Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/cafcb2cbf8238e383d1f5097867a4a/fi_workdir/tih_rna_sample_00635_B23MVV7LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/7c4e9e3b8571a4f31404d2e095908e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/7c4e9e3b8571a4f31404d2e095908e/.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: 4229
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4229
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:4229
=> 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:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AL512590.2--CCDC180 HAVANA gene 14599 56298 . + . FI_gene_label "CCDC180^ENSG00000197816.16" ; ID "AL512590.2--CCDC180^CCDC180^ENSG00000197816.16" ; exon_id "ENSE00003898006.1" ; exon_number 2 ; gene_id "AL512590.2--CCDC180^CCDC180^ENSG00000197816.16" ; gene_name CCDC180 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167001.3" ; havana_transcript "OTTHUMT00000383515.4" ; hgnc_id "HGNC:29303" ; level 2 ; orig_coord_info "chr9,97308064,97308132,+" ; protein_id "ENSP00000434727.2" ; tag basic MANE_Select appris_principal_1 ; transcript_id "AL512590.2--CCDC180^ENST00000529487.3" ; transcript_name "CCDC180-210" ; transcript_support_level 1 ; transcript_type protein_coding
AL512590.2--CCDC180 HAVANA mRNA 14599 56298 . + . FI_gene_label "CCDC180^ENSG00000197816.16" ; ID "AL512590.2--CCDC180^ENST00000529487.3" ; Parent "AL512590.2--CCDC180^CCDC180^ENSG00000197816.16" ; exon_id "ENSE00003898006.1" ; exon_number 2 ; gene_id "AL512590.2--CCDC180^CCDC180^ENSG00000197816.16" ; gene_name CCDC180 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167001.3" ; havana_transcript "OTTHUMT00000383515.4" ; hgnc_id "HGNC:29303" ; level 2 ; orig_coord_info "chr9,97308064,97308132,+" ; protein_id "ENSP00000434727.2" ; tag basic MANE_Select appris_principal_1 ; transcript_id "AL512590.2--CCDC180^ENST00000529487.3" ; transcript_name "CCDC180-210" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BOP1--ASB8 HAVANA gene 14083 20911 . + . FI_gene_label "ASB8^ENSG00000177981.11" ; ID "BOP1--ASB8^ASB8^ENSG00000177981.11" ; ccdsid "CCDS8761.1" ; exon_id "ENSE00001218337.3" ; exon_number 2 ; gene_id "BOP1--ASB8^ASB8^ENSG00000177981.11" ; gene_name ASB8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167834.4" ; havana_transcript "OTTHUMT00000396497.2" ; hgnc_id "HGNC:17183" ; level 2 ; orig_coord_info "chr12,48153368,48153496,-" ; protein_id "ENSP00000320893.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BOP1--ASB8^ENST00000317697.8" ; transcript_name "ASB8-201" ; transcript_support_level 1 ; transcript_type protein_coding
BOP1--ASB8 HAVANA mRNA 14083 20911 . + . FI_gene_label "ASB8^ENSG00000177981.11" ; ID "BOP1--ASB8^ENST00000317697.8" ; Parent "BOP1--ASB8^ASB8^ENSG00000177981.11" ; ccdsid "CCDS8761.1" ; exon_id "ENSE00001218337.3" ; exon_number 2 ; gene_id "BOP1--ASB8^ASB8^ENSG00000177981.11" ; gene_name ASB8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167834.4" ; havana_transcript "OTTHUMT00000396497.2" ; hgnc_id "HGNC:17183" ; level 2 ; orig_coord_info "chr12,48153368,48153496,-" ; protein_id "ENSP00000320893.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BOP1--ASB8^ENST00000317697.8" ; transcript_name "ASB8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BOP1--ASB8 HAVANA gene 1069 7453 . + . FI_gene_label "BOP1^ENSG00000261236.8" ; ID "BOP1--ASB8^BOP1^ENSG00000261236.8" ; exon_id "ENSE00002628286.1" ; exon_number 1 ; gene_id "BOP1--ASB8^BOP1^ENSG00000261236.8" ; gene_name BOP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000174603.5" ; havana_transcript "OTTHUMT00000426982.3" ; hgnc_id "HGNC:15519" ; level 2 ; orig_coord_info "chr8,144291272,144291370,-" ; protein_id "ENSP00000456082.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "BOP1--ASB8^ENST00000569403.1" ; transcript_name "BOP1-204" ; transcript_support_level 4 ; transcript_type protein_coding
BOP1--ASB8 HAVANA mRNA 1069 7453 . + . FI_gene_label "BOP1^ENSG00000261236.8" ; ID "BOP1--ASB8^ENST00000569403.1" ; Parent "BOP1--ASB8^BOP1^ENSG00000261236.8" ; exon_id "ENSE00002628286.1" ; exon_number 1 ; gene_id "BOP1--ASB8^BOP1^ENSG00000261236.8" ; gene_name BOP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000174603.5" ; havana_transcript "OTTHUMT00000426982.3" ; hgnc_id "HGNC:15519" ; level 2 ; orig_coord_info "chr8,144291272,144291370,-" ; protein_id "ENSP00000456082.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "BOP1--ASB8^ENST00000569403.1" ; transcript_name "BOP1-204" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
DNAJB6P1--GSAP HAVANA gene 4743 39125 . + . FI_gene_label "GSAP^ENSG00000186088.16" ; ID "DNAJB6P1--GSAP^GSAP^ENSG00000186088.16" ; ccdsid "CCDS34672.2" ; exon_id "ENSE00001519751.2" ; exon_number 1 ; gene_id "DNAJB6P1--GSAP^GSAP^ENSG00000186088.16" ; gene_name GSAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150504.7" ; havana_transcript "OTTHUMT00000318672.3" ; hgnc_id "HGNC:28042" ; level 2 ; orig_coord_info "chr7,77416213,77416321,-" ; protein_id "ENSP00000257626.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJB6P1--GSAP^ENST00000257626.12" ; transcript_name "GSAP-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNAJB6P1--GSAP HAVANA mRNA 4743 39125 . + . FI_gene_label "GSAP^ENSG00000186088.16" ; ID "DNAJB6P1--GSAP^ENST00000257626.12" ; Parent "DNAJB6P1--GSAP^GSAP^ENSG00000186088.16" ; ccdsid "CCDS34672.2" ; exon_id "ENSE00001519751.2" ; exon_number 1 ; gene_id "DNAJB6P1--GSAP^GSAP^ENSG00000186088.16" ; gene_name GSAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150504.7" ; havana_transcript "OTTHUMT00000318672.3" ; hgnc_id "HGNC:28042" ; level 2 ; orig_coord_info "chr7,77416213,77416321,-" ; protein_id "ENSP00000257626.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJB6P1--GSAP^ENST00000257626.12" ; transcript_name "GSAP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNAJB6P4--GSAP HAVANA gene 4729 39111 . + . FI_gene_label "GSAP^ENSG00000186088.16" ; ID "DNAJB6P4--GSAP^GSAP^ENSG00000186088.16" ; ccdsid "CCDS34672.2" ; exon_id "ENSE00001519751.2" ; exon_number 1 ; gene_id "DNAJB6P4--GSAP^GSAP^ENSG00000186088.16" ; gene_name GSAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150504.7" ; havana_transcript "OTTHUMT00000318672.3" ; hgnc_id "HGNC:28042" ; level 2 ; orig_coord_info "chr7,77416213,77416321,-" ; protein_id "ENSP00000257626.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJB6P4--GSAP^ENST00000257626.12" ; transcript_name "GSAP-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNAJB6P4--GSAP HAVANA mRNA 4729 39111 . + . FI_gene_label "GSAP^ENSG00000186088.16" ; ID "DNAJB6P4--GSAP^ENST00000257626.12" ; Parent "DNAJB6P4--GSAP^GSAP^ENSG00000186088.16" ; ccdsid "CCDS34672.2" ; exon_id "ENSE00001519751.2" ; exon_number 1 ; gene_id "DNAJB6P4--GSAP^GSAP^ENSG00000186088.16" ; gene_name GSAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150504.7" ; havana_transcript "OTTHUMT00000318672.3" ; hgnc_id "HGNC:28042" ; level 2 ; orig_coord_info "chr7,77416213,77416321,-" ; protein_id "ENSP00000257626.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJB6P4--GSAP^ENST00000257626.12" ; transcript_name "GSAP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERBIN--AC010280.1 HAVANA gene 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--AC010280.1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--AC010280.1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--AC010280.1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERBIN--AC010280.1 HAVANA mRNA 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--AC010280.1^ENST00000284037.10" ; Parent "ERBIN--AC010280.1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--AC010280.1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--AC010280.1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERBIN--AC093523.1 HAVANA gene 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--AC093523.1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--AC093523.1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--AC093523.1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERBIN--AC093523.1 HAVANA mRNA 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--AC093523.1^ENST00000284037.10" ; Parent "ERBIN--AC093523.1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--AC093523.1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--AC093523.1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MON1B--AC106733.1 HAVANA gene 1356 10336 . + . FI_gene_label "MON1B^ENSG00000103111.15" ; ID "MON1B--AC106733.1^MON1B^ENSG00000103111.15" ; ccdsid "CCDS10925.1" ; exon_id "ENSE00003626624.1" ; exon_number 2 ; gene_id "MON1B--AC106733.1^MON1B^ENSG00000103111.15" ; gene_name MON1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000137618.4" ; havana_transcript "OTTHUMT00000269036.3" ; hgnc_id "HGNC:25020" ; level 2 ; orig_coord_info "chr16,77191486,77191633,+" ; protein_id "ENSP00000248248.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MON1B--AC106733.1^ENST00000248248.8" ; transcript_name "MON1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
MON1B--AC106733.1 HAVANA mRNA 1356 10336 . + . FI_gene_label "MON1B^ENSG00000103111.15" ; ID "MON1B--AC106733.1^ENST00000248248.8" ; Parent "MON1B--AC106733.1^MON1B^ENSG00000103111.15" ; ccdsid "CCDS10925.1" ; exon_id "ENSE00003626624.1" ; exon_number 2 ; gene_id "MON1B--AC106733.1^MON1B^ENSG00000103111.15" ; gene_name MON1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000137618.4" ; havana_transcript "OTTHUMT00000269036.3" ; hgnc_id "HGNC:25020" ; level 2 ; orig_coord_info "chr16,77191486,77191633,+" ; protein_id "ENSP00000248248.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MON1B--AC106733.1^ENST00000248248.8" ; transcript_name "MON1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SMURF1--AC006148.1 HAVANA gene 1009 25933 . + . FI_gene_label "SMURF1^ENSG00000198742.10" ; ID "SMURF1--AC006148.1^SMURF1^ENSG00000198742.10" ; ccdsid "CCDS34690.1" ; exon_id "ENSE00001128723.4" ; exon_number 1 ; gene_id "SMURF1--AC006148.1^SMURF1^ENSG00000198742.10" ; gene_name SMURF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150272.3" ; havana_transcript "OTTHUMT00000335001.2" ; hgnc_id "HGNC:16807" ; level 2 ; orig_coord_info "chr7,99143726,99143780,-" ; protein_id "ENSP00000354621.1" ; tag basic CCDS ; transcript_id "SMURF1--AC006148.1^ENST00000361125.1" ; transcript_name "SMURF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SMURF1--AC006148.1 HAVANA mRNA 1009 25933 . + . FI_gene_label "SMURF1^ENSG00000198742.10" ; ID "SMURF1--AC006148.1^ENST00000361125.1" ; Parent "SMURF1--AC006148.1^SMURF1^ENSG00000198742.10" ; ccdsid "CCDS34690.1" ; exon_id "ENSE00001128723.4" ; exon_number 1 ; gene_id "SMURF1--AC006148.1^SMURF1^ENSG00000198742.10" ; gene_name SMURF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150272.3" ; havana_transcript "OTTHUMT00000335001.2" ; hgnc_id "HGNC:16807" ; level 2 ; orig_coord_info "chr7,99143726,99143780,-" ; protein_id "ENSP00000354621.1" ; tag basic CCDS ; transcript_id "SMURF1--AC006148.1^ENST00000361125.1" ; transcript_name "SMURF1-201" ; 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:
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:
TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRRAP--MAGI2 HAVANA gene 86355 168753 . + . FI_gene_label "MAGI2^ENSG00000187391.22" ; ID "TRRAP--MAGI2^MAGI2^ENSG00000187391.22" ; ccdsid "CCDS5594.1" ; exon_id "ENSE00001597225.2" ; exon_number 1 ; gene_id "TRRAP--MAGI2^MAGI2^ENSG00000187391.22" ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19" ; havana_transcript "OTTHUMT00000253197.5" ; hgnc_id "HGNC:18957" ; level 2 ; orig_coord_info "chr7,79453020,79453320,-" ; protein_id "ENSP00000346151.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TRRAP--MAGI2^ENST00000354212.9" ; transcript_name "MAGI2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRRAP--MAGI2 HAVANA mRNA 86355 168753 . + . FI_gene_label "MAGI2^ENSG00000187391.22" ; ID "TRRAP--MAGI2^ENST00000354212.9" ; Parent "TRRAP--MAGI2^MAGI2^ENSG00000187391.22" ; ccdsid "CCDS5594.1" ; exon_id "ENSE00001597225.2" ; exon_number 1 ; gene_id "TRRAP--MAGI2^MAGI2^ENSG00000187391.22" ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19" ; havana_transcript "OTTHUMT00000253197.5" ; hgnc_id "HGNC:18957" ; level 2 ; orig_coord_info "chr7,79453020,79453320,-" ; protein_id "ENSP00000346151.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TRRAP--MAGI2^ENST00000354212.9" ; transcript_name "MAGI2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRRAP--MAGI2 HAVANA gene 1558 71136 . + . FI_gene_label "TRRAP^ENSG00000196367.14" ; ID "TRRAP--MAGI2^TRRAP^ENSG00000196367.14" ; ccdsid "CCDS5659.1" ; exon_id "ENSE00001130521.1" ; exon_number 2 ; gene_id "TRRAP--MAGI2^TRRAP^ENSG00000196367.14" ; gene_name TRRAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150403.5" ; havana_transcript "OTTHUMT00000317979.1" ; hgnc_id "HGNC:12347" ; level 2 ; orig_coord_info "chr7,98881151,98881250,+" ; protein_id "ENSP00000347733.3" ; tag basic appris_principal_2 CCDS ; transcript_id "TRRAP--MAGI2^ENST00000355540.7" ; transcript_name "TRRAP-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRRAP--MAGI2 HAVANA mRNA 1558 71136 . + . FI_gene_label "TRRAP^ENSG00000196367.14" ; ID "TRRAP--MAGI2^ENST00000355540.7" ; Parent "TRRAP--MAGI2^TRRAP^ENSG00000196367.14" ; ccdsid "CCDS5659.1" ; exon_id "ENSE00001130521.1" ; exon_number 2 ; gene_id "TRRAP--MAGI2^TRRAP^ENSG00000196367.14" ; gene_name TRRAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000150403.5" ; havana_transcript "OTTHUMT00000317979.1" ; hgnc_id "HGNC:12347" ; level 2 ; orig_coord_info "chr7,98881151,98881250,+" ; protein_id "ENSP00000347733.3" ; tag basic appris_principal_2 CCDS ; transcript_id "TRRAP--MAGI2^ENST00000355540.7" ; transcript_name "TRRAP-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:
AC010329.1--OR7E140P HAVANA gene 12329 13354 . + . FI_gene_label "OR7E140P^ENSG00000238152.2" ; ID "AC010329.1--OR7E140P^OR7E140P^ENSG00000238152.2" ; exon_id "ENSE00002288068.1" ; exon_number 1 ; gene_id "AC010329.1--OR7E140P^OR7E140P^ENSG00000238152.2" ; gene_name OR7E140P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000168669.1" ; havana_transcript "OTTHUMT00000400559.1" ; hgnc_id "HGNC:19561" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr12,8414780,8415805,-" ; tag pseudo_consens basic ; transcript_id "AC010329.1--OR7E140P^ENST00000425390.2" ; transcript_name "OR7E140P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC010329.1--OR7E140P HAVANA RNA 12329 13354 . + . FI_gene_label "OR7E140P^ENSG00000238152.2" ; ID "AC010329.1--OR7E140P^ENST00000425390.2" ; Parent "AC010329.1--OR7E140P^OR7E140P^ENSG00000238152.2" ; exon_id "ENSE00002288068.1" ; exon_number 1 ; gene_id "AC010329.1--OR7E140P^OR7E140P^ENSG00000238152.2" ; gene_name OR7E140P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000168669.1" ; havana_transcript "OTTHUMT00000400559.1" ; hgnc_id "HGNC:19561" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr12,8414780,8415805,-" ; tag pseudo_consens basic ; transcript_id "AC010329.1--OR7E140P^ENST00000425390.2" ; transcript_name "OR7E140P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC010329.1--OR7E140P HAVANA gene 1001 9328 . + . FI_gene_label "AC010329.1^ENSG00000268416.1" ; ID "AC010329.1--OR7E140P^AC010329.1^ENSG00000268416.1" ; exon_id "ENSE00003149229.1" ; exon_number 1 ; gene_id "AC010329.1--OR7E140P^AC010329.1^ENSG00000268416.1" ; gene_name "AC010329.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182743.1" ; havana_transcript "OTTHUMT00000463423.1" ; level 2 ; orig_coord_info "chr19,20746923,20755250,-" ; tag basic ; transcript_id "AC010329.1--OR7E140P^ENST00000593903.1" ; transcript_name "AC010329.1-201" ; transcript_support_level NA ; transcript_type lncRNA
AC010329.1--OR7E140P HAVANA RNA 1001 9328 . + . FI_gene_label "AC010329.1^ENSG00000268416.1" ; ID "AC010329.1--OR7E140P^ENST00000593903.1" ; Parent "AC010329.1--OR7E140P^AC010329.1^ENSG00000268416.1" ; exon_id "ENSE00003149229.1" ; exon_number 1 ; gene_id "AC010329.1--OR7E140P^AC010329.1^ENSG00000268416.1" ; gene_name "AC010329.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182743.1" ; havana_transcript "OTTHUMT00000463423.1" ; level 2 ; orig_coord_info "chr19,20746923,20755250,-" ; tag basic ; transcript_id "AC010329.1--OR7E140P^ENST00000593903.1" ; transcript_name "AC010329.1-201" ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
AL512590.2--CCDC180 HAVANA gene 1001 11243 . + . FI_gene_label "AL512590.2^ENSG00000254633.2" ; ID "AL512590.2--CCDC180^AL512590.2^ENSG00000254633.2" ; exon_id "ENSE00002146032.2" ; exon_number 1 ; gene_id "AL512590.2--CCDC180^AL512590.2^ENSG00000254633.2" ; gene_name "AL512590.2" ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000167000.2" ; havana_transcript "OTTHUMT00000392365.2" ; level 2 ; orig_coord_info "chr9,97276569,97276697,+" ; tag basic ; transcript_id "AL512590.2--CCDC180^ENST00000531758.2" ; transcript_name "AL512590.2-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
AL512590.2--CCDC180 HAVANA RNA 1001 11243 . + . FI_gene_label "AL512590.2^ENSG00000254633.2" ; ID "AL512590.2--CCDC180^ENST00000531758.2" ; Parent "AL512590.2--CCDC180^AL512590.2^ENSG00000254633.2" ; exon_id "ENSE00002146032.2" ; exon_number 1 ; gene_id "AL512590.2--CCDC180^AL512590.2^ENSG00000254633.2" ; gene_name "AL512590.2" ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000167000.2" ; havana_transcript "OTTHUMT00000392365.2" ; level 2 ; orig_coord_info "chr9,97276569,97276697,+" ; tag basic ; transcript_id "AL512590.2--CCDC180^ENST00000531758.2" ; transcript_name "AL512590.2-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
BMS1P7--AGAP14P HAVANA gene 1001 7575 . + . FI_gene_label "BMS1P7^ENSG00000270025.2" ; ID "BMS1P7--AGAP14P^BMS1P7^ENSG00000270025.2" ; exon_id "ENSE00001675840.2" ; exon_number 1 ; gene_id "BMS1P7--AGAP14P^BMS1P7^ENSG00000270025.2" ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3" ; havana_transcript "OTTHUMT00000047911.2" ; hgnc_id "HGNC:23655" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48059827,48060016,-" ; tag basic ; transcript_id "BMS1P7--AGAP14P^ENST00000602440.2" ; transcript_name "BMS1P7-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
BMS1P7--AGAP14P HAVANA RNA 1001 7575 . + . FI_gene_label "BMS1P7^ENSG00000270025.2" ; ID "BMS1P7--AGAP14P^ENST00000602440.2" ; Parent "BMS1P7--AGAP14P^BMS1P7^ENSG00000270025.2" ; exon_id "ENSE00001675840.2" ; exon_number 1 ; gene_id "BMS1P7--AGAP14P^BMS1P7^ENSG00000270025.2" ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3" ; havana_transcript "OTTHUMT00000047911.2" ; hgnc_id "HGNC:23655" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48059827,48060016,-" ; tag basic ; transcript_id "BMS1P7--AGAP14P^ENST00000602440.2" ; transcript_name "BMS1P7-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
BMS1P7--AGAP14P HAVANA gene 10576 18649 . + . FI_gene_label "AGAP14P^ENSG00000279058.2" ; ID "BMS1P7--AGAP14P^AGAP14P^ENSG00000279058.2" ; exon_id "ENSE00003760240.1" ; exon_number 1 ; gene_id "BMS1P7--AGAP14P^AGAP14P^ENSG00000279058.2" ; gene_name AGAP14P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000192004.1" ; havana_transcript "OTTHUMT00000491977.1" ; hgnc_id "HGNC:23660" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr10,46337224,46337446,+" ; tag basic ; transcript_id "BMS1P7--AGAP14P^ENST00000624701.2" ; transcript_name "AGAP14P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
BMS1P7--AGAP14P HAVANA RNA 10576 18649 . + . FI_gene_label "AGAP14P^ENSG00000279058.2" ; ID "BMS1P7--AGAP14P^ENST00000624701.2" ; Parent "BMS1P7--AGAP14P^AGAP14P^ENSG00000279058.2" ; exon_id "ENSE00003760240.1" ; exon_number 1 ; gene_id "BMS1P7--AGAP14P^AGAP14P^ENSG00000279058.2" ; gene_name AGAP14P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000192004.1" ; havana_transcript "OTTHUMT00000491977.1" ; hgnc_id "HGNC:23660" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr10,46337224,46337446,+" ; tag basic ; transcript_id "BMS1P7--AGAP14P^ENST00000624701.2" ; transcript_name "AGAP14P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
DNAJB6P1--GSAP HAVANA gene 1001 1742 . + . FI_gene_label "DNAJB6P1^ENSG00000254612.2" ; ID "DNAJB6P1--GSAP^DNAJB6P1^ENSG00000254612.2" ; exon_id "ENSE00002179110.2" ; exon_number 1 ; gene_id "DNAJB6P1--GSAP^DNAJB6P1^ENSG00000254612.2" ; gene_name DNAJB6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000165798.2" ; havana_transcript "OTTHUMT00000386266.2" ; hgnc_id "HGNC:54754" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr11,127940913,127941654,-" ; tag pseudo_consens basic ; transcript_id "DNAJB6P1--GSAP^ENST00000526843.2" ; transcript_name "DNAJB6P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
DNAJB6P1--GSAP HAVANA RNA 1001 1742 . + . FI_gene_label "DNAJB6P1^ENSG00000254612.2" ; ID "DNAJB6P1--GSAP^ENST00000526843.2" ; Parent "DNAJB6P1--GSAP^DNAJB6P1^ENSG00000254612.2" ; exon_id "ENSE00002179110.2" ; exon_number 1 ; gene_id "DNAJB6P1--GSAP^DNAJB6P1^ENSG00000254612.2" ; gene_name DNAJB6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000165798.2" ; havana_transcript "OTTHUMT00000386266.2" ; hgnc_id "HGNC:54754" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr11,127940913,127941654,-" ; tag pseudo_consens basic ; transcript_id "DNAJB6P1--GSAP^ENST00000526843.2" ; transcript_name "DNAJB6P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
DNAJB6P4--GSAP HAVANA gene 1001 1728 . + . FI_gene_label "DNAJB6P4^ENSG00000228523.1" ; ID "DNAJB6P4--GSAP^DNAJB6P4^ENSG00000228523.1" ; exon_id "ENSE00001727291.1" ; exon_number 1 ; gene_id "DNAJB6P4--GSAP^DNAJB6P4^ENSG00000228523.1" ; gene_name DNAJB6P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000009093.2" ; havana_transcript "OTTHUMT00000025201.2" ; hgnc_id "HGNC:54757" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,67278052,67278779,+" ; tag pseudo_consens basic ; transcript_id "DNAJB6P4--GSAP^ENST00000432257.1" ; transcript_name "DNAJB6P4-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
DNAJB6P4--GSAP HAVANA RNA 1001 1728 . + . FI_gene_label "DNAJB6P4^ENSG00000228523.1" ; ID "DNAJB6P4--GSAP^ENST00000432257.1" ; Parent "DNAJB6P4--GSAP^DNAJB6P4^ENSG00000228523.1" ; exon_id "ENSE00001727291.1" ; exon_number 1 ; gene_id "DNAJB6P4--GSAP^DNAJB6P4^ENSG00000228523.1" ; gene_name DNAJB6P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000009093.2" ; havana_transcript "OTTHUMT00000025201.2" ; hgnc_id "HGNC:54757" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,67278052,67278779,+" ; tag pseudo_consens basic ; transcript_id "DNAJB6P4--GSAP^ENST00000432257.1" ; transcript_name "DNAJB6P4-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
ERBIN--AC010280.1 HAVANA gene 39651 40990 . + . FI_gene_label "AC010280.1^ENSG00000248359.2" ; ID "ERBIN--AC010280.1^AC010280.1^ENSG00000248359.2" ; exon_id "ENSE00002043391.1" ; exon_number 1 ; gene_id "ERBIN--AC010280.1^AC010280.1^ENSG00000248359.2" ; gene_name "AC010280.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000162335.3" ; havana_transcript "OTTHUMT00000368584.1" ; level 1 ; orig_coord_info "chr5,68533419,68533530,-" ; tag basic exp_conf ; transcript_id "ERBIN--AC010280.1^ENST00000515199.1" ; transcript_name "AC010280.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
ERBIN--AC010280.1 HAVANA RNA 39651 40990 . + . FI_gene_label "AC010280.1^ENSG00000248359.2" ; ID "ERBIN--AC010280.1^ENST00000515199.1" ; Parent "ERBIN--AC010280.1^AC010280.1^ENSG00000248359.2" ; exon_id "ENSE00002043391.1" ; exon_number 1 ; gene_id "ERBIN--AC010280.1^AC010280.1^ENSG00000248359.2" ; gene_name "AC010280.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000162335.3" ; havana_transcript "OTTHUMT00000368584.1" ; level 1 ; orig_coord_info "chr5,68533419,68533530,-" ; tag basic exp_conf ; transcript_id "ERBIN--AC010280.1^ENST00000515199.1" ; transcript_name "AC010280.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
ERBIN--AC093523.1 HAVANA gene 38475 46499 . + . FI_gene_label "AC093523.1^ENSG00000249335.2" ; ID "ERBIN--AC093523.1^AC093523.1^ENSG00000249335.2" ; exon_id "ENSE00003880822.1" ; exon_number 1 ; gene_id "ERBIN--AC093523.1^AC093523.1^ENSG00000249335.2" ; gene_name "AC093523.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000162332.3" ; havana_transcript "OTTHUMT00000524529.1" ; level 2 ; orig_coord_info "chr5,69007027,69007185,-" ; tag basic TAGENE ; transcript_id "ERBIN--AC093523.1^ENST00000503268.2" ; transcript_name "AC093523.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
ERBIN--AC093523.1 HAVANA RNA 38475 46499 . + . FI_gene_label "AC093523.1^ENSG00000249335.2" ; ID "ERBIN--AC093523.1^ENST00000503268.2" ; Parent "ERBIN--AC093523.1^AC093523.1^ENSG00000249335.2" ; exon_id "ENSE00003880822.1" ; exon_number 1 ; gene_id "ERBIN--AC093523.1^AC093523.1^ENSG00000249335.2" ; gene_name "AC093523.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000162332.3" ; havana_transcript "OTTHUMT00000524529.1" ; level 2 ; orig_coord_info "chr5,69007027,69007185,-" ; tag basic TAGENE ; transcript_id "ERBIN--AC093523.1^ENST00000503268.2" ; transcript_name "AC093523.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
MON1B--AC106733.1 HAVANA gene 13337 14374 . + . FI_gene_label "AC106733.1^ENSG00000279856.1" ; ID "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1" ; exon_id "ENSE00003756467.1" ; exon_number 1 ; gene_id "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1" ; gene_name "AC106733.1" ; gene_type TEC ; havana_gene "OTTHUMG00000176663.1" ; havana_transcript "OTTHUMT00000433025.1" ; level 2 ; orig_coord_info "chr16,77104260,77105297,+" ; tag basic ; transcript_id "MON1B--AC106733.1^ENST00000624476.1" ; transcript_name "AC106733.1-201" ; transcript_support_level NA ; transcript_type TEC
MON1B--AC106733.1 HAVANA RNA 13337 14374 . + . FI_gene_label "AC106733.1^ENSG00000279856.1" ; ID "MON1B--AC106733.1^ENST00000624476.1" ; Parent "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1" ; exon_id "ENSE00003756467.1" ; exon_number 1 ; gene_id "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1" ; gene_name "AC106733.1" ; gene_type TEC ; havana_gene "OTTHUMG00000176663.1" ; havana_transcript "OTTHUMT00000433025.1" ; level 2 ; orig_coord_info "chr16,77104260,77105297,+" ; tag basic ; transcript_id "MON1B--AC106733.1^ENST00000624476.1" ; transcript_name "AC106733.1-201" ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created:
SMURF1--AC006148.1 HAVANA gene 29014 63954 . + . FI_gene_label "AC006148.1^ENSG00000242593.7" ; ID "SMURF1--AC006148.1^AC006148.1^ENSG00000242593.7" ; exon_id "ENSE00001818688.1" ; exon_number 1 ; gene_id "SMURF1--AC006148.1^AC006148.1^ENSG00000242593.7" ; gene_name "AC006148.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000157321.5" ; havana_transcript "OTTHUMT00000348433.1" ; level 2 ; orig_coord_info "chr7,124032205,124032279,+" ; tag basic ; transcript_id "SMURF1--AC006148.1^ENST00000484322.5" ; transcript_name "AC006148.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
SMURF1--AC006148.1 HAVANA RNA 29014 63954 . + . FI_gene_label "AC006148.1^ENSG00000242593.7" ; ID "SMURF1--AC006148.1^ENST00000484322.5" ; Parent "SMURF1--AC006148.1^AC006148.1^ENSG00000242593.7" ; exon_id "ENSE00001818688.1" ; exon_number 1 ; gene_id "SMURF1--AC006148.1^AC006148.1^ENSG00000242593.7" ; gene_name "AC006148.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000157321.5" ; havana_transcript "OTTHUMT00000348433.1" ; level 2 ; orig_coord_info "chr7,124032205,124032279,+" ; tag basic ; transcript_id "SMURF1--AC006148.1^ENST00000484322.5" ; transcript_name "AC006148.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
281 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 ------------------------------
429 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 19 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed