.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_mK-T1-TRNA-2_B23MHV2LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/9f7a217b48372b48324cd65095d960/.command.out
Size: 65.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_mK-T1-TRNA-2_B23MHV2LT4_1)
Attempt
Content

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: 5756
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5756
=> 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:5756
  => 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: 
ARHGAP17--IL21R-AS1	HAVANA	gene	1298	31886	.	+	.	FI_gene_label "ARHGAP17^ENSG00000140750.17"  ; ID "ARHGAP17--IL21R-AS1^ARHGAP17^ENSG00000140750.17"  ; ccdsid "CCDS32409.1"  ; exon_id "ENSE00003850028.1"  ; exon_number 1 ; gene_id "ARHGAP17--IL21R-AS1^ARHGAP17^ENSG00000140750.17"  ; gene_name ARHGAP17 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177372.11"  ; havana_transcript "OTTHUMT00000436548.4"  ; hgnc_id "HGNC:18239"  ; level 2 ; orig_coord_info "chr16,25015209,25015261,-"  ; protein_id "ENSP00000289968.6"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "ARHGAP17--IL21R-AS1^ENST00000289968.11"  ; transcript_name "ARHGAP17-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP17--IL21R-AS1	HAVANA	mRNA	1298	31886	.	+	.	FI_gene_label "ARHGAP17^ENSG00000140750.17"  ; ID "ARHGAP17--IL21R-AS1^ENST00000289968.11"  ; Parent "ARHGAP17--IL21R-AS1^ARHGAP17^ENSG00000140750.17"  ; ccdsid "CCDS32409.1"  ; exon_id "ENSE00003850028.1"  ; exon_number 1 ; gene_id "ARHGAP17--IL21R-AS1^ARHGAP17^ENSG00000140750.17"  ; gene_name ARHGAP17 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177372.11"  ; havana_transcript "OTTHUMT00000436548.4"  ; hgnc_id "HGNC:18239"  ; level 2 ; orig_coord_info "chr16,25015209,25015261,-"  ; protein_id "ENSP00000289968.6"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "ARHGAP17--IL21R-AS1^ENST00000289968.11"  ; transcript_name "ARHGAP17-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARID2--MIR4527HG	HAVANA	gene	1001	29970	.	+	.	FI_gene_label "ARID2^ENSG00000189079.17"  ; ID "ARID2--MIR4527HG^ARID2^ENSG00000189079.17"  ; ccdsid "CCDS31783.1"  ; exon_id "ENSE00002363600.2"  ; exon_number 1 ; gene_id "ARID2--MIR4527HG^ARID2^ENSG00000189079.17"  ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6"  ; havana_transcript "OTTHUMT00000318380.3"  ; hgnc_id "HGNC:18037"  ; level 2 ; orig_coord_info "chr12,45729837,45729928,+"  ; protein_id "ENSP00000335044.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARID2--MIR4527HG^ENST00000334344.11"  ; transcript_name "ARID2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARID2--MIR4527HG	HAVANA	mRNA	1001	29970	.	+	.	FI_gene_label "ARID2^ENSG00000189079.17"  ; ID "ARID2--MIR4527HG^ENST00000334344.11"  ; Parent "ARID2--MIR4527HG^ARID2^ENSG00000189079.17"  ; ccdsid "CCDS31783.1"  ; exon_id "ENSE00002363600.2"  ; exon_number 1 ; gene_id "ARID2--MIR4527HG^ARID2^ENSG00000189079.17"  ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6"  ; havana_transcript "OTTHUMT00000318380.3"  ; hgnc_id "HGNC:18037"  ; level 2 ; orig_coord_info "chr12,45729837,45729928,+"  ; protein_id "ENSP00000335044.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARID2--MIR4527HG^ENST00000334344.11"  ; transcript_name "ARID2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARID2--TPMTP1	HAVANA	gene	1001	29970	.	+	.	FI_gene_label "ARID2^ENSG00000189079.17"  ; ID "ARID2--TPMTP1^ARID2^ENSG00000189079.17"  ; ccdsid "CCDS31783.1"  ; exon_id "ENSE00002363600.2"  ; exon_number 1 ; gene_id "ARID2--TPMTP1^ARID2^ENSG00000189079.17"  ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6"  ; havana_transcript "OTTHUMT00000318380.3"  ; hgnc_id "HGNC:18037"  ; level 2 ; orig_coord_info "chr12,45729837,45729928,+"  ; protein_id "ENSP00000335044.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARID2--TPMTP1^ENST00000334344.11"  ; transcript_name "ARID2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARID2--TPMTP1	HAVANA	mRNA	1001	29970	.	+	.	FI_gene_label "ARID2^ENSG00000189079.17"  ; ID "ARID2--TPMTP1^ENST00000334344.11"  ; Parent "ARID2--TPMTP1^ARID2^ENSG00000189079.17"  ; ccdsid "CCDS31783.1"  ; exon_id "ENSE00002363600.2"  ; exon_number 1 ; gene_id "ARID2--TPMTP1^ARID2^ENSG00000189079.17"  ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6"  ; havana_transcript "OTTHUMT00000318380.3"  ; hgnc_id "HGNC:18037"  ; level 2 ; orig_coord_info "chr12,45729837,45729928,+"  ; protein_id "ENSP00000335044.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARID2--TPMTP1^ENST00000334344.11"  ; transcript_name "ARID2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CLPTM1L--AC115100.1	HAVANA	gene	1001	18913	.	+	.	FI_gene_label "CLPTM1L^ENSG00000049656.14"  ; ID "CLPTM1L--AC115100.1^CLPTM1L^ENSG00000049656.14"  ; ccdsid "CCDS3862.1"  ; exon_id "ENSE00001830316.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC115100.1^CLPTM1L^ENSG00000049656.14"  ; gene_name CLPTM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000131015.5"  ; havana_transcript "OTTHUMT00000253649.3"  ; hgnc_id "HGNC:24308"  ; level 2 ; orig_coord_info "chr5,1344680,1344841,-"  ; protein_id "ENSP00000313854.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLPTM1L--AC115100.1^ENST00000320895.10"  ; transcript_name "CLPTM1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CLPTM1L--AC115100.1	HAVANA	mRNA	1001	18913	.	+	.	FI_gene_label "CLPTM1L^ENSG00000049656.14"  ; ID "CLPTM1L--AC115100.1^ENST00000320895.10"  ; Parent "CLPTM1L--AC115100.1^CLPTM1L^ENSG00000049656.14"  ; ccdsid "CCDS3862.1"  ; exon_id "ENSE00001830316.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC115100.1^CLPTM1L^ENSG00000049656.14"  ; gene_name CLPTM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000131015.5"  ; havana_transcript "OTTHUMT00000253649.3"  ; hgnc_id "HGNC:24308"  ; level 2 ; orig_coord_info "chr5,1344680,1344841,-"  ; protein_id "ENSP00000313854.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLPTM1L--AC115100.1^ENST00000320895.10"  ; transcript_name "CLPTM1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CLPTM1L--AC117569.2	HAVANA	gene	1001	18913	.	+	.	FI_gene_label "CLPTM1L^ENSG00000049656.14"  ; ID "CLPTM1L--AC117569.2^CLPTM1L^ENSG00000049656.14"  ; ccdsid "CCDS3862.1"  ; exon_id "ENSE00001830316.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC117569.2^CLPTM1L^ENSG00000049656.14"  ; gene_name CLPTM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000131015.5"  ; havana_transcript "OTTHUMT00000253649.3"  ; hgnc_id "HGNC:24308"  ; level 2 ; orig_coord_info "chr5,1344680,1344841,-"  ; protein_id "ENSP00000313854.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLPTM1L--AC117569.2^ENST00000320895.10"  ; transcript_name "CLPTM1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CLPTM1L--AC117569.2	HAVANA	mRNA	1001	18913	.	+	.	FI_gene_label "CLPTM1L^ENSG00000049656.14"  ; ID "CLPTM1L--AC117569.2^ENST00000320895.10"  ; Parent "CLPTM1L--AC117569.2^CLPTM1L^ENSG00000049656.14"  ; ccdsid "CCDS3862.1"  ; exon_id "ENSE00001830316.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC117569.2^CLPTM1L^ENSG00000049656.14"  ; gene_name CLPTM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000131015.5"  ; havana_transcript "OTTHUMT00000253649.3"  ; hgnc_id "HGNC:24308"  ; level 2 ; orig_coord_info "chr5,1344680,1344841,-"  ; protein_id "ENSP00000313854.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLPTM1L--AC117569.2^ENST00000320895.10"  ; transcript_name "CLPTM1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EML4--ALK	HAVANA	gene	1001	31063	.	+	.	FI_gene_label "EML4^ENSG00000143924.19"  ; ID "EML4--ALK^EML4^ENSG00000143924.19"  ; ccdsid "CCDS1807.1"  ; exon_id "ENSE00001548738.1"  ; exon_number 1 ; gene_id "EML4--ALK^EML4^ENSG00000143924.19"  ; gene_name EML4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128603.7"  ; havana_transcript "OTTHUMT00000250463.4"  ; hgnc_id "HGNC:1316"  ; level 2 ; orig_coord_info "chr2,42169612,42169636,+"  ; protein_id "ENSP00000320663.5"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "EML4--ALK^ENST00000318522.10"  ; transcript_name "EML4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EML4--ALK	HAVANA	mRNA	1001	31063	.	+	.	FI_gene_label "EML4^ENSG00000143924.19"  ; ID "EML4--ALK^ENST00000318522.10"  ; Parent "EML4--ALK^EML4^ENSG00000143924.19"  ; ccdsid "CCDS1807.1"  ; exon_id "ENSE00001548738.1"  ; exon_number 1 ; gene_id "EML4--ALK^EML4^ENSG00000143924.19"  ; gene_name EML4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128603.7"  ; havana_transcript "OTTHUMT00000250463.4"  ; hgnc_id "HGNC:1316"  ; level 2 ; orig_coord_info "chr2,42169612,42169636,+"  ; protein_id "ENSP00000320663.5"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "EML4--ALK^ENST00000318522.10"  ; transcript_name "EML4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EML4--ALK	HAVANA	gene	34064	69068	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "EML4--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "EML4--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EML4--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EML4--ALK	HAVANA	mRNA	34064	69068	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "EML4--ALK^ENST00000389048.8"  ; Parent "EML4--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "EML4--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EML4--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LTA4H--FOCAD	HAVANA	gene	2287	23475	.	+	.	FI_gene_label "LTA4H^ENSG00000111144.10"  ; ID "LTA4H--FOCAD^LTA4H^ENSG00000111144.10"  ; ccdsid "CCDS9059.1"  ; exon_id "ENSE00002370169.2"  ; exon_number 1 ; gene_id "LTA4H--FOCAD^LTA4H^ENSG00000111144.10"  ; gene_name LTA4H ; gene_type protein_coding ; havana_gene "OTTHUMG00000170355.2"  ; havana_transcript "OTTHUMT00000408655.2"  ; hgnc_id "HGNC:6710"  ; level 2 ; orig_coord_info "chr12,96035361,96035519,-"  ; protein_id "ENSP00000228740.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LTA4H--FOCAD^ENST00000228740.7"  ; transcript_name "LTA4H-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LTA4H--FOCAD	HAVANA	mRNA	2287	23475	.	+	.	FI_gene_label "LTA4H^ENSG00000111144.10"  ; ID "LTA4H--FOCAD^ENST00000228740.7"  ; Parent "LTA4H--FOCAD^LTA4H^ENSG00000111144.10"  ; ccdsid "CCDS9059.1"  ; exon_id "ENSE00002370169.2"  ; exon_number 1 ; gene_id "LTA4H--FOCAD^LTA4H^ENSG00000111144.10"  ; gene_name LTA4H ; gene_type protein_coding ; havana_gene "OTTHUMG00000170355.2"  ; havana_transcript "OTTHUMT00000408655.2"  ; hgnc_id "HGNC:6710"  ; level 2 ; orig_coord_info "chr12,96035361,96035519,-"  ; protein_id "ENSP00000228740.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LTA4H--FOCAD^ENST00000228740.7"  ; transcript_name "LTA4H-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LTA4H--FOCAD	ENSEMBL	gene	30355	85392	.	+	.	FI_gene_label "FOCAD^ENSG00000188352.12"  ; ID "LTA4H--FOCAD^FOCAD^ENSG00000188352.12"  ; ccdsid "CCDS34993.1"  ; exon_id "ENSE00002283239.2"  ; exon_number 1 ; gene_id "LTA4H--FOCAD^FOCAD^ENSG00000188352.12"  ; gene_name FOCAD ; gene_type protein_coding ; havana_gene "OTTHUMG00000066930.4"  ; hgnc_id "HGNC:23377"  ; level 3 ; orig_coord_info "chr9,20715354,20715410,+"  ; protein_id "ENSP00000344307.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "LTA4H--FOCAD^ENST00000338382.10"  ; transcript_name "FOCAD-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LTA4H--FOCAD	ENSEMBL	mRNA	30355	85392	.	+	.	FI_gene_label "FOCAD^ENSG00000188352.12"  ; ID "LTA4H--FOCAD^ENST00000338382.10"  ; Parent "LTA4H--FOCAD^FOCAD^ENSG00000188352.12"  ; ccdsid "CCDS34993.1"  ; exon_id "ENSE00002283239.2"  ; exon_number 1 ; gene_id "LTA4H--FOCAD^FOCAD^ENSG00000188352.12"  ; gene_name FOCAD ; gene_type protein_coding ; havana_gene "OTTHUMG00000066930.4"  ; hgnc_id "HGNC:23377"  ; level 3 ; orig_coord_info "chr9,20715354,20715410,+"  ; protein_id "ENSP00000344307.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "LTA4H--FOCAD^ENST00000338382.10"  ; transcript_name "FOCAD-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MAP4K4--ARPP19P2	ENSEMBL	gene	2177	40764	.	+	.	FI_gene_label "MAP4K4^ENSG00000071054.16"  ; ID "MAP4K4--ARPP19P2^MAP4K4^ENSG00000071054.16"  ; exon_id "ENSE00003726002.1"  ; exon_number 3 ; gene_id "MAP4K4--ARPP19P2^MAP4K4^ENSG00000071054.16"  ; gene_name MAP4K4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155394.5"  ; hgnc_id "HGNC:6866"  ; level 3 ; orig_coord_info "chr2,101790762,101790776,+"  ; protein_id "ENSP00000303600.6"  ; tag basic ; transcript_id "MAP4K4--ARPP19P2^ENST00000302217.9"  ; transcript_name "MAP4K4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP4K4--ARPP19P2	ENSEMBL	mRNA	2177	40764	.	+	.	FI_gene_label "MAP4K4^ENSG00000071054.16"  ; ID "MAP4K4--ARPP19P2^ENST00000302217.9"  ; Parent "MAP4K4--ARPP19P2^MAP4K4^ENSG00000071054.16"  ; exon_id "ENSE00003726002.1"  ; exon_number 3 ; gene_id "MAP4K4--ARPP19P2^MAP4K4^ENSG00000071054.16"  ; gene_name MAP4K4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155394.5"  ; hgnc_id "HGNC:6866"  ; level 3 ; orig_coord_info "chr2,101790762,101790776,+"  ; protein_id "ENSP00000303600.6"  ; tag basic ; transcript_id "MAP4K4--ARPP19P2^ENST00000302217.9"  ; transcript_name "MAP4K4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP4K4--PDCL3	HAVANA	gene	43765	50036	.	+	.	FI_gene_label "PDCL3^ENSG00000115539.14"  ; ID "MAP4K4--PDCL3^PDCL3^ENSG00000115539.14"  ; ccdsid "CCDS33261.1"  ; exon_id "ENSE00001072179.9"  ; exon_number 1 ; gene_id "MAP4K4--PDCL3^PDCL3^ENSG00000115539.14"  ; gene_name PDCL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153141.5"  ; havana_transcript "OTTHUMT00000329734.2"  ; hgnc_id "HGNC:28860"  ; level 2 ; orig_coord_info "chr2,100563068,100563073,+"  ; protein_id "ENSP00000264254.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP4K4--PDCL3^ENST00000264254.11"  ; transcript_name "PDCL3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP4K4--PDCL3	HAVANA	mRNA	43765	50036	.	+	.	FI_gene_label "PDCL3^ENSG00000115539.14"  ; ID "MAP4K4--PDCL3^ENST00000264254.11"  ; Parent "MAP4K4--PDCL3^PDCL3^ENSG00000115539.14"  ; ccdsid "CCDS33261.1"  ; exon_id "ENSE00001072179.9"  ; exon_number 1 ; gene_id "MAP4K4--PDCL3^PDCL3^ENSG00000115539.14"  ; gene_name PDCL3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153141.5"  ; havana_transcript "OTTHUMT00000329734.2"  ; hgnc_id "HGNC:28860"  ; level 2 ; orig_coord_info "chr2,100563068,100563073,+"  ; protein_id "ENSP00000264254.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP4K4--PDCL3^ENST00000264254.11"  ; transcript_name "PDCL3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP4K4--PDCL3	ENSEMBL	gene	2177	40764	.	+	.	FI_gene_label "MAP4K4^ENSG00000071054.16"  ; ID "MAP4K4--PDCL3^MAP4K4^ENSG00000071054.16"  ; exon_id "ENSE00003726002.1"  ; exon_number 3 ; gene_id "MAP4K4--PDCL3^MAP4K4^ENSG00000071054.16"  ; gene_name MAP4K4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155394.5"  ; hgnc_id "HGNC:6866"  ; level 3 ; orig_coord_info "chr2,101790762,101790776,+"  ; protein_id "ENSP00000303600.6"  ; tag basic ; transcript_id "MAP4K4--PDCL3^ENST00000302217.9"  ; transcript_name "MAP4K4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP4K4--PDCL3	ENSEMBL	mRNA	2177	40764	.	+	.	FI_gene_label "MAP4K4^ENSG00000071054.16"  ; ID "MAP4K4--PDCL3^ENST00000302217.9"  ; Parent "MAP4K4--PDCL3^MAP4K4^ENSG00000071054.16"  ; exon_id "ENSE00003726002.1"  ; exon_number 3 ; gene_id "MAP4K4--PDCL3^MAP4K4^ENSG00000071054.16"  ; gene_name MAP4K4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155394.5"  ; hgnc_id "HGNC:6866"  ; level 3 ; orig_coord_info "chr2,101790762,101790776,+"  ; protein_id "ENSP00000303600.6"  ; tag basic ; transcript_id "MAP4K4--PDCL3^ENST00000302217.9"  ; transcript_name "MAP4K4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MET--RNA5-8SP6	HAVANA	gene	1001	27300	.	+	.	FI_gene_label "MET^ENSG00000105976.16"  ; ID "MET--RNA5-8SP6^MET^ENSG00000105976.16"  ; ccdsid "CCDS47689.1"  ; exon_id "ENSE00001238915.3"  ; exon_number 2 ; gene_id "MET--RNA5-8SP6^MET^ENSG00000105976.16"  ; gene_name MET ; gene_type protein_coding ; havana_gene "OTTHUMG00000023299.10"  ; havana_transcript "OTTHUMT00000059620.4"  ; hgnc_id "HGNC:7029"  ; level 2 ; orig_coord_info "chr7,116699085,116700284,+"  ; protein_id "ENSP00000317272.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "MET--RNA5-8SP6^ENST00000318493.11"  ; transcript_name "MET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MET--RNA5-8SP6	HAVANA	mRNA	1001	27300	.	+	.	FI_gene_label "MET^ENSG00000105976.16"  ; ID "MET--RNA5-8SP6^ENST00000318493.11"  ; Parent "MET--RNA5-8SP6^MET^ENSG00000105976.16"  ; ccdsid "CCDS47689.1"  ; exon_id "ENSE00001238915.3"  ; exon_number 2 ; gene_id "MET--RNA5-8SP6^MET^ENSG00000105976.16"  ; gene_name MET ; gene_type protein_coding ; havana_gene "OTTHUMG00000023299.10"  ; havana_transcript "OTTHUMT00000059620.4"  ; hgnc_id "HGNC:7029"  ; level 2 ; orig_coord_info "chr7,116699085,116700284,+"  ; protein_id "ENSP00000317272.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "MET--RNA5-8SP6^ENST00000318493.11"  ; transcript_name "MET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MOCOS--FHOD3	HAVANA	gene	24230	60606	.	+	.	FI_gene_label "FHOD3^ENSG00000134775.15"  ; ID "MOCOS--FHOD3^FHOD3^ENSG00000134775.15"  ; ccdsid "CCDS32816.1"  ; exon_id "ENSE00003647252.1"  ; exon_number 1 ; gene_id "MOCOS--FHOD3^FHOD3^ENSG00000134775.15"  ; gene_name FHOD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182381.5"  ; havana_transcript "OTTHUMT00000460885.3"  ; hgnc_id "HGNC:26178"  ; level 2 ; orig_coord_info "chr18,36297836,36298000,+"  ; protein_id "ENSP00000257209.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "MOCOS--FHOD3^ENST00000257209.8"  ; transcript_name "FHOD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MOCOS--FHOD3	HAVANA	mRNA	24230	60606	.	+	.	FI_gene_label "FHOD3^ENSG00000134775.15"  ; ID "MOCOS--FHOD3^ENST00000257209.8"  ; Parent "MOCOS--FHOD3^FHOD3^ENSG00000134775.15"  ; ccdsid "CCDS32816.1"  ; exon_id "ENSE00003647252.1"  ; exon_number 1 ; gene_id "MOCOS--FHOD3^FHOD3^ENSG00000134775.15"  ; gene_name FHOD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182381.5"  ; havana_transcript "OTTHUMT00000460885.3"  ; hgnc_id "HGNC:26178"  ; level 2 ; orig_coord_info "chr18,36297836,36298000,+"  ; protein_id "ENSP00000257209.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "MOCOS--FHOD3^ENST00000257209.8"  ; transcript_name "FHOD3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MOCOS--FHOD3	HAVANA	gene	1001	21229	.	+	.	FI_gene_label "MOCOS^ENSG00000075643.6"  ; ID "MOCOS--FHOD3^MOCOS^ENSG00000075643.6"  ; ccdsid "CCDS11919.1"  ; exon_id "ENSE00000916114.8"  ; exon_number 1 ; gene_id "MOCOS--FHOD3^MOCOS^ENSG00000075643.6"  ; gene_name MOCOS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132590.3"  ; havana_transcript "OTTHUMT00000255801.2"  ; hgnc_id "HGNC:18234"  ; level 2 ; orig_coord_info "chr18,36187540,36187681,+"  ; protein_id "ENSP00000261326.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MOCOS--FHOD3^ENST00000261326.6"  ; transcript_name "MOCOS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MOCOS--FHOD3	HAVANA	mRNA	1001	21229	.	+	.	FI_gene_label "MOCOS^ENSG00000075643.6"  ; ID "MOCOS--FHOD3^ENST00000261326.6"  ; Parent "MOCOS--FHOD3^MOCOS^ENSG00000075643.6"  ; ccdsid "CCDS11919.1"  ; exon_id "ENSE00000916114.8"  ; exon_number 1 ; gene_id "MOCOS--FHOD3^MOCOS^ENSG00000075643.6"  ; gene_name MOCOS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132590.3"  ; havana_transcript "OTTHUMT00000255801.2"  ; hgnc_id "HGNC:18234"  ; level 2 ; orig_coord_info "chr18,36187540,36187681,+"  ; protein_id "ENSP00000261326.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MOCOS--FHOD3^ENST00000261326.6"  ; transcript_name "MOCOS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TALDO1--EPS8L2	HAVANA	gene	14589	26541	.	+	.	FI_gene_label "EPS8L2^ENSG00000177106.16"  ; ID "TALDO1--EPS8L2^EPS8L2^ENSG00000177106.16"  ; ccdsid "CCDS31328.1"  ; exon_id "ENSE00003542299.1"  ; exon_number 2 ; gene_id "TALDO1--EPS8L2^EPS8L2^ENSG00000177106.16"  ; gene_name EPS8L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165165.12"  ; havana_transcript "OTTHUMT00000382343.2"  ; hgnc_id "HGNC:21296"  ; level 2 ; orig_coord_info "chr11,709408,709451,+"  ; protein_id "ENSP00000320828.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--EPS8L2^ENST00000318562.13"  ; transcript_name "EPS8L2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TALDO1--EPS8L2	HAVANA	mRNA	14589	26541	.	+	.	FI_gene_label "EPS8L2^ENSG00000177106.16"  ; ID "TALDO1--EPS8L2^ENST00000318562.13"  ; Parent "TALDO1--EPS8L2^EPS8L2^ENSG00000177106.16"  ; ccdsid "CCDS31328.1"  ; exon_id "ENSE00003542299.1"  ; exon_number 2 ; gene_id "TALDO1--EPS8L2^EPS8L2^ENSG00000177106.16"  ; gene_name EPS8L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165165.12"  ; havana_transcript "OTTHUMT00000382343.2"  ; hgnc_id "HGNC:21296"  ; level 2 ; orig_coord_info "chr11,709408,709451,+"  ; protein_id "ENSP00000320828.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--EPS8L2^ENST00000318562.13"  ; transcript_name "EPS8L2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TALDO1--EPS8L2	HAVANA	gene	1050	9536	.	+	.	FI_gene_label "TALDO1^ENSG00000177156.11"  ; ID "TALDO1--EPS8L2^TALDO1^ENSG00000177156.11"  ; ccdsid "CCDS7712.1"  ; exon_id "ENSE00001297974.7"  ; exon_number 1 ; gene_id "TALDO1--EPS8L2^TALDO1^ENSG00000177156.11"  ; gene_name TALDO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133318.5"  ; havana_transcript "OTTHUMT00000257116.2"  ; hgnc_id "HGNC:11559"  ; level 2 ; orig_coord_info "chr11,747482,747578,+"  ; protein_id "ENSP00000321259.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--EPS8L2^ENST00000319006.8"  ; transcript_name "TALDO1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TALDO1--EPS8L2	HAVANA	mRNA	1050	9536	.	+	.	FI_gene_label "TALDO1^ENSG00000177156.11"  ; ID "TALDO1--EPS8L2^ENST00000319006.8"  ; Parent "TALDO1--EPS8L2^TALDO1^ENSG00000177156.11"  ; ccdsid "CCDS7712.1"  ; exon_id "ENSE00001297974.7"  ; exon_number 1 ; gene_id "TALDO1--EPS8L2^TALDO1^ENSG00000177156.11"  ; gene_name TALDO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133318.5"  ; havana_transcript "OTTHUMT00000257116.2"  ; hgnc_id "HGNC:11559"  ; level 2 ; orig_coord_info "chr11,747482,747578,+"  ; protein_id "ENSP00000321259.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--EPS8L2^ENST00000319006.8"  ; transcript_name "TALDO1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TBP--ATXN3	HAVANA	gene	1078	10356	.	+	.	FI_gene_label "TBP^ENSG00000112592.14"  ; ID "TBP--ATXN3^TBP^ENSG00000112592.14"  ; ccdsid "CCDS5315.1"  ; exon_id "ENSE00000854356.1"  ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14"  ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6"  ; havana_transcript "OTTHUMT00000043271.2"  ; hgnc_id "HGNC:11588"  ; level 2 ; orig_coord_info "chr6,170557030,170557083,+"  ; protein_id "ENSP00000230354.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10"  ; transcript_name "TBP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TBP--ATXN3	HAVANA	mRNA	1078	10356	.	+	.	FI_gene_label "TBP^ENSG00000112592.14"  ; ID "TBP--ATXN3^ENST00000230354.10"  ; Parent "TBP--ATXN3^TBP^ENSG00000112592.14"  ; ccdsid "CCDS5315.1"  ; exon_id "ENSE00000854356.1"  ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14"  ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6"  ; havana_transcript "OTTHUMT00000043271.2"  ; hgnc_id "HGNC:11588"  ; level 2 ; orig_coord_info "chr6,170557030,170557083,+"  ; protein_id "ENSP00000230354.5"  ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10"  ; transcript_name "TBP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TBP--ATXN3	HAVANA	gene	13368	28517	.	+	.	FI_gene_label "ATXN3^ENSG00000066427.24"  ; ID "TBP--ATXN3^ATXN3^ENSG00000066427.24"  ; ccdsid "CCDS32143.1"  ; exon_id "ENSE00002073369.1"  ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24"  ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16"  ; havana_transcript "OTTHUMT00000367924.2"  ; hgnc_id "HGNC:7106"  ; level 2 ; orig_coord_info "chr14,92106529,92106552,-"  ; protein_id "ENSP00000339110.6"  ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10"  ; transcript_name "ATXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TBP--ATXN3	HAVANA	mRNA	13368	28517	.	+	.	FI_gene_label "ATXN3^ENSG00000066427.24"  ; ID "TBP--ATXN3^ENST00000340660.10"  ; Parent "TBP--ATXN3^ATXN3^ENSG00000066427.24"  ; ccdsid "CCDS32143.1"  ; exon_id "ENSE00002073369.1"  ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24"  ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16"  ; havana_transcript "OTTHUMT00000367924.2"  ; hgnc_id "HGNC:7106"  ; level 2 ; orig_coord_info "chr14,92106529,92106552,-"  ; protein_id "ENSP00000339110.6"  ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10"  ; transcript_name "ATXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRIM41--AC008620.2	HAVANA	gene	1783	14310	.	+	.	FI_gene_label "TRIM41^ENSG00000146063.20"  ; ID "TRIM41--AC008620.2^TRIM41^ENSG00000146063.20"  ; ccdsid "CCDS4466.1"  ; exon_id "ENSE00003844969.1"  ; exon_number 1 ; gene_id "TRIM41--AC008620.2^TRIM41^ENSG00000146063.20"  ; gene_name TRIM41 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130965.10"  ; havana_transcript "OTTHUMT00000253574.4"  ; hgnc_id "HGNC:19013"  ; level 2 ; orig_coord_info "chr5,181224000,181224812,+"  ; protein_id "ENSP00000320869.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM41--AC008620.2^ENST00000315073.10"  ; transcript_name "TRIM41-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRIM41--AC008620.2	HAVANA	mRNA	1783	14310	.	+	.	FI_gene_label "TRIM41^ENSG00000146063.20"  ; ID "TRIM41--AC008620.2^ENST00000315073.10"  ; Parent "TRIM41--AC008620.2^TRIM41^ENSG00000146063.20"  ; ccdsid "CCDS4466.1"  ; exon_id "ENSE00003844969.1"  ; exon_number 1 ; gene_id "TRIM41--AC008620.2^TRIM41^ENSG00000146063.20"  ; gene_name TRIM41 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130965.10"  ; havana_transcript "OTTHUMT00000253574.4"  ; hgnc_id "HGNC:19013"  ; level 2 ; orig_coord_info "chr5,181224000,181224812,+"  ; protein_id "ENSP00000320869.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM41--AC008620.2^ENST00000315073.10"  ; transcript_name "TRIM41-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRIM41--OR2V1	HAVANA	gene	1783	14310	.	+	.	FI_gene_label "TRIM41^ENSG00000146063.20"  ; ID "TRIM41--OR2V1^TRIM41^ENSG00000146063.20"  ; ccdsid "CCDS4466.1"  ; exon_id "ENSE00003844969.1"  ; exon_number 1 ; gene_id "TRIM41--OR2V1^TRIM41^ENSG00000146063.20"  ; gene_name TRIM41 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130965.10"  ; havana_transcript "OTTHUMT00000253574.4"  ; hgnc_id "HGNC:19013"  ; level 2 ; orig_coord_info "chr5,181224000,181224812,+"  ; protein_id "ENSP00000320869.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM41--OR2V1^ENST00000315073.10"  ; transcript_name "TRIM41-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TRIM41--OR2V1	HAVANA	mRNA	1783	14310	.	+	.	FI_gene_label "TRIM41^ENSG00000146063.20"  ; ID "TRIM41--OR2V1^ENST00000315073.10"  ; Parent "TRIM41--OR2V1^TRIM41^ENSG00000146063.20"  ; ccdsid "CCDS4466.1"  ; exon_id "ENSE00003844969.1"  ; exon_number 1 ; gene_id "TRIM41--OR2V1^TRIM41^ENSG00000146063.20"  ; gene_name TRIM41 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130965.10"  ; havana_transcript "OTTHUMT00000253574.4"  ; hgnc_id "HGNC:19013"  ; level 2 ; orig_coord_info "chr5,181224000,181224812,+"  ; protein_id "ENSP00000320869.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM41--OR2V1^ENST00000315073.10"  ; transcript_name "TRIM41-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRIM41--OR2V1	ENSEMBL	gene	19982	20929	.	+	.	FI_gene_label "OR2V1^ENSG00000185372.3"  ; ID "TRIM41--OR2V1^OR2V1^ENSG00000185372.3"  ; ccdsid "CCDS58992.1"  ; exon_id "ENSE00002471304.1"  ; exon_number 1 ; gene_id "TRIM41--OR2V1^OR2V1^ENSG00000185372.3"  ; gene_name OR2V1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162118.4"  ; hgnc_id "HGNC:8280"  ; level 3 ; orig_coord_info "chr5,181124360,181125304,-"  ; protein_id "ENSP00000404102.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "TRIM41--OR2V1^ENST00000329365.2"  ; transcript_name "OR2V1-201"  ; transcript_support_level NA ; transcript_type protein_coding
TRIM41--OR2V1	ENSEMBL	mRNA	19982	20929	.	+	.	FI_gene_label "OR2V1^ENSG00000185372.3"  ; ID "TRIM41--OR2V1^ENST00000329365.2"  ; Parent "TRIM41--OR2V1^OR2V1^ENSG00000185372.3"  ; ccdsid "CCDS58992.1"  ; exon_id "ENSE00002471304.1"  ; exon_number 1 ; gene_id "TRIM41--OR2V1^OR2V1^ENSG00000185372.3"  ; gene_name OR2V1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162118.4"  ; hgnc_id "HGNC:8280"  ; level 3 ; orig_coord_info "chr5,181124360,181125304,-"  ; protein_id "ENSP00000404102.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "TRIM41--OR2V1^ENST00000329365.2"  ; transcript_name "OR2V1-201"  ; transcript_support_level NA ; 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: 
WDR70--LINC00603	HAVANA	gene	1034	23383	.	+	.	FI_gene_label "WDR70^ENSG00000082068.9"  ; ID "WDR70--LINC00603^WDR70^ENSG00000082068.9"  ; ccdsid "CCDS34147.1"  ; exon_id "ENSE00002056284.2"  ; exon_number 1 ; gene_id "WDR70--LINC00603^WDR70^ENSG00000082068.9"  ; gene_name WDR70 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162263.2"  ; havana_transcript "OTTHUMT00000368294.2"  ; hgnc_id "HGNC:25495"  ; level 2 ; orig_coord_info "chr5,37379368,37379392,+"  ; protein_id "ENSP00000265107.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR70--LINC00603^ENST00000265107.9"  ; transcript_name "WDR70-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WDR70--LINC00603	HAVANA	mRNA	1034	23383	.	+	.	FI_gene_label "WDR70^ENSG00000082068.9"  ; ID "WDR70--LINC00603^ENST00000265107.9"  ; Parent "WDR70--LINC00603^WDR70^ENSG00000082068.9"  ; ccdsid "CCDS34147.1"  ; exon_id "ENSE00002056284.2"  ; exon_number 1 ; gene_id "WDR70--LINC00603^WDR70^ENSG00000082068.9"  ; gene_name WDR70 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162263.2"  ; havana_transcript "OTTHUMT00000368294.2"  ; hgnc_id "HGNC:25495"  ; level 2 ; orig_coord_info "chr5,37379368,37379392,+"  ; protein_id "ENSP00000265107.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR70--LINC00603^ENST00000265107.9"  ; transcript_name "WDR70-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP17--IL21R-AS1	HAVANA	gene	34887	38675	.	+	.	FI_gene_label "IL21R-AS1^ENSG00000259954.1"  ; ID "ARHGAP17--IL21R-AS1^IL21R-AS1^ENSG00000259954.1"  ; exon_id "ENSE00002591700.1"  ; exon_number 1 ; gene_id "ARHGAP17--IL21R-AS1^IL21R-AS1^ENSG00000259954.1"  ; gene_name "IL21R-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000176806.1"  ; havana_transcript "OTTHUMT00000433868.1"  ; hgnc_id "HGNC:27551"  ; level 2 ; orig_coord_info "chr16,27453097,27453393,-"  ; tag basic ; transcript_id "ARHGAP17--IL21R-AS1^ENST00000563191.1"  ; transcript_name "IL21R-AS1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
ARHGAP17--IL21R-AS1	HAVANA	RNA	34887	38675	.	+	.	FI_gene_label "IL21R-AS1^ENSG00000259954.1"  ; ID "ARHGAP17--IL21R-AS1^ENST00000563191.1"  ; Parent "ARHGAP17--IL21R-AS1^IL21R-AS1^ENSG00000259954.1"  ; exon_id "ENSE00002591700.1"  ; exon_number 1 ; gene_id "ARHGAP17--IL21R-AS1^IL21R-AS1^ENSG00000259954.1"  ; gene_name "IL21R-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000176806.1"  ; havana_transcript "OTTHUMT00000433868.1"  ; hgnc_id "HGNC:27551"  ; level 2 ; orig_coord_info "chr16,27453097,27453393,-"  ; tag basic ; transcript_id "ARHGAP17--IL21R-AS1^ENST00000563191.1"  ; transcript_name "IL21R-AS1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
ARID2--MIR4527HG	HAVANA	gene	32974	40370	.	+	.	FI_gene_label "MIR4527HG^ENSG00000267761.3"  ; ID "ARID2--MIR4527HG^MIR4527HG^ENSG00000267761.3"  ; exon_id "ENSE00003017591.1"  ; exon_number 1 ; gene_id "ARID2--MIR4527HG^MIR4527HG^ENSG00000267761.3"  ; gene_name MIR4527HG ; gene_type lncRNA ; havana_gene "OTTHUMG00000180284.4"  ; havana_transcript "OTTHUMT00000450570.4"  ; hgnc_id "HGNC:31724"  ; level 2 ; orig_coord_info "chr18,47285725,47285761,+"  ; tag basic ; transcript_id "ARID2--MIR4527HG^ENST00000586905.3"  ; transcript_name "MIR4527HG-201"  ; transcript_support_level 1 ; transcript_type lncRNA
ARID2--MIR4527HG	HAVANA	RNA	32974	40370	.	+	.	FI_gene_label "MIR4527HG^ENSG00000267761.3"  ; ID "ARID2--MIR4527HG^ENST00000586905.3"  ; Parent "ARID2--MIR4527HG^MIR4527HG^ENSG00000267761.3"  ; exon_id "ENSE00003017591.1"  ; exon_number 1 ; gene_id "ARID2--MIR4527HG^MIR4527HG^ENSG00000267761.3"  ; gene_name MIR4527HG ; gene_type lncRNA ; havana_gene "OTTHUMG00000180284.4"  ; havana_transcript "OTTHUMT00000450570.4"  ; hgnc_id "HGNC:31724"  ; level 2 ; orig_coord_info "chr18,47285725,47285761,+"  ; tag basic ; transcript_id "ARID2--MIR4527HG^ENST00000586905.3"  ; transcript_name "MIR4527HG-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
ARID2--TPMTP1	HAVANA	gene	32974	33710	.	+	.	FI_gene_label "TPMTP1^ENSG00000267156.1"  ; ID "ARID2--TPMTP1^TPMTP1^ENSG00000267156.1"  ; exon_id "ENSE00002817915.1"  ; exon_number 1 ; gene_id "ARID2--TPMTP1^TPMTP1^ENSG00000267156.1"  ; gene_name TPMTP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000180321.1"  ; havana_transcript "OTTHUMT00000450729.1"  ; hgnc_id "HGNC:17490"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr18,47630112,47630848,+"  ; tag pseudo_consens basic ; transcript_id "ARID2--TPMTP1^ENST00000592307.1"  ; transcript_name "TPMTP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ARID2--TPMTP1	HAVANA	RNA	32974	33710	.	+	.	FI_gene_label "TPMTP1^ENSG00000267156.1"  ; ID "ARID2--TPMTP1^ENST00000592307.1"  ; Parent "ARID2--TPMTP1^TPMTP1^ENSG00000267156.1"  ; exon_id "ENSE00002817915.1"  ; exon_number 1 ; gene_id "ARID2--TPMTP1^TPMTP1^ENSG00000267156.1"  ; gene_name TPMTP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000180321.1"  ; havana_transcript "OTTHUMT00000450729.1"  ; hgnc_id "HGNC:17490"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr18,47630112,47630848,+"  ; tag pseudo_consens basic ; transcript_id "ARID2--TPMTP1^ENST00000592307.1"  ; transcript_name "TPMTP1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
CLPTM1L--AC115100.1	HAVANA	gene	21914	26643	.	+	.	FI_gene_label "AC115100.1^ENSG00000286605.1"  ; ID "CLPTM1L--AC115100.1^AC115100.1^ENSG00000286605.1"  ; exon_id "ENSE00003857895.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC115100.1^AC115100.1^ENSG00000286605.1"  ; gene_name "AC115100.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194799.1"  ; havana_transcript "OTTHUMT00000522161.1"  ; level 2 ; orig_coord_info "chr18,30290161,30290422,+"  ; tag basic TAGENE ; transcript_id "CLPTM1L--AC115100.1^ENST00000657542.1"  ; transcript_name "AC115100.1-201"  ; transcript_type lncRNA
CLPTM1L--AC115100.1	HAVANA	RNA	21914	26643	.	+	.	FI_gene_label "AC115100.1^ENSG00000286605.1"  ; ID "CLPTM1L--AC115100.1^ENST00000657542.1"  ; Parent "CLPTM1L--AC115100.1^AC115100.1^ENSG00000286605.1"  ; exon_id "ENSE00003857895.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC115100.1^AC115100.1^ENSG00000286605.1"  ; gene_name "AC115100.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194799.1"  ; havana_transcript "OTTHUMT00000522161.1"  ; level 2 ; orig_coord_info "chr18,30290161,30290422,+"  ; tag basic TAGENE ; transcript_id "CLPTM1L--AC115100.1^ENST00000657542.1"  ; transcript_name "AC115100.1-201"  ; transcript_type lncRNA
L1 and L2 created: 
CLPTM1L--AC117569.2	HAVANA	gene	21914	25250	.	+	.	FI_gene_label "AC117569.2^ENSG00000287803.1"  ; ID "CLPTM1L--AC117569.2^AC117569.2^ENSG00000287803.1"  ; exon_id "ENSE00003871240.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC117569.2^AC117569.2^ENSG00000287803.1"  ; gene_name "AC117569.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194445.1"  ; havana_transcript "OTTHUMT00000516449.1"  ; level 2 ; orig_coord_info "chr18,29629842,29629964,+"  ; tag basic TAGENE ; transcript_id "CLPTM1L--AC117569.2^ENST00000666254.1"  ; transcript_name "AC117569.2-201"  ; transcript_type lncRNA
CLPTM1L--AC117569.2	HAVANA	RNA	21914	25250	.	+	.	FI_gene_label "AC117569.2^ENSG00000287803.1"  ; ID "CLPTM1L--AC117569.2^ENST00000666254.1"  ; Parent "CLPTM1L--AC117569.2^AC117569.2^ENSG00000287803.1"  ; exon_id "ENSE00003871240.1"  ; exon_number 1 ; gene_id "CLPTM1L--AC117569.2^AC117569.2^ENSG00000287803.1"  ; gene_name "AC117569.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000194445.1"  ; havana_transcript "OTTHUMT00000516449.1"  ; level 2 ; orig_coord_info "chr18,29629842,29629964,+"  ; tag basic TAGENE ; transcript_id "CLPTM1L--AC117569.2^ENST00000666254.1"  ; transcript_name "AC117569.2-201"  ; transcript_type lncRNA
L1 and L2 created: 
MAP4K4--ARPP19P2	HAVANA	gene	43765	44100	.	+	.	FI_gene_label "ARPP19P2^ENSG00000204637.4"  ; ID "MAP4K4--ARPP19P2^ARPP19P2^ENSG00000204637.4"  ; exon_id "ENSE00001471940.2"  ; exon_number 1 ; gene_id "MAP4K4--ARPP19P2^ARPP19P2^ENSG00000204637.4"  ; gene_name ARPP19P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153139.2"  ; havana_transcript "OTTHUMT00000329732.1"  ; hgnc_id "HGNC:54699"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr2,100509277,100509612,+"  ; tag pseudo_consens basic ; transcript_id "MAP4K4--ARPP19P2^ENST00000376856.2"  ; transcript_name "ARPP19P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MAP4K4--ARPP19P2	HAVANA	RNA	43765	44100	.	+	.	FI_gene_label "ARPP19P2^ENSG00000204637.4"  ; ID "MAP4K4--ARPP19P2^ENST00000376856.2"  ; Parent "MAP4K4--ARPP19P2^ARPP19P2^ENSG00000204637.4"  ; exon_id "ENSE00001471940.2"  ; exon_number 1 ; gene_id "MAP4K4--ARPP19P2^ARPP19P2^ENSG00000204637.4"  ; gene_name ARPP19P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153139.2"  ; havana_transcript "OTTHUMT00000329732.1"  ; hgnc_id "HGNC:54699"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr2,100509277,100509612,+"  ; tag pseudo_consens basic ; transcript_id "MAP4K4--ARPP19P2^ENST00000376856.2"  ; transcript_name "ARPP19P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
MET--RNA5-8SP6	ENSEMBL	gene	30301	30452	.	+	.	FI_gene_label "RNA5-8SP6^ENSG00000251705.1"  ; ID "MET--RNA5-8SP6^RNA5-8SP6^ENSG00000251705.1"  ; exon_id "ENSE00002088173.1"  ; exon_number 1 ; gene_id "MET--RNA5-8SP6^RNA5-8SP6^ENSG00000251705.1"  ; gene_name "RNA5-8SP6"  ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41960"  ; level 3 ; orig_coord_info "chrY,10200155,10200306,+"  ; tag basic ; transcript_id "MET--RNA5-8SP6^ENST00000515896.1"  ; transcript_name "RNA5-8SP6-201"  ; transcript_support_level NA ; transcript_type rRNA_pseudogene
MET--RNA5-8SP6	ENSEMBL	RNA	30301	30452	.	+	.	FI_gene_label "RNA5-8SP6^ENSG00000251705.1"  ; ID "MET--RNA5-8SP6^ENST00000515896.1"  ; Parent "MET--RNA5-8SP6^RNA5-8SP6^ENSG00000251705.1"  ; exon_id "ENSE00002088173.1"  ; exon_number 1 ; gene_id "MET--RNA5-8SP6^RNA5-8SP6^ENSG00000251705.1"  ; gene_name "RNA5-8SP6"  ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41960"  ; level 3 ; orig_coord_info "chrY,10200155,10200306,+"  ; tag basic ; transcript_id "MET--RNA5-8SP6^ENST00000515896.1"  ; transcript_name "RNA5-8SP6-201"  ; transcript_support_level NA ; transcript_type rRNA_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
TRIM41--AC008620.2	HAVANA	gene	17311	18879	.	+	.	FI_gene_label "AC008620.2^ENSG00000248560.1"  ; ID "TRIM41--AC008620.2^AC008620.2^ENSG00000248560.1"  ; exon_id "ENSE00002069086.1"  ; exon_number 1 ; gene_id "TRIM41--AC008620.2^AC008620.2^ENSG00000248560.1"  ; gene_name "AC008620.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162100.1"  ; havana_transcript "OTTHUMT00000367312.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,181114106,181115674,+"  ; tag pseudo_consens basic ; transcript_id "TRIM41--AC008620.2^ENST00000510294.1"  ; transcript_name "AC008620.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TRIM41--AC008620.2	HAVANA	RNA	17311	18879	.	+	.	FI_gene_label "AC008620.2^ENSG00000248560.1"  ; ID "TRIM41--AC008620.2^ENST00000510294.1"  ; Parent "TRIM41--AC008620.2^AC008620.2^ENSG00000248560.1"  ; exon_id "ENSE00002069086.1"  ; exon_number 1 ; gene_id "TRIM41--AC008620.2^AC008620.2^ENSG00000248560.1"  ; gene_name "AC008620.2"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162100.1"  ; havana_transcript "OTTHUMT00000367312.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,181114106,181115674,+"  ; tag pseudo_consens basic ; transcript_id "TRIM41--AC008620.2^ENST00000510294.1"  ; transcript_name "AC008620.2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
WDR70--LINC00603	HAVANA	gene	28587	31059	.	+	.	FI_gene_label "LINC00603^ENSG00000250048.2"  ; ID "WDR70--LINC00603^LINC00603^ENSG00000250048.2"  ; exon_id "ENSE00003795156.1"  ; exon_number 1 ; gene_id "WDR70--LINC00603^LINC00603^ENSG00000250048.2"  ; gene_name LINC00603 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162195.2"  ; havana_transcript "OTTHUMT00000367830.2"  ; hgnc_id "HGNC:43918"  ; level 2 ; orig_coord_info "chr5,40010912,40011010,+"  ; tag RNA_Seq_supported_only basic ; transcript_id "WDR70--LINC00603^ENST00000507027.2"  ; transcript_name "LINC00603-201"  ; transcript_support_level 5 ; transcript_type lncRNA
WDR70--LINC00603	HAVANA	RNA	28587	31059	.	+	.	FI_gene_label "LINC00603^ENSG00000250048.2"  ; ID "WDR70--LINC00603^ENST00000507027.2"  ; Parent "WDR70--LINC00603^LINC00603^ENSG00000250048.2"  ; exon_id "ENSE00003795156.1"  ; exon_number 1 ; gene_id "WDR70--LINC00603^LINC00603^ENSG00000250048.2"  ; gene_name LINC00603 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162195.2"  ; havana_transcript "OTTHUMT00000367830.2"  ; hgnc_id "HGNC:43918"  ; level 2 ; orig_coord_info "chr5,40010912,40011010,+"  ; tag RNA_Seq_supported_only basic ; transcript_id "WDR70--LINC00603^ENST00000507027.2"  ; transcript_name "LINC00603-201"  ; transcript_support_level 5 ; transcript_type lncRNA
377 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------

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

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

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

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

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

----------------------------- Check10: check utrs ------------------------------
605 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 23 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 1 seconds -------------------------------
                  ------ End checks (done in 1 second) ------                   


GFF3 file parsed