ; ccdsid "CCDS45085.1"  ; exon_id "ENSE00003478704.2"  ; exon_number 1 ; gene_id "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9"  ; gene_name HOMEZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000172122.9"  ; havana_transcript "OTTHUMT00000416939.4"  ; hgnc_id "HGNC:20164"  ; level 2 ; orig_coord_info "chr14,23285913,23285952,-"  ; protein_id "ENSP00000350049.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000357460.7"  ; transcript_name "HOMEZ-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ACIN1--HOMEZ	HAVANA	mRNA	26161	33068	.	+	.	FI_gene_label "HOMEZ^ENSG00000215271.9"  ; ID "ACIN1--HOMEZ^ENST00000357460.7"  ; Parent "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9"  ; ccdsid "CCDS45085.1"  ; exon_id "ENSE00003478704.2"  ; exon_number 1 ; gene_id "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9"  ; gene_name HOMEZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000172122.9"  ; havana_transcript "OTTHUMT00000416939.4"  ; hgnc_id "HGNC:20164"  ; level 2 ; orig_coord_info "chr14,23285913,23285952,-"  ; protein_id "ENSP00000350049.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000357460.7"  ; transcript_name "HOMEZ-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CLTC--VMP1	HAVANA	gene	39205	57907	.	+	.	FI_gene_label "VMP1^ENSG00000062716.13"  ; ID "CLTC--VMP1^VMP1^ENSG00000062716.13"  ; ccdsid "CCDS11619.1"  ; exon_id "ENSE00003550286.1"  ; exon_number 2 ; gene_id "CLTC--VMP1^VMP1^ENSG00000062716.13"  ; gene_name VMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179882.4"  ; havana_transcript "OTTHUMT00000448793.2"  ; hgnc_id "HGNC:29559"  ; level 2 ; orig_coord_info "chr17,59731447,59731522,+"  ; protein_id "ENSP00000262291.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000262291.9"  ; transcript_name "VMP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CLTC--VMP1	HAVANA	mRNA	39205	57907	.	+	.	FI_gene_label "VMP1^ENSG00000062716.13"  ; ID "CLTC--VMP1^ENST00000262291.9"  ; Parent "CLTC--VMP1^VMP1^ENSG00000062716.13"  ; ccdsid "CCDS11619.1"  ; exon_id "ENSE00003550286.1"  ; exon_number 2 ; gene_id "CLTC--VMP1^VMP1^ENSG00000062716.13"  ; gene_name VMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179882.4"  ; havana_transcript "OTTHUMT00000448793.2"  ; hgnc_id "HGNC:29559"  ; level 2 ; orig_coord_info "chr17,59731447,59731522,+"  ; protein_id "ENSP00000262291.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000262291.9"  ; transcript_name "VMP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CLTC--VMP1	HAVANA	gene	1207	35742	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "CLTC--VMP1^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "CLTC--VMP1^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CLTC--VMP1	HAVANA	mRNA	1207	35742	.	+	.	FI_gene_label "CLTC^ENSG00000141367.12"  ; ID "CLTC--VMP1^ENST00000269122.8"  ; Parent "CLTC--VMP1^CLTC^ENSG00000141367.12"  ; ccdsid "CCDS32696.1"  ; exon_id "ENSE00003895422.1"  ; exon_number 1 ; gene_id "CLTC--VMP1^CLTC^ENSG00000141367.12"  ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5"  ; havana_transcript "OTTHUMT00000258859.2"  ; hgnc_id "HGNC:2092"  ; level 2 ; orig_coord_info "chr17,59620132,59620173,+"  ; protein_id "ENSP00000269122.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000269122.8"  ; transcript_name "CLTC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPSF6--FRA10AC1	HAVANA	gene	1048	12978	.	+	.	FI_gene_label "CPSF6^ENSG00000111605.18"  ; ID "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18"  ; ccdsid "CCDS73494.1"  ; exon_id "ENSE00002424959.1"  ; exon_number 1 ; gene_id "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18"  ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4"  ; havana_transcript "OTTHUMT00000403613.1"  ; hgnc_id "HGNC:13871"  ; level 2 ; orig_coord_info "chr12,69239647,69239706,+"  ; protein_id "ENSP00000266679.8"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000266679.8"  ; transcript_name "CPSF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPSF6--FRA10AC1	HAVANA	mRNA	1048	12978	.	+	.	FI_gene_label "CPSF6^ENSG00000111605.18"  ; ID "CPSF6--FRA10AC1^ENST00000266679.8"  ; Parent "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18"  ; ccdsid "CCDS73494.1"  ; exon_id "ENSE00002424959.1"  ; exon_number 1 ; gene_id "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18"  ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4"  ; havana_transcript "OTTHUMT00000403613.1"  ; hgnc_id "HGNC:13871"  ; level 2 ; orig_coord_info "chr12,69239647,69239706,+"  ; protein_id "ENSP00000266679.8"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000266679.8"  ; transcript_name "CPSF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPSF6--FRA10AC1	HAVANA	gene	20398	40131	.	+	.	FI_gene_label "FRA10AC1^ENSG00000148690.12"  ; ID "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12"  ; ccdsid "CCDS7430.1"  ; exon_id "ENSE00003459004.1"  ; exon_number 2 ; gene_id "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12"  ; gene_name FRA10AC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018776.2"  ; havana_transcript "OTTHUMT00000049439.2"  ; hgnc_id "HGNC:1162"  ; level 2 ; orig_coord_info "chr10,93700030,93700106,-"  ; protein_id "ENSP00000360488.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000359204.5"  ; transcript_name "FRA10AC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPSF6--FRA10AC1	HAVANA	mRNA	20398	40131	.	+	.	FI_gene_label "FRA10AC1^ENSG00000148690.12"  ; ID "CPSF6--FRA10AC1^ENST00000359204.5"  ; Parent "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12"  ; ccdsid "CCDS7430.1"  ; exon_id "ENSE00003459004.1"  ; exon_number 2 ; gene_id "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12"  ; gene_name FRA10AC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018776.2"  ; havana_transcript "OTTHUMT00000049439.2"  ; hgnc_id "HGNC:1162"  ; level 2 ; orig_coord_info "chr10,93700030,93700106,-"  ; protein_id "ENSP00000360488.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000359204.5"  ; transcript_name "FRA10AC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
E2F1--ZNF341	HAVANA	gene	9922	28921	.	+	.	FI_gene_label "ZNF341^ENSG00000131061.14"  ; ID "E2F1--ZNF341^ZNF341^ENSG00000131061.14"  ; ccdsid "CCDS13227.1"  ; exon_id "ENSE00001660419.1"  ; exon_number 1 ; gene_id "E2F1--ZNF341^ZNF341^ENSG00000131061.14"  ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5"  ; havana_transcript "OTTHUMT00000078741.2"  ; hgnc_id "HGNC:15992"  ; level 2 ; orig_coord_info "chr20,33732022,33732052,+"  ; protein_id "ENSP00000344308.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "E2F1--ZNF341^ENST00000342427.6"  ; transcript_name "ZNF341-201"  ; transcript_support_level 1 ; transcript_type protein_coding
E2F1--ZNF341	HAVANA	mRNA	9922	28921	.	+	.	FI_gene_label "ZNF341^ENSG00000131061.14"  ; ID "E2F1--ZNF341^ENST00000342427.6"  ; Parent "E2F1--ZNF341^ZNF341^ENSG00000131061.14"  ; ccdsid "CCDS13227.1"  ; exon_id "ENSE00001660419.1"  ; exon_number 1 ; gene_id "E2F1--ZNF341^ZNF341^ENSG00000131061.14"  ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5"  ; havana_transcript "OTTHUMT00000078741.2"  ; hgnc_id "HGNC:15992"  ; level 2 ; orig_coord_info "chr20,33732022,33732052,+"  ; protein_id "ENSP00000344308.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "E2F1--ZNF341^ENST00000342427.6"  ; transcript_name "ZNF341-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
E2F1--ZNF341	HAVANA	gene	1001	6921	.	+	.	FI_gene_label "E2F1^ENSG00000101412.13"  ; ID "E2F1--ZNF341^E2F1^ENSG00000101412.13"  ; ccdsid "CCDS13224.1"  ; exon_id "ENSE00001667355.2"  ; exon_number 1 ; gene_id "E2F1--ZNF341^E2F1^ENSG00000101412.13"  ; gene_name E2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032265.3"  ; havana_transcript "OTTHUMT00000078731.3"  ; hgnc_id "HGNC:3113"  ; level 2 ; orig_coord_info "chr20,33686004,33686264,-"  ; protein_id "ENSP00000345571.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F1--ZNF341^ENST00000343380.6"  ; transcript_name "E2F1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
E2F1--ZNF341	HAVANA	mRNA	1001	6921	.	+	.	FI_gene_label "E2F1^ENSG00000101412.13"  ; ID "E2F1--ZNF341^ENST00000343380.6"  ; Parent "E2F1--ZNF341^E2F1^ENSG00000101412.13"  ; ccdsid "CCDS13224.1"  ; exon_id "ENSE00001667355.2"  ; exon_number 1 ; gene_id "E2F1--ZNF341^E2F1^ENSG00000101412.13"  ; gene_name E2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032265.3"  ; havana_transcript "OTTHUMT00000078731.3"  ; hgnc_id "HGNC:3113"  ; level 2 ; orig_coord_info "chr20,33686004,33686264,-"  ; protein_id "ENSP00000345571.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F1--ZNF341^ENST00000343380.6"  ; transcript_name "E2F1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
F8--IKBKG	HAVANA	gene	29435	39341	.	+	.	FI_gene_label "F8^ENSG00000185010.15"  ; ID "F8--IKBKG^F8^ENSG00000185010.15"  ; ccdsid "CCDS44026.1"  ; exon_id "ENSE00001515616.3"  ; exon_number 1 ; gene_id "F8--IKBKG^F8^ENSG00000185010.15"  ; gene_name F8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022688.16"  ; havana_transcript "OTTHUMT00000083107.7"  ; hgnc_id "HGNC:3546"  ; level 1 ; orig_coord_info "chrX,154886134,154886157,-"  ; protein_id "ENSP00000327895.6"  ; tag basic exp_conf CCDS ; transcript_id "F8--IKBKG^ENST00000330287.10"  ; transcript_name "F8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
F8--IKBKG	HAVANA	mRNA	29435	39341	.	+	.	FI_gene_label "F8^ENSG00000185010.15"  ; ID "F8--IKBKG^ENST00000330287.10"  ; Parent "F8--IKBKG^F8^ENSG00000185010.15"  ; ccdsid "CCDS44026.1"  ; exon_id "ENSE00001515616.3"  ; exon_number 1 ; gene_id "F8--IKBKG^F8^ENSG00000185010.15"  ; gene_name F8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022688.16"  ; havana_transcript "OTTHUMT00000083107.7"  ; hgnc_id "HGNC:3546"  ; level 1 ; orig_coord_info "chrX,154886134,154886157,-"  ; protein_id "ENSP00000327895.6"  ; tag basic exp_conf CCDS ; transcript_id "F8--IKBKG^ENST00000330287.10"  ; transcript_name "F8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
F8--IKBKG	HAVANA	gene	45860	51712	.	+	.	FI_gene_label "IKBKG^ENSG00000269335.6"  ; ID "F8--IKBKG^IKBKG^ENSG00000269335.6"  ; exon_id "ENSE00001651956.1"  ; exon_number 2 ; gene_id "F8--IKBKG^IKBKG^ENSG00000269335.6"  ; gene_name IKBKG ; gene_type protein_coding ; havana_gene "OTTHUMG00000024234.17"  ; havana_transcript "OTTHUMT00000061161.2"  ; hgnc_id "HGNC:5961"  ; level 2 ; orig_coord_info "chrX,154552039,154552189,+"  ; protein_id "ENSP00000398579.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "F8--IKBKG^ENST00000413620.5"  ; transcript_name "IKBKG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
F8--IKBKG	HAVANA	mRNA	45860	51712	.	+	.	FI_gene_label "IKBKG^ENSG00000269335.6"  ; ID "F8--IKBKG^ENST00000413620.5"  ; Parent "F8--IKBKG^IKBKG^ENSG00000269335.6"  ; exon_id "ENSE00001651956.1"  ; exon_number 2 ; gene_id "F8--IKBKG^IKBKG^ENSG00000269335.6"  ; gene_name IKBKG ; gene_type protein_coding ; havana_gene "OTTHUMG00000024234.17"  ; havana_transcript "OTTHUMT00000061161.2"  ; hgnc_id "HGNC:5961"  ; level 2 ; orig_coord_info "chrX,154552039,154552189,+"  ; protein_id "ENSP00000398579.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "F8--IKBKG^ENST00000413620.5"  ; transcript_name "IKBKG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
FANCI--ABHD2	HAVANA	gene	1005	41482	.	+	.	FI_gene_label "FANCI^ENSG00000140525.19"  ; ID "FANCI--ABHD2^FANCI^ENSG00000140525.19"  ; ccdsid "CCDS10349.2"  ; exon_id "ENSE00003645183.1"  ; exon_number 2 ; gene_id "FANCI--ABHD2^FANCI^ENSG00000140525.19"  ; gene_name FANCI ; gene_type protein_coding ; havana_gene "OTTHUMG00000132993.7"  ; havana_transcript "OTTHUMT00000256568.2"  ; hgnc_id "HGNC:25568"  ; level 2 ; orig_coord_info "chr15,89247648,89247731,+"  ; protein_id "ENSP00000300027.8"  ; tag basic CCDS ; transcript_id "FANCI--ABHD2^ENST00000300027.12"  ; transcript_name "FANCI-201"  ; transcript_support_level 5 ; transcript_type protein_coding
FANCI--ABHD2	HAVANA	mRNA	1005	41482	.	+	.	FI_gene_label "FANCI^ENSG00000140525.19"  ; ID "FANCI--ABHD2^ENST00000300027.12"  ; Parent "FANCI--ABHD2^FANCI^ENSG00000140525.19"  ; ccdsid "CCDS10349.2"  ; exon_id "ENSE00003645183.1"  ; exon_number 2 ; gene_id "FANCI--ABHD2^FANCI^ENSG00000140525.19"  ; gene_name FANCI ; gene_type protein_coding ; havana_gene "OTTHUMG00000132993.7"  ; havana_transcript "OTTHUMT00000256568.2"  ; hgnc_id "HGNC:25568"  ; level 2 ; orig_coord_info "chr15,89247648,89247731,+"  ; protein_id "ENSP00000300027.8"  ; tag basic CCDS ; transcript_id "FANCI--ABHD2^ENST00000300027.12"  ; transcript_name "FANCI-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
FANCI--ABHD2	HAVANA	gene	45480	71592	.	+	.	FI_gene_label "ABHD2^ENSG00000140526.18"  ; ID "FANCI--ABHD2^ABHD2^ENSG00000140526.18"  ; ccdsid "CCDS10348.1"  ; exon_id "ENSE00000943593.2"  ; exon_number 3 ; gene_id "FANCI--ABHD2^ABHD2^ENSG00000140526.18"  ; gene_name ABHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148684.6"  ; havana_transcript "OTTHUMT00000309074.3"  ; hgnc_id "HGNC:18717"  ; level 2 ; orig_coord_info "chr15,89116328,89116521,+"  ; protein_id "ENSP00000268129.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FANCI--ABHD2^ENST00000352732.10"  ; transcript_name "ABHD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FANCI--ABHD2	HAVANA	mRNA	45480	71592	.	+	.	FI_gene_label "ABHD2^ENSG00000140526.18"  ; ID "FANCI--ABHD2^ENST00000352732.10"  ; Parent "FANCI--ABHD2^ABHD2^ENSG00000140526.18"  ; ccdsid "CCDS10348.1"  ; exon_id "ENSE00000943593.2"  ; exon_number 3 ; gene_id "FANCI--ABHD2^ABHD2^ENSG00000140526.18"  ; gene_name ABHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148684.6"  ; havana_transcript "OTTHUMT00000309074.3"  ; hgnc_id "HGNC:18717"  ; level 2 ; orig_coord_info "chr15,89116328,89116521,+"  ; protein_id "ENSP00000268129.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FANCI--ABHD2^ENST00000352732.10"  ; transcript_name "ABHD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KANSL1--ARL17B	HAVANA	gene	7306	43177	.	+	.	FI_gene_label "KANSL1^ENSG00000120071.15"  ; ID "KANSL1--ARL17B^KANSL1^ENSG00000120071.15"  ; ccdsid "CCDS11503.2"  ; exon_id "ENSE00003614505.1"  ; exon_number 2 ; gene_id "KANSL1--ARL17B^KANSL1^ENSG00000120071.15"  ; gene_name KANSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178026.11"  ; havana_transcript "OTTHUMT00000440274.2"  ; hgnc_id "HGNC:24565"  ; level 2 ; orig_coord_info "chr17,46170855,46172143,-"  ; protein_id "ENSP00000262419.6"  ; tag alternative_5_UTR NAGNAG_splice_site basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000262419.10"  ; transcript_name "KANSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KANSL1--ARL17B	HAVANA	mRNA	7306	43177	.	+	.	FI_gene_label "KANSL1^ENSG00000120071.15"  ; ID "KANSL1--ARL17B^ENST00000262419.10"  ; Parent "KANSL1--ARL17B^KANSL1^ENSG00000120071.15"  ; ccdsid "CCDS11503.2"  ; exon_id "ENSE00003614505.1"  ; exon_number 2 ; gene_id "KANSL1--ARL17B^KANSL1^ENSG00000120071.15"  ; gene_name KANSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178026.11"  ; havana_transcript "OTTHUMT00000440274.2"  ; hgnc_id "HGNC:24565"  ; level 2 ; orig_coord_info "chr17,46170855,46172143,-"  ; protein_id "ENSP00000262419.6"  ; tag alternative_5_UTR NAGNAG_splice_site basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000262419.10"  ; transcript_name "KANSL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KANSL1--ARL17B	HAVANA	gene	46270	61341	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "KANSL1--ARL17B^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "KANSL1--ARL17B^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KANSL1--ARL17B	HAVANA	mRNA	46270	61341	.	+	.	FI_gene_label "ARL17B^ENSG00000228696.10"  ; ID "KANSL1--ARL17B^ENST00000434041.6"  ; Parent "KANSL1--ARL17B^ARL17B^ENSG00000228696.10"  ; ccdsid "CCDS54137.1"  ; exon_id "ENSE00002352294.1"  ; exon_number 2 ; gene_id "KANSL1--ARL17B^ARL17B^ENSG00000228696.10"  ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2"  ; havana_transcript "OTTHUMT00000440292.1"  ; hgnc_id "HGNC:32387"  ; level 2 ; orig_coord_info "chr17,46358250,46358397,-"  ; protein_id "ENSP00000391751.2"  ; tag basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000434041.6"  ; transcript_name "ARL17B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MTAP--H3P30	HAVANA	gene	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--H3P30^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--H3P30^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--H3P30^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--H3P30	HAVANA	mRNA	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--H3P30^ENST00000419385.5"  ; Parent "MTAP--H3P30^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--H3P30^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--H3P30^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
MTAP--KHSRPP1	HAVANA	gene	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--KHSRPP1^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--KHSRPP1^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--KHSRPP1^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--KHSRPP1	HAVANA	mRNA	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--KHSRPP1^ENST00000419385.5"  ; Parent "MTAP--KHSRPP1^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--KHSRPP1^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--KHSRPP1^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
PHF12--JMJD1C	HAVANA	gene	1282	15732	.	+	.	FI_gene_label "PHF12^ENSG00000109118.14"  ; ID "PHF12--JMJD1C^PHF12^ENSG00000109118.14"  ; ccdsid "CCDS11247.1"  ; exon_id "ENSE00001124814.3"  ; exon_number 1 ; gene_id "PHF12--JMJD1C^PHF12^ENSG00000109118.14"  ; gene_name PHF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132676.7"  ; havana_transcript "OTTHUMT00000255942.2"  ; hgnc_id "HGNC:20816"  ; level 2 ; orig_coord_info "chr17,28950895,28950960,-"  ; protein_id "ENSP00000268756.3"  ; tag basic CCDS ; transcript_id "PHF12--JMJD1C^ENST00000268756.7"  ; transcript_name "PHF12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF12--JMJD1C	HAVANA	mRNA	1282	15732	.	+	.	FI_gene_label "PHF12^ENSG00000109118.14"  ; ID "PHF12--JMJD1C^ENST00000268756.7"  ; Parent "PHF12--JMJD1C^PHF12^ENSG00000109118.14"  ; ccdsid "CCDS11247.1"  ; exon_id "ENSE00001124814.3"  ; exon_number 1 ; gene_id "PHF12--JMJD1C^PHF12^ENSG00000109118.14"  ; gene_name PHF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132676.7"  ; havana_transcript "OTTHUMT00000255942.2"  ; hgnc_id "HGNC:20816"  ; level 2 ; orig_coord_info "chr17,28950895,28950960,-"  ; protein_id "ENSP00000268756.3"  ; tag basic CCDS ; transcript_id "PHF12--JMJD1C^ENST00000268756.7"  ; transcript_name "PHF12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF12--JMJD1C	HAVANA	gene	39439	55295	.	+	.	FI_gene_label "JMJD1C^ENSG00000171988.19"  ; ID "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19"  ; exon_id "ENSE00001605128.1"  ; exon_number 1 ; gene_id "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19"  ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7"  ; havana_transcript "OTTHUMT00000048250.1"  ; hgnc_id "HGNC:12313"  ; level 1 ; orig_coord_info "chr10,63206595,63207725,-"  ; protein_id "ENSP00000335929.5"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PHF12--JMJD1C^ENST00000327520.7"  ; transcript_name "JMJD1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PHF12--JMJD1C	HAVANA	mRNA	39439	55295	.	+	.	FI_gene_label "JMJD1C^ENSG00000171988.19"  ; ID "PHF12--JMJD1C^ENST00000327520.7"  ; Parent "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19"  ; exon_id "ENSE00001605128.1"  ; exon_number 1 ; gene_id "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19"  ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7"  ; havana_transcript "OTTHUMT00000048250.1"  ; hgnc_id "HGNC:12313"  ; level 1 ; orig_coord_info "chr10,63206595,63207725,-"  ; protein_id "ENSP00000335929.5"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PHF12--JMJD1C^ENST00000327520.7"  ; transcript_name "JMJD1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PXMP4--ZNF341	HAVANA	gene	1010	4988	.	+	.	FI_gene_label "PXMP4^ENSG00000101417.12"  ; ID "PXMP4--ZNF341^PXMP4^ENSG00000101417.12"  ; exon_id "ENSE00001925420.1"  ; exon_number 1 ; gene_id "PXMP4--ZNF341^PXMP4^ENSG00000101417.12"  ; gene_name PXMP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032273.5"  ; havana_transcript "OTTHUMT00000334677.1"  ; hgnc_id "HGNC:15920"  ; level 2 ; orig_coord_info "chr20,33720095,33720207,-"  ; protein_id "ENSP00000217398.3"  ; tag basic ; transcript_id "PXMP4--ZNF341^ENST00000217398.3"  ; transcript_name "PXMP4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PXMP4--ZNF341	HAVANA	mRNA	1010	4988	.	+	.	FI_gene_label "PXMP4^ENSG00000101417.12"  ; ID "PXMP4--ZNF341^ENST00000217398.3"  ; Parent "PXMP4--ZNF341^PXMP4^ENSG00000101417.12"  ; exon_id "ENSE00001925420.1"  ; exon_number 1 ; gene_id "PXMP4--ZNF341^PXMP4^ENSG00000101417.12"  ; gene_name PXMP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032273.5"  ; havana_transcript "OTTHUMT00000334677.1"  ; hgnc_id "HGNC:15920"  ; level 2 ; orig_coord_info "chr20,33720095,33720207,-"  ; protein_id "ENSP00000217398.3"  ; tag basic ; transcript_id "PXMP4--ZNF341^ENST00000217398.3"  ; transcript_name "PXMP4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PXMP4--ZNF341	HAVANA	gene	12720	31719	.	+	.	FI_gene_label "ZNF341^ENSG00000131061.14"  ; ID "PXMP4--ZNF341^ZNF341^ENSG00000131061.14"  ; ccdsid "CCDS13227.1"  ; exon_id "ENSE00001660419.1"  ; exon_number 1 ; gene_id "PXMP4--ZNF341^ZNF341^ENSG00000131061.14"  ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5"  ; havana_transcript "OTTHUMT00000078741.2"  ; hgnc_id "HGNC:15992"  ; level 2 ; orig_coord_info "chr20,33732022,33732052,+"  ; protein_id "ENSP00000344308.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PXMP4--ZNF341^ENST00000342427.6"  ; transcript_name "ZNF341-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PXMP4--ZNF341	HAVANA	mRNA	12720	31719	.	+	.	FI_gene_label "ZNF341^ENSG00000131061.14"  ; ID "PXMP4--ZNF341^ENST00000342427.6"  ; Parent "PXMP4--ZNF341^ZNF341^ENSG00000131061.14"  ; ccdsid "CCDS13227.1"  ; exon_id "ENSE00001660419.1"  ; exon_number 1 ; gene_id "PXMP4--ZNF341^ZNF341^ENSG00000131061.14"  ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5"  ; havana_transcript "OTTHUMT00000078741.2"  ; hgnc_id "HGNC:15992"  ; level 2 ; orig_coord_info "chr20,33732022,33732052,+"  ; protein_id "ENSP00000344308.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "PXMP4--ZNF341^ENST00000342427.6"  ; transcript_name "ZNF341-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RABGAP1L--CACYBP	HAVANA	gene	1108	42636	.	+	.	FI_gene_label "RABGAP1L^ENSG00000152061.23"  ; ID "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23"  ; ccdsid "CCDS1314.1"  ; exon_id "ENSE00001445393.1"  ; exon_number 2 ; gene_id "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23"  ; gene_name RABGAP1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000034899.9"  ; havana_transcript "OTTHUMT00000084497.1"  ; hgnc_id "HGNC:24663"  ; level 2 ; orig_coord_info "chr1,174219158,174219295,+"  ; protein_id "ENSP00000251507.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000251507.8"  ; transcript_name "RABGAP1L-201"  ; transcript_support_level 2 ; transcript_type protein_coding
RABGAP1L--CACYBP	HAVANA	mRNA	1108	42636	.	+	.	FI_gene_label "RABGAP1L^ENSG00000152061.23"  ; ID "RABGAP1L--CACYBP^ENST00000251507.8"  ; Parent "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23"  ; ccdsid "CCDS1314.1"  ; exon_id "ENSE00001445393.1"  ; exon_number 2 ; gene_id "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23"  ; gene_name RABGAP1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000034899.9"  ; havana_transcript "OTTHUMT00000084497.1"  ; hgnc_id "HGNC:24663"  ; level 2 ; orig_coord_info "chr1,174219158,174219295,+"  ; protein_id "ENSP00000251507.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000251507.8"  ; transcript_name "RABGAP1L-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RABGAP1L--CACYBP	HAVANA	gene	59723	67821	.	+	.	FI_gene_label "CACYBP^ENSG00000116161.18"  ; ID "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18"  ; ccdsid "CCDS1315.1"  ; exon_id "ENSE00001273868.9"  ; exon_number 1 ; gene_id "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18"  ; gene_name CACYBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000034941.8"  ; havana_transcript "OTTHUMT00000084583.4"  ; hgnc_id "HGNC:30423"  ; level 2 ; orig_coord_info "chr1,175000181,175000195,+"  ; protein_id "ENSP00000356652.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000367679.7"  ; transcript_name "CACYBP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RABGAP1L--CACYBP	HAVANA	mRNA	59723	67821	.	+	.	FI_gene_label "CACYBP^ENSG00000116161.18"  ; ID "RABGAP1L--CACYBP^ENST00000367679.7"  ; Parent "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18"  ; ccdsid "CCDS1315.1"  ; exon_id "ENSE00001273868.9"  ; exon_number 1 ; gene_id "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18"  ; gene_name CACYBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000034941.8"  ; havana_transcript "OTTHUMT00000084583.4"  ; hgnc_id "HGNC:30423"  ; level 2 ; orig_coord_info "chr1,175000181,175000195,+"  ; protein_id "ENSP00000356652.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000367679.7"  ; transcript_name "CACYBP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNASE10--CD38	HAVANA	gene	6254	19390	.	+	.	FI_gene_label "CD38^ENSG00000004468.13"  ; ID "RNASE10--CD38^CD38^ENSG00000004468.13"  ; ccdsid "CCDS3417.1"  ; exon_id "ENSE00001131145.4"  ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13"  ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6"  ; havana_transcript "OTTHUMT00000250322.3"  ; hgnc_id "HGNC:1667"  ; level 2 ; orig_coord_info "chr4,15778415,15778647,+"  ; protein_id "ENSP00000226279.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8"  ; transcript_name "CD38-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RNASE10--CD38	HAVANA	mRNA	6254	19390	.	+	.	FI_gene_label "CD38^ENSG00000004468.13"  ; ID "RNASE10--CD38^ENST00000226279.8"  ; Parent "RNASE10--CD38^CD38^ENSG00000004468.13"  ; ccdsid "CCDS3417.1"  ; exon_id "ENSE00001131145.4"  ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13"  ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6"  ; havana_transcript "OTTHUMT00000250322.3"  ; hgnc_id "HGNC:1667"  ; level 2 ; orig_coord_info "chr4,15778415,15778647,+"  ; protein_id "ENSP00000226279.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8"  ; transcript_name "CD38-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNASE10--CD38	HAVANA	gene	2484	3200	.	+	.	FI_gene_label "RNASE10^ENSG00000182545.6"  ; ID "RNASE10--CD38^RNASE10^ENSG00000182545.6"  ; ccdsid "CCDS32035.1"  ; exon_id "ENSE00001299018.5"  ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6"  ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1"  ; havana_transcript "OTTHUMT00000411088.1"  ; hgnc_id "HGNC:19275"  ; level 2 ; orig_coord_info "chr14,20510472,20511119,+"  ; protein_id "ENSP00000333358.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5"  ; transcript_name "RNASE10-201"  ; transcript_support_level NA ; transcript_type protein_coding
RNASE10--CD38	HAVANA	mRNA	2484	3200	.	+	.	FI_gene_label "RNASE10^ENSG00000182545.6"  ; ID "RNASE10--CD38^ENST00000328444.5"  ; Parent "RNASE10--CD38^RNASE10^ENSG00000182545.6"  ; ccdsid "CCDS32035.1"  ; exon_id "ENSE00001299018.5"  ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6"  ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1"  ; havana_transcript "OTTHUMT00000411088.1"  ; hgnc_id "HGNC:19275"  ; level 2 ; orig_coord_info "chr14,20510472,20511119,+"  ; protein_id "ENSP00000333358.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5"  ; transcript_name "RNASE10-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
RPSAP52--HMGA2	HAVANA	gene	7036	17922	.	+	.	FI_gene_label "HMGA2^ENSG00000149948.14"  ; ID "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14"  ; ccdsid "CCDS31854.1"  ; exon_id "ENSE00001242304.6"  ; exon_number 1 ; gene_id "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14"  ; gene_name HMGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168936.2"  ; havana_transcript "OTTHUMT00000401660.1"  ; hgnc_id "HGNC:5009"  ; level 2 ; orig_coord_info "chr12,65825271,65825381,+"  ; protein_id "ENSP00000346658.3"  ; tag basic CCDS ; transcript_id "RPSAP52--HMGA2^ENST00000354636.7"  ; transcript_name "HMGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RPSAP52--HMGA2	HAVANA	mRNA	7036	17922	.	+	.	FI_gene_label "HMGA2^ENSG00000149948.14"  ; ID "RPSAP52--HMGA2^ENST00000354636.7"  ; Parent "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14"  ; ccdsid "CCDS31854.1"  ; exon_id "ENSE00001242304.6"  ; exon_number 1 ; gene_id "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14"  ; gene_name HMGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168936.2"  ; havana_transcript "OTTHUMT00000401660.1"  ; hgnc_id "HGNC:5009"  ; level 2 ; orig_coord_info "chr12,65825271,65825381,+"  ; protein_id "ENSP00000346658.3"  ; tag basic CCDS ; transcript_id "RPSAP52--HMGA2^ENST00000354636.7"  ; transcript_name "HMGA2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^ENST00000326270.13"  ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; 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: 
AC015712.1--KLK9	HAVANA	gene	1001	5743	.	+	.	FI_gene_label "AC015712.1^ENSG00000232386.9"  ; ID "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9"  ; exon_id "ENSE00002547857.1"  ; exon_number 1 ; gene_id "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9"  ; gene_name "AC015712.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186438.3"  ; havana_transcript "OTTHUMT00000416693.1"  ; level 2 ; orig_coord_info "chr15,100849561,100849910,+"  ; transcript_id "AC015712.1--KLK9^ENST00000557962.1"  ; transcript_name "AC015712.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
AC015712.1--KLK9	HAVANA	RNA	1001	5743	.	+	.	FI_gene_label "AC015712.1^ENSG00000232386.9"  ; ID "AC015712.1--KLK9^ENST00000557962.1"  ; Parent "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9"  ; exon_id "ENSE00002547857.1"  ; exon_number 1 ; gene_id "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9"  ; gene_name "AC015712.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000186438.3"  ; havana_transcript "OTTHUMT00000416693.1"  ; level 2 ; orig_coord_info "chr15,100849561,100849910,+"  ; transcript_id "AC015712.1--KLK9^ENST00000557962.1"  ; transcript_name "AC015712.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
AC015911.9--SLFN12L	HAVANA	gene	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L	HAVANA	RNA	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^ENST00000650652.2"  ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC015911.9--SLFN12L	ENSEMBL	gene	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
AC015911.9--SLFN12L	ENSEMBL	RNA	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^ENST00000675965.1"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
L1 and L2 created: 
MTAP--H3P30	HAVANA	gene	29696	30087	.	+	.	FI_gene_label "H3P30^ENSG00000227443.2"  ; ID "MTAP--H3P30^H3P30^ENSG00000227443.2"  ; exon_id "ENSE00001628925.2"  ; exon_number 1 ; gene_id "MTAP--H3P30^H3P30^ENSG00000227443.2"  ; gene_name H3P30 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019682.2"  ; havana_transcript "OTTHUMT00000051911.2"  ; hgnc_id "HGNC:54463"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,21638285,21638676,+"  ; tag pseudo_consens basic ; transcript_id "MTAP--H3P30^ENST00000424386.2"  ; transcript_name "H3P30-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MTAP--H3P30	HAVANA	RNA	29696	30087	.	+	.	FI_gene_label "H3P30^ENSG00000227443.2"  ; ID "MTAP--H3P30^ENST00000424386.2"  ; Parent "MTAP--H3P30^H3P30^ENSG00000227443.2"  ; exon_id "ENSE00001628925.2"  ; exon_number 1 ; gene_id "MTAP--H3P30^H3P30^ENSG00000227443.2"  ; gene_name H3P30 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019682.2"  ; havana_transcript "OTTHUMT00000051911.2"  ; hgnc_id "HGNC:54463"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,21638285,21638676,+"  ; tag pseudo_consens basic ; transcript_id "MTAP--H3P30^ENST00000424386.2"  ; transcript_name "H3P30-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
MTAP--KHSRPP1	HAVANA	gene	29696	31463	.	+	.	FI_gene_label "KHSRPP1^ENSG00000229835.2"  ; ID "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2"  ; exon_id "ENSE00001689429.2"  ; exon_number 1 ; gene_id "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2"  ; gene_name KHSRPP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019683.2"  ; havana_transcript "OTTHUMT00000051912.2"  ; hgnc_id "HGNC:39198"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,21695176,21696943,+"  ; tag pseudo_consens basic ; transcript_id "MTAP--KHSRPP1^ENST00000427983.2"  ; transcript_name "KHSRPP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MTAP--KHSRPP1	HAVANA	RNA	29696	31463	.	+	.	FI_gene_label "KHSRPP1^ENSG00000229835.2"  ; ID "MTAP--KHSRPP1^ENST00000427983.2"  ; Parent "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2"  ; exon_id "ENSE00001689429.2"  ; exon_number 1 ; gene_id "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2"  ; gene_name KHSRPP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019683.2"  ; havana_transcript "OTTHUMT00000051912.2"  ; hgnc_id "HGNC:39198"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,21695176,21696943,+"  ; tag pseudo_consens basic ; transcript_id "MTAP--KHSRPP1^ENST00000427983.2"  ; transcript_name "KHSRPP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
RPSAP52--HMGA2	HAVANA	gene	1024	4035	.	+	.	FI_gene_label "RPSAP52^ENSG00000241749.4"  ; ID "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4"  ; exon_id "ENSE00001887935.1"  ; exon_number 1 ; gene_id "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4"  ; gene_name RPSAP52 ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000157608.3"  ; havana_transcript "OTTHUMT00000349256.2"  ; hgnc_id "HGNC:35752"  ; level 2 ; orig_coord_info "chr12,65826843,65826974,-"  ; tag basic ; transcript_id "RPSAP52--HMGA2^ENST00000489520.2"  ; transcript_name "RPSAP52-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
RPSAP52--HMGA2	HAVANA	RNA	1024	4035	.	+	.	FI_gene_label "RPSAP52^ENSG00000241749.4"  ; ID "RPSAP52--HMGA2^ENST00000489520.2"  ; Parent "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4"  ; exon_id "ENSE00001887935.1"  ; exon_number 1 ; gene_id "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4"  ; gene_name RPSAP52 ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000157608.3"  ; havana_transcript "OTTHUMT00000349256.2"  ; hgnc_id "HGNC:35752"  ; level 2 ; orig_coord_info "chr12,65826843,65826974,-"  ; tag basic ; transcript_id "RPSAP52--HMGA2^ENST00000489520.2"  ; transcript_name "RPSAP52-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A	HAVANA	RNA	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^ENST00000437428.3"  ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
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
344 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 1 seconds -------------------------------

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

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

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

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

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

----------------------------- Check10: check utrs ------------------------------
611 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 28 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