Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/75ed5a56f2c375bf04af7bc46ba856/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/c1cbbf54ceae8f20480eb60f499105/fi_workdir/aih-tih-sc-62dadb-R1_B23WHYVLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/75ed5a56f2c375bf04af7bc46ba856/.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: 3159
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3159
=> 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:3159
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 2 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
ASB1--AC079612.1 HAVANA gene 1186 12859 . + . FI_gene_label "ASB1^ENSG00000065802.12" ; ID "ASB1--AC079612.1^ASB1^ENSG00000065802.12" ; ccdsid "CCDS33416.1" ; exon_id "ENSE00001883621.2" ; exon_number 1 ; gene_id "ASB1--AC079612.1^ASB1^ENSG00000065802.12" ; gene_name ASB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152866.2" ; havana_transcript "OTTHUMT00000328294.2" ; hgnc_id "HGNC:16011" ; level 2 ; orig_coord_info "chr2,238427071,238427119,+" ; protein_id "ENSP00000264607.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASB1--AC079612.1^ENST00000264607.9" ; transcript_name "ASB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ASB1--AC079612.1 HAVANA mRNA 1186 12859 . + . FI_gene_label "ASB1^ENSG00000065802.12" ; ID "ASB1--AC079612.1^ENST00000264607.9" ; Parent "ASB1--AC079612.1^ASB1^ENSG00000065802.12" ; ccdsid "CCDS33416.1" ; exon_id "ENSE00001883621.2" ; exon_number 1 ; gene_id "ASB1--AC079612.1^ASB1^ENSG00000065802.12" ; gene_name ASB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152866.2" ; havana_transcript "OTTHUMT00000328294.2" ; hgnc_id "HGNC:16011" ; level 2 ; orig_coord_info "chr2,238427071,238427119,+" ; protein_id "ENSP00000264607.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASB1--AC079612.1^ENST00000264607.9" ; transcript_name "ASB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ASB1--AC079612.2 HAVANA gene 1186 12859 . + . FI_gene_label "ASB1^ENSG00000065802.12" ; ID "ASB1--AC079612.2^ASB1^ENSG00000065802.12" ; ccdsid "CCDS33416.1" ; exon_id "ENSE00001883621.2" ; exon_number 1 ; gene_id "ASB1--AC079612.2^ASB1^ENSG00000065802.12" ; gene_name ASB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152866.2" ; havana_transcript "OTTHUMT00000328294.2" ; hgnc_id "HGNC:16011" ; level 2 ; orig_coord_info "chr2,238427071,238427119,+" ; protein_id "ENSP00000264607.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASB1--AC079612.2^ENST00000264607.9" ; transcript_name "ASB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ASB1--AC079612.2 HAVANA mRNA 1186 12859 . + . FI_gene_label "ASB1^ENSG00000065802.12" ; ID "ASB1--AC079612.2^ENST00000264607.9" ; Parent "ASB1--AC079612.2^ASB1^ENSG00000065802.12" ; ccdsid "CCDS33416.1" ; exon_id "ENSE00001883621.2" ; exon_number 1 ; gene_id "ASB1--AC079612.2^ASB1^ENSG00000065802.12" ; gene_name ASB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152866.2" ; havana_transcript "OTTHUMT00000328294.2" ; hgnc_id "HGNC:16011" ; level 2 ; orig_coord_info "chr2,238427071,238427119,+" ; protein_id "ENSP00000264607.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASB1--AC079612.2^ENST00000264607.9" ; transcript_name "ASB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CLPB--SHANK2 HAVANA gene 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--SHANK2^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--SHANK2^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--SHANK2^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
CLPB--SHANK2 HAVANA mRNA 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--SHANK2^ENST00000294053.9" ; Parent "CLPB--SHANK2^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--SHANK2^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--SHANK2^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CLPB--SHANK2 HAVANA gene 71411 94836 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "CLPB--SHANK2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "CLPB--SHANK2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "CLPB--SHANK2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
CLPB--SHANK2 HAVANA mRNA 71411 94836 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "CLPB--SHANK2^ENST00000338508.8" ; Parent "CLPB--SHANK2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "CLPB--SHANK2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "CLPB--SHANK2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
DAG1--ACTR2 HAVANA gene 18356 32058 . + . FI_gene_label "ACTR2^ENSG00000138071.14" ; ID "DAG1--ACTR2^ACTR2^ENSG00000138071.14" ; ccdsid "CCDS1881.1" ; exon_id "ENSE00001006428.8" ; exon_number 1 ; gene_id "DAG1--ACTR2^ACTR2^ENSG00000138071.14" ; gene_name ACTR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129540.3" ; havana_transcript "OTTHUMT00000251730.1" ; hgnc_id "HGNC:169" ; level 2 ; orig_coord_info "chr2,65227910,65227957,+" ; protein_id "ENSP00000260641.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DAG1--ACTR2^ENST00000260641.10" ; transcript_name "ACTR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DAG1--ACTR2 HAVANA mRNA 18356 32058 . + . FI_gene_label "ACTR2^ENSG00000138071.14" ; ID "DAG1--ACTR2^ENST00000260641.10" ; Parent "DAG1--ACTR2^ACTR2^ENSG00000138071.14" ; ccdsid "CCDS1881.1" ; exon_id "ENSE00001006428.8" ; exon_number 1 ; gene_id "DAG1--ACTR2^ACTR2^ENSG00000138071.14" ; gene_name ACTR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129540.3" ; havana_transcript "OTTHUMT00000251730.1" ; hgnc_id "HGNC:169" ; level 2 ; orig_coord_info "chr2,65227910,65227957,+" ; protein_id "ENSP00000260641.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DAG1--ACTR2^ENST00000260641.10" ; transcript_name "ACTR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DAG1--ACTR2 HAVANA gene 2489 15309 . + . FI_gene_label "DAG1^ENSG00000173402.12" ; ID "DAG1--ACTR2^DAG1^ENSG00000173402.12" ; ccdsid "CCDS2799.1" ; exon_id "ENSE00001204501.1" ; exon_number 2 ; gene_id "DAG1--ACTR2^DAG1^ENSG00000173402.12" ; gene_name DAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156869.11" ; havana_transcript "OTTHUMT00000346326.4" ; hgnc_id "HGNC:2666" ; level 2 ; orig_coord_info "chr3,49510535,49510819,+" ; protein_id "ENSP00000312435.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DAG1--ACTR2^ENST00000308775.7" ; transcript_name "DAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DAG1--ACTR2 HAVANA mRNA 2489 15309 . + . FI_gene_label "DAG1^ENSG00000173402.12" ; ID "DAG1--ACTR2^ENST00000308775.7" ; Parent "DAG1--ACTR2^DAG1^ENSG00000173402.12" ; ccdsid "CCDS2799.1" ; exon_id "ENSE00001204501.1" ; exon_number 2 ; gene_id "DAG1--ACTR2^DAG1^ENSG00000173402.12" ; gene_name DAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156869.11" ; havana_transcript "OTTHUMT00000346326.4" ; hgnc_id "HGNC:2666" ; level 2 ; orig_coord_info "chr3,49510535,49510819,+" ; protein_id "ENSP00000312435.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DAG1--ACTR2^ENST00000308775.7" ; transcript_name "DAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KDM1A--EPHB2 HAVANA gene 1006 22471 . + . FI_gene_label "KDM1A^ENSG00000004487.17" ; ID "KDM1A--EPHB2^KDM1A^ENSG00000004487.17" ; ccdsid "CCDS30627.1" ; exon_id "ENSE00001422377.3" ; exon_number 1 ; gene_id "KDM1A--EPHB2^KDM1A^ENSG00000004487.17" ; gene_name KDM1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000003220.7" ; havana_transcript "OTTHUMT00000008880.3" ; hgnc_id "HGNC:29079" ; level 2 ; orig_coord_info "chr1,23019597,23019947,+" ; protein_id "ENSP00000349049.3" ; tag basic CCDS ; transcript_id "KDM1A--EPHB2^ENST00000356634.7" ; transcript_name "KDM1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
KDM1A--EPHB2 HAVANA mRNA 1006 22471 . + . FI_gene_label "KDM1A^ENSG00000004487.17" ; ID "KDM1A--EPHB2^ENST00000356634.7" ; Parent "KDM1A--EPHB2^KDM1A^ENSG00000004487.17" ; ccdsid "CCDS30627.1" ; exon_id "ENSE00001422377.3" ; exon_number 1 ; gene_id "KDM1A--EPHB2^KDM1A^ENSG00000004487.17" ; gene_name KDM1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000003220.7" ; havana_transcript "OTTHUMT00000008880.3" ; hgnc_id "HGNC:29079" ; level 2 ; orig_coord_info "chr1,23019597,23019947,+" ; protein_id "ENSP00000349049.3" ; tag basic CCDS ; transcript_id "KDM1A--EPHB2^ENST00000356634.7" ; transcript_name "KDM1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KDM1A--EPHB2 HAVANA gene 26677 46517 . + . FI_gene_label "EPHB2^ENSG00000133216.17" ; ID "KDM1A--EPHB2^EPHB2^ENSG00000133216.17" ; exon_id "ENSE00001464053.1" ; exon_number 1 ; gene_id "KDM1A--EPHB2^EPHB2^ENSG00000133216.17" ; gene_name EPHB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002881.4" ; havana_transcript "OTTHUMT00000008062.2" ; hgnc_id "HGNC:3393" ; level 2 ; orig_coord_info "chr1,22775202,22775244,+" ; protein_id "ENSP00000363758.1" ; tag non_canonical_polymorphism dotter_confirmed basic ; transcript_id "KDM1A--EPHB2^ENST00000374627.1" ; transcript_name "EPHB2-201" ; transcript_support_level 5 ; transcript_type protein_coding
KDM1A--EPHB2 HAVANA mRNA 26677 46517 . + . FI_gene_label "EPHB2^ENSG00000133216.17" ; ID "KDM1A--EPHB2^ENST00000374627.1" ; Parent "KDM1A--EPHB2^EPHB2^ENSG00000133216.17" ; exon_id "ENSE00001464053.1" ; exon_number 1 ; gene_id "KDM1A--EPHB2^EPHB2^ENSG00000133216.17" ; gene_name EPHB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002881.4" ; havana_transcript "OTTHUMT00000008062.2" ; hgnc_id "HGNC:3393" ; level 2 ; orig_coord_info "chr1,22775202,22775244,+" ; protein_id "ENSP00000363758.1" ; tag non_canonical_polymorphism dotter_confirmed basic ; transcript_id "KDM1A--EPHB2^ENST00000374627.1" ; transcript_name "EPHB2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
LINC00511--BORCS5 HAVANA gene 76850 80642 . + . FI_gene_label "BORCS5^ENSG00000165714.11" ; ID "LINC00511--BORCS5^BORCS5^ENSG00000165714.11" ; ccdsid "CCDS81669.1" ; exon_id "ENSE00002312579.1" ; exon_number 1 ; gene_id "LINC00511--BORCS5^BORCS5^ENSG00000165714.11" ; gene_name BORCS5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168542.3" ; havana_transcript "OTTHUMT00000400152.1" ; hgnc_id "HGNC:17950" ; level 2 ; orig_coord_info "chr12,12357452,12357509,+" ; protein_id "ENSP00000298571.6" ; tag basic CCDS ; transcript_id "LINC00511--BORCS5^ENST00000298571.6" ; transcript_name "BORCS5-201" ; transcript_support_level 1 ; transcript_type protein_coding
LINC00511--BORCS5 HAVANA mRNA 76850 80642 . + . FI_gene_label "BORCS5^ENSG00000165714.11" ; ID "LINC00511--BORCS5^ENST00000298571.6" ; Parent "LINC00511--BORCS5^BORCS5^ENSG00000165714.11" ; ccdsid "CCDS81669.1" ; exon_id "ENSE00002312579.1" ; exon_number 1 ; gene_id "LINC00511--BORCS5^BORCS5^ENSG00000165714.11" ; gene_name BORCS5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168542.3" ; havana_transcript "OTTHUMT00000400152.1" ; hgnc_id "HGNC:17950" ; level 2 ; orig_coord_info "chr12,12357452,12357509,+" ; protein_id "ENSP00000298571.6" ; tag basic CCDS ; transcript_id "LINC00511--BORCS5^ENST00000298571.6" ; transcript_name "BORCS5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LRP1B--FAM178B HAVANA gene 1001 103254 . + . FI_gene_label "LRP1B^ENSG00000168702.18" ; ID "LRP1B--FAM178B^LRP1B^ENSG00000168702.18" ; ccdsid "CCDS2182.1" ; exon_id "ENSE00001794248.2" ; exon_number 1 ; gene_id "LRP1B--FAM178B^LRP1B^ENSG00000168702.18" ; gene_name LRP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000131799.6" ; havana_transcript "OTTHUMT00000254736.3" ; hgnc_id "HGNC:6693" ; level 2 ; orig_coord_info "chr2,142130648,142130729,-" ; protein_id "ENSP00000374135.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP1B--FAM178B^ENST00000389484.8" ; transcript_name "LRP1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
LRP1B--FAM178B HAVANA mRNA 1001 103254 . + . FI_gene_label "LRP1B^ENSG00000168702.18" ; ID "LRP1B--FAM178B^ENST00000389484.8" ; Parent "LRP1B--FAM178B^LRP1B^ENSG00000168702.18" ; ccdsid "CCDS2182.1" ; exon_id "ENSE00001794248.2" ; exon_number 1 ; gene_id "LRP1B--FAM178B^LRP1B^ENSG00000168702.18" ; gene_name LRP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000131799.6" ; havana_transcript "OTTHUMT00000254736.3" ; hgnc_id "HGNC:6693" ; level 2 ; orig_coord_info "chr2,142130648,142130729,-" ; protein_id "ENSP00000374135.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRP1B--FAM178B^ENST00000389484.8" ; transcript_name "LRP1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LRP1B--FAM178B HAVANA gene 121177 126788 . + . FI_gene_label "FAM178B^ENSG00000168754.15" ; ID "LRP1B--FAM178B^FAM178B^ENSG00000168754.15" ; ccdsid "CCDS33252.1" ; exon_id "ENSE00003487710.1" ; exon_number 2 ; gene_id "LRP1B--FAM178B^FAM178B^ENSG00000168754.15" ; gene_name FAM178B ; gene_type protein_coding ; havana_gene "OTTHUMG00000155257.5" ; havana_transcript "OTTHUMT00000339493.2" ; hgnc_id "HGNC:28036" ; level 2 ; orig_coord_info "chr2,96893926,96894021,-" ; protein_id "ENSP00000377160.2" ; tag basic CCDS ; transcript_id "LRP1B--FAM178B^ENST00000393526.6" ; transcript_name "FAM178B-201" ; transcript_support_level 1 ; transcript_type protein_coding
LRP1B--FAM178B HAVANA mRNA 121177 126788 . + . FI_gene_label "FAM178B^ENSG00000168754.15" ; ID "LRP1B--FAM178B^ENST00000393526.6" ; Parent "LRP1B--FAM178B^FAM178B^ENSG00000168754.15" ; ccdsid "CCDS33252.1" ; exon_id "ENSE00003487710.1" ; exon_number 2 ; gene_id "LRP1B--FAM178B^FAM178B^ENSG00000168754.15" ; gene_name FAM178B ; gene_type protein_coding ; havana_gene "OTTHUMG00000155257.5" ; havana_transcript "OTTHUMT00000339493.2" ; hgnc_id "HGNC:28036" ; level 2 ; orig_coord_info "chr2,96893926,96894021,-" ; protein_id "ENSP00000377160.2" ; tag basic CCDS ; transcript_id "LRP1B--FAM178B^ENST00000393526.6" ; transcript_name "FAM178B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NPHP3--ACAD11 HAVANA gene 34363 56719 . + . FI_gene_label "ACAD11^ENSG00000240303.8" ; ID "NPHP3--ACAD11^ACAD11^ENSG00000240303.8" ; ccdsid "CCDS3074.1" ; exon_id "ENSE00001878063.2" ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8" ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6" ; havana_transcript "OTTHUMT00000357279.4" ; hgnc_id "HGNC:30211" ; level 2 ; orig_coord_info "chr3,132659603,132659751,-" ; protein_id "ENSP00000264990.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11" ; transcript_name "ACAD11-201" ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11 HAVANA mRNA 34363 56719 . + . FI_gene_label "ACAD11^ENSG00000240303.8" ; ID "NPHP3--ACAD11^ENST00000264990.11" ; Parent "NPHP3--ACAD11^ACAD11^ENSG00000240303.8" ; ccdsid "CCDS3074.1" ; exon_id "ENSE00001878063.2" ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8" ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6" ; havana_transcript "OTTHUMT00000357279.4" ; hgnc_id "HGNC:30211" ; level 2 ; orig_coord_info "chr3,132659603,132659751,-" ; protein_id "ENSP00000264990.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11" ; transcript_name "ACAD11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NPHP3--ACAD11 HAVANA gene 1006 31089 . + . FI_gene_label "NPHP3^ENSG00000113971.20" ; ID "NPHP3--ACAD11^NPHP3^ENSG00000113971.20" ; ccdsid "CCDS3078.1" ; exon_id "ENSE00001810363.2" ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20" ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4" ; havana_transcript "OTTHUMT00000357020.3" ; hgnc_id "HGNC:7907" ; level 2 ; orig_coord_info "chr3,132721963,132722355,-" ; protein_id "ENSP00000338766.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10" ; transcript_name "NPHP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11 HAVANA mRNA 1006 31089 . + . FI_gene_label "NPHP3^ENSG00000113971.20" ; ID "NPHP3--ACAD11^ENST00000337331.10" ; Parent "NPHP3--ACAD11^NPHP3^ENSG00000113971.20" ; ccdsid "CCDS3078.1" ; exon_id "ENSE00001810363.2" ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20" ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4" ; havana_transcript "OTTHUMT00000357020.3" ; hgnc_id "HGNC:7907" ; level 2 ; orig_coord_info "chr3,132721963,132722355,-" ; protein_id "ENSP00000338766.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10" ; transcript_name "NPHP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWTR1--DPP10 HAVANA gene 37350 66091 . + . FI_gene_label "DPP10^ENSG00000175497.17" ; ID "WWTR1--DPP10^DPP10^ENSG00000175497.17" ; ccdsid "CCDS33278.1" ; exon_id "ENSE00001957895.1" ; exon_number 1 ; gene_id "WWTR1--DPP10^DPP10^ENSG00000175497.17" ; gene_name DPP10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153294.10" ; havana_transcript "OTTHUMT00000330691.1" ; hgnc_id "HGNC:20823" ; level 2 ; orig_coord_info "chr2,115162234,115162272,+" ; protein_id "ENSP00000309066.8" ; tag basic CCDS ; transcript_id "WWTR1--DPP10^ENST00000310323.12" ; transcript_name "DPP10-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWTR1--DPP10 HAVANA mRNA 37350 66091 . + . FI_gene_label "DPP10^ENSG00000175497.17" ; ID "WWTR1--DPP10^ENST00000310323.12" ; Parent "WWTR1--DPP10^DPP10^ENSG00000175497.17" ; ccdsid "CCDS33278.1" ; exon_id "ENSE00001957895.1" ; exon_number 1 ; gene_id "WWTR1--DPP10^DPP10^ENSG00000175497.17" ; gene_name DPP10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153294.10" ; havana_transcript "OTTHUMT00000330691.1" ; hgnc_id "HGNC:20823" ; level 2 ; orig_coord_info "chr2,115162234,115162272,+" ; protein_id "ENSP00000309066.8" ; tag basic CCDS ; transcript_id "WWTR1--DPP10^ENST00000310323.12" ; transcript_name "DPP10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWTR1--DPP10 HAVANA gene 10616 24379 . + . FI_gene_label "WWTR1^ENSG00000018408.15" ; ID "WWTR1--DPP10^WWTR1^ENSG00000018408.15" ; ccdsid "CCDS3144.1" ; exon_id "ENSE00001078038.4" ; exon_number 2 ; gene_id "WWTR1--DPP10^WWTR1^ENSG00000018408.15" ; gene_name WWTR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159614.13" ; havana_transcript "OTTHUMT00000356501.1" ; hgnc_id "HGNC:24042" ; level 2 ; orig_coord_info "chr3,149656876,149657306,-" ; protein_id "ENSP00000353847.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWTR1--DPP10^ENST00000360632.8" ; transcript_name "WWTR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWTR1--DPP10 HAVANA mRNA 10616 24379 . + . FI_gene_label "WWTR1^ENSG00000018408.15" ; ID "WWTR1--DPP10^ENST00000360632.8" ; Parent "WWTR1--DPP10^WWTR1^ENSG00000018408.15" ; ccdsid "CCDS3144.1" ; exon_id "ENSE00001078038.4" ; exon_number 2 ; gene_id "WWTR1--DPP10^WWTR1^ENSG00000018408.15" ; gene_name WWTR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159614.13" ; havana_transcript "OTTHUMT00000356501.1" ; hgnc_id "HGNC:24042" ; level 2 ; orig_coord_info "chr3,149656876,149657306,-" ; protein_id "ENSP00000353847.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWTR1--DPP10^ENST00000360632.8" ; transcript_name "WWTR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ASB1--AC079612.1 HAVANA gene 15860 20559 . + . FI_gene_label "AC079612.1^ENSG00000196758.3" ; ID "ASB1--AC079612.1^AC079612.1^ENSG00000196758.3" ; exon_id "ENSE00003005995.1" ; exon_number 1 ; gene_id "ASB1--AC079612.1^AC079612.1^ENSG00000196758.3" ; gene_name "AC079612.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000133345.2" ; havana_transcript "OTTHUMT00000257175.2" ; level 1 ; orig_coord_info "chr2,239578301,239578924,+" ; tag basic exp_conf ; transcript_id "ASB1--AC079612.1^ENST00000358775.1" ; transcript_name "AC079612.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
ASB1--AC079612.1 HAVANA RNA 15860 20559 . + . FI_gene_label "AC079612.1^ENSG00000196758.3" ; ID "ASB1--AC079612.1^ENST00000358775.1" ; Parent "ASB1--AC079612.1^AC079612.1^ENSG00000196758.3" ; exon_id "ENSE00003005995.1" ; exon_number 1 ; gene_id "ASB1--AC079612.1^AC079612.1^ENSG00000196758.3" ; gene_name "AC079612.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000133345.2" ; havana_transcript "OTTHUMT00000257175.2" ; level 1 ; orig_coord_info "chr2,239578301,239578924,+" ; tag basic exp_conf ; transcript_id "ASB1--AC079612.1^ENST00000358775.1" ; transcript_name "AC079612.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
ASB1--AC079612.2 HAVANA gene 15860 17207 . + . FI_gene_label "AC079612.2^ENSG00000227459.1" ; ID "ASB1--AC079612.2^AC079612.2^ENSG00000227459.1" ; exon_id "ENSE00001623809.1" ; exon_number 1 ; gene_id "ASB1--AC079612.2^AC079612.2^ENSG00000227459.1" ; gene_name "AC079612.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000152416.1" ; havana_transcript "OTTHUMT00000326162.1" ; level 2 ; orig_coord_info "chr2,239625698,239625783,+" ; tag basic ; transcript_id "ASB1--AC079612.2^ENST00000446029.1" ; transcript_name "AC079612.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
ASB1--AC079612.2 HAVANA RNA 15860 17207 . + . FI_gene_label "AC079612.2^ENSG00000227459.1" ; ID "ASB1--AC079612.2^ENST00000446029.1" ; Parent "ASB1--AC079612.2^AC079612.2^ENSG00000227459.1" ; exon_id "ENSE00001623809.1" ; exon_number 1 ; gene_id "ASB1--AC079612.2^AC079612.2^ENSG00000227459.1" ; gene_name "AC079612.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000152416.1" ; havana_transcript "OTTHUMT00000326162.1" ; level 2 ; orig_coord_info "chr2,239625698,239625783,+" ; tag basic ; transcript_id "ASB1--AC079612.2^ENST00000446029.1" ; transcript_name "AC079612.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
LINC00511--BORCS5 HAVANA gene 10811 55018 . + . FI_gene_label "LINC00511^ENSG00000227036.8" ; ID "LINC00511--BORCS5^LINC00511^ENSG00000227036.8" ; exon_id "ENSE00001629418.1" ; exon_number 1 ; gene_id "LINC00511--BORCS5^LINC00511^ENSG00000227036.8" ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20" ; havana_transcript "OTTHUMT00000255287.2" ; hgnc_id "HGNC:43564" ; level 2 ; orig_coord_info "chr17,72592203,72592804,-" ; transcript_id "LINC00511--BORCS5^ENST00000453722.6" ; transcript_name "LINC00511-201" ; transcript_support_level 2 ; transcript_type lncRNA
LINC00511--BORCS5 HAVANA RNA 10811 55018 . + . FI_gene_label "LINC00511^ENSG00000227036.8" ; ID "LINC00511--BORCS5^ENST00000453722.6" ; Parent "LINC00511--BORCS5^LINC00511^ENSG00000227036.8" ; exon_id "ENSE00001629418.1" ; exon_number 1 ; gene_id "LINC00511--BORCS5^LINC00511^ENSG00000227036.8" ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20" ; havana_transcript "OTTHUMT00000255287.2" ; hgnc_id "HGNC:43564" ; level 2 ; orig_coord_info "chr17,72592203,72592804,-" ; transcript_id "LINC00511--BORCS5^ENST00000453722.6" ; transcript_name "LINC00511-201" ; transcript_support_level 2 ; 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
317 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 ------------------------------
391 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