Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/933dbd25d9f0333fdc30a77955ed43/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/eb1dea6f62a808bd52127dec2d59f5/fi_workdir/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/933dbd25d9f0333fdc30a77955ed43/.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: 2580 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 2580 => 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:2580 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 1 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: AL669831.1--SEPTIN14 HAVANA gene 24499 38046 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.1--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding AL669831.1--SEPTIN14 HAVANA mRNA 24499 38046 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.1--SEPTIN14^ENST00000388975.4" ; Parent "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.1--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.1--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: AL669831.4--SEPTIN14 HAVANA gene 8876 22423 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding AL669831.4--SEPTIN14 HAVANA mRNA 8876 22423 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.4--SEPTIN14^ENST00000388975.4" ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: BFAR--APC2 ENSEMBL gene 16498 35959 . + . FI_gene_label "APC2^ENSG00000115266.12" ; ID "BFAR--APC2^APC2^ENSG00000115266.12" ; ccdsid "CCDS12068.1" ; exon_id "ENSE00003508879.1" ; exon_number 2 ; gene_id "BFAR--APC2^APC2^ENSG00000115266.12" ; gene_name APC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180059.11" ; hgnc_id "HGNC:24036" ; level 3 ; orig_coord_info "chr19,1453002,1453142,+" ; protein_id "ENSP00000233607.2" ; tag basic appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000233607.6" ; transcript_name "APC2-201" ; transcript_support_level 1 ; transcript_type protein_coding BFAR--APC2 ENSEMBL mRNA 16498 35959 . + . FI_gene_label "APC2^ENSG00000115266.12" ; ID "BFAR--APC2^ENST00000233607.6" ; Parent "BFAR--APC2^APC2^ENSG00000115266.12" ; ccdsid "CCDS12068.1" ; exon_id "ENSE00003508879.1" ; exon_number 2 ; gene_id "BFAR--APC2^APC2^ENSG00000115266.12" ; gene_name APC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180059.11" ; hgnc_id "HGNC:24036" ; level 3 ; orig_coord_info "chr19,1453002,1453142,+" ; protein_id "ENSP00000233607.2" ; tag basic appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000233607.6" ; transcript_name "APC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BFAR--APC2 HAVANA gene 1021 12429 . + . FI_gene_label "BFAR^ENSG00000103429.11" ; ID "BFAR--APC2^BFAR^ENSG00000103429.11" ; ccdsid "CCDS10554.1" ; exon_id "ENSE00003646355.1" ; exon_number 2 ; gene_id "BFAR--APC2^BFAR^ENSG00000103429.11" ; gene_name BFAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000129848.5" ; havana_transcript "OTTHUMT00000252088.2" ; hgnc_id "HGNC:17613" ; level 2 ; orig_coord_info "chr16,14644347,14644609,+" ; protein_id "ENSP00000261658.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000261658.7" ; transcript_name "BFAR-201" ; transcript_support_level 1 ; transcript_type protein_coding BFAR--APC2 HAVANA mRNA 1021 12429 . + . FI_gene_label "BFAR^ENSG00000103429.11" ; ID "BFAR--APC2^ENST00000261658.7" ; Parent "BFAR--APC2^BFAR^ENSG00000103429.11" ; ccdsid "CCDS10554.1" ; exon_id "ENSE00003646355.1" ; exon_number 2 ; gene_id "BFAR--APC2^BFAR^ENSG00000103429.11" ; gene_name BFAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000129848.5" ; havana_transcript "OTTHUMT00000252088.2" ; hgnc_id "HGNC:17613" ; level 2 ; orig_coord_info "chr16,14644347,14644609,+" ; protein_id "ENSP00000261658.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BFAR--APC2^ENST00000261658.7" ; transcript_name "BFAR-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: DNAJC6--PDE1C ENSEMBL gene 3274 27911 . + . FI_gene_label "DNAJC6^ENSG00000116675.16" ; ID "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16" ; ccdsid "CCDS58005.1" ; exon_id "ENSE00003684627.1" ; exon_number 3 ; gene_id "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16" ; gene_name DNAJC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009066.4" ; hgnc_id "HGNC:15469" ; level 3 ; orig_coord_info "chr1,65364652,65364785,+" ; protein_id "ENSP00000263441.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000263441.11" ; transcript_name "DNAJC6-201" ; transcript_support_level 2 ; transcript_type protein_coding DNAJC6--PDE1C ENSEMBL mRNA 3274 27911 . + . FI_gene_label "DNAJC6^ENSG00000116675.16" ; ID "DNAJC6--PDE1C^ENST00000263441.11" ; Parent "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16" ; ccdsid "CCDS58005.1" ; exon_id "ENSE00003684627.1" ; exon_number 3 ; gene_id "DNAJC6--PDE1C^DNAJC6^ENSG00000116675.16" ; gene_name DNAJC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009066.4" ; hgnc_id "HGNC:15469" ; level 3 ; orig_coord_info "chr1,65364652,65364785,+" ; protein_id "ENSP00000263441.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000263441.11" ; transcript_name "DNAJC6-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: DNAJC6--PDE1C HAVANA gene 37267 68688 . + . FI_gene_label "PDE1C^ENSG00000154678.18" ; ID "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18" ; ccdsid "CCDS55099.1" ; exon_id "ENSE00001281920.2" ; exon_number 2 ; gene_id "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18" ; gene_name PDE1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000023836.10" ; havana_transcript "OTTHUMT00000215076.2" ; hgnc_id "HGNC:8776" ; level 2 ; orig_coord_info "chr7,32070293,32070393,-" ; protein_id "ENSP00000318105.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000321453.12" ; transcript_name "PDE1C-201" ; transcript_support_level 2 ; transcript_type protein_coding DNAJC6--PDE1C HAVANA mRNA 37267 68688 . + . FI_gene_label "PDE1C^ENSG00000154678.18" ; ID "DNAJC6--PDE1C^ENST00000321453.12" ; Parent "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18" ; ccdsid "CCDS55099.1" ; exon_id "ENSE00001281920.2" ; exon_number 2 ; gene_id "DNAJC6--PDE1C^PDE1C^ENSG00000154678.18" ; gene_name PDE1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000023836.10" ; havana_transcript "OTTHUMT00000215076.2" ; hgnc_id "HGNC:8776" ; level 2 ; orig_coord_info "chr7,32070293,32070393,-" ; protein_id "ENSP00000318105.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNAJC6--PDE1C^ENST00000321453.12" ; transcript_name "PDE1C-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: GTF2A1L--STON1-GTF2A1L HAVANA gene 1059 10137 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "GTF2A1L--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 "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding GTF2A1L--STON1-GTF2A1L HAVANA mRNA 1059 10137 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; Parent "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "GTF2A1L--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 "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ME1--UBE3D HAVANA gene 20339 39653 . + . FI_gene_label "UBE3D^ENSG00000118420.17" ; ID "ME1--UBE3D^UBE3D^ENSG00000118420.17" ; exon_id "ENSE00002062478.1" ; exon_number 1 ; gene_id "ME1--UBE3D^UBE3D^ENSG00000118420.17" ; gene_name UBE3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000015108.8" ; havana_transcript "OTTHUMT00000366290.1" ; hgnc_id "HGNC:21381" ; level 2 ; orig_coord_info "chr6,83065680,83065718,-" ; protein_id "ENSP00000237186.6" ; transcript_id "ME1--UBE3D^ENST00000237186.10" ; transcript_name "UBE3D-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay ME1--UBE3D HAVANA mRNA 20339 39653 . + . FI_gene_label "UBE3D^ENSG00000118420.17" ; ID "ME1--UBE3D^ENST00000237186.10" ; Parent "ME1--UBE3D^UBE3D^ENSG00000118420.17" ; exon_id "ENSE00002062478.1" ; exon_number 1 ; gene_id "ME1--UBE3D^UBE3D^ENSG00000118420.17" ; gene_name UBE3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000015108.8" ; havana_transcript "OTTHUMT00000366290.1" ; hgnc_id "HGNC:21381" ; level 2 ; orig_coord_info "chr6,83065680,83065718,-" ; protein_id "ENSP00000237186.6" ; transcript_id "ME1--UBE3D^ENST00000237186.10" ; transcript_name "UBE3D-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay L1 and L2 created: ME1--UBE3D HAVANA gene 1001 17338 . + . FI_gene_label "ME1^ENSG00000065833.9" ; ID "ME1--UBE3D^ME1^ENSG00000065833.9" ; ccdsid "CCDS34492.1" ; exon_id "ENSE00000760044.5" ; exon_number 1 ; gene_id "ME1--UBE3D^ME1^ENSG00000065833.9" ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3" ; havana_transcript "OTTHUMT00000041350.3" ; hgnc_id "HGNC:6983" ; level 2 ; orig_coord_info "chr6,83430877,83430954,-" ; protein_id "ENSP00000358719.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--UBE3D^ENST00000369705.4" ; transcript_name "ME1-201" ; transcript_support_level 1 ; transcript_type protein_coding ME1--UBE3D HAVANA mRNA 1001 17338 . + . FI_gene_label "ME1^ENSG00000065833.9" ; ID "ME1--UBE3D^ENST00000369705.4" ; Parent "ME1--UBE3D^ME1^ENSG00000065833.9" ; ccdsid "CCDS34492.1" ; exon_id "ENSE00000760044.5" ; exon_number 1 ; gene_id "ME1--UBE3D^ME1^ENSG00000065833.9" ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3" ; havana_transcript "OTTHUMT00000041350.3" ; hgnc_id "HGNC:6983" ; level 2 ; orig_coord_info "chr6,83430877,83430954,-" ; protein_id "ENSP00000358719.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--UBE3D^ENST00000369705.4" ; transcript_name "ME1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MYO18A--KRT18P55 HAVANA gene 1001 48046 . + . FI_gene_label "MYO18A^ENSG00000196535.17" ; ID "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17" ; ccdsid "CCDS45642.1" ; exon_id "ENSE00002189252.1" ; exon_number 2 ; gene_id "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17" ; gene_name MYO18A ; gene_type protein_coding ; havana_gene "OTTHUMG00000166360.11" ; havana_transcript "OTTHUMT00000389396.2" ; hgnc_id "HGNC:31104" ; level 2 ; orig_coord_info "chr17,29165942,29166940,-" ; protein_id "ENSP00000437073.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18A--KRT18P55^ENST00000527372.7" ; transcript_name "MYO18A-202" ; transcript_support_level 1 ; transcript_type protein_coding MYO18A--KRT18P55 HAVANA mRNA 1001 48046 . + . FI_gene_label "MYO18A^ENSG00000196535.17" ; ID "MYO18A--KRT18P55^ENST00000527372.7" ; Parent "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17" ; ccdsid "CCDS45642.1" ; exon_id "ENSE00002189252.1" ; exon_number 2 ; gene_id "MYO18A--KRT18P55^MYO18A^ENSG00000196535.17" ; gene_name MYO18A ; gene_type protein_coding ; havana_gene "OTTHUMG00000166360.11" ; havana_transcript "OTTHUMT00000389396.2" ; hgnc_id "HGNC:31104" ; level 2 ; orig_coord_info "chr17,29165942,29166940,-" ; protein_id "ENSP00000437073.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18A--KRT18P55^ENST00000527372.7" ; transcript_name "MYO18A-202" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PLEKHG1--MTHFD1L HAVANA gene 11157 31558 . + . FI_gene_label "PLEKHG1^ENSG00000120278.16" ; ID "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; ccdsid "CCDS34552.1" ; exon_id "ENSE00001444243.1" ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7" ; havana_transcript "OTTHUMT00000042691.3" ; hgnc_id "HGNC:20884" ; level 2 ; orig_coord_info "chr6,150733682,150734092,+" ; protein_id "ENSP00000351318.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6" ; transcript_name "PLEKHG1-201" ; transcript_support_level 5 ; transcript_type protein_coding PLEKHG1--MTHFD1L HAVANA mRNA 11157 31558 . + . FI_gene_label "PLEKHG1^ENSG00000120278.16" ; ID "PLEKHG1--MTHFD1L^ENST00000358517.6" ; Parent "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; ccdsid "CCDS34552.1" ; exon_id "ENSE00001444243.1" ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7" ; havana_transcript "OTTHUMT00000042691.3" ; hgnc_id "HGNC:20884" ; level 2 ; orig_coord_info "chr6,150733682,150734092,+" ; protein_id "ENSP00000351318.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6" ; transcript_name "PLEKHG1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PLEKHG1--MTHFD1L HAVANA gene 34596 42321 . + . FI_gene_label "MTHFD1L^ENSG00000120254.16" ; ID "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; ccdsid "CCDS56457.1" ; exon_id "ENSE00003713432.1" ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4" ; havana_transcript "OTTHUMT00000474291.1" ; hgnc_id "HGNC:21055" ; level 2 ; orig_coord_info "chr6,150865823,150866049,+" ; protein_id "ENSP00000356276.4" ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8" ; transcript_name "MTHFD1L-201" ; transcript_support_level 1 ; transcript_type protein_coding PLEKHG1--MTHFD1L HAVANA mRNA 34596 42321 . + . FI_gene_label "MTHFD1L^ENSG00000120254.16" ; ID "PLEKHG1--MTHFD1L^ENST00000367307.8" ; Parent "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; ccdsid "CCDS56457.1" ; exon_id "ENSE00003713432.1" ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4" ; havana_transcript "OTTHUMT00000474291.1" ; hgnc_id "HGNC:21055" ; level 2 ; orig_coord_info "chr6,150865823,150866049,+" ; protein_id "ENSP00000356276.4" ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8" ; transcript_name "MTHFD1L-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RNF135--AC005552.1 HAVANA gene 1040 8369 . + . FI_gene_label "RNF135^ENSG00000181481.14" ; ID "RNF135--AC005552.1^RNF135^ENSG00000181481.14" ; ccdsid "CCDS11263.1" ; exon_id "ENSE00001315229.5" ; exon_number 1 ; gene_id "RNF135--AC005552.1^RNF135^ENSG00000181481.14" ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7" ; havana_transcript "OTTHUMT00000256344.2" ; hgnc_id "HGNC:21158" ; level 2 ; orig_coord_info "chr17,30971074,30971445,+" ; protein_id "ENSP00000323693.4" ; tag basic CCDS ; transcript_id "RNF135--AC005552.1^ENST00000324689.8" ; transcript_name "RNF135-201" ; transcript_support_level 1 ; transcript_type protein_coding RNF135--AC005552.1 HAVANA mRNA 1040 8369 . + . FI_gene_label "RNF135^ENSG00000181481.14" ; ID "RNF135--AC005552.1^ENST00000324689.8" ; Parent "RNF135--AC005552.1^RNF135^ENSG00000181481.14" ; ccdsid "CCDS11263.1" ; exon_id "ENSE00001315229.5" ; exon_number 1 ; gene_id "RNF135--AC005552.1^RNF135^ENSG00000181481.14" ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7" ; havana_transcript "OTTHUMT00000256344.2" ; hgnc_id "HGNC:21158" ; level 2 ; orig_coord_info "chr17,30971074,30971445,+" ; protein_id "ENSP00000323693.4" ; tag basic CCDS ; transcript_id "RNF135--AC005552.1^ENST00000324689.8" ; transcript_name "RNF135-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RNF135--TMEM132E HAVANA gene 11372 24274 . + . FI_gene_label "TMEM132E^ENSG00000181291.8" ; ID "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8" ; exon_id "ENSE00001405658.4" ; exon_number 1 ; gene_id "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8" ; gene_name TMEM132E ; gene_type protein_coding ; havana_gene "OTTHUMG00000132927.4" ; havana_transcript "OTTHUMT00000256440.3" ; hgnc_id "HGNC:26991" ; level 2 ; orig_coord_info "chr17,34581077,34581143,+" ; protein_id "ENSP00000316532.5" ; tag basic appris_alternative_2 ; transcript_id "RNF135--TMEM132E^ENST00000321639.7" ; transcript_name "TMEM132E-201" ; transcript_support_level 5 ; transcript_type protein_coding RNF135--TMEM132E HAVANA mRNA 11372 24274 . + . FI_gene_label "TMEM132E^ENSG00000181291.8" ; ID "RNF135--TMEM132E^ENST00000321639.7" ; Parent "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8" ; exon_id "ENSE00001405658.4" ; exon_number 1 ; gene_id "RNF135--TMEM132E^TMEM132E^ENSG00000181291.8" ; gene_name TMEM132E ; gene_type protein_coding ; havana_gene "OTTHUMG00000132927.4" ; havana_transcript "OTTHUMT00000256440.3" ; hgnc_id "HGNC:26991" ; level 2 ; orig_coord_info "chr17,34581077,34581143,+" ; protein_id "ENSP00000316532.5" ; tag basic appris_alternative_2 ; transcript_id "RNF135--TMEM132E^ENST00000321639.7" ; transcript_name "TMEM132E-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: RNF135--TMEM132E HAVANA gene 1040 8369 . + . FI_gene_label "RNF135^ENSG00000181481.14" ; ID "RNF135--TMEM132E^RNF135^ENSG00000181481.14" ; ccdsid "CCDS11263.1" ; exon_id "ENSE00001315229.5" ; exon_number 1 ; gene_id "RNF135--TMEM132E^RNF135^ENSG00000181481.14" ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7" ; havana_transcript "OTTHUMT00000256344.2" ; hgnc_id "HGNC:21158" ; level 2 ; orig_coord_info "chr17,30971074,30971445,+" ; protein_id "ENSP00000323693.4" ; tag basic CCDS ; transcript_id "RNF135--TMEM132E^ENST00000324689.8" ; transcript_name "RNF135-201" ; transcript_support_level 1 ; transcript_type protein_coding RNF135--TMEM132E HAVANA mRNA 1040 8369 . + . FI_gene_label "RNF135^ENSG00000181481.14" ; ID "RNF135--TMEM132E^ENST00000324689.8" ; Parent "RNF135--TMEM132E^RNF135^ENSG00000181481.14" ; ccdsid "CCDS11263.1" ; exon_id "ENSE00001315229.5" ; exon_number 1 ; gene_id "RNF135--TMEM132E^RNF135^ENSG00000181481.14" ; gene_name RNF135 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132867.7" ; havana_transcript "OTTHUMT00000256344.2" ; hgnc_id "HGNC:21158" ; level 2 ; orig_coord_info "chr17,30971074,30971445,+" ; protein_id "ENSP00000323693.4" ; tag basic CCDS ; transcript_id "RNF135--TMEM132E^ENST00000324689.8" ; transcript_name "RNF135-201" ; transcript_support_level 1 ; 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: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TRAF4--AC011840.1 HAVANA gene 1007 7728 . + . FI_gene_label "TRAF4^ENSG00000076604.15" ; ID "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15" ; ccdsid "CCDS11243.1" ; exon_id "ENSE00002729975.2" ; exon_number 1 ; gene_id "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15" ; gene_name TRAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132677.8" ; havana_transcript "OTTHUMT00000255944.4" ; hgnc_id "HGNC:12034" ; level 2 ; orig_coord_info "chr17,28744113,28744255,+" ; protein_id "ENSP00000262395.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRAF4--AC011840.1^ENST00000262395.10" ; transcript_name "TRAF4-201" ; transcript_support_level 1 ; transcript_type protein_coding TRAF4--AC011840.1 HAVANA mRNA 1007 7728 . + . FI_gene_label "TRAF4^ENSG00000076604.15" ; ID "TRAF4--AC011840.1^ENST00000262395.10" ; Parent "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15" ; ccdsid "CCDS11243.1" ; exon_id "ENSE00002729975.2" ; exon_number 1 ; gene_id "TRAF4--AC011840.1^TRAF4^ENSG00000076604.15" ; gene_name TRAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132677.8" ; havana_transcript "OTTHUMT00000255944.4" ; hgnc_id "HGNC:12034" ; level 2 ; orig_coord_info "chr17,28744113,28744255,+" ; protein_id "ENSP00000262395.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRAF4--AC011840.1^ENST00000262395.10" ; transcript_name "TRAF4-201" ; 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: AL669831.1--SEPTIN14 HAVANA gene 2344 8334 . + . FI_gene_label "AL669831.1^ENSG00000228327.3" ; ID "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3" ; exon_id "ENSE00001630466.1" ; exon_number 1 ; gene_id "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3" ; gene_name "AL669831.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2" ; havana_transcript "OTTHUMT00000488438.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,774171,774280,-" ; tag basic ; transcript_id "AL669831.1--SEPTIN14^ENST00000428504.2" ; transcript_name "AL669831.1-202" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene AL669831.1--SEPTIN14 HAVANA RNA 2344 8334 . + . FI_gene_label "AL669831.1^ENSG00000228327.3" ; ID "AL669831.1--SEPTIN14^ENST00000428504.2" ; Parent "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3" ; exon_id "ENSE00001630466.1" ; exon_number 1 ; gene_id "AL669831.1--SEPTIN14^AL669831.1^ENSG00000228327.3" ; gene_name "AL669831.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2" ; havana_transcript "OTTHUMT00000488438.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,774171,774280,-" ; tag basic ; transcript_id "AL669831.1--SEPTIN14^ENST00000428504.2" ; transcript_name "AL669831.1-202" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: AL669831.4--SEPTIN14 HAVANA gene 1001 5872 . + . FI_gene_label "AL669831.4^ENSG00000230092.7" ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; exon_id "ENSE00001746491.1" ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; gene_name "AL669831.4" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3" ; havana_transcript "OTTHUMT00000448550.2" ; level 2 ; orig_coord_info "chr1,817373,817712,-" ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4" ; transcript_name "AL669831.4-201" ; transcript_support_level 5 ; transcript_type processed_transcript AL669831.4--SEPTIN14 HAVANA RNA 1001 5872 . + . FI_gene_label "AL669831.4^ENSG00000230092.7" ; ID "AL669831.4--SEPTIN14^ENST00000447500.4" ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; exon_id "ENSE00001746491.1" ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; gene_name "AL669831.4" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3" ; havana_transcript "OTTHUMT00000448550.2" ; level 2 ; orig_coord_info "chr1,817373,817712,-" ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4" ; transcript_name "AL669831.4-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: GTF2A1L--STON1-GTF2A1L HAVANA gene 14395 15764 . + . FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21" ; ID "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; exon_id "ENSE00001916353.1" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; gene_name "STON1-GTF2A1L" ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6" ; havana_transcript "OTTHUMT00000325207.1" ; hgnc_id "HGNC:30651" ; level 1 ; orig_coord_info "chr2,48768954,48769121,+" ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; transcript_name "STON1-GTF2A1L-205" ; transcript_support_level 5 ; transcript_type processed_transcript GTF2A1L--STON1-GTF2A1L HAVANA RNA 14395 15764 . + . FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21" ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; Parent "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; exon_id "ENSE00001916353.1" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; gene_name "STON1-GTF2A1L" ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6" ; havana_transcript "OTTHUMT00000325207.1" ; hgnc_id "HGNC:30651" ; level 1 ; orig_coord_info "chr2,48768954,48769121,+" ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; transcript_name "STON1-GTF2A1L-205" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: MYO18A--KRT18P55 HAVANA gene 52133 56897 . + . FI_gene_label "KRT18P55^ENSG00000265480.5" ; ID "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5" ; exon_id "ENSE00002724983.1" ; exon_number 1 ; gene_id "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5" ; gene_name KRT18P55 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000179422.3" ; havana_transcript "OTTHUMT00000446194.1" ; hgnc_id "HGNC:26874" ; level 2 ; orig_coord_info "chr17,28306976,28307382,-" ; tag basic ; transcript_id "MYO18A--KRT18P55^ENST00000577198.5" ; transcript_name "KRT18P55-201" ; transcript_support_level 1 ; transcript_type processed_transcript MYO18A--KRT18P55 HAVANA RNA 52133 56897 . + . FI_gene_label "KRT18P55^ENSG00000265480.5" ; ID "MYO18A--KRT18P55^ENST00000577198.5" ; Parent "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5" ; exon_id "ENSE00002724983.1" ; exon_number 1 ; gene_id "MYO18A--KRT18P55^KRT18P55^ENSG00000265480.5" ; gene_name KRT18P55 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000179422.3" ; havana_transcript "OTTHUMT00000446194.1" ; hgnc_id "HGNC:26874" ; level 2 ; orig_coord_info "chr17,28306976,28307382,-" ; tag basic ; transcript_id "MYO18A--KRT18P55^ENST00000577198.5" ; transcript_name "KRT18P55-201" ; transcript_support_level 1 ; transcript_type processed_transcript L1 and L2 created: RNF135--AC005552.1 HAVANA gene 11372 12033 . + . FI_gene_label "AC005552.1^ENSG00000264174.1" ; ID "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1" ; exon_id "ENSE00002719564.1" ; exon_number 1 ; gene_id "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1" ; gene_name "AC005552.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179768.1" ; havana_transcript "OTTHUMT00000448011.1" ; level 2 ; orig_coord_info "chr17,34725509,34726170,-" ; tag basic ; transcript_id "RNF135--AC005552.1^ENST00000577556.1" ; transcript_name "AC005552.1-201" ; transcript_support_level NA ; transcript_type lncRNA RNF135--AC005552.1 HAVANA RNA 11372 12033 . + . FI_gene_label "AC005552.1^ENSG00000264174.1" ; ID "RNF135--AC005552.1^ENST00000577556.1" ; Parent "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1" ; exon_id "ENSE00002719564.1" ; exon_number 1 ; gene_id "RNF135--AC005552.1^AC005552.1^ENSG00000264174.1" ; gene_name "AC005552.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179768.1" ; havana_transcript "OTTHUMT00000448011.1" ; level 2 ; orig_coord_info "chr17,34725509,34726170,-" ; tag basic ; transcript_id "RNF135--AC005552.1^ENST00000577556.1" ; transcript_name "AC005552.1-201" ; transcript_support_level NA ; transcript_type lncRNA L1 and L2 created: TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: TRAF4--AC011840.1 HAVANA gene 10729 13673 . + . FI_gene_label "AC011840.1^ENSG00000231421.8" ; ID "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8" ; exon_id "ENSE00001595653.2" ; exon_number 1 ; gene_id "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8" ; gene_name "AC011840.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000132806.4" ; havana_transcript "OTTHUMT00000256223.3" ; level 2 ; orig_coord_info "chr17,30576006,30577000,-" ; tag basic TAGENE ; transcript_id "TRAF4--AC011840.1^ENST00000436477.7" ; transcript_name "AC011840.1-202" ; transcript_support_level 2 ; transcript_type lncRNA TRAF4--AC011840.1 HAVANA RNA 10729 13673 . + . FI_gene_label "AC011840.1^ENSG00000231421.8" ; ID "TRAF4--AC011840.1^ENST00000436477.7" ; Parent "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8" ; exon_id "ENSE00001595653.2" ; exon_number 1 ; gene_id "TRAF4--AC011840.1^AC011840.1^ENSG00000231421.8" ; gene_name "AC011840.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000132806.4" ; havana_transcript "OTTHUMT00000256223.3" ; level 2 ; orig_coord_info "chr17,30576006,30577000,-" ; tag basic TAGENE ; transcript_id "TRAF4--AC011840.1^ENST00000436477.7" ; transcript_name "AC011840.1-202" ; transcript_support_level 2 ; transcript_type lncRNA 215 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 ------------------------------ 385 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 24 wrong level1 location cases ------------------------------ done in 0 seconds ------------------------------- ---------------------- Check13: remove identical isoforms ---------------------- Lets remove isoform PLEKHG1--MTHFD1L^ENST00000643692.1 1 identical isoforms removed ------------------------------ done in 0 seconds ------------------------------- ------ End checks (done in 0 second) ------ GFF3 file parsed