.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-06a169-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/b76f24aa84c9c7dea38d4cfbd7b8a8/.command.log
Size: 58.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-06a169-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/b91878d73718e9ad9441d25883b44f/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/b76f24aa84c9c7dea38d4cfbd7b8a8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/b76f24aa84c9c7dea38d4cfbd7b8a8/.command.run
==> STAGING COMPLETE (3 inputs)

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 4699
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4699
=> 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:4699
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 2 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
APPL1--LINC02531	HAVANA	gene	1004	25535	.	+	.	FI_gene_label "APPL1^ENSG00000157500.12"  ; ID "APPL1--LINC02531^APPL1^ENSG00000157500.12"  ; ccdsid "CCDS2882.1"  ; exon_id "ENSE00001277615.7"  ; exon_number 1 ; gene_id "APPL1--LINC02531^APPL1^ENSG00000157500.12"  ; gene_name APPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133756.14"  ; havana_transcript "OTTHUMT00000258196.3"  ; hgnc_id "HGNC:24035"  ; level 2 ; orig_coord_info "chr3,57227884,57227937,+"  ; protein_id "ENSP00000288266.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "APPL1--LINC02531^ENST00000288266.8"  ; transcript_name "APPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
APPL1--LINC02531	HAVANA	mRNA	1004	25535	.	+	.	FI_gene_label "APPL1^ENSG00000157500.12"  ; ID "APPL1--LINC02531^ENST00000288266.8"  ; Parent "APPL1--LINC02531^APPL1^ENSG00000157500.12"  ; ccdsid "CCDS2882.1"  ; exon_id "ENSE00001277615.7"  ; exon_number 1 ; gene_id "APPL1--LINC02531^APPL1^ENSG00000157500.12"  ; gene_name APPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133756.14"  ; havana_transcript "OTTHUMT00000258196.3"  ; hgnc_id "HGNC:24035"  ; level 2 ; orig_coord_info "chr3,57227884,57227937,+"  ; protein_id "ENSP00000288266.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "APPL1--LINC02531^ENST00000288266.8"  ; transcript_name "APPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF10L--DLGAP3	HAVANA	gene	18785	37949	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "ARHGEF10L--DLGAP3^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "ARHGEF10L--DLGAP3^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ARHGEF10L--DLGAP3^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ARHGEF10L--DLGAP3	HAVANA	mRNA	18785	37949	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "ARHGEF10L--DLGAP3^ENST00000167825.5"  ; Parent "ARHGEF10L--DLGAP3^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "ARHGEF10L--DLGAP3^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ARHGEF10L--DLGAP3^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ARHGEF10L--DLGAP3	ENSEMBL	gene	44411	54084	.	+	.	FI_gene_label "DLGAP3^ENSG00000116544.12"  ; ID "ARHGEF10L--DLGAP3^DLGAP3^ENSG00000116544.12"  ; ccdsid "CCDS30670.1"  ; exon_id "ENSE00001460327.1"  ; exon_number 1 ; gene_id "ARHGEF10L--DLGAP3^DLGAP3^ENSG00000116544.12"  ; gene_name DLGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004049.2"  ; hgnc_id "HGNC:30368"  ; level 3 ; orig_coord_info "chr1,34904277,34905383,-"  ; protein_id "ENSP00000235180.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGEF10L--DLGAP3^ENST00000235180.4"  ; transcript_name "DLGAP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ARHGEF10L--DLGAP3	ENSEMBL	mRNA	44411	54084	.	+	.	FI_gene_label "DLGAP3^ENSG00000116544.12"  ; ID "ARHGEF10L--DLGAP3^ENST00000235180.4"  ; Parent "ARHGEF10L--DLGAP3^DLGAP3^ENSG00000116544.12"  ; ccdsid "CCDS30670.1"  ; exon_id "ENSE00001460327.1"  ; exon_number 1 ; gene_id "ARHGEF10L--DLGAP3^DLGAP3^ENSG00000116544.12"  ; gene_name DLGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004049.2"  ; hgnc_id "HGNC:30368"  ; level 3 ; orig_coord_info "chr1,34904277,34905383,-"  ; protein_id "ENSP00000235180.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGEF10L--DLGAP3^ENST00000235180.4"  ; transcript_name "DLGAP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF10L--NKAIN1	HAVANA	gene	18785	37949	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "ARHGEF10L--NKAIN1^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "ARHGEF10L--NKAIN1^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ARHGEF10L--NKAIN1^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ARHGEF10L--NKAIN1	HAVANA	mRNA	18785	37949	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "ARHGEF10L--NKAIN1^ENST00000167825.5"  ; Parent "ARHGEF10L--NKAIN1^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "ARHGEF10L--NKAIN1^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "ARHGEF10L--NKAIN1^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
ARHGEF10L--NKAIN1	HAVANA	gene	40956	50010	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "ARHGEF10L--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "ARHGEF10L--NKAIN1^NKAIN1^ENSG00000084628.10"  ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5"  ; havana_transcript "OTTHUMT00000010655.3"  ; hgnc_id "HGNC:25743"  ; level 2 ; orig_coord_info "chr1,31239494,31239547,-"  ; protein_id "ENSP00000362841.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF10L--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ARHGEF10L--NKAIN1	HAVANA	mRNA	40956	50010	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "ARHGEF10L--NKAIN1^ENST00000373736.7"  ; Parent "ARHGEF10L--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "ARHGEF10L--NKAIN1^NKAIN1^ENSG00000084628.10"  ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5"  ; havana_transcript "OTTHUMT00000010655.3"  ; hgnc_id "HGNC:25743"  ; level 2 ; orig_coord_info "chr1,31239494,31239547,-"  ; protein_id "ENSP00000362841.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF10L--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CDC27--AL162376.1	HAVANA	gene	1128	25238	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "CDC27--AL162376.1^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "CDC27--AL162376.1^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CDC27--AL162376.1^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CDC27--AL162376.1	HAVANA	mRNA	1128	25238	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "CDC27--AL162376.1^ENST00000066544.8"  ; Parent "CDC27--AL162376.1^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "CDC27--AL162376.1^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CDC27--AL162376.1^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CDC27--RNY1P8	HAVANA	gene	1128	25238	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "CDC27--RNY1P8^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "CDC27--RNY1P8^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CDC27--RNY1P8^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CDC27--RNY1P8	HAVANA	mRNA	1128	25238	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "CDC27--RNY1P8^ENST00000066544.8"  ; Parent "CDC27--RNY1P8^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "CDC27--RNY1P8^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CDC27--RNY1P8^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CHMP4B--LINC02219	HAVANA	gene	1001	6602	.	+	.	FI_gene_label "CHMP4B^ENSG00000101421.4"  ; ID "CHMP4B--LINC02219^CHMP4B^ENSG00000101421.4"  ; ccdsid "CCDS13228.1"  ; exon_id "ENSE00000661352.7"  ; exon_number 1 ; gene_id "CHMP4B--LINC02219^CHMP4B^ENSG00000101421.4"  ; gene_name CHMP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000032272.3"  ; havana_transcript "OTTHUMT00000078738.3"  ; hgnc_id "HGNC:16171"  ; level 2 ; orig_coord_info "chr20,33811469,33811658,+"  ; protein_id "ENSP00000217402.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CHMP4B--LINC02219^ENST00000217402.3"  ; transcript_name "CHMP4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CHMP4B--LINC02219	HAVANA	mRNA	1001	6602	.	+	.	FI_gene_label "CHMP4B^ENSG00000101421.4"  ; ID "CHMP4B--LINC02219^ENST00000217402.3"  ; Parent "CHMP4B--LINC02219^CHMP4B^ENSG00000101421.4"  ; ccdsid "CCDS13228.1"  ; exon_id "ENSE00000661352.7"  ; exon_number 1 ; gene_id "CHMP4B--LINC02219^CHMP4B^ENSG00000101421.4"  ; gene_name CHMP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000032272.3"  ; havana_transcript "OTTHUMT00000078738.3"  ; hgnc_id "HGNC:16171"  ; level 2 ; orig_coord_info "chr20,33811469,33811658,+"  ; protein_id "ENSP00000217402.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CHMP4B--LINC02219^ENST00000217402.3"  ; transcript_name "CHMP4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B	HAVANA	mRNA	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^ENST00000308284.10"  ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FAM185A--DPY19L2P2	HAVANA	gene	1058	12344	.	+	.	FI_gene_label "FAM185A^ENSG00000222011.9"  ; ID "FAM185A--DPY19L2P2^FAM185A^ENSG00000222011.9"  ; ccdsid "CCDS47677.1"  ; exon_id "ENSE00001622968.2"  ; exon_number 1 ; gene_id "FAM185A--DPY19L2P2^FAM185A^ENSG00000222011.9"  ; gene_name FAM185A ; gene_type protein_coding ; havana_gene "OTTHUMG00000154140.4"  ; havana_transcript "OTTHUMT00000334053.1"  ; hgnc_id "HGNC:22412"  ; level 2 ; orig_coord_info "chr7,102749208,102749417,+"  ; protein_id "ENSP00000387066.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "FAM185A--DPY19L2P2^ENST00000409231.7"  ; transcript_name "FAM185A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
FAM185A--DPY19L2P2	HAVANA	mRNA	1058	12344	.	+	.	FI_gene_label "FAM185A^ENSG00000222011.9"  ; ID "FAM185A--DPY19L2P2^ENST00000409231.7"  ; Parent "FAM185A--DPY19L2P2^FAM185A^ENSG00000222011.9"  ; ccdsid "CCDS47677.1"  ; exon_id "ENSE00001622968.2"  ; exon_number 1 ; gene_id "FAM185A--DPY19L2P2^FAM185A^ENSG00000222011.9"  ; gene_name FAM185A ; gene_type protein_coding ; havana_gene "OTTHUMG00000154140.4"  ; havana_transcript "OTTHUMT00000334053.1"  ; hgnc_id "HGNC:22412"  ; level 2 ; orig_coord_info "chr7,102749208,102749417,+"  ; protein_id "ENSP00000387066.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "FAM185A--DPY19L2P2^ENST00000409231.7"  ; transcript_name "FAM185A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GOLPH3--PDZD2	HAVANA	gene	1001	6742	.	+	.	FI_gene_label "GOLPH3^ENSG00000113384.14"  ; ID "GOLPH3--PDZD2^GOLPH3^ENSG00000113384.14"  ; ccdsid "CCDS3896.1"  ; exon_id "ENSE00002031824.2"  ; exon_number 1 ; gene_id "GOLPH3--PDZD2^GOLPH3^ENSG00000113384.14"  ; gene_name GOLPH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090679.4"  ; havana_transcript "OTTHUMT00000207363.3"  ; hgnc_id "HGNC:15452"  ; level 2 ; orig_coord_info "chr5,32173810,32174034,-"  ; protein_id "ENSP00000265070.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GOLPH3--PDZD2^ENST00000265070.7"  ; transcript_name "GOLPH3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GOLPH3--PDZD2	HAVANA	mRNA	1001	6742	.	+	.	FI_gene_label "GOLPH3^ENSG00000113384.14"  ; ID "GOLPH3--PDZD2^ENST00000265070.7"  ; Parent "GOLPH3--PDZD2^GOLPH3^ENSG00000113384.14"  ; ccdsid "CCDS3896.1"  ; exon_id "ENSE00002031824.2"  ; exon_number 1 ; gene_id "GOLPH3--PDZD2^GOLPH3^ENSG00000113384.14"  ; gene_name GOLPH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090679.4"  ; havana_transcript "OTTHUMT00000207363.3"  ; hgnc_id "HGNC:15452"  ; level 2 ; orig_coord_info "chr5,32173810,32174034,-"  ; protein_id "ENSP00000265070.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GOLPH3--PDZD2^ENST00000265070.7"  ; transcript_name "GOLPH3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GOLPH3--PDZD2	HAVANA	gene	9743	55726	.	+	.	FI_gene_label "PDZD2^ENSG00000133401.16"  ; ID "GOLPH3--PDZD2^PDZD2^ENSG00000133401.16"  ; ccdsid "CCDS34137.1"  ; exon_id "ENSE00003550471.1"  ; exon_number 2 ; gene_id "GOLPH3--PDZD2^PDZD2^ENSG00000133401.16"  ; gene_name PDZD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161981.7"  ; havana_transcript "OTTHUMT00000366608.2"  ; hgnc_id "HGNC:18486"  ; level 2 ; orig_coord_info "chr5,31799249,31799724,+"  ; protein_id "ENSP00000402033.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GOLPH3--PDZD2^ENST00000438447.2"  ; transcript_name "PDZD2-202"  ; transcript_support_level 1 ; transcript_type protein_coding
GOLPH3--PDZD2	HAVANA	mRNA	9743	55726	.	+	.	FI_gene_label "PDZD2^ENSG00000133401.16"  ; ID "GOLPH3--PDZD2^ENST00000438447.2"  ; Parent "GOLPH3--PDZD2^PDZD2^ENSG00000133401.16"  ; ccdsid "CCDS34137.1"  ; exon_id "ENSE00003550471.1"  ; exon_number 2 ; gene_id "GOLPH3--PDZD2^PDZD2^ENSG00000133401.16"  ; gene_name PDZD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161981.7"  ; havana_transcript "OTTHUMT00000366608.2"  ; hgnc_id "HGNC:18486"  ; level 2 ; orig_coord_info "chr5,31799249,31799724,+"  ; protein_id "ENSP00000402033.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GOLPH3--PDZD2^ENST00000438447.2"  ; transcript_name "PDZD2-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GUCY1B2--NKAIN2	HAVANA	gene	24657	32303	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GUCY1B2--NKAIN2	HAVANA	mRNA	24657	32303	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "GUCY1B2--NKAIN2^ENST00000368416.5"  ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAX7--ARHGEF10L	HAVANA	gene	35826	54990	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "PAX7--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "PAX7--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "PAX7--ARHGEF10L^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
PAX7--ARHGEF10L	HAVANA	mRNA	35826	54990	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "PAX7--ARHGEF10L^ENST00000167825.5"  ; Parent "PAX7--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "PAX7--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "PAX7--ARHGEF10L^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
PAX7--ARHGEF10L	HAVANA	gene	1161	9988	.	+	.	FI_gene_label "PAX7^ENSG00000009709.12"  ; ID "PAX7--ARHGEF10L^PAX7^ENSG00000009709.12"  ; ccdsid "CCDS186.1"  ; exon_id "ENSE00001466882.1"  ; exon_number 1 ; gene_id "PAX7--ARHGEF10L^PAX7^ENSG00000009709.12"  ; gene_name PAX7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002433.3"  ; havana_transcript "OTTHUMT00000006928.1"  ; hgnc_id "HGNC:8621"  ; level 2 ; orig_coord_info "chr1,18631604,18631688,+"  ; protein_id "ENSP00000364524.3"  ; tag basic CCDS ; transcript_id "PAX7--ARHGEF10L^ENST00000375375.7"  ; transcript_name "PAX7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAX7--ARHGEF10L	HAVANA	mRNA	1161	9988	.	+	.	FI_gene_label "PAX7^ENSG00000009709.12"  ; ID "PAX7--ARHGEF10L^ENST00000375375.7"  ; Parent "PAX7--ARHGEF10L^PAX7^ENSG00000009709.12"  ; ccdsid "CCDS186.1"  ; exon_id "ENSE00001466882.1"  ; exon_number 1 ; gene_id "PAX7--ARHGEF10L^PAX7^ENSG00000009709.12"  ; gene_name PAX7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002433.3"  ; havana_transcript "OTTHUMT00000006928.1"  ; hgnc_id "HGNC:8621"  ; level 2 ; orig_coord_info "chr1,18631604,18631688,+"  ; protein_id "ENSP00000364524.3"  ; tag basic CCDS ; transcript_id "PAX7--ARHGEF10L^ENST00000375375.7"  ; transcript_name "PAX7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRPF8--BEST1	HAVANA	gene	1001	24961	.	+	.	FI_gene_label "PRPF8^ENSG00000174231.17"  ; ID "PRPF8--BEST1^PRPF8^ENSG00000174231.17"  ; ccdsid "CCDS11010.1"  ; exon_id "ENSE00003537012.1"  ; exon_number 2 ; gene_id "PRPF8--BEST1^PRPF8^ENSG00000174231.17"  ; gene_name PRPF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090553.7"  ; havana_transcript "OTTHUMT00000207079.4"  ; hgnc_id "HGNC:17340"  ; level 2 ; orig_coord_info "chr17,1684472,1684571,-"  ; protein_id "ENSP00000304350.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF8--BEST1^ENST00000304992.11"  ; transcript_name "PRPF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRPF8--BEST1	HAVANA	mRNA	1001	24961	.	+	.	FI_gene_label "PRPF8^ENSG00000174231.17"  ; ID "PRPF8--BEST1^ENST00000304992.11"  ; Parent "PRPF8--BEST1^PRPF8^ENSG00000174231.17"  ; ccdsid "CCDS11010.1"  ; exon_id "ENSE00003537012.1"  ; exon_number 2 ; gene_id "PRPF8--BEST1^PRPF8^ENSG00000174231.17"  ; gene_name PRPF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090553.7"  ; havana_transcript "OTTHUMT00000207079.4"  ; hgnc_id "HGNC:17340"  ; level 2 ; orig_coord_info "chr17,1684472,1684571,-"  ; protein_id "ENSP00000304350.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF8--BEST1^ENST00000304992.11"  ; transcript_name "PRPF8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRPF8--BEST1	HAVANA	gene	28250	39869	.	+	.	FI_gene_label "BEST1^ENSG00000167995.17"  ; ID "PRPF8--BEST1^BEST1^ENSG00000167995.17"  ; ccdsid "CCDS31580.1"  ; exon_id "ENSE00003658293.1"  ; exon_number 2 ; gene_id "PRPF8--BEST1^BEST1^ENSG00000167995.17"  ; gene_name BEST1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167469.4"  ; havana_transcript "OTTHUMT00000394715.2"  ; hgnc_id "HGNC:12703"  ; level 2 ; orig_coord_info "chr11,61951807,61951958,+"  ; protein_id "ENSP00000367282.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF8--BEST1^ENST00000378043.9"  ; transcript_name "BEST1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRPF8--BEST1	HAVANA	mRNA	28250	39869	.	+	.	FI_gene_label "BEST1^ENSG00000167995.17"  ; ID "PRPF8--BEST1^ENST00000378043.9"  ; Parent "PRPF8--BEST1^BEST1^ENSG00000167995.17"  ; ccdsid "CCDS31580.1"  ; exon_id "ENSE00003658293.1"  ; exon_number 2 ; gene_id "PRPF8--BEST1^BEST1^ENSG00000167995.17"  ; gene_name BEST1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167469.4"  ; havana_transcript "OTTHUMT00000394715.2"  ; hgnc_id "HGNC:12703"  ; level 2 ; orig_coord_info "chr11,61951807,61951958,+"  ; protein_id "ENSP00000367282.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF8--BEST1^ENST00000378043.9"  ; transcript_name "BEST1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SH3GLB2--CDC27	HAVANA	gene	16468	40578	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "SH3GLB2--CDC27^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "SH3GLB2--CDC27^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SH3GLB2--CDC27^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SH3GLB2--CDC27	HAVANA	mRNA	16468	40578	.	+	.	FI_gene_label "CDC27^ENSG00000004897.12"  ; ID "SH3GLB2--CDC27^ENST00000066544.8"  ; Parent "SH3GLB2--CDC27^CDC27^ENSG00000004897.12"  ; ccdsid "CCDS11509.1"  ; exon_id "ENSE00002166699.2"  ; exon_number 1 ; gene_id "SH3GLB2--CDC27^CDC27^ENSG00000004897.12"  ; gene_name CDC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166429.8"  ; havana_transcript "OTTHUMT00000389742.3"  ; hgnc_id "HGNC:1728"  ; level 2 ; orig_coord_info "chr17,47189146,47189172,-"  ; protein_id "ENSP00000066544.3"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SH3GLB2--CDC27^ENST00000066544.8"  ; transcript_name "CDC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SH3GLB2--CDC27	HAVANA	gene	1053	12337	.	+	.	FI_gene_label "SH3GLB2^ENSG00000148341.18"  ; ID "SH3GLB2--CDC27^SH3GLB2^ENSG00000148341.18"  ; ccdsid "CCDS69680.1"  ; exon_id "ENSE00001954305.1"  ; exon_number 1 ; gene_id "SH3GLB2--CDC27^SH3GLB2^ENSG00000148341.18"  ; gene_name SH3GLB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020769.8"  ; havana_transcript "OTTHUMT00000106248.1"  ; hgnc_id "HGNC:10834"  ; level 2 ; orig_coord_info "chr9,129028092,129028154,-"  ; protein_id "ENSP00000361634.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "SH3GLB2--CDC27^ENST00000372554.8"  ; transcript_name "SH3GLB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SH3GLB2--CDC27	HAVANA	mRNA	1053	12337	.	+	.	FI_gene_label "SH3GLB2^ENSG00000148341.18"  ; ID "SH3GLB2--CDC27^ENST00000372554.8"  ; Parent "SH3GLB2--CDC27^SH3GLB2^ENSG00000148341.18"  ; ccdsid "CCDS69680.1"  ; exon_id "ENSE00001954305.1"  ; exon_number 1 ; gene_id "SH3GLB2--CDC27^SH3GLB2^ENSG00000148341.18"  ; gene_name SH3GLB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020769.8"  ; havana_transcript "OTTHUMT00000106248.1"  ; hgnc_id "HGNC:10834"  ; level 2 ; orig_coord_info "chr9,129028092,129028154,-"  ; protein_id "ENSP00000361634.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "SH3GLB2--CDC27^ENST00000372554.8"  ; transcript_name "SH3GLB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLC39A11--LINC00511	HAVANA	gene	1020	24927	.	+	.	FI_gene_label "SLC39A11^ENSG00000133195.11"  ; ID "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11"  ; ccdsid "CCDS11690.1"  ; exon_id "ENSE00003519818.1"  ; exon_number 2 ; gene_id "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11"  ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5"  ; havana_transcript "OTTHUMT00000441441.1"  ; hgnc_id "HGNC:14463"  ; level 2 ; orig_coord_info "chr17,73088657,73088764,-"  ; protein_id "ENSP00000255559.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--LINC00511^ENST00000255559.7"  ; transcript_name "SLC39A11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC39A11--LINC00511	HAVANA	mRNA	1020	24927	.	+	.	FI_gene_label "SLC39A11^ENSG00000133195.11"  ; ID "SLC39A11--LINC00511^ENST00000255559.7"  ; Parent "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11"  ; ccdsid "CCDS11690.1"  ; exon_id "ENSE00003519818.1"  ; exon_number 2 ; gene_id "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11"  ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5"  ; havana_transcript "OTTHUMT00000441441.1"  ; hgnc_id "HGNC:14463"  ; level 2 ; orig_coord_info "chr17,73088657,73088764,-"  ; protein_id "ENSP00000255559.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--LINC00511^ENST00000255559.7"  ; transcript_name "SLC39A11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TAS1R2--ARHGEF10L	HAVANA	gene	29327	48491	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "TAS1R2--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "TAS1R2--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAS1R2--ARHGEF10L^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
TAS1R2--ARHGEF10L	HAVANA	mRNA	29327	48491	.	+	.	FI_gene_label "ARHGEF10L^ENSG00000074964.17"  ; ID "TAS1R2--ARHGEF10L^ENST00000167825.5"  ; Parent "TAS1R2--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; exon_id "ENSE00001833298.1"  ; exon_number 1 ; gene_id "TAS1R2--ARHGEF10L^ARHGEF10L^ENSG00000074964.17"  ; gene_name ARHGEF10L ; gene_type protein_coding ; havana_gene "OTTHUMG00000002514.4"  ; havana_transcript "OTTHUMT00000007151.2"  ; hgnc_id "HGNC:25540"  ; level 2 ; orig_coord_info "chr1,17626007,17626048,+"  ; protein_id "ENSP00000167825.5"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAS1R2--ARHGEF10L^ENST00000167825.5"  ; transcript_name "ARHGEF10L-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
TAS1R2--ARHGEF10L	HAVANA	gene	1001	8542	.	+	.	FI_gene_label "TAS1R2^ENSG00000179002.5"  ; ID "TAS1R2--ARHGEF10L^TAS1R2^ENSG00000179002.5"  ; ccdsid "CCDS187.1"  ; exon_id "ENSE00001466844.3"  ; exon_number 1 ; gene_id "TAS1R2--ARHGEF10L^TAS1R2^ENSG00000179002.5"  ; gene_name TAS1R2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002442.2"  ; havana_transcript "OTTHUMT00000006953.2"  ; hgnc_id "HGNC:14905"  ; level 1 ; orig_coord_info "chr1,18859479,18859660,-"  ; protein_id "ENSP00000364520.3"  ; tag basic appris_principal_1 exp_conf CCDS ; transcript_id "TAS1R2--ARHGEF10L^ENST00000375371.3"  ; transcript_name "TAS1R2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TAS1R2--ARHGEF10L	HAVANA	mRNA	1001	8542	.	+	.	FI_gene_label "TAS1R2^ENSG00000179002.5"  ; ID "TAS1R2--ARHGEF10L^ENST00000375371.3"  ; Parent "TAS1R2--ARHGEF10L^TAS1R2^ENSG00000179002.5"  ; ccdsid "CCDS187.1"  ; exon_id "ENSE00001466844.3"  ; exon_number 1 ; gene_id "TAS1R2--ARHGEF10L^TAS1R2^ENSG00000179002.5"  ; gene_name TAS1R2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002442.2"  ; havana_transcript "OTTHUMT00000006953.2"  ; hgnc_id "HGNC:14905"  ; level 1 ; orig_coord_info "chr1,18859479,18859660,-"  ; protein_id "ENSP00000364520.3"  ; tag basic appris_principal_1 exp_conf CCDS ; transcript_id "TAS1R2--ARHGEF10L^ENST00000375371.3"  ; transcript_name "TAS1R2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TP53--CLDN7	HAVANA	gene	1049	11797	.	+	.	FI_gene_label "TP53^ENSG00000141510.18"  ; ID "TP53--CLDN7^TP53^ENSG00000141510.18"  ; ccdsid "CCDS11118.1"  ; exon_id "ENSE00002667911.1"  ; exon_number 2 ; gene_id "TP53--CLDN7^TP53^ENSG00000141510.18"  ; gene_name TP53 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162125.10"  ; havana_transcript "OTTHUMT00000367397.3"  ; hgnc_id "HGNC:11998"  ; level 2 ; orig_coord_info "chr17,7676521,7676594,-"  ; protein_id "ENSP00000269305.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TP53--CLDN7^ENST00000269305.9"  ; transcript_name "TP53-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TP53--CLDN7	HAVANA	mRNA	1049	11797	.	+	.	FI_gene_label "TP53^ENSG00000141510.18"  ; ID "TP53--CLDN7^ENST00000269305.9"  ; Parent "TP53--CLDN7^TP53^ENSG00000141510.18"  ; ccdsid "CCDS11118.1"  ; exon_id "ENSE00002667911.1"  ; exon_number 2 ; gene_id "TP53--CLDN7^TP53^ENSG00000141510.18"  ; gene_name TP53 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162125.10"  ; havana_transcript "OTTHUMT00000367397.3"  ; hgnc_id "HGNC:11998"  ; level 2 ; orig_coord_info "chr17,7676521,7676594,-"  ; protein_id "ENSP00000269305.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TP53--CLDN7^ENST00000269305.9"  ; transcript_name "TP53-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TP53--CLDN7	HAVANA	gene	20544	23119	.	+	.	FI_gene_label "CLDN7^ENSG00000181885.18"  ; ID "TP53--CLDN7^CLDN7^ENSG00000181885.18"  ; ccdsid "CCDS11096.1"  ; exon_id "ENSE00002675597.1"  ; exon_number 1 ; gene_id "TP53--CLDN7^CLDN7^ENSG00000181885.18"  ; gene_name CLDN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178005.4"  ; havana_transcript "OTTHUMT00000440204.2"  ; hgnc_id "HGNC:2049"  ; level 2 ; orig_coord_info "chr17,7261821,7262043,-"  ; protein_id "ENSP00000353475.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TP53--CLDN7^ENST00000360325.11"  ; transcript_name "CLDN7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TP53--CLDN7	HAVANA	mRNA	20544	23119	.	+	.	FI_gene_label "CLDN7^ENSG00000181885.18"  ; ID "TP53--CLDN7^ENST00000360325.11"  ; Parent "TP53--CLDN7^CLDN7^ENSG00000181885.18"  ; ccdsid "CCDS11096.1"  ; exon_id "ENSE00002675597.1"  ; exon_number 1 ; gene_id "TP53--CLDN7^CLDN7^ENSG00000181885.18"  ; gene_name CLDN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178005.4"  ; havana_transcript "OTTHUMT00000440204.2"  ; hgnc_id "HGNC:2049"  ; level 2 ; orig_coord_info "chr17,7261821,7262043,-"  ; protein_id "ENSP00000353475.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TP53--CLDN7^ENST00000360325.11"  ; transcript_name "CLDN7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
APPL1--LINC02531	HAVANA	gene	31005	31831	.	+	.	FI_gene_label "LINC02531^ENSG00000220908.2"  ; ID "APPL1--LINC02531^LINC02531^ENSG00000220908.2"  ; exon_id "ENSE00001564266.2"  ; exon_number 1 ; gene_id "APPL1--LINC02531^LINC02531^ENSG00000220908.2"  ; gene_name LINC02531 ; gene_type lncRNA ; havana_gene "OTTHUMG00000015224.1"  ; havana_transcript "OTTHUMT00000041541.1"  ; hgnc_id "HGNC:53557"  ; level 1 ; orig_coord_info "chr6,92723322,92723829,-"  ; tag basic exp_conf ; transcript_id "APPL1--LINC02531^ENST00000404689.2"  ; transcript_name "LINC02531-201"  ; transcript_support_level 5 ; transcript_type lncRNA
APPL1--LINC02531	HAVANA	RNA	31005	31831	.	+	.	FI_gene_label "LINC02531^ENSG00000220908.2"  ; ID "APPL1--LINC02531^ENST00000404689.2"  ; Parent "APPL1--LINC02531^LINC02531^ENSG00000220908.2"  ; exon_id "ENSE00001564266.2"  ; exon_number 1 ; gene_id "APPL1--LINC02531^LINC02531^ENSG00000220908.2"  ; gene_name LINC02531 ; gene_type lncRNA ; havana_gene "OTTHUMG00000015224.1"  ; havana_transcript "OTTHUMT00000041541.1"  ; hgnc_id "HGNC:53557"  ; level 1 ; orig_coord_info "chr6,92723322,92723829,-"  ; tag basic exp_conf ; transcript_id "APPL1--LINC02531^ENST00000404689.2"  ; transcript_name "LINC02531-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
CDC27--AL162376.1	HAVANA	gene	28239	28413	.	+	.	FI_gene_label "AL162376.1^ENSG00000279754.1"  ; ID "CDC27--AL162376.1^AL162376.1^ENSG00000279754.1"  ; exon_id "ENSE00003757562.1"  ; exon_number 1 ; gene_id "CDC27--AL162376.1^AL162376.1^ENSG00000279754.1"  ; gene_name "AL162376.1"  ; gene_type TEC ; havana_gene "OTTHUMG00000176037.1"  ; havana_transcript "OTTHUMT00000431410.1"  ; level 2 ; orig_coord_info "chr13,73399031,73399205,+"  ; tag basic ; transcript_id "CDC27--AL162376.1^ENST00000624117.1"  ; transcript_name "AL162376.1-201"  ; transcript_support_level NA ; transcript_type TEC
CDC27--AL162376.1	HAVANA	RNA	28239	28413	.	+	.	FI_gene_label "AL162376.1^ENSG00000279754.1"  ; ID "CDC27--AL162376.1^ENST00000624117.1"  ; Parent "CDC27--AL162376.1^AL162376.1^ENSG00000279754.1"  ; exon_id "ENSE00003757562.1"  ; exon_number 1 ; gene_id "CDC27--AL162376.1^AL162376.1^ENSG00000279754.1"  ; gene_name "AL162376.1"  ; gene_type TEC ; havana_gene "OTTHUMG00000176037.1"  ; havana_transcript "OTTHUMT00000431410.1"  ; level 2 ; orig_coord_info "chr13,73399031,73399205,+"  ; tag basic ; transcript_id "CDC27--AL162376.1^ENST00000624117.1"  ; transcript_name "AL162376.1-201"  ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created: 
CDC27--RNY1P8	ENSEMBL	gene	28239	28352	.	+	.	FI_gene_label "RNY1P8^ENSG00000206697.1"  ; ID "CDC27--RNY1P8^RNY1P8^ENSG00000206697.1"  ; exon_id "ENSE00001498980.1"  ; exon_number 1 ; gene_id "CDC27--RNY1P8^RNY1P8^ENSG00000206697.1"  ; gene_name RNY1P8 ; gene_type misc_RNA ; hgnc_id "HGNC:42485"  ; level 3 ; orig_coord_info "chr13,73227147,73227260,+"  ; tag basic ; transcript_id "CDC27--RNY1P8^ENST00000383970.1"  ; transcript_name "RNY1P8-201"  ; transcript_support_level NA ; transcript_type misc_RNA
CDC27--RNY1P8	ENSEMBL	RNA	28239	28352	.	+	.	FI_gene_label "RNY1P8^ENSG00000206697.1"  ; ID "CDC27--RNY1P8^ENST00000383970.1"  ; Parent "CDC27--RNY1P8^RNY1P8^ENSG00000206697.1"  ; exon_id "ENSE00001498980.1"  ; exon_number 1 ; gene_id "CDC27--RNY1P8^RNY1P8^ENSG00000206697.1"  ; gene_name RNY1P8 ; gene_type misc_RNA ; hgnc_id "HGNC:42485"  ; level 3 ; orig_coord_info "chr13,73227147,73227260,+"  ; tag basic ; transcript_id "CDC27--RNY1P8^ENST00000383970.1"  ; transcript_name "RNY1P8-201"  ; transcript_support_level NA ; transcript_type misc_RNA
L1 and L2 created: 
CHMP4B--LINC02219	HAVANA	gene	9603	12056	.	+	.	FI_gene_label "LINC02219^ENSG00000253787.1"  ; ID "CHMP4B--LINC02219^LINC02219^ENSG00000253787.1"  ; exon_id "ENSE00002094451.1"  ; exon_number 1 ; gene_id "CHMP4B--LINC02219^LINC02219^ENSG00000253787.1"  ; gene_name LINC02219 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164191.1"  ; havana_transcript "OTTHUMT00000377721.1"  ; hgnc_id "HGNC:53086"  ; level 2 ; orig_coord_info "chr5,68189876,68189991,+"  ; tag basic ; transcript_id "CHMP4B--LINC02219^ENST00000520762.1"  ; transcript_name "LINC02219-201"  ; transcript_support_level 2 ; transcript_type lncRNA
CHMP4B--LINC02219	HAVANA	RNA	9603	12056	.	+	.	FI_gene_label "LINC02219^ENSG00000253787.1"  ; ID "CHMP4B--LINC02219^ENST00000520762.1"  ; Parent "CHMP4B--LINC02219^LINC02219^ENSG00000253787.1"  ; exon_id "ENSE00002094451.1"  ; exon_number 1 ; gene_id "CHMP4B--LINC02219^LINC02219^ENSG00000253787.1"  ; gene_name LINC02219 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164191.1"  ; havana_transcript "OTTHUMT00000377721.1"  ; hgnc_id "HGNC:53086"  ; level 2 ; orig_coord_info "chr5,68189876,68189991,+"  ; tag basic ; transcript_id "CHMP4B--LINC02219^ENST00000520762.1"  ; transcript_name "LINC02219-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B	HAVANA	RNA	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^ENST00000462729.2"  ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created: 
FAM185A--DPY19L2P2	HAVANA	gene	15730	45203	.	+	.	FI_gene_label "DPY19L2P2^ENSG00000170629.14"  ; ID "FAM185A--DPY19L2P2^DPY19L2P2^ENSG00000170629.14"  ; exon_id "ENSE00001240945.4"  ; exon_number 1 ; gene_id "FAM185A--DPY19L2P2^DPY19L2P2^ENSG00000170629.14"  ; gene_name DPY19L2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000157200.1"  ; havana_transcript "OTTHUMT00000347877.1"  ; hgnc_id "HGNC:21764"  ; level 2 ; orig_coord_info "chr7,103279833,103280410,-"  ; tag basic ; transcript_id "FAM185A--DPY19L2P2^ENST00000312132.8"  ; transcript_name "DPY19L2P2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
FAM185A--DPY19L2P2	HAVANA	RNA	15730	45203	.	+	.	FI_gene_label "DPY19L2P2^ENSG00000170629.14"  ; ID "FAM185A--DPY19L2P2^ENST00000312132.8"  ; Parent "FAM185A--DPY19L2P2^DPY19L2P2^ENSG00000170629.14"  ; exon_id "ENSE00001240945.4"  ; exon_number 1 ; gene_id "FAM185A--DPY19L2P2^DPY19L2P2^ENSG00000170629.14"  ; gene_name DPY19L2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000157200.1"  ; havana_transcript "OTTHUMT00000347877.1"  ; hgnc_id "HGNC:21764"  ; level 2 ; orig_coord_info "chr7,103279833,103280410,-"  ; tag basic ; transcript_id "FAM185A--DPY19L2P2^ENST00000312132.8"  ; transcript_name "DPY19L2P2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
GUCY1B2--NKAIN2	HAVANA	gene	2157	15439	.	+	.	FI_gene_label "GUCY1B2^ENSG00000123201.14"  ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; exon_id "ENSE00001531871.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5"  ; havana_transcript "OTTHUMT00000045017.2"  ; hgnc_id "HGNC:4686"  ; level 2 ; orig_coord_info "chr13,51065951,51066207,-"  ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6"  ; transcript_name "GUCY1B2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
GUCY1B2--NKAIN2	HAVANA	RNA	2157	15439	.	+	.	FI_gene_label "GUCY1B2^ENSG00000123201.14"  ; ID "GUCY1B2--NKAIN2^ENST00000389600.6"  ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; exon_id "ENSE00001531871.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5"  ; havana_transcript "OTTHUMT00000045017.2"  ; hgnc_id "HGNC:4686"  ; level 2 ; orig_coord_info "chr13,51065951,51066207,-"  ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6"  ; transcript_name "GUCY1B2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
SLC39A11--LINC00511	HAVANA	gene	37738	81945	.	+	.	FI_gene_label "LINC00511^ENSG00000227036.8"  ; ID "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8"  ; exon_id "ENSE00001629418.1"  ; exon_number 1 ; gene_id "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8"  ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20"  ; havana_transcript "OTTHUMT00000255287.2"  ; hgnc_id "HGNC:43564"  ; level 2 ; orig_coord_info "chr17,72592203,72592804,-"  ; transcript_id "SLC39A11--LINC00511^ENST00000453722.6"  ; transcript_name "LINC00511-201"  ; transcript_support_level 2 ; transcript_type lncRNA
SLC39A11--LINC00511	HAVANA	RNA	37738	81945	.	+	.	FI_gene_label "LINC00511^ENSG00000227036.8"  ; ID "SLC39A11--LINC00511^ENST00000453722.6"  ; Parent "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8"  ; exon_id "ENSE00001629418.1"  ; exon_number 1 ; gene_id "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8"  ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20"  ; havana_transcript "OTTHUMT00000255287.2"  ; hgnc_id "HGNC:43564"  ; level 2 ; orig_coord_info "chr17,72592203,72592804,-"  ; transcript_id "SLC39A11--LINC00511^ENST00000453722.6"  ; transcript_name "LINC00511-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
417 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------

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

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

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

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

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

----------------------------- Check10: check utrs ------------------------------
583 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 25 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