.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/7b4ac196d059685190ef9663abce25/.command.log
Size: 72.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/d3bf23d4943a02b9e699ec341cfe6e/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/7b4ac196d059685190ef9663abce25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/7b4ac196d059685190ef9663abce25/.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: 6010
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6010
=> 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:6010
  => 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: 
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: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AMDHD1--PROCR	HAVANA	gene	15221	18820	.	+	.	FI_gene_label "PROCR^ENSG00000101000.6"  ; ID "AMDHD1--PROCR^PROCR^ENSG00000101000.6"  ; ccdsid "CCDS13248.1"  ; exon_id "ENSE00001049003.5"  ; exon_number 1 ; gene_id "AMDHD1--PROCR^PROCR^ENSG00000101000.6"  ; gene_name PROCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000032323.5"  ; havana_transcript "OTTHUMT00000078843.4"  ; hgnc_id "HGNC:9452"  ; level 2 ; orig_coord_info "chr20,35172155,35172224,+"  ; protein_id "ENSP00000216968.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AMDHD1--PROCR^ENST00000216968.5"  ; transcript_name "PROCR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AMDHD1--PROCR	HAVANA	mRNA	15221	18820	.	+	.	FI_gene_label "PROCR^ENSG00000101000.6"  ; ID "AMDHD1--PROCR^ENST00000216968.5"  ; Parent "AMDHD1--PROCR^PROCR^ENSG00000101000.6"  ; ccdsid "CCDS13248.1"  ; exon_id "ENSE00001049003.5"  ; exon_number 1 ; gene_id "AMDHD1--PROCR^PROCR^ENSG00000101000.6"  ; gene_name PROCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000032323.5"  ; havana_transcript "OTTHUMT00000078843.4"  ; hgnc_id "HGNC:9452"  ; level 2 ; orig_coord_info "chr20,35172155,35172224,+"  ; protein_id "ENSP00000216968.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AMDHD1--PROCR^ENST00000216968.5"  ; transcript_name "PROCR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AMDHD1--PROCR	HAVANA	gene	1001	12220	.	+	.	FI_gene_label "AMDHD1^ENSG00000139344.8"  ; ID "AMDHD1--PROCR^AMDHD1^ENSG00000139344.8"  ; ccdsid "CCDS9057.1"  ; exon_id "ENSE00001280254.4"  ; exon_number 1 ; gene_id "AMDHD1--PROCR^AMDHD1^ENSG00000139344.8"  ; gene_name AMDHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170353.4"  ; havana_transcript "OTTHUMT00000408640.3"  ; hgnc_id "HGNC:28577"  ; level 2 ; orig_coord_info "chr12,95943399,95943535,+"  ; protein_id "ENSP00000266736.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AMDHD1--PROCR^ENST00000266736.7"  ; transcript_name "AMDHD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AMDHD1--PROCR	HAVANA	mRNA	1001	12220	.	+	.	FI_gene_label "AMDHD1^ENSG00000139344.8"  ; ID "AMDHD1--PROCR^ENST00000266736.7"  ; Parent "AMDHD1--PROCR^AMDHD1^ENSG00000139344.8"  ; ccdsid "CCDS9057.1"  ; exon_id "ENSE00001280254.4"  ; exon_number 1 ; gene_id "AMDHD1--PROCR^AMDHD1^ENSG00000139344.8"  ; gene_name AMDHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170353.4"  ; havana_transcript "OTTHUMT00000408640.3"  ; hgnc_id "HGNC:28577"  ; level 2 ; orig_coord_info "chr12,95943399,95943535,+"  ; protein_id "ENSP00000266736.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AMDHD1--PROCR^ENST00000266736.7"  ; transcript_name "AMDHD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ASAP1--CCDC26	ENSEMBL	gene	1015	44661	.	+	.	FI_gene_label "ASAP1^ENSG00000153317.15"  ; ID "ASAP1--CCDC26^ASAP1^ENSG00000153317.15"  ; ccdsid "CCDS75788.1"  ; exon_id "ENSE00003501495.1"  ; exon_number 3 ; gene_id "ASAP1--CCDC26^ASAP1^ENSG00000153317.15"  ; gene_name ASAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164772.4"  ; hgnc_id "HGNC:2720"  ; level 3 ; orig_coord_info "chr8,130361670,130361707,-"  ; protein_id "ENSP00000350297.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ASAP1--CCDC26^ENST00000357668.2"  ; transcript_name "ASAP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ASAP1--CCDC26	ENSEMBL	mRNA	1015	44661	.	+	.	FI_gene_label "ASAP1^ENSG00000153317.15"  ; ID "ASAP1--CCDC26^ENST00000357668.2"  ; Parent "ASAP1--CCDC26^ASAP1^ENSG00000153317.15"  ; ccdsid "CCDS75788.1"  ; exon_id "ENSE00003501495.1"  ; exon_number 3 ; gene_id "ASAP1--CCDC26^ASAP1^ENSG00000153317.15"  ; gene_name ASAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164772.4"  ; hgnc_id "HGNC:2720"  ; level 3 ; orig_coord_info "chr8,130361670,130361707,-"  ; protein_id "ENSP00000350297.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "ASAP1--CCDC26^ENST00000357668.2"  ; transcript_name "ASAP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
BBOX1-AS1--ADGRL3	HAVANA	gene	26117	48520	.	+	.	FI_gene_label "ADGRL3^ENSG00000150471.16"  ; ID "BBOX1-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; exon_id "ENSE00002088156.1"  ; exon_number 1 ; gene_id "BBOX1-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; gene_name ADGRL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160690.2"  ; havana_transcript "OTTHUMT00000361764.1"  ; hgnc_id "HGNC:20974"  ; level 2 ; orig_coord_info "chr4,61895741,61895834,+"  ; protein_id "ENSP00000424402.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "BBOX1-AS1--ADGRL3^ENST00000502815.1"  ; transcript_name "ADGRL3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
BBOX1-AS1--ADGRL3	HAVANA	mRNA	26117	48520	.	+	.	FI_gene_label "ADGRL3^ENSG00000150471.16"  ; ID "BBOX1-AS1--ADGRL3^ENST00000502815.1"  ; Parent "BBOX1-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; exon_id "ENSE00002088156.1"  ; exon_number 1 ; gene_id "BBOX1-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; gene_name ADGRL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160690.2"  ; havana_transcript "OTTHUMT00000361764.1"  ; hgnc_id "HGNC:20974"  ; level 2 ; orig_coord_info "chr4,61895741,61895834,+"  ; protein_id "ENSP00000424402.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "BBOX1-AS1--ADGRL3^ENST00000502815.1"  ; transcript_name "ADGRL3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CYCTP--PDE11A	HAVANA	gene	5632	45178	.	+	.	FI_gene_label "PDE11A^ENSG00000128655.18"  ; ID "CYCTP--PDE11A^PDE11A^ENSG00000128655.18"  ; ccdsid "CCDS33334.1"  ; exon_id "ENSE00001125342.6"  ; exon_number 1 ; gene_id "CYCTP--PDE11A^PDE11A^ENSG00000128655.18"  ; gene_name PDE11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000154188.8"  ; havana_transcript "OTTHUMT00000334313.3"  ; hgnc_id "HGNC:8773"  ; level 2 ; orig_coord_info "chr2,178071526,178072437,-"  ; protein_id "ENSP00000286063.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYCTP--PDE11A^ENST00000286063.11"  ; transcript_name "PDE11A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CYCTP--PDE11A	HAVANA	mRNA	5632	45178	.	+	.	FI_gene_label "PDE11A^ENSG00000128655.18"  ; ID "CYCTP--PDE11A^ENST00000286063.11"  ; Parent "CYCTP--PDE11A^PDE11A^ENSG00000128655.18"  ; ccdsid "CCDS33334.1"  ; exon_id "ENSE00001125342.6"  ; exon_number 1 ; gene_id "CYCTP--PDE11A^PDE11A^ENSG00000128655.18"  ; gene_name PDE11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000154188.8"  ; havana_transcript "OTTHUMT00000334313.3"  ; hgnc_id "HGNC:8773"  ; level 2 ; orig_coord_info "chr2,178071526,178072437,-"  ; protein_id "ENSP00000286063.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYCTP--PDE11A^ENST00000286063.11"  ; transcript_name "PDE11A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXO25--AC240565.1	HAVANA	gene	2640	15007	.	+	.	FI_gene_label "FBXO25^ENSG00000147364.17"  ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; ccdsid "CCDS5954.1"  ; exon_id "ENSE00003460930.1"  ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8"  ; havana_transcript "OTTHUMT00000206713.2"  ; hgnc_id "HGNC:13596"  ; level 2 ; orig_coord_info "chr8,431358,431444,+"  ; protein_id "ENSP00000276326.6"  ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9"  ; transcript_name "FBXO25-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1	HAVANA	mRNA	2640	15007	.	+	.	FI_gene_label "FBXO25^ENSG00000147364.17"  ; ID "FBXO25--AC240565.1^ENST00000276326.9"  ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; ccdsid "CCDS5954.1"  ; exon_id "ENSE00003460930.1"  ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8"  ; havana_transcript "OTTHUMT00000206713.2"  ; hgnc_id "HGNC:13596"  ; level 2 ; orig_coord_info "chr8,431358,431444,+"  ; protein_id "ENSP00000276326.6"  ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9"  ; transcript_name "FBXO25-201"  ; 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: 
KCNMB2-AS1--ADGRL3	HAVANA	gene	36740	59143	.	+	.	FI_gene_label "ADGRL3^ENSG00000150471.16"  ; ID "KCNMB2-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; exon_id "ENSE00002088156.1"  ; exon_number 1 ; gene_id "KCNMB2-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; gene_name ADGRL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160690.2"  ; havana_transcript "OTTHUMT00000361764.1"  ; hgnc_id "HGNC:20974"  ; level 2 ; orig_coord_info "chr4,61895741,61895834,+"  ; protein_id "ENSP00000424402.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "KCNMB2-AS1--ADGRL3^ENST00000502815.1"  ; transcript_name "ADGRL3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
KCNMB2-AS1--ADGRL3	HAVANA	mRNA	36740	59143	.	+	.	FI_gene_label "ADGRL3^ENSG00000150471.16"  ; ID "KCNMB2-AS1--ADGRL3^ENST00000502815.1"  ; Parent "KCNMB2-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; exon_id "ENSE00002088156.1"  ; exon_number 1 ; gene_id "KCNMB2-AS1--ADGRL3^ADGRL3^ENSG00000150471.16"  ; gene_name ADGRL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160690.2"  ; havana_transcript "OTTHUMT00000361764.1"  ; hgnc_id "HGNC:20974"  ; level 2 ; orig_coord_info "chr4,61895741,61895834,+"  ; protein_id "ENSP00000424402.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "KCNMB2-AS1--ADGRL3^ENST00000502815.1"  ; transcript_name "ADGRL3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
LINC00381--NKAIN2	HAVANA	gene	10218	17864	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "LINC00381--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 "LINC00381--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC00381--NKAIN2	HAVANA	mRNA	10218	17864	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "LINC00381--NKAIN2^ENST00000368416.5"  ; Parent "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "LINC00381--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 "LINC00381--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRCH1--GRID1	HAVANA	gene	1001	29521	.	+	.	FI_gene_label "LRCH1^ENSG00000136141.15"  ; ID "LRCH1--GRID1^LRCH1^ENSG00000136141.15"  ; ccdsid "CCDS53866.1"  ; exon_id "ENSE00001156067.3"  ; exon_number 1 ; gene_id "LRCH1--GRID1^LRCH1^ENSG00000136141.15"  ; gene_name LRCH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016877.8"  ; havana_transcript "OTTHUMT00000044825.3"  ; hgnc_id "HGNC:20309"  ; level 2 ; orig_coord_info "chr13,46553397,46553703,+"  ; protein_id "ENSP00000308493.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "LRCH1--GRID1^ENST00000311191.10"  ; transcript_name "LRCH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LRCH1--GRID1	HAVANA	mRNA	1001	29521	.	+	.	FI_gene_label "LRCH1^ENSG00000136141.15"  ; ID "LRCH1--GRID1^ENST00000311191.10"  ; Parent "LRCH1--GRID1^LRCH1^ENSG00000136141.15"  ; ccdsid "CCDS53866.1"  ; exon_id "ENSE00001156067.3"  ; exon_number 1 ; gene_id "LRCH1--GRID1^LRCH1^ENSG00000136141.15"  ; gene_name LRCH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016877.8"  ; havana_transcript "OTTHUMT00000044825.3"  ; hgnc_id "HGNC:20309"  ; level 2 ; orig_coord_info "chr13,46553397,46553703,+"  ; protein_id "ENSP00000308493.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "LRCH1--GRID1^ENST00000311191.10"  ; transcript_name "LRCH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LRCH1--GRID1	HAVANA	gene	32522	54026	.	+	.	FI_gene_label "GRID1^ENSG00000182771.19"  ; ID "LRCH1--GRID1^GRID1^ENSG00000182771.19"  ; ccdsid "CCDS31236.1"  ; exon_id "ENSE00001328131.3"  ; exon_number 1 ; gene_id "LRCH1--GRID1^GRID1^ENSG00000182771.19"  ; gene_name GRID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018650.7"  ; havana_transcript "OTTHUMT00000049148.4"  ; hgnc_id "HGNC:4575"  ; level 2 ; orig_coord_info "chr10,86366314,86366392,-"  ; protein_id "ENSP00000330148.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRCH1--GRID1^ENST00000327946.12"  ; transcript_name "GRID1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
LRCH1--GRID1	HAVANA	mRNA	32522	54026	.	+	.	FI_gene_label "GRID1^ENSG00000182771.19"  ; ID "LRCH1--GRID1^ENST00000327946.12"  ; Parent "LRCH1--GRID1^GRID1^ENSG00000182771.19"  ; ccdsid "CCDS31236.1"  ; exon_id "ENSE00001328131.3"  ; exon_number 1 ; gene_id "LRCH1--GRID1^GRID1^ENSG00000182771.19"  ; gene_name GRID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018650.7"  ; havana_transcript "OTTHUMT00000049148.4"  ; hgnc_id "HGNC:4575"  ; level 2 ; orig_coord_info "chr10,86366314,86366392,-"  ; protein_id "ENSP00000330148.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRCH1--GRID1^ENST00000327946.12"  ; transcript_name "GRID1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NECTIN3--PHLDB2	HAVANA	gene	2312	13064	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "NECTIN3--PHLDB2^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "NECTIN3--PHLDB2^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PHLDB2^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NECTIN3--PHLDB2	HAVANA	mRNA	2312	13064	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "NECTIN3--PHLDB2^ENST00000319792.7"  ; Parent "NECTIN3--PHLDB2^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "NECTIN3--PHLDB2^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PHLDB2^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NECTIN3--PHLDB2	HAVANA	gene	25296	60371	.	+	.	FI_gene_label "PHLDB2^ENSG00000144824.21"  ; ID "NECTIN3--PHLDB2^PHLDB2^ENSG00000144824.21"  ; ccdsid "CCDS46885.1"  ; exon_id "ENSE00001231345.4"  ; exon_number 2 ; gene_id "NECTIN3--PHLDB2^PHLDB2^ENSG00000144824.21"  ; gene_name PHLDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159282.4"  ; havana_transcript "OTTHUMT00000354338.1"  ; hgnc_id "HGNC:29573"  ; level 2 ; orig_coord_info "chr3,111845869,111845935,+"  ; protein_id "ENSP00000377500.3"  ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "NECTIN3--PHLDB2^ENST00000393923.7"  ; transcript_name "PHLDB2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NECTIN3--PHLDB2	HAVANA	mRNA	25296	60371	.	+	.	FI_gene_label "PHLDB2^ENSG00000144824.21"  ; ID "NECTIN3--PHLDB2^ENST00000393923.7"  ; Parent "NECTIN3--PHLDB2^PHLDB2^ENSG00000144824.21"  ; ccdsid "CCDS46885.1"  ; exon_id "ENSE00001231345.4"  ; exon_number 2 ; gene_id "NECTIN3--PHLDB2^PHLDB2^ENSG00000144824.21"  ; gene_name PHLDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159282.4"  ; havana_transcript "OTTHUMT00000354338.1"  ; hgnc_id "HGNC:29573"  ; level 2 ; orig_coord_info "chr3,111845869,111845935,+"  ; protein_id "ENSP00000377500.3"  ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "NECTIN3--PHLDB2^ENST00000393923.7"  ; transcript_name "PHLDB2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NECTIN3--PLCXD2	HAVANA	gene	2312	13064	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "NECTIN3--PLCXD2^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "NECTIN3--PLCXD2^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PLCXD2^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NECTIN3--PLCXD2	HAVANA	mRNA	2312	13064	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "NECTIN3--PLCXD2^ENST00000319792.7"  ; Parent "NECTIN3--PLCXD2^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "NECTIN3--PLCXD2^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PLCXD2^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NECTIN3--PLCXD2	HAVANA	gene	25296	42248	.	+	.	FI_gene_label "PLCXD2^ENSG00000240891.8"  ; ID "NECTIN3--PLCXD2^PLCXD2^ENSG00000240891.8"  ; ccdsid "CCDS2961.1"  ; exon_id "ENSE00001900737.1"  ; exon_number 1 ; gene_id "NECTIN3--PLCXD2^PLCXD2^ENSG00000240891.8"  ; gene_name PLCXD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159279.5"  ; havana_transcript "OTTHUMT00000354321.1"  ; hgnc_id "HGNC:26462"  ; level 2 ; orig_coord_info "chr3,111675246,111675408,+"  ; protein_id "ENSP00000377511.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PLCXD2^ENST00000393934.7"  ; transcript_name "PLCXD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NECTIN3--PLCXD2	HAVANA	mRNA	25296	42248	.	+	.	FI_gene_label "PLCXD2^ENSG00000240891.8"  ; ID "NECTIN3--PLCXD2^ENST00000393934.7"  ; Parent "NECTIN3--PLCXD2^PLCXD2^ENSG00000240891.8"  ; ccdsid "CCDS2961.1"  ; exon_id "ENSE00001900737.1"  ; exon_number 1 ; gene_id "NECTIN3--PLCXD2^PLCXD2^ENSG00000240891.8"  ; gene_name PLCXD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159279.5"  ; havana_transcript "OTTHUMT00000354321.1"  ; hgnc_id "HGNC:26462"  ; level 2 ; orig_coord_info "chr3,111675246,111675408,+"  ; protein_id "ENSP00000377511.3"  ; tag basic CCDS ; transcript_id "NECTIN3--PLCXD2^ENST00000393934.7"  ; transcript_name "PLCXD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHLDB2--NECTIN3	HAVANA	gene	40638	51390	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "PHLDB2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "PHLDB2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "PHLDB2--NECTIN3^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHLDB2--NECTIN3	HAVANA	mRNA	40638	51390	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "PHLDB2--NECTIN3^ENST00000319792.7"  ; Parent "PHLDB2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "PHLDB2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "PHLDB2--NECTIN3^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHLDB2--NECTIN3	HAVANA	gene	1001	36076	.	+	.	FI_gene_label "PHLDB2^ENSG00000144824.21"  ; ID "PHLDB2--NECTIN3^PHLDB2^ENSG00000144824.21"  ; ccdsid "CCDS46885.1"  ; exon_id "ENSE00001231345.4"  ; exon_number 2 ; gene_id "PHLDB2--NECTIN3^PHLDB2^ENSG00000144824.21"  ; gene_name PHLDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159282.4"  ; havana_transcript "OTTHUMT00000354338.1"  ; hgnc_id "HGNC:29573"  ; level 2 ; orig_coord_info "chr3,111845869,111845935,+"  ; protein_id "ENSP00000377500.3"  ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "PHLDB2--NECTIN3^ENST00000393923.7"  ; transcript_name "PHLDB2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PHLDB2--NECTIN3	HAVANA	mRNA	1001	36076	.	+	.	FI_gene_label "PHLDB2^ENSG00000144824.21"  ; ID "PHLDB2--NECTIN3^ENST00000393923.7"  ; Parent "PHLDB2--NECTIN3^PHLDB2^ENSG00000144824.21"  ; ccdsid "CCDS46885.1"  ; exon_id "ENSE00001231345.4"  ; exon_number 2 ; gene_id "PHLDB2--NECTIN3^PHLDB2^ENSG00000144824.21"  ; gene_name PHLDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159282.4"  ; havana_transcript "OTTHUMT00000354338.1"  ; hgnc_id "HGNC:29573"  ; level 2 ; orig_coord_info "chr3,111845869,111845935,+"  ; protein_id "ENSP00000377500.3"  ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "PHLDB2--NECTIN3^ENST00000393923.7"  ; transcript_name "PHLDB2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PLCXD2--NECTIN3	HAVANA	gene	22265	33017	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "PLCXD2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "PLCXD2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "PLCXD2--NECTIN3^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLCXD2--NECTIN3	HAVANA	mRNA	22265	33017	.	+	.	FI_gene_label "NECTIN3^ENSG00000177707.11"  ; ID "PLCXD2--NECTIN3^ENST00000319792.7"  ; Parent "PLCXD2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; ccdsid "CCDS58842.1"  ; exon_id "ENSE00001240544.4"  ; exon_number 1 ; gene_id "PLCXD2--NECTIN3^NECTIN3^ENSG00000177707.11"  ; gene_name NECTIN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159239.4"  ; havana_transcript "OTTHUMT00000354044.1"  ; hgnc_id "HGNC:17664"  ; level 2 ; orig_coord_info "chr3,111072018,111072177,+"  ; protein_id "ENSP00000321514.3"  ; tag basic CCDS ; transcript_id "PLCXD2--NECTIN3^ENST00000319792.7"  ; transcript_name "NECTIN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PLCXD2--NECTIN3	HAVANA	gene	1001	17953	.	+	.	FI_gene_label "PLCXD2^ENSG00000240891.8"  ; ID "PLCXD2--NECTIN3^PLCXD2^ENSG00000240891.8"  ; ccdsid "CCDS2961.1"  ; exon_id "ENSE00001900737.1"  ; exon_number 1 ; gene_id "PLCXD2--NECTIN3^PLCXD2^ENSG00000240891.8"  ; gene_name PLCXD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159279.5"  ; havana_transcript "OTTHUMT00000354321.1"  ; hgnc_id "HGNC:26462"  ; level 2 ; orig_coord_info "chr3,111675246,111675408,+"  ; protein_id "ENSP00000377511.3"  ; tag basic CCDS ; transcript_id "PLCXD2--NECTIN3^ENST00000393934.7"  ; transcript_name "PLCXD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PLCXD2--NECTIN3	HAVANA	mRNA	1001	17953	.	+	.	FI_gene_label "PLCXD2^ENSG00000240891.8"  ; ID "PLCXD2--NECTIN3^ENST00000393934.7"  ; Parent "PLCXD2--NECTIN3^PLCXD2^ENSG00000240891.8"  ; ccdsid "CCDS2961.1"  ; exon_id "ENSE00001900737.1"  ; exon_number 1 ; gene_id "PLCXD2--NECTIN3^PLCXD2^ENSG00000240891.8"  ; gene_name PLCXD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159279.5"  ; havana_transcript "OTTHUMT00000354321.1"  ; hgnc_id "HGNC:26462"  ; level 2 ; orig_coord_info "chr3,111675246,111675408,+"  ; protein_id "ENSP00000377511.3"  ; tag basic CCDS ; transcript_id "PLCXD2--NECTIN3^ENST00000393934.7"  ; transcript_name "PLCXD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146	HAVANA	mRNA	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^ENST00000285871.5"  ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^ENST00000302641.8"  ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^ENST00000606293.5"  ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SELENOO--TUBGCP6	HAVANA	gene	11677	27664	.	+	.	FI_gene_label "TUBGCP6^ENSG00000128159.12"  ; ID "SELENOO--TUBGCP6^TUBGCP6^ENSG00000128159.12"  ; ccdsid "CCDS14087.1"  ; exon_id "ENSE00001892806.2"  ; exon_number 1 ; gene_id "SELENOO--TUBGCP6^TUBGCP6^ENSG00000128159.12"  ; gene_name TUBGCP6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030150.7"  ; havana_transcript "OTTHUMT00000075004.4"  ; hgnc_id "HGNC:18127"  ; level 2 ; orig_coord_info "chr22,50243719,50244459,-"  ; protein_id "ENSP00000248846.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENOO--TUBGCP6^ENST00000248846.10"  ; transcript_name "TUBGCP6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SELENOO--TUBGCP6	HAVANA	mRNA	11677	27664	.	+	.	FI_gene_label "TUBGCP6^ENSG00000128159.12"  ; ID "SELENOO--TUBGCP6^ENST00000248846.10"  ; Parent "SELENOO--TUBGCP6^TUBGCP6^ENSG00000128159.12"  ; ccdsid "CCDS14087.1"  ; exon_id "ENSE00001892806.2"  ; exon_number 1 ; gene_id "SELENOO--TUBGCP6^TUBGCP6^ENSG00000128159.12"  ; gene_name TUBGCP6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030150.7"  ; havana_transcript "OTTHUMT00000075004.4"  ; hgnc_id "HGNC:18127"  ; level 2 ; orig_coord_info "chr22,50243719,50244459,-"  ; protein_id "ENSP00000248846.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENOO--TUBGCP6^ENST00000248846.10"  ; transcript_name "TUBGCP6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SELENOO--TUBGCP6	HAVANA	gene	1033	8676	.	+	.	FI_gene_label "SELENOO^ENSG00000073169.14"  ; ID "SELENOO--TUBGCP6^SELENOO^ENSG00000073169.14"  ; ccdsid "CCDS43034.1"  ; exon_id "ENSE00003849499.1"  ; exon_number 1 ; gene_id "SELENOO--TUBGCP6^SELENOO^ENSG00000073169.14"  ; gene_name SELENOO ; gene_type protein_coding ; havana_gene "OTTHUMG00000044645.4"  ; havana_transcript "OTTHUMT00000075003.3"  ; hgnc_id "HGNC:30395"  ; level 2 ; orig_coord_info "chr22,50201037,50201590,+"  ; protein_id "ENSP00000370288.2"  ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "SELENOO--TUBGCP6^ENST00000380903.7"  ; transcript_name "SELENOO-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SELENOO--TUBGCP6	HAVANA	mRNA	1033	8676	.	+	.	FI_gene_label "SELENOO^ENSG00000073169.14"  ; ID "SELENOO--TUBGCP6^ENST00000380903.7"  ; Parent "SELENOO--TUBGCP6^SELENOO^ENSG00000073169.14"  ; ccdsid "CCDS43034.1"  ; exon_id "ENSE00003849499.1"  ; exon_number 1 ; gene_id "SELENOO--TUBGCP6^SELENOO^ENSG00000073169.14"  ; gene_name SELENOO ; gene_type protein_coding ; havana_gene "OTTHUMG00000044645.4"  ; havana_transcript "OTTHUMT00000075003.3"  ; hgnc_id "HGNC:30395"  ; level 2 ; orig_coord_info "chr22,50201037,50201590,+"  ; protein_id "ENSP00000370288.2"  ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "SELENOO--TUBGCP6^ENST00000380903.7"  ; transcript_name "SELENOO-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: 
SVEP1--MYLK	HAVANA	gene	61804	112489	.	+	.	FI_gene_label "MYLK^ENSG00000065534.19"  ; ID "SVEP1--MYLK^MYLK^ENSG00000065534.19"  ; ccdsid "CCDS43141.1"  ; exon_id "ENSE00003544345.1"  ; exon_number 4 ; gene_id "SVEP1--MYLK^MYLK^ENSG00000065534.19"  ; gene_name MYLK ; gene_type protein_coding ; havana_gene "OTTHUMG00000141304.13"  ; havana_transcript "OTTHUMT00000280601.1"  ; hgnc_id "HGNC:7590"  ; level 2 ; orig_coord_info "chr3,123793677,123793841,-"  ; protein_id "ENSP00000320622.5"  ; tag basic CCDS ; transcript_id "SVEP1--MYLK^ENST00000346322.9"  ; transcript_name "MYLK-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SVEP1--MYLK	HAVANA	mRNA	61804	112489	.	+	.	FI_gene_label "MYLK^ENSG00000065534.19"  ; ID "SVEP1--MYLK^ENST00000346322.9"  ; Parent "SVEP1--MYLK^MYLK^ENSG00000065534.19"  ; ccdsid "CCDS43141.1"  ; exon_id "ENSE00003544345.1"  ; exon_number 4 ; gene_id "SVEP1--MYLK^MYLK^ENSG00000065534.19"  ; gene_name MYLK ; gene_type protein_coding ; havana_gene "OTTHUMG00000141304.13"  ; havana_transcript "OTTHUMT00000280601.1"  ; hgnc_id "HGNC:7590"  ; level 2 ; orig_coord_info "chr3,123793677,123793841,-"  ; protein_id "ENSP00000320622.5"  ; tag basic CCDS ; transcript_id "SVEP1--MYLK^ENST00000346322.9"  ; transcript_name "MYLK-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SVEP1--MYLK	HAVANA	gene	1001	17023	.	+	.	FI_gene_label "SVEP1^ENSG00000165124.18"  ; ID "SVEP1--MYLK^SVEP1^ENSG00000165124.18"  ; exon_id "ENSE00001463572.1"  ; exon_number 1 ; gene_id "SVEP1--MYLK^SVEP1^ENSG00000165124.18"  ; gene_name SVEP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020482.3"  ; havana_transcript "OTTHUMT00000053620.2"  ; hgnc_id "HGNC:15985"  ; level 2 ; orig_coord_info "chr9,110579013,110579543,-"  ; protein_id "ENSP00000363585.2"  ; tag basic ; transcript_id "SVEP1--MYLK^ENST00000374461.1"  ; transcript_name "SVEP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SVEP1--MYLK	HAVANA	mRNA	1001	17023	.	+	.	FI_gene_label "SVEP1^ENSG00000165124.18"  ; ID "SVEP1--MYLK^ENST00000374461.1"  ; Parent "SVEP1--MYLK^SVEP1^ENSG00000165124.18"  ; exon_id "ENSE00001463572.1"  ; exon_number 1 ; gene_id "SVEP1--MYLK^SVEP1^ENSG00000165124.18"  ; gene_name SVEP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020482.3"  ; havana_transcript "OTTHUMT00000053620.2"  ; hgnc_id "HGNC:15985"  ; level 2 ; orig_coord_info "chr9,110579013,110579543,-"  ; protein_id "ENSP00000363585.2"  ; tag basic ; transcript_id "SVEP1--MYLK^ENST00000374461.1"  ; transcript_name "SVEP1-201"  ; 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: 
UBE2Q2P1--GOLGA6L10	HAVANA	gene	16591	25371	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
UBE2Q2P1--GOLGA6L10	HAVANA	mRNA	16591	25371	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "UBE2Q2P1--GOLGA6L10^ENST00000610657.2"  ; Parent "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
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: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
ASAP1--CCDC26	HAVANA	gene	50131	95453	.	+	.	FI_gene_label "CCDC26^ENSG00000229140.11"  ; ID "ASAP1--CCDC26^CCDC26^ENSG00000229140.11"  ; exon_id "ENSE00002063024.1"  ; exon_number 1 ; gene_id "ASAP1--CCDC26^CCDC26^ENSG00000229140.11"  ; gene_name CCDC26 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164848.68"  ; havana_transcript "OTTHUMT00000380581.1"  ; hgnc_id "HGNC:28416"  ; level 2 ; orig_coord_info "chr8,129679928,129680239,-"  ; tag non_canonical_polymorphism dotter_confirmed ; transcript_id "ASAP1--CCDC26^ENST00000446592.7"  ; transcript_name "CCDC26-201"  ; transcript_support_level 1 ; transcript_type lncRNA
ASAP1--CCDC26	HAVANA	RNA	50131	95453	.	+	.	FI_gene_label "CCDC26^ENSG00000229140.11"  ; ID "ASAP1--CCDC26^ENST00000446592.7"  ; Parent "ASAP1--CCDC26^CCDC26^ENSG00000229140.11"  ; exon_id "ENSE00002063024.1"  ; exon_number 1 ; gene_id "ASAP1--CCDC26^CCDC26^ENSG00000229140.11"  ; gene_name CCDC26 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164848.68"  ; havana_transcript "OTTHUMT00000380581.1"  ; hgnc_id "HGNC:28416"  ; level 2 ; orig_coord_info "chr8,129679928,129680239,-"  ; tag non_canonical_polymorphism dotter_confirmed ; transcript_id "ASAP1--CCDC26^ENST00000446592.7"  ; transcript_name "CCDC26-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
BBOX1-AS1--ADGRL3	HAVANA	gene	1001	7167	.	+	.	FI_gene_label "BBOX1-AS1^ENSG00000254560.6"  ; ID "BBOX1-AS1--ADGRL3^BBOX1-AS1^ENSG00000254560.6"  ; exon_id "ENSE00002196313.1"  ; exon_number 1 ; gene_id "BBOX1-AS1--ADGRL3^BBOX1-AS1^ENSG00000254560.6"  ; gene_name "BBOX1-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166122.2"  ; havana_transcript "OTTHUMT00000387954.1"  ; hgnc_id "HGNC:50700"  ; level 2 ; orig_coord_info "chr11,27220047,27220113,-"  ; transcript_id "BBOX1-AS1--ADGRL3^ENST00000525302.5"  ; transcript_name "BBOX1-AS1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
BBOX1-AS1--ADGRL3	HAVANA	RNA	1001	7167	.	+	.	FI_gene_label "BBOX1-AS1^ENSG00000254560.6"  ; ID "BBOX1-AS1--ADGRL3^ENST00000525302.5"  ; Parent "BBOX1-AS1--ADGRL3^BBOX1-AS1^ENSG00000254560.6"  ; exon_id "ENSE00002196313.1"  ; exon_number 1 ; gene_id "BBOX1-AS1--ADGRL3^BBOX1-AS1^ENSG00000254560.6"  ; gene_name "BBOX1-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166122.2"  ; havana_transcript "OTTHUMT00000387954.1"  ; hgnc_id "HGNC:50700"  ; level 2 ; orig_coord_info "chr11,27220047,27220113,-"  ; transcript_id "BBOX1-AS1--ADGRL3^ENST00000525302.5"  ; transcript_name "BBOX1-AS1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
CYCTP--PDE11A	HAVANA	gene	1001	2631	.	+	.	FI_gene_label "CYCTP^ENSG00000249909.1"  ; ID "CYCTP--PDE11A^CYCTP^ENSG00000249909.1"  ; exon_id "ENSE00002053327.1"  ; exon_number 1 ; gene_id "CYCTP--PDE11A^CYCTP^ENSG00000249909.1"  ; gene_name CYCTP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000154943.1"  ; havana_transcript "OTTHUMT00000337764.1"  ; hgnc_id "HGNC:24424"  ; level 2 ; ont "PGO:0000006"  ; orig_coord_info "chr2,178104302,178104470,-"  ; tag basic ; transcript_id "CYCTP--PDE11A^ENST00000504253.1"  ; transcript_name "CYCTP-201"  ; transcript_support_level NA ; transcript_type unitary_pseudogene
CYCTP--PDE11A	HAVANA	RNA	1001	2631	.	+	.	FI_gene_label "CYCTP^ENSG00000249909.1"  ; ID "CYCTP--PDE11A^ENST00000504253.1"  ; Parent "CYCTP--PDE11A^CYCTP^ENSG00000249909.1"  ; exon_id "ENSE00002053327.1"  ; exon_number 1 ; gene_id "CYCTP--PDE11A^CYCTP^ENSG00000249909.1"  ; gene_name CYCTP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000154943.1"  ; havana_transcript "OTTHUMT00000337764.1"  ; hgnc_id "HGNC:24424"  ; level 2 ; ont "PGO:0000006"  ; orig_coord_info "chr2,178104302,178104470,-"  ; tag basic ; transcript_id "CYCTP--PDE11A^ENST00000504253.1"  ; transcript_name "CYCTP-201"  ; transcript_support_level NA ; transcript_type unitary_pseudogene
L1 and L2 created: 
FBXO25--AC240565.1	HAVANA	gene	26102	34357	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1	HAVANA	RNA	26102	34357	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "FBXO25--AC240565.1^ENST00000624936.2"  ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
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: 
KCNMB2-AS1--ADGRL3	HAVANA	gene	9953	12402	.	+	.	FI_gene_label "KCNMB2-AS1^ENSG00000237978.6"  ; ID "KCNMB2-AS1--ADGRL3^KCNMB2-AS1^ENSG00000237978.6"  ; exon_id "ENSE00001737090.1"  ; exon_number 1 ; gene_id "KCNMB2-AS1--ADGRL3^KCNMB2-AS1^ENSG00000237978.6"  ; gene_name "KCNMB2-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000157289.2"  ; havana_transcript "OTTHUMT00000348333.1"  ; hgnc_id "HGNC:51409"  ; level 2 ; orig_coord_info "chr3,178801793,178801936,-"  ; transcript_id "KCNMB2-AS1--ADGRL3^ENST00000421498.1"  ; transcript_name "KCNMB2-AS1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
KCNMB2-AS1--ADGRL3	HAVANA	RNA	9953	12402	.	+	.	FI_gene_label "KCNMB2-AS1^ENSG00000237978.6"  ; ID "KCNMB2-AS1--ADGRL3^ENST00000421498.1"  ; Parent "KCNMB2-AS1--ADGRL3^KCNMB2-AS1^ENSG00000237978.6"  ; exon_id "ENSE00001737090.1"  ; exon_number 1 ; gene_id "KCNMB2-AS1--ADGRL3^KCNMB2-AS1^ENSG00000237978.6"  ; gene_name "KCNMB2-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000157289.2"  ; havana_transcript "OTTHUMT00000348333.1"  ; hgnc_id "HGNC:51409"  ; level 2 ; orig_coord_info "chr3,178801793,178801936,-"  ; transcript_id "KCNMB2-AS1--ADGRL3^ENST00000421498.1"  ; transcript_name "KCNMB2-AS1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
LINC00381--NKAIN2	HAVANA	gene	1016	4365	.	+	.	FI_gene_label "LINC00381^ENSG00000226240.2"  ; ID "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; exon_id "ENSE00001743371.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2"  ; havana_transcript "OTTHUMT00000045275.1"  ; hgnc_id "HGNC:42708"  ; level 2 ; orig_coord_info "chr13,74419173,74419228,+"  ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1"  ; transcript_name "LINC00381-201"  ; transcript_support_level 5 ; transcript_type lncRNA
LINC00381--NKAIN2	HAVANA	RNA	1016	4365	.	+	.	FI_gene_label "LINC00381^ENSG00000226240.2"  ; ID "LINC00381--NKAIN2^ENST00000423629.1"  ; Parent "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; exon_id "ENSE00001743371.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2"  ; havana_transcript "OTTHUMT00000045275.1"  ; hgnc_id "HGNC:42708"  ; level 2 ; orig_coord_info "chr13,74419173,74419228,+"  ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1"  ; transcript_name "LINC00381-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146	HAVANA	RNA	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^ENST00000333674.5"  ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
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
L1 and L2 created: 
UBE2Q2P1--GOLGA6L10	HAVANA	gene	1422	13175	.	+	.	FI_gene_label "UBE2Q2P1^ENSG00000189136.9"  ; ID "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9"  ; exon_id "ENSE00002026145.1"  ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9"  ; gene_name UBE2Q2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000148662.3"  ; havana_transcript "OTTHUMT00000308970.2"  ; hgnc_id "HGNC:37439"  ; level 2 ; orig_coord_info "chr15,84569505,84570795,-"  ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000339094.5"  ; transcript_name "UBE2Q2P1-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
UBE2Q2P1--GOLGA6L10	HAVANA	RNA	1422	13175	.	+	.	FI_gene_label "UBE2Q2P1^ENSG00000189136.9"  ; ID "UBE2Q2P1--GOLGA6L10^ENST00000339094.5"  ; Parent "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9"  ; exon_id "ENSE00002026145.1"  ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9"  ; gene_name UBE2Q2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000148662.3"  ; havana_transcript "OTTHUMT00000308970.2"  ; hgnc_id "HGNC:37439"  ; level 2 ; orig_coord_info "chr15,84569505,84570795,-"  ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000339094.5"  ; transcript_name "UBE2Q2P1-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
496 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
568 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 34 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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                  ------ End checks (done in 0 second) ------                   


GFF3 file parsed