Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/062dc33fdfaaf08f3efe5a523815c3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/062dc33fdfaaf08f3efe5a523815c3/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/534a8beab8cc1940b36ceda78eb8a8/fi_workdir/659_gK-T1-TRNA-1_B23MHV2LT4_1.gtf
==> 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: 5034
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5034
=> 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:5034
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 2 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AK3--CDKN2A HAVANA gene 16703 21805 . + . FI_gene_label "CDKN2A^ENSG00000147889.18" ; ID "AK3--CDKN2A^CDKN2A^ENSG00000147889.18" ; ccdsid "CCDS6510.1" ; exon_id "ENSE00001833804.2" ; exon_number 1 ; gene_id "AK3--CDKN2A^CDKN2A^ENSG00000147889.18" ; gene_name CDKN2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000019686.7" ; havana_transcript "OTTHUMT00000051915.1" ; hgnc_id "HGNC:1787" ; level 2 ; orig_coord_info "chr9,21974678,21974827,-" ; protein_id "ENSP00000307101.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AK3--CDKN2A^ENST00000304494.10" ; transcript_name "CDKN2A-201" ; transcript_support_level 1 ; transcript_type protein_coding
AK3--CDKN2A HAVANA mRNA 16703 21805 . + . FI_gene_label "CDKN2A^ENSG00000147889.18" ; ID "AK3--CDKN2A^ENST00000304494.10" ; Parent "AK3--CDKN2A^CDKN2A^ENSG00000147889.18" ; ccdsid "CCDS6510.1" ; exon_id "ENSE00001833804.2" ; exon_number 1 ; gene_id "AK3--CDKN2A^CDKN2A^ENSG00000147889.18" ; gene_name CDKN2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000019686.7" ; havana_transcript "OTTHUMT00000051915.1" ; hgnc_id "HGNC:1787" ; level 2 ; orig_coord_info "chr9,21974678,21974827,-" ; protein_id "ENSP00000307101.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AK3--CDKN2A^ENST00000304494.10" ; transcript_name "CDKN2A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AK3--CDKN2A HAVANA gene 1001 7168 . + . FI_gene_label "AK3^ENSG00000147853.17" ; ID "AK3--CDKN2A^AK3^ENSG00000147853.17" ; ccdsid "CCDS56561.1" ; exon_id "ENSE00003474218.1" ; exon_number 2 ; gene_id "AK3--CDKN2A^AK3^ENSG00000147853.17" ; gene_name AK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019472.3" ; havana_transcript "OTTHUMT00000051584.1" ; hgnc_id "HGNC:17376" ; level 2 ; orig_coord_info "chr9,4722506,4722566,-" ; protein_id "ENSP00000352948.2" ; tag basic CCDS ; transcript_id "AK3--CDKN2A^ENST00000359883.6" ; transcript_name "AK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
AK3--CDKN2A HAVANA mRNA 1001 7168 . + . FI_gene_label "AK3^ENSG00000147853.17" ; ID "AK3--CDKN2A^ENST00000359883.6" ; Parent "AK3--CDKN2A^AK3^ENSG00000147853.17" ; ccdsid "CCDS56561.1" ; exon_id "ENSE00003474218.1" ; exon_number 2 ; gene_id "AK3--CDKN2A^AK3^ENSG00000147853.17" ; gene_name AK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019472.3" ; havana_transcript "OTTHUMT00000051584.1" ; hgnc_id "HGNC:17376" ; level 2 ; orig_coord_info "chr9,4722506,4722566,-" ; protein_id "ENSP00000352948.2" ; tag basic CCDS ; transcript_id "AK3--CDKN2A^ENST00000359883.6" ; transcript_name "AK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1 HAVANA mRNA 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^ENST00000276326.9" ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUSBP13--NAIP ENSEMBL gene 10656 31835 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8" ; transcript_name "NAIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUSBP13--NAIP ENSEMBL mRNA 10656 31835 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSBP13--NAIP^ENST00000194097.8" ; Parent "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8" ; transcript_name "NAIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KDM4C--AL358053.1 HAVANA gene 2151 38844 . + . FI_gene_label "KDM4C^ENSG00000107077.19" ; ID "KDM4C--AL358053.1^KDM4C^ENSG00000107077.19" ; exon_id "ENSE00003498584.1" ; exon_number 2 ; gene_id "KDM4C--AL358053.1^KDM4C^ENSG00000107077.19" ; gene_name KDM4C ; gene_type protein_coding ; havana_gene "OTTHUMG00000019536.6" ; havana_transcript "OTTHUMT00000051693.1" ; hgnc_id "HGNC:17071" ; level 2 ; orig_coord_info "chr9,6792989,6793132,+" ; protein_id "ENSP00000370707.3" ; tag basic appris_alternative_2 ; transcript_id "KDM4C--AL358053.1^ENST00000381306.7" ; transcript_name "KDM4C-201" ; transcript_support_level 2 ; transcript_type protein_coding
KDM4C--AL358053.1 HAVANA mRNA 2151 38844 . + . FI_gene_label "KDM4C^ENSG00000107077.19" ; ID "KDM4C--AL358053.1^ENST00000381306.7" ; Parent "KDM4C--AL358053.1^KDM4C^ENSG00000107077.19" ; exon_id "ENSE00003498584.1" ; exon_number 2 ; gene_id "KDM4C--AL358053.1^KDM4C^ENSG00000107077.19" ; gene_name KDM4C ; gene_type protein_coding ; havana_gene "OTTHUMG00000019536.6" ; havana_transcript "OTTHUMT00000051693.1" ; hgnc_id "HGNC:17071" ; level 2 ; orig_coord_info "chr9,6792989,6793132,+" ; protein_id "ENSP00000370707.3" ; tag basic appris_alternative_2 ; transcript_id "KDM4C--AL358053.1^ENST00000381306.7" ; transcript_name "KDM4C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
KDM4C--AL591644.1 HAVANA gene 2151 38844 . + . FI_gene_label "KDM4C^ENSG00000107077.19" ; ID "KDM4C--AL591644.1^KDM4C^ENSG00000107077.19" ; exon_id "ENSE00003498584.1" ; exon_number 2 ; gene_id "KDM4C--AL591644.1^KDM4C^ENSG00000107077.19" ; gene_name KDM4C ; gene_type protein_coding ; havana_gene "OTTHUMG00000019536.6" ; havana_transcript "OTTHUMT00000051693.1" ; hgnc_id "HGNC:17071" ; level 2 ; orig_coord_info "chr9,6792989,6793132,+" ; protein_id "ENSP00000370707.3" ; tag basic appris_alternative_2 ; transcript_id "KDM4C--AL591644.1^ENST00000381306.7" ; transcript_name "KDM4C-201" ; transcript_support_level 2 ; transcript_type protein_coding
KDM4C--AL591644.1 HAVANA mRNA 2151 38844 . + . FI_gene_label "KDM4C^ENSG00000107077.19" ; ID "KDM4C--AL591644.1^ENST00000381306.7" ; Parent "KDM4C--AL591644.1^KDM4C^ENSG00000107077.19" ; exon_id "ENSE00003498584.1" ; exon_number 2 ; gene_id "KDM4C--AL591644.1^KDM4C^ENSG00000107077.19" ; gene_name KDM4C ; gene_type protein_coding ; havana_gene "OTTHUMG00000019536.6" ; havana_transcript "OTTHUMT00000051693.1" ; hgnc_id "HGNC:17071" ; level 2 ; orig_coord_info "chr9,6792989,6793132,+" ; protein_id "ENSP00000370707.3" ; tag basic appris_alternative_2 ; transcript_id "KDM4C--AL591644.1^ENST00000381306.7" ; transcript_name "KDM4C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
LMNA--NTRK1 HAVANA gene 31461 45545 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding
LMNA--NTRK1 HAVANA mRNA 31461 45545 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "LMNA--NTRK1^ENST00000358660.3" ; Parent "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
LMNA--NTRK1 HAVANA gene 11719 23624 . + . FI_gene_label "LMNA^ENSG00000160789.23" ; ID "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; ccdsid "CCDS1129.1" ; exon_id "ENSE00001554780.1" ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6" ; hgnc_id "HGNC:6636" ; level 2 ; orig_coord_info "chr1,156114919,156115274,+" ; protein_id "ENSP00000355292.6" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9" ; transcript_name "LMNA-201" ; transcript_support_level 5 ; transcript_type protein_coding
LMNA--NTRK1 HAVANA mRNA 11719 23624 . + . FI_gene_label "LMNA^ENSG00000160789.23" ; ID "LMNA--NTRK1^ENST00000361308.9" ; Parent "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; ccdsid "CCDS1129.1" ; exon_id "ENSE00001554780.1" ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6" ; hgnc_id "HGNC:6636" ; level 2 ; orig_coord_info "chr1,156114919,156115274,+" ; protein_id "ENSP00000355292.6" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9" ; transcript_name "LMNA-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^ENST00000302641.8" ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^ENST00000606293.5" ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--AL356534.1 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--AL356534.1^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--AL356534.1^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--AL356534.1^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--AL356534.1 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--AL356534.1^ENST00000368207.7" ; Parent "PTPRK--AL356534.1^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--AL356534.1^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--AL356534.1^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^ENST00000356698.9" ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^ENST00000368207.7" ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RCL1--AL161449.2 HAVANA gene 7988 12914 . + . FI_gene_label "RCL1^ENSG00000120158.12" ; ID "RCL1--AL161449.2^RCL1^ENSG00000120158.12" ; ccdsid "CCDS69565.1" ; exon_id "ENSE00003577400.1" ; exon_number 2 ; gene_id "RCL1--AL161449.2^RCL1^ENSG00000120158.12" ; gene_name RCL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019474.5" ; havana_transcript "OTTHUMT00000051592.1" ; hgnc_id "HGNC:17687" ; level 2 ; orig_coord_info "chr9,4841206,4841357,+" ; protein_id "ENSP00000371147.1" ; tag basic CCDS ; transcript_id "RCL1--AL161449.2^ENST00000381728.5" ; transcript_name "RCL1-201" ; transcript_support_level 3 ; transcript_type protein_coding
RCL1--AL161449.2 HAVANA mRNA 7988 12914 . + . FI_gene_label "RCL1^ENSG00000120158.12" ; ID "RCL1--AL161449.2^ENST00000381728.5" ; Parent "RCL1--AL161449.2^RCL1^ENSG00000120158.12" ; ccdsid "CCDS69565.1" ; exon_id "ENSE00003577400.1" ; exon_number 2 ; gene_id "RCL1--AL161449.2^RCL1^ENSG00000120158.12" ; gene_name RCL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019474.5" ; havana_transcript "OTTHUMT00000051592.1" ; hgnc_id "HGNC:17687" ; level 2 ; orig_coord_info "chr9,4841206,4841357,+" ; protein_id "ENSP00000371147.1" ; tag basic CCDS ; transcript_id "RCL1--AL161449.2^ENST00000381728.5" ; transcript_name "RCL1-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
RCL1--MPDZ HAVANA gene 19128 71761 . + . FI_gene_label "MPDZ^ENSG00000107186.17" ; ID "RCL1--MPDZ^MPDZ^ENSG00000107186.17" ; ccdsid "CCDS83342.1" ; exon_id "ENSE00002297104.1" ; exon_number 2 ; gene_id "RCL1--MPDZ^MPDZ^ENSG00000107186.17" ; gene_name MPDZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000021031.6" ; havana_transcript "OTTHUMT00000055485.3" ; hgnc_id "HGNC:7208" ; level 2 ; orig_coord_info "chr9,13250300,13250315,-" ; protein_id "ENSP00000320006.7" ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_2 CCDS ; transcript_id "RCL1--MPDZ^ENST00000319217.12" ; transcript_name "MPDZ-202" ; transcript_support_level 5 ; transcript_type protein_coding
RCL1--MPDZ HAVANA mRNA 19128 71761 . + . FI_gene_label "MPDZ^ENSG00000107186.17" ; ID "RCL1--MPDZ^ENST00000319217.12" ; Parent "RCL1--MPDZ^MPDZ^ENSG00000107186.17" ; ccdsid "CCDS83342.1" ; exon_id "ENSE00002297104.1" ; exon_number 2 ; gene_id "RCL1--MPDZ^MPDZ^ENSG00000107186.17" ; gene_name MPDZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000021031.6" ; havana_transcript "OTTHUMT00000055485.3" ; hgnc_id "HGNC:7208" ; level 2 ; orig_coord_info "chr9,13250300,13250315,-" ; protein_id "ENSP00000320006.7" ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_2 CCDS ; transcript_id "RCL1--MPDZ^ENST00000319217.12" ; transcript_name "MPDZ-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RCL1--MPDZ HAVANA gene 7988 12914 . + . FI_gene_label "RCL1^ENSG00000120158.12" ; ID "RCL1--MPDZ^RCL1^ENSG00000120158.12" ; ccdsid "CCDS69565.1" ; exon_id "ENSE00003577400.1" ; exon_number 2 ; gene_id "RCL1--MPDZ^RCL1^ENSG00000120158.12" ; gene_name RCL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019474.5" ; havana_transcript "OTTHUMT00000051592.1" ; hgnc_id "HGNC:17687" ; level 2 ; orig_coord_info "chr9,4841206,4841357,+" ; protein_id "ENSP00000371147.1" ; tag basic CCDS ; transcript_id "RCL1--MPDZ^ENST00000381728.5" ; transcript_name "RCL1-201" ; transcript_support_level 3 ; transcript_type protein_coding
RCL1--MPDZ HAVANA mRNA 7988 12914 . + . FI_gene_label "RCL1^ENSG00000120158.12" ; ID "RCL1--MPDZ^ENST00000381728.5" ; Parent "RCL1--MPDZ^RCL1^ENSG00000120158.12" ; ccdsid "CCDS69565.1" ; exon_id "ENSE00003577400.1" ; exon_number 2 ; gene_id "RCL1--MPDZ^RCL1^ENSG00000120158.12" ; gene_name RCL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019474.5" ; havana_transcript "OTTHUMT00000051592.1" ; hgnc_id "HGNC:17687" ; level 2 ; orig_coord_info "chr9,4841206,4841357,+" ; protein_id "ENSP00000371147.1" ; tag basic CCDS ; transcript_id "RCL1--MPDZ^ENST00000381728.5" ; transcript_name "RCL1-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STON1--GTF2A1L HAVANA gene 15060 24138 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8" ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17" ; havana_transcript "OTTHUMT00000323852.5" ; hgnc_id "HGNC:30727" ; level 2 ; orig_coord_info "chr2,48617875,48617895,+" ; protein_id "ENSP00000384597.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L HAVANA mRNA 15060 24138 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "STON1--GTF2A1L^ENST00000403751.8" ; Parent "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8" ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17" ; havana_transcript "OTTHUMT00000323852.5" ; hgnc_id "HGNC:30727" ; level 2 ; orig_coord_info "chr2,48617875,48617895,+" ; protein_id "ENSP00000384597.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STON1--GTF2A1L HAVANA gene 1772 12001 . + . FI_gene_label "STON1^ENSG00000243244.7" ; ID "STON1--GTF2A1L^STON1^ENSG00000243244.7" ; ccdsid "CCDS1841.1" ; exon_id "ENSE00003530448.1" ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7" ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7" ; havana_transcript "OTTHUMT00000325006.1" ; hgnc_id "HGNC:17003" ; level 2 ; orig_coord_info "chr2,48580634,48582563,+" ; protein_id "ENSP00000385273.1" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6" ; transcript_name "STON1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L HAVANA mRNA 1772 12001 . + . FI_gene_label "STON1^ENSG00000243244.7" ; ID "STON1--GTF2A1L^ENST00000404752.6" ; Parent "STON1--GTF2A1L^STON1^ENSG00000243244.7" ; ccdsid "CCDS1841.1" ; exon_id "ENSE00003530448.1" ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7" ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7" ; havana_transcript "OTTHUMT00000325006.1" ; hgnc_id "HGNC:17003" ; level 2 ; orig_coord_info "chr2,48580634,48582563,+" ; protein_id "ENSP00000385273.1" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6" ; transcript_name "STON1-201" ; 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--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
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:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1 HAVANA RNA 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^ENST00000624936.2" ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
GUSBP13--NAIP HAVANA gene 1001 5633 . + . FI_gene_label "GUSBP13^ENSG00000198237.8" ; ID "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; exon_id "ENSE00002091111.1" ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1" ; havana_transcript "OTTHUMT00000379319.1" ; hgnc_id "HGNC:54495" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr5,69875271,69875319,+" ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2" ; transcript_name "GUSBP13-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GUSBP13--NAIP HAVANA RNA 1001 5633 . + . FI_gene_label "GUSBP13^ENSG00000198237.8" ; ID "GUSBP13--NAIP^ENST00000506490.2" ; Parent "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; exon_id "ENSE00002091111.1" ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1" ; havana_transcript "OTTHUMT00000379319.1" ; hgnc_id "HGNC:54495" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr5,69875271,69875319,+" ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2" ; transcript_name "GUSBP13-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
KDM4C--AL358053.1 HAVANA gene 43941 45456 . + . FI_gene_label "AL358053.1^ENSG00000287465.1" ; ID "KDM4C--AL358053.1^AL358053.1^ENSG00000287465.1" ; exon_id "ENSE00003880761.1" ; exon_number 1 ; gene_id "KDM4C--AL358053.1^AL358053.1^ENSG00000287465.1" ; gene_name "AL358053.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194930.1" ; havana_transcript "OTTHUMT00000523209.1" ; level 2 ; orig_coord_info "chr9,1549869,1550103,-" ; tag basic TAGENE ; transcript_id "KDM4C--AL358053.1^ENST00000660579.1" ; transcript_name "AL358053.1-201" ; transcript_type lncRNA
KDM4C--AL358053.1 HAVANA RNA 43941 45456 . + . FI_gene_label "AL358053.1^ENSG00000287465.1" ; ID "KDM4C--AL358053.1^ENST00000660579.1" ; Parent "KDM4C--AL358053.1^AL358053.1^ENSG00000287465.1" ; exon_id "ENSE00003880761.1" ; exon_number 1 ; gene_id "KDM4C--AL358053.1^AL358053.1^ENSG00000287465.1" ; gene_name "AL358053.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194930.1" ; havana_transcript "OTTHUMT00000523209.1" ; level 2 ; orig_coord_info "chr9,1549869,1550103,-" ; tag basic TAGENE ; transcript_id "KDM4C--AL358053.1^ENST00000660579.1" ; transcript_name "AL358053.1-201" ; transcript_type lncRNA
L1 and L2 created:
KDM4C--AL591644.1 HAVANA gene 43941 44704 . + . FI_gene_label "AL591644.1^ENSG00000224092.1" ; ID "KDM4C--AL591644.1^AL591644.1^ENSG00000224092.1" ; exon_id "ENSE00001760147.1" ; exon_number 1 ; gene_id "KDM4C--AL591644.1^AL591644.1^ENSG00000224092.1" ; gene_name "AL591644.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019443.1" ; havana_transcript "OTTHUMT00000051501.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,1977784,1978547,-" ; tag basic ; transcript_id "KDM4C--AL591644.1^ENST00000436102.1" ; transcript_name "AL591644.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
KDM4C--AL591644.1 HAVANA RNA 43941 44704 . + . FI_gene_label "AL591644.1^ENSG00000224092.1" ; ID "KDM4C--AL591644.1^ENST00000436102.1" ; Parent "KDM4C--AL591644.1^AL591644.1^ENSG00000224092.1" ; exon_id "ENSE00001760147.1" ; exon_number 1 ; gene_id "KDM4C--AL591644.1^AL591644.1^ENSG00000224092.1" ; gene_name "AL591644.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019443.1" ; havana_transcript "OTTHUMT00000051501.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,1977784,1978547,-" ; tag basic ; transcript_id "KDM4C--AL591644.1^ENST00000436102.1" ; transcript_name "AL591644.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
PTPRK--AL356534.1 HAVANA gene 120183 121476 . + . FI_gene_label "AL356534.1^ENSG00000286215.1" ; ID "PTPRK--AL356534.1^AL356534.1^ENSG00000286215.1" ; exon_id "ENSE00001556513.3" ; exon_number 1 ; gene_id "PTPRK--AL356534.1^AL356534.1^ENSG00000286215.1" ; gene_name "AL356534.1" ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000015519.5" ; havana_transcript "OTTHUMT00000042107.4" ; level 1 ; ont "PGO:0000004" "PGO:0000019" ; orig_coord_info "chr6,126602356,126603649,-" ; tag pseudo_consens basic ; transcript_id "PTPRK--AL356534.1^ENST00000402383.3" ; transcript_name "AL356534.1-205" ; transcript_support_level NA ; transcript_type transcribed_processed_pseudogene
PTPRK--AL356534.1 HAVANA RNA 120183 121476 . + . FI_gene_label "AL356534.1^ENSG00000286215.1" ; ID "PTPRK--AL356534.1^ENST00000402383.3" ; Parent "PTPRK--AL356534.1^AL356534.1^ENSG00000286215.1" ; exon_id "ENSE00001556513.3" ; exon_number 1 ; gene_id "PTPRK--AL356534.1^AL356534.1^ENSG00000286215.1" ; gene_name "AL356534.1" ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000015519.5" ; havana_transcript "OTTHUMT00000042107.4" ; level 1 ; ont "PGO:0000004" "PGO:0000019" ; orig_coord_info "chr6,126602356,126603649,-" ; tag pseudo_consens basic ; transcript_id "PTPRK--AL356534.1^ENST00000402383.3" ; transcript_name "AL356534.1-205" ; transcript_support_level NA ; transcript_type transcribed_processed_pseudogene
L1 and L2 created:
RCL1--AL161449.2 HAVANA gene 19128 29413 . + . FI_gene_label "AL161449.2^ENSG00000285637.2" ; ID "RCL1--AL161449.2^AL161449.2^ENSG00000285637.2" ; exon_id "ENSE00003832995.1" ; exon_number 1 ; gene_id "RCL1--AL161449.2^AL161449.2^ENSG00000285637.2" ; gene_name "AL161449.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192712.2" ; havana_transcript "OTTHUMT00000498917.1" ; level 2 ; orig_coord_info "chr9,13034171,13034326,-" ; tag basic ; transcript_id "RCL1--AL161449.2^ENST00000649120.1" ; transcript_name "AL161449.2-201" ; transcript_type lncRNA
RCL1--AL161449.2 HAVANA RNA 19128 29413 . + . FI_gene_label "AL161449.2^ENSG00000285637.2" ; ID "RCL1--AL161449.2^ENST00000649120.1" ; Parent "RCL1--AL161449.2^AL161449.2^ENSG00000285637.2" ; exon_id "ENSE00003832995.1" ; exon_number 1 ; gene_id "RCL1--AL161449.2^AL161449.2^ENSG00000285637.2" ; gene_name "AL161449.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192712.2" ; havana_transcript "OTTHUMT00000498917.1" ; level 2 ; orig_coord_info "chr9,13034171,13034326,-" ; tag basic ; transcript_id "RCL1--AL161449.2^ENST00000649120.1" ; transcript_name "AL161449.2-201" ; 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
352 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 ------------------------------
660 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 27 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