.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-3b54a2-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/799eb6e5309f61f658bae50a6aa744/.command.log
Size: 56.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-3b54a2-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/071fc6350f4c7b6cf17cf31146cfaa/fi_workdir/aih-tih-sc-3b54a2-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/799eb6e5309f61f658bae50a6aa744/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/799eb6e5309f61f658bae50a6aa744/.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: 4017
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4017
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:4017
  => Some common attributes and some Parent attributes missing.
  /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
  see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote).  see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html 
  !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
                  ------ End parsing (done in 1 second) ------                  


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

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

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

--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created: 
AC004980.3--UPK3BL1	HAVANA	gene	6366	11192	.	+	.	FI_gene_label "UPK3BL1^ENSG00000267368.1"  ; ID "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; ccdsid "CCDS47675.1"  ; exon_id "ENSE00001683829.2"  ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2"  ; havana_transcript "OTTHUMT00000381510.1"  ; hgnc_id "HGNC:37278"  ; level 2 ; orig_coord_info "chr7,102642630,102642741,-"  ; protein_id "ENSP00000342938.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8"  ; transcript_name "UPK3BL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC004980.3--UPK3BL1	HAVANA	mRNA	6366	11192	.	+	.	FI_gene_label "UPK3BL1^ENSG00000267368.1"  ; ID "AC004980.3--UPK3BL1^ENST00000340457.8"  ; Parent "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; ccdsid "CCDS47675.1"  ; exon_id "ENSE00001683829.2"  ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2"  ; havana_transcript "OTTHUMT00000381510.1"  ; hgnc_id "HGNC:37278"  ; level 2 ; orig_coord_info "chr7,102642630,102642741,-"  ; protein_id "ENSP00000342938.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8"  ; transcript_name "UPK3BL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPSF6--ANKRD36C	HAVANA	gene	1048	12978	.	+	.	FI_gene_label "CPSF6^ENSG00000111605.18"  ; ID "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18"  ; ccdsid "CCDS73494.1"  ; exon_id "ENSE00002424959.1"  ; exon_number 1 ; gene_id "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18"  ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4"  ; havana_transcript "OTTHUMT00000403613.1"  ; hgnc_id "HGNC:13871"  ; level 2 ; orig_coord_info "chr12,69239647,69239706,+"  ; protein_id "ENSP00000266679.8"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--ANKRD36C^ENST00000266679.8"  ; transcript_name "CPSF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CPSF6--ANKRD36C	HAVANA	mRNA	1048	12978	.	+	.	FI_gene_label "CPSF6^ENSG00000111605.18"  ; ID "CPSF6--ANKRD36C^ENST00000266679.8"  ; Parent "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18"  ; ccdsid "CCDS73494.1"  ; exon_id "ENSE00002424959.1"  ; exon_number 1 ; gene_id "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18"  ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4"  ; havana_transcript "OTTHUMT00000403613.1"  ; hgnc_id "HGNC:13871"  ; level 2 ; orig_coord_info "chr12,69239647,69239706,+"  ; protein_id "ENSP00000266679.8"  ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--ANKRD36C^ENST00000266679.8"  ; transcript_name "CPSF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CPSF6--ANKRD36C	ENSEMBL	gene	35506	73554	.	+	.	FI_gene_label "ANKRD36C^ENSG00000174501.14"  ; ID "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14"  ; exon_id "ENSE00003729919.1"  ; exon_number 5 ; gene_id "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14"  ; gene_name ANKRD36C ; gene_type protein_coding ; havana_gene "OTTHUMG00000155211.2"  ; hgnc_id "HGNC:32946"  ; level 3 ; orig_coord_info "chr2,95935454,95935487,-"  ; protein_id "ENSP00000295246.6"  ; tag basic ; transcript_id "CPSF6--ANKRD36C^ENST00000295246.6"  ; transcript_name "ANKRD36C-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CPSF6--ANKRD36C	ENSEMBL	mRNA	35506	73554	.	+	.	FI_gene_label "ANKRD36C^ENSG00000174501.14"  ; ID "CPSF6--ANKRD36C^ENST00000295246.6"  ; Parent "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14"  ; exon_id "ENSE00003729919.1"  ; exon_number 5 ; gene_id "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14"  ; gene_name ANKRD36C ; gene_type protein_coding ; havana_gene "OTTHUMG00000155211.2"  ; hgnc_id "HGNC:32946"  ; level 3 ; orig_coord_info "chr2,95935454,95935487,-"  ; protein_id "ENSP00000295246.6"  ; tag basic ; transcript_id "CPSF6--ANKRD36C^ENST00000295246.6"  ; transcript_name "ANKRD36C-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
EFL1--GOLGA6L11P	HAVANA	gene	1001	25062	.	+	.	FI_gene_label "EFL1^ENSG00000140598.15"  ; ID "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; ccdsid "CCDS42071.1"  ; exon_id "ENSE00003786417.1"  ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5"  ; havana_transcript "OTTHUMT00000419252.2"  ; hgnc_id "HGNC:25789"  ; level 2 ; orig_coord_info "chr15,82261688,82261778,-"  ; protein_id "ENSP00000268206.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12"  ; transcript_name "EFL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EFL1--GOLGA6L11P	HAVANA	mRNA	1001	25062	.	+	.	FI_gene_label "EFL1^ENSG00000140598.15"  ; ID "EFL1--GOLGA6L11P^ENST00000268206.12"  ; Parent "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; ccdsid "CCDS42071.1"  ; exon_id "ENSE00003786417.1"  ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5"  ; havana_transcript "OTTHUMT00000419252.2"  ; hgnc_id "HGNC:25789"  ; level 2 ; orig_coord_info "chr15,82261688,82261778,-"  ; protein_id "ENSP00000268206.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12"  ; transcript_name "EFL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EIF4G3--HP1BP3	HAVANA	gene	10142	51670	.	+	.	FI_gene_label "EIF4G3^ENSG00000075151.22"  ; ID "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22"  ; ccdsid "CCDS214.1"  ; exon_id "ENSE00003337316.1"  ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22"  ; gene_name EIF4G3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002624.7"  ; havana_transcript "OTTHUMT00000007467.3"  ; hgnc_id "HGNC:3298"  ; level 2 ; orig_coord_info "chr1,21002713,21002742,-"  ; protein_id "ENSP00000264211.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000264211.12"  ; transcript_name "EIF4G3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
EIF4G3--HP1BP3	HAVANA	mRNA	10142	51670	.	+	.	FI_gene_label "EIF4G3^ENSG00000075151.22"  ; ID "EIF4G3--HP1BP3^ENST00000264211.12"  ; Parent "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22"  ; ccdsid "CCDS214.1"  ; exon_id "ENSE00003337316.1"  ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22"  ; gene_name EIF4G3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002624.7"  ; havana_transcript "OTTHUMT00000007467.3"  ; hgnc_id "HGNC:3298"  ; level 2 ; orig_coord_info "chr1,21002713,21002742,-"  ; protein_id "ENSP00000264211.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000264211.12"  ; transcript_name "EIF4G3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
EIF4G3--HP1BP3	HAVANA	gene	55520	73106	.	+	.	FI_gene_label "HP1BP3^ENSG00000127483.19"  ; ID "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19"  ; ccdsid "CCDS30621.1"  ; exon_id "ENSE00002245255.1"  ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19"  ; gene_name HP1BP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002622.10"  ; havana_transcript "OTTHUMT00000007457.3"  ; hgnc_id "HGNC:24973"  ; level 2 ; orig_coord_info "chr1,20780345,20780440,-"  ; protein_id "ENSP00000312625.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000312239.10"  ; transcript_name "HP1BP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
EIF4G3--HP1BP3	HAVANA	mRNA	55520	73106	.	+	.	FI_gene_label "HP1BP3^ENSG00000127483.19"  ; ID "EIF4G3--HP1BP3^ENST00000312239.10"  ; Parent "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19"  ; ccdsid "CCDS30621.1"  ; exon_id "ENSE00002245255.1"  ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19"  ; gene_name HP1BP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002622.10"  ; havana_transcript "OTTHUMT00000007457.3"  ; hgnc_id "HGNC:24973"  ; level 2 ; orig_coord_info "chr1,20780345,20780440,-"  ; protein_id "ENSP00000312625.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000312239.10"  ; transcript_name "HP1BP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GINS2--AC025822.2	HAVANA	gene	2120	8183	.	+	.	FI_gene_label "GINS2^ENSG00000131153.9"  ; ID "GINS2--AC025822.2^GINS2^ENSG00000131153.9"  ; ccdsid "CCDS10953.1"  ; exon_id "ENSE00001303150.3"  ; exon_number 1 ; gene_id "GINS2--AC025822.2^GINS2^ENSG00000131153.9"  ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4"  ; havana_transcript "OTTHUMT00000269098.2"  ; hgnc_id "HGNC:24575"  ; level 2 ; orig_coord_info "chr16,85688809,85688898,-"  ; protein_id "ENSP00000253462.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--AC025822.2^ENST00000253462.8"  ; transcript_name "GINS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GINS2--AC025822.2	HAVANA	mRNA	2120	8183	.	+	.	FI_gene_label "GINS2^ENSG00000131153.9"  ; ID "GINS2--AC025822.2^ENST00000253462.8"  ; Parent "GINS2--AC025822.2^GINS2^ENSG00000131153.9"  ; ccdsid "CCDS10953.1"  ; exon_id "ENSE00001303150.3"  ; exon_number 1 ; gene_id "GINS2--AC025822.2^GINS2^ENSG00000131153.9"  ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4"  ; havana_transcript "OTTHUMT00000269098.2"  ; hgnc_id "HGNC:24575"  ; level 2 ; orig_coord_info "chr16,85688809,85688898,-"  ; protein_id "ENSP00000253462.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--AC025822.2^ENST00000253462.8"  ; transcript_name "GINS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GINS2--LINC00702	HAVANA	gene	2120	8183	.	+	.	FI_gene_label "GINS2^ENSG00000131153.9"  ; ID "GINS2--LINC00702^GINS2^ENSG00000131153.9"  ; ccdsid "CCDS10953.1"  ; exon_id "ENSE00001303150.3"  ; exon_number 1 ; gene_id "GINS2--LINC00702^GINS2^ENSG00000131153.9"  ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4"  ; havana_transcript "OTTHUMT00000269098.2"  ; hgnc_id "HGNC:24575"  ; level 2 ; orig_coord_info "chr16,85688809,85688898,-"  ; protein_id "ENSP00000253462.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--LINC00702^ENST00000253462.8"  ; transcript_name "GINS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GINS2--LINC00702	HAVANA	mRNA	2120	8183	.	+	.	FI_gene_label "GINS2^ENSG00000131153.9"  ; ID "GINS2--LINC00702^ENST00000253462.8"  ; Parent "GINS2--LINC00702^GINS2^ENSG00000131153.9"  ; ccdsid "CCDS10953.1"  ; exon_id "ENSE00001303150.3"  ; exon_number 1 ; gene_id "GINS2--LINC00702^GINS2^ENSG00000131153.9"  ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4"  ; havana_transcript "OTTHUMT00000269098.2"  ; hgnc_id "HGNC:24575"  ; level 2 ; orig_coord_info "chr16,85688809,85688898,-"  ; protein_id "ENSP00000253462.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--LINC00702^ENST00000253462.8"  ; transcript_name "GINS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^ENST00000616325.1"  ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PKD1--NPIPB12	HAVANA	gene	1001	30973	.	+	.	FI_gene_label "PKD1^ENSG00000008710.20"  ; ID "PKD1--NPIPB12^PKD1^ENSG00000008710.20"  ; ccdsid "CCDS32369.1"  ; exon_id "ENSE00002710399.1"  ; exon_number 1 ; gene_id "PKD1--NPIPB12^PKD1^ENSG00000008710.20"  ; gene_name PKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155795.6"  ; havana_transcript "OTTHUMT00000341688.2"  ; hgnc_id "HGNC:9008"  ; level 2 ; orig_coord_info "chr16,2135475,2135689,-"  ; protein_id "ENSP00000262304.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PKD1--NPIPB12^ENST00000262304.9"  ; transcript_name "PKD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PKD1--NPIPB12	HAVANA	mRNA	1001	30973	.	+	.	FI_gene_label "PKD1^ENSG00000008710.20"  ; ID "PKD1--NPIPB12^ENST00000262304.9"  ; Parent "PKD1--NPIPB12^PKD1^ENSG00000008710.20"  ; ccdsid "CCDS32369.1"  ; exon_id "ENSE00002710399.1"  ; exon_number 1 ; gene_id "PKD1--NPIPB12^PKD1^ENSG00000008710.20"  ; gene_name PKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155795.6"  ; havana_transcript "OTTHUMT00000341688.2"  ; hgnc_id "HGNC:9008"  ; level 2 ; orig_coord_info "chr16,2135475,2135689,-"  ; protein_id "ENSP00000262304.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PKD1--NPIPB12^ENST00000262304.9"  ; transcript_name "PKD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PKD1--NPIPB12	ENSEMBL	gene	42932	45149	.	+	.	FI_gene_label "NPIPB12^ENSG00000169203.16"  ; ID "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16"  ; exon_id "ENSE00001744303.2"  ; exon_number 1 ; gene_id "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16"  ; gene_name NPIPB12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163547.2"  ; hgnc_id "HGNC:37491"  ; level 3 ; orig_coord_info "chr16,29485263,29485827,-"  ; protein_id "ENSP00000399107.3"  ; tag basic appris_alternative_2 ; transcript_id "PKD1--NPIPB12^ENST00000458643.3"  ; transcript_name "NPIPB12-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PKD1--NPIPB12	ENSEMBL	mRNA	42932	45149	.	+	.	FI_gene_label "NPIPB12^ENSG00000169203.16"  ; ID "PKD1--NPIPB12^ENST00000458643.3"  ; Parent "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16"  ; exon_id "ENSE00001744303.2"  ; exon_number 1 ; gene_id "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16"  ; gene_name NPIPB12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163547.2"  ; hgnc_id "HGNC:37491"  ; level 3 ; orig_coord_info "chr16,29485263,29485827,-"  ; protein_id "ENSP00000399107.3"  ; tag basic appris_alternative_2 ; transcript_id "PKD1--NPIPB12^ENST00000458643.3"  ; transcript_name "NPIPB12-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PMS2P1--UPK3BL1	HAVANA	gene	14962	19788	.	+	.	FI_gene_label "UPK3BL1^ENSG00000267368.1"  ; ID "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; ccdsid "CCDS47675.1"  ; exon_id "ENSE00001683829.2"  ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2"  ; havana_transcript "OTTHUMT00000381510.1"  ; hgnc_id "HGNC:37278"  ; level 2 ; orig_coord_info "chr7,102642630,102642741,-"  ; protein_id "ENSP00000342938.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P1--UPK3BL1^ENST00000340457.8"  ; transcript_name "UPK3BL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P1--UPK3BL1	HAVANA	mRNA	14962	19788	.	+	.	FI_gene_label "UPK3BL1^ENSG00000267368.1"  ; ID "PMS2P1--UPK3BL1^ENST00000340457.8"  ; Parent "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; ccdsid "CCDS47675.1"  ; exon_id "ENSE00001683829.2"  ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1"  ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2"  ; havana_transcript "OTTHUMT00000381510.1"  ; hgnc_id "HGNC:37278"  ; level 2 ; orig_coord_info "chr7,102642630,102642741,-"  ; protein_id "ENSP00000342938.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P1--UPK3BL1^ENST00000340457.8"  ; transcript_name "UPK3BL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PSG5--CD177	HAVANA	gene	1001	12284	.	+	.	FI_gene_label "PSG5^ENSG00000204941.14"  ; ID "PSG5--CD177^PSG5^ENSG00000204941.14"  ; ccdsid "CCDS12617.1"  ; exon_id "ENSE00001564066.1"  ; exon_number 1 ; gene_id "PSG5--CD177^PSG5^ENSG00000204941.14"  ; gene_name PSG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151539.3"  ; havana_transcript "OTTHUMT00000323057.1"  ; hgnc_id "HGNC:9522"  ; level 2 ; orig_coord_info "chr19,43186342,43186405,-"  ; protein_id "ENSP00000344413.6"  ; tag alternative_3_UTR basic MANE_Select CCDS ; transcript_id "PSG5--CD177^ENST00000342951.11"  ; transcript_name "PSG5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PSG5--CD177	HAVANA	mRNA	1001	12284	.	+	.	FI_gene_label "PSG5^ENSG00000204941.14"  ; ID "PSG5--CD177^ENST00000342951.11"  ; Parent "PSG5--CD177^PSG5^ENSG00000204941.14"  ; ccdsid "CCDS12617.1"  ; exon_id "ENSE00001564066.1"  ; exon_number 1 ; gene_id "PSG5--CD177^PSG5^ENSG00000204941.14"  ; gene_name PSG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151539.3"  ; havana_transcript "OTTHUMT00000323057.1"  ; hgnc_id "HGNC:9522"  ; level 2 ; orig_coord_info "chr19,43186342,43186405,-"  ; protein_id "ENSP00000344413.6"  ; tag alternative_3_UTR basic MANE_Select CCDS ; transcript_id "PSG5--CD177^ENST00000342951.11"  ; transcript_name "PSG5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PSG5--CD177	HAVANA	gene	16801	22302	.	+	.	FI_gene_label "CD177^ENSG00000204936.10"  ; ID "PSG5--CD177^CD177^ENSG00000204936.10"  ; exon_id "ENSE00003739430.1"  ; exon_number 1 ; gene_id "PSG5--CD177^CD177^ENSG00000204936.10"  ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4"  ; havana_transcript "OTTHUMT00000470164.2"  ; hgnc_id "HGNC:30072"  ; level 2 ; orig_coord_info "chr19,43353715,43353766,+"  ; protein_id "ENSP00000367251.2"  ; transcript_id "PSG5--CD177^ENST00000378012.3"  ; transcript_name "CD177-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
PSG5--CD177	HAVANA	mRNA	16801	22302	.	+	.	FI_gene_label "CD177^ENSG00000204936.10"  ; ID "PSG5--CD177^ENST00000378012.3"  ; Parent "PSG5--CD177^CD177^ENSG00000204936.10"  ; exon_id "ENSE00003739430.1"  ; exon_number 1 ; gene_id "PSG5--CD177^CD177^ENSG00000204936.10"  ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4"  ; havana_transcript "OTTHUMT00000470164.2"  ; hgnc_id "HGNC:30072"  ; level 2 ; orig_coord_info "chr19,43353715,43353766,+"  ; protein_id "ENSP00000367251.2"  ; transcript_id "PSG5--CD177^ENST00000378012.3"  ; transcript_name "CD177-201"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
PUM1--NKAIN1	HAVANA	gene	1294	30447	.	+	.	FI_gene_label "PUM1^ENSG00000134644.16"  ; ID "PUM1--NKAIN1^PUM1^ENSG00000134644.16"  ; ccdsid "CCDS338.1"  ; exon_id "ENSE00003607854.1"  ; exon_number 2 ; gene_id "PUM1--NKAIN1^PUM1^ENSG00000134644.16"  ; gene_name PUM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003795.5"  ; havana_transcript "OTTHUMT00000010671.1"  ; hgnc_id "HGNC:14957"  ; level 2 ; orig_coord_info "chr1,31059204,31059566,-"  ; protein_id "ENSP00000257075.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000257075.9"  ; transcript_name "PUM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PUM1--NKAIN1	HAVANA	mRNA	1294	30447	.	+	.	FI_gene_label "PUM1^ENSG00000134644.16"  ; ID "PUM1--NKAIN1^ENST00000257075.9"  ; Parent "PUM1--NKAIN1^PUM1^ENSG00000134644.16"  ; ccdsid "CCDS338.1"  ; exon_id "ENSE00003607854.1"  ; exon_number 2 ; gene_id "PUM1--NKAIN1^PUM1^ENSG00000134644.16"  ; gene_name PUM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003795.5"  ; havana_transcript "OTTHUMT00000010671.1"  ; hgnc_id "HGNC:14957"  ; level 2 ; orig_coord_info "chr1,31059204,31059566,-"  ; protein_id "ENSP00000257075.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000257075.9"  ; transcript_name "PUM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PUM1--NKAIN1	HAVANA	gene	33448	42502	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "PUM1--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 "PUM1--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PUM1--NKAIN1	HAVANA	mRNA	33448	42502	.	+	.	FI_gene_label "NKAIN1^ENSG00000084628.10"  ; ID "PUM1--NKAIN1^ENST00000373736.7"  ; Parent "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10"  ; ccdsid "CCDS339.2"  ; exon_id "ENSE00001461423.3"  ; exon_number 1 ; gene_id "PUM1--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 "PUM1--NKAIN1^ENST00000373736.7"  ; transcript_name "NKAIN1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RAB3B--SSBP3	HAVANA	gene	22749	45544	.	+	.	FI_gene_label "SSBP3^ENSG00000157216.16"  ; ID "RAB3B--SSBP3^SSBP3^ENSG00000157216.16"  ; ccdsid "CCDS590.1"  ; exon_id "ENSE00001894230.1"  ; exon_number 1 ; gene_id "RAB3B--SSBP3^SSBP3^ENSG00000157216.16"  ; gene_name SSBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008264.5"  ; havana_transcript "OTTHUMT00000022720.2"  ; hgnc_id "HGNC:15674"  ; level 2 ; orig_coord_info "chr1,54405953,54406008,-"  ; protein_id "ENSP00000350067.4"  ; tag basic CCDS ; transcript_id "RAB3B--SSBP3^ENST00000357475.9"  ; transcript_name "SSBP3-202"  ; transcript_support_level 1 ; transcript_type protein_coding
RAB3B--SSBP3	HAVANA	mRNA	22749	45544	.	+	.	FI_gene_label "SSBP3^ENSG00000157216.16"  ; ID "RAB3B--SSBP3^ENST00000357475.9"  ; Parent "RAB3B--SSBP3^SSBP3^ENSG00000157216.16"  ; ccdsid "CCDS590.1"  ; exon_id "ENSE00001894230.1"  ; exon_number 1 ; gene_id "RAB3B--SSBP3^SSBP3^ENSG00000157216.16"  ; gene_name SSBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008264.5"  ; havana_transcript "OTTHUMT00000022720.2"  ; hgnc_id "HGNC:15674"  ; level 2 ; orig_coord_info "chr1,54405953,54406008,-"  ; protein_id "ENSP00000350067.4"  ; tag basic CCDS ; transcript_id "RAB3B--SSBP3^ENST00000357475.9"  ; transcript_name "SSBP3-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAB3B--SSBP3	HAVANA	gene	1001	17780	.	+	.	FI_gene_label "RAB3B^ENSG00000169213.7"  ; ID "RAB3B--SSBP3^RAB3B^ENSG00000169213.7"  ; ccdsid "CCDS560.1"  ; exon_id "ENSE00003281431.1"  ; exon_number 2 ; gene_id "RAB3B--SSBP3^RAB3B^ENSG00000169213.7"  ; gene_name RAB3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000008627.2"  ; havana_transcript "OTTHUMT00000023816.2"  ; hgnc_id "HGNC:9778"  ; level 2 ; orig_coord_info "chr1,51976890,51977117,-"  ; protein_id "ENSP00000360718.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB3B--SSBP3^ENST00000371655.4"  ; transcript_name "RAB3B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAB3B--SSBP3	HAVANA	mRNA	1001	17780	.	+	.	FI_gene_label "RAB3B^ENSG00000169213.7"  ; ID "RAB3B--SSBP3^ENST00000371655.4"  ; Parent "RAB3B--SSBP3^RAB3B^ENSG00000169213.7"  ; ccdsid "CCDS560.1"  ; exon_id "ENSE00003281431.1"  ; exon_number 2 ; gene_id "RAB3B--SSBP3^RAB3B^ENSG00000169213.7"  ; gene_name RAB3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000008627.2"  ; havana_transcript "OTTHUMT00000023816.2"  ; hgnc_id "HGNC:9778"  ; level 2 ; orig_coord_info "chr1,51976890,51977117,-"  ; protein_id "ENSP00000360718.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB3B--SSBP3^ENST00000371655.4"  ; transcript_name "RAB3B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SBF2--RIC3	HAVANA	gene	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--RIC3^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--RIC3^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--RIC3^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--RIC3	HAVANA	mRNA	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--RIC3^ENST00000256190.13"  ; Parent "SBF2--RIC3^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--RIC3^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--RIC3^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SBF2--RIC3	HAVANA	gene	62844	77582	.	+	.	FI_gene_label "RIC3^ENSG00000166405.15"  ; ID "SBF2--RIC3^RIC3^ENSG00000166405.15"  ; ccdsid "CCDS55742.1"  ; exon_id "ENSE00003848333.1"  ; exon_number 1 ; gene_id "SBF2--RIC3^RIC3^ENSG00000166405.15"  ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6"  ; havana_transcript "OTTHUMT00000385900.3"  ; hgnc_id "HGNC:30338"  ; level 2 ; orig_coord_info "chr11,8168866,8168989,-"  ; protein_id "ENSP00000308820.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SBF2--RIC3^ENST00000309737.11"  ; transcript_name "RIC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--RIC3	HAVANA	mRNA	62844	77582	.	+	.	FI_gene_label "RIC3^ENSG00000166405.15"  ; ID "SBF2--RIC3^ENST00000309737.11"  ; Parent "SBF2--RIC3^RIC3^ENSG00000166405.15"  ; ccdsid "CCDS55742.1"  ; exon_id "ENSE00003848333.1"  ; exon_number 1 ; gene_id "SBF2--RIC3^RIC3^ENSG00000166405.15"  ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6"  ; havana_transcript "OTTHUMT00000385900.3"  ; hgnc_id "HGNC:30338"  ; level 2 ; orig_coord_info "chr11,8168866,8168989,-"  ; protein_id "ENSP00000308820.6"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SBF2--RIC3^ENST00000309737.11"  ; transcript_name "RIC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLFN11--SLFN12	HAVANA	gene	14962	22369	.	+	.	FI_gene_label "SLFN12^ENSG00000172123.13"  ; ID "SLFN11--SLFN12^SLFN12^ENSG00000172123.13"  ; ccdsid "CCDS11295.1"  ; exon_id "ENSE00001160241.4"  ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN12^ENSG00000172123.13"  ; gene_name SLFN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132952.3"  ; havana_transcript "OTTHUMT00000256490.1"  ; hgnc_id "HGNC:25500"  ; level 2 ; orig_coord_info "chr17,35421990,35423028,-"  ; protein_id "ENSP00000302077.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000304905.10"  ; transcript_name "SLFN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLFN11--SLFN12	HAVANA	mRNA	14962	22369	.	+	.	FI_gene_label "SLFN12^ENSG00000172123.13"  ; ID "SLFN11--SLFN12^ENST00000304905.10"  ; Parent "SLFN11--SLFN12^SLFN12^ENSG00000172123.13"  ; ccdsid "CCDS11295.1"  ; exon_id "ENSE00001160241.4"  ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN12^ENSG00000172123.13"  ; gene_name SLFN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132952.3"  ; havana_transcript "OTTHUMT00000256490.1"  ; hgnc_id "HGNC:25500"  ; level 2 ; orig_coord_info "chr17,35421990,35423028,-"  ; protein_id "ENSP00000302077.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000304905.10"  ; transcript_name "SLFN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SLFN11--SLFN12	HAVANA	gene	1095	11178	.	+	.	FI_gene_label "SLFN11^ENSG00000172716.16"  ; ID "SLFN11--SLFN12^SLFN11^ENSG00000172716.16"  ; ccdsid "CCDS11294.1"  ; exon_id "ENSE00001186651.3"  ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN11^ENSG00000172716.16"  ; gene_name SLFN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132948.3"  ; havana_transcript "OTTHUMT00000256481.1"  ; hgnc_id "HGNC:26633"  ; level 2 ; orig_coord_info "chr17,35362739,35363807,-"  ; protein_id "ENSP00000312402.4"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000308377.8"  ; transcript_name "SLFN11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLFN11--SLFN12	HAVANA	mRNA	1095	11178	.	+	.	FI_gene_label "SLFN11^ENSG00000172716.16"  ; ID "SLFN11--SLFN12^ENST00000308377.8"  ; Parent "SLFN11--SLFN12^SLFN11^ENSG00000172716.16"  ; ccdsid "CCDS11294.1"  ; exon_id "ENSE00001186651.3"  ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN11^ENSG00000172716.16"  ; gene_name SLFN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132948.3"  ; havana_transcript "OTTHUMT00000256481.1"  ; hgnc_id "HGNC:26633"  ; level 2 ; orig_coord_info "chr17,35362739,35363807,-"  ; protein_id "ENSP00000312402.4"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000308377.8"  ; transcript_name "SLFN11-201"  ; 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: 
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: 
AC004980.3--UPK3BL1	HAVANA	gene	1001	3365	.	+	.	FI_gene_label "AC004980.3^ENSG00000230305.2"  ; ID "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2"  ; exon_id "ENSE00002500030.1"  ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2"  ; gene_name "AC004980.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2"  ; havana_transcript "OTTHUMT00000341407.2"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,76524515,76524698,+"  ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1"  ; transcript_name "AC004980.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC004980.3--UPK3BL1	HAVANA	RNA	1001	3365	.	+	.	FI_gene_label "AC004980.3^ENSG00000230305.2"  ; ID "AC004980.3--UPK3BL1^ENST00000447046.1"  ; Parent "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2"  ; exon_id "ENSE00002500030.1"  ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2"  ; gene_name "AC004980.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2"  ; havana_transcript "OTTHUMT00000341407.2"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,76524515,76524698,+"  ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1"  ; transcript_name "AC004980.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
EFL1--GOLGA6L11P	HAVANA	gene	28063	33687	.	+	.	FI_gene_label "GOLGA6L11P^ENSG00000223698.3"  ; ID "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; exon_id "ENSE00001742768.1"  ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2"  ; havana_transcript "OTTHUMT00000104689.2"  ; hgnc_id "HGNC:23958"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chrY,24168187,24168270,+"  ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2"  ; transcript_name "GOLGA6L11P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EFL1--GOLGA6L11P	HAVANA	RNA	28063	33687	.	+	.	FI_gene_label "GOLGA6L11P^ENSG00000223698.3"  ; ID "EFL1--GOLGA6L11P^ENST00000417252.2"  ; Parent "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; exon_id "ENSE00001742768.1"  ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2"  ; havana_transcript "OTTHUMT00000104689.2"  ; hgnc_id "HGNC:23958"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chrY,24168187,24168270,+"  ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2"  ; transcript_name "GOLGA6L11P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
GINS2--AC025822.2	HAVANA	gene	11184	15782	.	+	.	FI_gene_label "AC025822.2^ENSG00000236990.1"  ; ID "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1"  ; exon_id "ENSE00001647260.1"  ; exon_number 1 ; gene_id "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1"  ; gene_name "AC025822.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017571.1"  ; havana_transcript "OTTHUMT00000046505.1"  ; level 2 ; orig_coord_info "chr10,4051726,4052157,+"  ; tag basic ; transcript_id "GINS2--AC025822.2^ENST00000455199.1"  ; transcript_name "AC025822.2-201"  ; transcript_support_level 2 ; transcript_type lncRNA
GINS2--AC025822.2	HAVANA	RNA	11184	15782	.	+	.	FI_gene_label "AC025822.2^ENSG00000236990.1"  ; ID "GINS2--AC025822.2^ENST00000455199.1"  ; Parent "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1"  ; exon_id "ENSE00001647260.1"  ; exon_number 1 ; gene_id "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1"  ; gene_name "AC025822.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017571.1"  ; havana_transcript "OTTHUMT00000046505.1"  ; level 2 ; orig_coord_info "chr10,4051726,4052157,+"  ; tag basic ; transcript_id "GINS2--AC025822.2^ENST00000455199.1"  ; transcript_name "AC025822.2-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
GINS2--LINC00702	HAVANA	gene	11307	12146	.	+	.	FI_gene_label "LINC00702^ENSG00000233117.4"  ; ID "GINS2--LINC00702^LINC00702^ENSG00000233117.4"  ; exon_id "ENSE00001727453.1"  ; exon_number 1 ; gene_id "GINS2--LINC00702^LINC00702^ENSG00000233117.4"  ; gene_name LINC00702 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017572.17"  ; havana_transcript "OTTHUMT00000046506.1"  ; hgnc_id "HGNC:44676"  ; level 1 ; orig_coord_info "chr10,4243504,4243789,-"  ; tag exp_conf ; transcript_id "GINS2--LINC00702^ENST00000418372.1"  ; transcript_name "LINC00702-201"  ; transcript_support_level 3 ; transcript_type lncRNA
GINS2--LINC00702	HAVANA	RNA	11307	12146	.	+	.	FI_gene_label "LINC00702^ENSG00000233117.4"  ; ID "GINS2--LINC00702^ENST00000418372.1"  ; Parent "GINS2--LINC00702^LINC00702^ENSG00000233117.4"  ; exon_id "ENSE00001727453.1"  ; exon_number 1 ; gene_id "GINS2--LINC00702^LINC00702^ENSG00000233117.4"  ; gene_name LINC00702 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017572.17"  ; havana_transcript "OTTHUMT00000046506.1"  ; hgnc_id "HGNC:44676"  ; level 1 ; orig_coord_info "chr10,4243504,4243789,-"  ; tag exp_conf ; transcript_id "GINS2--LINC00702^ENST00000418372.1"  ; transcript_name "LINC00702-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PMS2P1--UPK3BL1	HAVANA	gene	1448	6845	.	+	.	FI_gene_label "PMS2P1^ENSG00000078319.10"  ; ID "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10"  ; exon_id "ENSE00003899279.1"  ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10"  ; gene_name PMS2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156885.3"  ; havana_transcript "OTTHUMT00000346451.2"  ; hgnc_id "HGNC:9123"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr7,100335838,100335860,-"  ; tag basic ; transcript_id "PMS2P1--UPK3BL1^ENST00000431037.3"  ; transcript_name "PMS2P1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
PMS2P1--UPK3BL1	HAVANA	RNA	1448	6845	.	+	.	FI_gene_label "PMS2P1^ENSG00000078319.10"  ; ID "PMS2P1--UPK3BL1^ENST00000431037.3"  ; Parent "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10"  ; exon_id "ENSE00003899279.1"  ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10"  ; gene_name PMS2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156885.3"  ; havana_transcript "OTTHUMT00000346451.2"  ; hgnc_id "HGNC:9123"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr7,100335838,100335860,-"  ; tag basic ; transcript_id "PMS2P1--UPK3BL1^ENST00000431037.3"  ; transcript_name "PMS2P1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
323 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 ------------------------------
647 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 22 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