Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/46e3f68552e475bbccf61fd70bca03/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/0281707304675ac77d260ee8a80a87/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/46e3f68552e475bbccf61fd70bca03/.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: 3375 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3375 => 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:3375 => 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: AC020637.1--TMEM243 HAVANA gene 12778 19800 . + . FI_gene_label "TMEM243^ENSG00000135185.12" ; ID "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12" ; ccdsid "CCDS5602.1" ; exon_id "ENSE00001207780.5" ; exon_number 1 ; gene_id "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12" ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8" ; havana_transcript "OTTHUMT00000253377.4" ; hgnc_id "HGNC:21707" ; level 2 ; orig_coord_info "chr7,87219426,87219503,-" ; protein_id "ENSP00000257637.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC020637.1--TMEM243^ENST00000257637.8" ; transcript_name "TMEM243-201" ; transcript_support_level 1 ; transcript_type protein_coding AC020637.1--TMEM243 HAVANA mRNA 12778 19800 . + . FI_gene_label "TMEM243^ENSG00000135185.12" ; ID "AC020637.1--TMEM243^ENST00000257637.8" ; Parent "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12" ; ccdsid "CCDS5602.1" ; exon_id "ENSE00001207780.5" ; exon_number 1 ; gene_id "AC020637.1--TMEM243^TMEM243^ENSG00000135185.12" ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8" ; havana_transcript "OTTHUMT00000253377.4" ; hgnc_id "HGNC:21707" ; level 2 ; orig_coord_info "chr7,87219426,87219503,-" ; protein_id "ENSP00000257637.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC020637.1--TMEM243^ENST00000257637.8" ; transcript_name "TMEM243-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC083805.1--EEF1AKMT3 HAVANA gene 14982 19922 . + . FI_gene_label "EEF1AKMT3^ENSG00000123427.17" ; ID "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17" ; ccdsid "CCDS8957.1" ; exon_id "ENSE00002301479.2" ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17" ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2" ; havana_transcript "OTTHUMT00000409268.2" ; hgnc_id "HGNC:24936" ; level 2 ; orig_coord_info "chr12,57772725,57772901,+" ; protein_id "ENSP00000300209.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000300209.13" ; transcript_name "EEF1AKMT3-201" ; transcript_support_level 1 ; transcript_type protein_coding AC083805.1--EEF1AKMT3 HAVANA mRNA 14982 19922 . + . FI_gene_label "EEF1AKMT3^ENSG00000123427.17" ; ID "AC083805.1--EEF1AKMT3^ENST00000300209.13" ; Parent "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17" ; ccdsid "CCDS8957.1" ; exon_id "ENSE00002301479.2" ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^EEF1AKMT3^ENSG00000123427.17" ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2" ; havana_transcript "OTTHUMT00000409268.2" ; hgnc_id "HGNC:24936" ; level 2 ; orig_coord_info "chr12,57772725,57772901,+" ; protein_id "ENSP00000300209.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000300209.13" ; transcript_name "EEF1AKMT3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC083805.1--TSFM HAVANA gene 13875 20936 . + . FI_gene_label "TSFM^ENSG00000123297.20" ; ID "AC083805.1--TSFM^TSFM^ENSG00000123297.20" ; ccdsid "CCDS53809.1" ; exon_id "ENSE00001479920.3" ; exon_number 1 ; gene_id "AC083805.1--TSFM^TSFM^ENSG00000123297.20" ; gene_name TSFM ; gene_type protein_coding ; havana_gene "OTTHUMG00000153042.13" ; havana_transcript "OTTHUMT00000329193.1" ; hgnc_id "HGNC:12367" ; level 2 ; orig_coord_info "chr12,57782802,57782858,+" ; protein_id "ENSP00000313877.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "AC083805.1--TSFM^ENST00000323833.12" ; transcript_name "TSFM-201" ; transcript_support_level 1 ; transcript_type protein_coding AC083805.1--TSFM HAVANA mRNA 13875 20936 . + . FI_gene_label "TSFM^ENSG00000123297.20" ; ID "AC083805.1--TSFM^ENST00000323833.12" ; Parent "AC083805.1--TSFM^TSFM^ENSG00000123297.20" ; ccdsid "CCDS53809.1" ; exon_id "ENSE00001479920.3" ; exon_number 1 ; gene_id "AC083805.1--TSFM^TSFM^ENSG00000123297.20" ; gene_name TSFM ; gene_type protein_coding ; havana_gene "OTTHUMG00000153042.13" ; havana_transcript "OTTHUMT00000329193.1" ; hgnc_id "HGNC:12367" ; level 2 ; orig_coord_info "chr12,57782802,57782858,+" ; protein_id "ENSP00000313877.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "AC083805.1--TSFM^ENST00000323833.12" ; transcript_name "TSFM-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC093890.1--SOS2 HAVANA gene 4541 33009 . + . FI_gene_label "SOS2^ENSG00000100485.12" ; ID "AC093890.1--SOS2^SOS2^ENSG00000100485.12" ; ccdsid "CCDS9697.1" ; exon_id "ENSE00002525812.2" ; exon_number 1 ; gene_id "AC093890.1--SOS2^SOS2^ENSG00000100485.12" ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5" ; havana_transcript "OTTHUMT00000276878.4" ; hgnc_id "HGNC:11188" ; level 2 ; orig_coord_info "chr14,50231197,50231283,-" ; protein_id "ENSP00000216373.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC093890.1--SOS2^ENST00000216373.10" ; transcript_name "SOS2-201" ; transcript_support_level 1 ; transcript_type protein_coding AC093890.1--SOS2 HAVANA mRNA 4541 33009 . + . FI_gene_label "SOS2^ENSG00000100485.12" ; ID "AC093890.1--SOS2^ENST00000216373.10" ; Parent "AC093890.1--SOS2^SOS2^ENSG00000100485.12" ; ccdsid "CCDS9697.1" ; exon_id "ENSE00002525812.2" ; exon_number 1 ; gene_id "AC093890.1--SOS2^SOS2^ENSG00000100485.12" ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5" ; havana_transcript "OTTHUMT00000276878.4" ; hgnc_id "HGNC:11188" ; level 2 ; orig_coord_info "chr14,50231197,50231283,-" ; protein_id "ENSP00000216373.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC093890.1--SOS2^ENST00000216373.10" ; transcript_name "SOS2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCNY--AL353600.1 ENSEMBL gene 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--AL353600.1^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--AL353600.1^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--AL353600.1^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding CCNY--AL353600.1 ENSEMBL mRNA 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--AL353600.1^ENST00000265375.13" ; Parent "CCNY--AL353600.1^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--AL353600.1^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--AL353600.1^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCNY--AL353600.2 ENSEMBL gene 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--AL353600.2^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--AL353600.2^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--AL353600.2^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding CCNY--AL353600.2 ENSEMBL mRNA 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--AL353600.2^ENST00000265375.13" ; Parent "CCNY--AL353600.2^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--AL353600.2^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--AL353600.2^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCNY--NRP1 HAVANA gene 27174 58914 . + . FI_gene_label "NRP1^ENSG00000099250.18" ; ID "CCNY--NRP1^NRP1^ENSG00000099250.18" ; ccdsid "CCDS7177.1" ; exon_id "ENSE00001465117.2" ; exon_number 2 ; gene_id "CCNY--NRP1^NRP1^ENSG00000099250.18" ; gene_name NRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019343.8" ; havana_transcript "OTTHUMT00000051203.2" ; hgnc_id "HGNC:8004" ; level 2 ; orig_coord_info "chr10,33334310,33334382,-" ; protein_id "ENSP00000265371.3" ; tag alternative_5_UTR basic appris_principal_3 CCDS ; transcript_id "CCNY--NRP1^ENST00000265371.8" ; transcript_name "NRP1-201" ; transcript_support_level 5 ; transcript_type protein_coding CCNY--NRP1 HAVANA mRNA 27174 58914 . + . FI_gene_label "NRP1^ENSG00000099250.18" ; ID "CCNY--NRP1^ENST00000265371.8" ; Parent "CCNY--NRP1^NRP1^ENSG00000099250.18" ; ccdsid "CCDS7177.1" ; exon_id "ENSE00001465117.2" ; exon_number 2 ; gene_id "CCNY--NRP1^NRP1^ENSG00000099250.18" ; gene_name NRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019343.8" ; havana_transcript "OTTHUMT00000051203.2" ; hgnc_id "HGNC:8004" ; level 2 ; orig_coord_info "chr10,33334310,33334382,-" ; protein_id "ENSP00000265371.3" ; tag alternative_5_UTR basic appris_principal_3 CCDS ; transcript_id "CCNY--NRP1^ENST00000265371.8" ; transcript_name "NRP1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: CCNY--NRP1 ENSEMBL gene 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--NRP1^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--NRP1^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--NRP1^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding CCNY--NRP1 ENSEMBL mRNA 7867 24173 . + . FI_gene_label "CCNY^ENSG00000108100.18" ; ID "CCNY--NRP1^ENST00000265375.13" ; Parent "CCNY--NRP1^CCNY^ENSG00000108100.18" ; ccdsid "CCDS7190.1" ; exon_id "ENSE00003652968.1" ; exon_number 3 ; gene_id "CCNY--NRP1^CCNY^ENSG00000108100.18" ; gene_name CCNY ; gene_type protein_coding ; havana_gene "OTTHUMG00000017955.5" ; hgnc_id "HGNC:23354" ; level 3 ; orig_coord_info "chr10,35483412,35483478,+" ; protein_id "ENSP00000265375.9" ; tag basic CCDS ; transcript_id "CCNY--NRP1^ENST00000265375.13" ; transcript_name "CCNY-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EEF1AKMT3--CTDSP2 HAVANA gene 2123 7063 . + . FI_gene_label "EEF1AKMT3^ENSG00000123427.17" ; ID "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17" ; ccdsid "CCDS8957.1" ; exon_id "ENSE00002301479.2" ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17" ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2" ; havana_transcript "OTTHUMT00000409268.2" ; hgnc_id "HGNC:24936" ; level 2 ; orig_coord_info "chr12,57772725,57772901,+" ; protein_id "ENSP00000300209.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000300209.13" ; transcript_name "EEF1AKMT3-201" ; transcript_support_level 1 ; transcript_type protein_coding EEF1AKMT3--CTDSP2 HAVANA mRNA 2123 7063 . + . FI_gene_label "EEF1AKMT3^ENSG00000123427.17" ; ID "EEF1AKMT3--CTDSP2^ENST00000300209.13" ; Parent "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17" ; ccdsid "CCDS8957.1" ; exon_id "ENSE00002301479.2" ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^EEF1AKMT3^ENSG00000123427.17" ; gene_name EEF1AKMT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170459.2" ; havana_transcript "OTTHUMT00000409268.2" ; hgnc_id "HGNC:24936" ; level 2 ; orig_coord_info "chr12,57772725,57772901,+" ; protein_id "ENSP00000300209.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000300209.13" ; transcript_name "EEF1AKMT3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EEF1AKMT3--CTDSP2 HAVANA gene 10064 20364 . + . FI_gene_label "CTDSP2^ENSG00000175215.11" ; ID "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11" ; ccdsid "CCDS41801.1" ; exon_id "ENSE00001377388.4" ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11" ; gene_name CTDSP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170483.3" ; havana_transcript "OTTHUMT00000409353.2" ; hgnc_id "HGNC:17077" ; level 2 ; orig_coord_info "chr12,57846372,57846435,-" ; protein_id "ENSP00000381148.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000398073.7" ; transcript_name "CTDSP2-201" ; transcript_support_level 1 ; transcript_type protein_coding EEF1AKMT3--CTDSP2 HAVANA mRNA 10064 20364 . + . FI_gene_label "CTDSP2^ENSG00000175215.11" ; ID "EEF1AKMT3--CTDSP2^ENST00000398073.7" ; Parent "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11" ; ccdsid "CCDS41801.1" ; exon_id "ENSE00001377388.4" ; exon_number 1 ; gene_id "EEF1AKMT3--CTDSP2^CTDSP2^ENSG00000175215.11" ; gene_name CTDSP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170483.3" ; havana_transcript "OTTHUMT00000409353.2" ; hgnc_id "HGNC:17077" ; level 2 ; orig_coord_info "chr12,57846372,57846435,-" ; protein_id "ENSP00000381148.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1AKMT3--CTDSP2^ENST00000398073.7" ; transcript_name "CTDSP2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MRPS35--TMTC1 HAVANA gene 1011 10930 . + . FI_gene_label "MRPS35^ENSG00000061794.13" ; ID "MRPS35--TMTC1^MRPS35^ENSG00000061794.13" ; ccdsid "CCDS8714.1" ; exon_id "ENSE00001008074.3" ; exon_number 1 ; gene_id "MRPS35--TMTC1^MRPS35^ENSG00000061794.13" ; gene_name MRPS35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169215.2" ; havana_transcript "OTTHUMT00000402897.2" ; hgnc_id "HGNC:16635" ; level 2 ; orig_coord_info "chr12,27710844,27710955,+" ; protein_id "ENSP00000081029.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS35--TMTC1^ENST00000081029.8" ; transcript_name "MRPS35-201" ; transcript_support_level 1 ; transcript_type protein_coding MRPS35--TMTC1 HAVANA mRNA 1011 10930 . + . FI_gene_label "MRPS35^ENSG00000061794.13" ; ID "MRPS35--TMTC1^ENST00000081029.8" ; Parent "MRPS35--TMTC1^MRPS35^ENSG00000061794.13" ; ccdsid "CCDS8714.1" ; exon_id "ENSE00001008074.3" ; exon_number 1 ; gene_id "MRPS35--TMTC1^MRPS35^ENSG00000061794.13" ; gene_name MRPS35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169215.2" ; havana_transcript "OTTHUMT00000402897.2" ; hgnc_id "HGNC:16635" ; level 2 ; orig_coord_info "chr12,27710844,27710955,+" ; protein_id "ENSP00000081029.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS35--TMTC1^ENST00000081029.8" ; transcript_name "MRPS35-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MRPS35--TMTC1 HAVANA gene 13931 51649 . + . FI_gene_label "TMTC1^ENSG00000133687.16" ; ID "MRPS35--TMTC1^TMTC1^ENSG00000133687.16" ; ccdsid "CCDS8718.1" ; exon_id "ENSE00003646738.1" ; exon_number 2 ; gene_id "MRPS35--TMTC1^TMTC1^ENSG00000133687.16" ; gene_name TMTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169324.2" ; havana_transcript "OTTHUMT00000403503.1" ; hgnc_id "HGNC:24099" ; level 2 ; orig_coord_info "chr12,29767898,29768053,-" ; protein_id "ENSP00000256062.5" ; tag basic CCDS ; transcript_id "MRPS35--TMTC1^ENST00000256062.9" ; transcript_name "TMTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding MRPS35--TMTC1 HAVANA mRNA 13931 51649 . + . FI_gene_label "TMTC1^ENSG00000133687.16" ; ID "MRPS35--TMTC1^ENST00000256062.9" ; Parent "MRPS35--TMTC1^TMTC1^ENSG00000133687.16" ; ccdsid "CCDS8718.1" ; exon_id "ENSE00003646738.1" ; exon_number 2 ; gene_id "MRPS35--TMTC1^TMTC1^ENSG00000133687.16" ; gene_name TMTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169324.2" ; havana_transcript "OTTHUMT00000403503.1" ; hgnc_id "HGNC:24099" ; level 2 ; orig_coord_info "chr12,29767898,29768053,-" ; protein_id "ENSP00000256062.5" ; tag basic CCDS ; transcript_id "MRPS35--TMTC1^ENST00000256062.9" ; transcript_name "TMTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PPP2R3B--TMLHE HAVANA gene 22666 34361 . + . FI_gene_label "TMLHE^ENSG00000185973.12" ; ID "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12" ; ccdsid "CCDS14768.1" ; exon_id "ENSE00003660615.1" ; exon_number 2 ; gene_id "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12" ; gene_name TMLHE ; gene_type protein_coding ; havana_gene "OTTHUMG00000022674.3" ; havana_transcript "OTTHUMT00000058817.2" ; hgnc_id "HGNC:18308" ; level 2 ; orig_coord_info "chrX,155545096,155545276,-" ; protein_id "ENSP00000335261.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP2R3B--TMLHE^ENST00000334398.8" ; transcript_name "TMLHE-201" ; transcript_support_level 1 ; transcript_type protein_coding PPP2R3B--TMLHE HAVANA mRNA 22666 34361 . + . FI_gene_label "TMLHE^ENSG00000185973.12" ; ID "PPP2R3B--TMLHE^ENST00000334398.8" ; Parent "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12" ; ccdsid "CCDS14768.1" ; exon_id "ENSE00003660615.1" ; exon_number 2 ; gene_id "PPP2R3B--TMLHE^TMLHE^ENSG00000185973.12" ; gene_name TMLHE ; gene_type protein_coding ; havana_gene "OTTHUMG00000022674.3" ; havana_transcript "OTTHUMT00000058817.2" ; hgnc_id "HGNC:18308" ; level 2 ; orig_coord_info "chrX,155545096,155545276,-" ; protein_id "ENSP00000335261.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP2R3B--TMLHE^ENST00000334398.8" ; transcript_name "TMLHE-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PPP2R3B--TMLHE HAVANA gene 2589 6257 . + . FI_gene_label "PPP2R3B^ENSG00000167393.18" ; ID "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18" ; exon_id "ENSE00001489321.3" ; exon_number 1 ; gene_id "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18" ; gene_name PPP2R3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000021052.4" ; havana_transcript "OTTHUMT00000055578.3" ; hgnc_id "HGNC:13417" ; level 2 ; orig_coord_info "chrX,373532,373771,-" ; protein_id "ENSP00000371038.4" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PPP2R3B--TMLHE^ENST00000381625.9" ; transcript_name "PPP2R3B-201" ; transcript_support_level 5 ; transcript_type protein_coding PPP2R3B--TMLHE HAVANA mRNA 2589 6257 . + . FI_gene_label "PPP2R3B^ENSG00000167393.18" ; ID "PPP2R3B--TMLHE^ENST00000381625.9" ; Parent "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18" ; exon_id "ENSE00001489321.3" ; exon_number 1 ; gene_id "PPP2R3B--TMLHE^PPP2R3B^ENSG00000167393.18" ; gene_name PPP2R3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000021052.4" ; havana_transcript "OTTHUMT00000055578.3" ; hgnc_id "HGNC:13417" ; level 2 ; orig_coord_info "chrX,373532,373771,-" ; protein_id "ENSP00000371038.4" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PPP2R3B--TMLHE^ENST00000381625.9" ; transcript_name "PPP2R3B-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: RAP1B--SRGAP1 HAVANA gene 1045 26964 . + . FI_gene_label "RAP1B^ENSG00000127314.18" ; ID "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18" ; ccdsid "CCDS8984.1" ; exon_id "ENSE00003505440.1" ; exon_number 2 ; gene_id "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18" ; gene_name RAP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133660.8" ; havana_transcript "OTTHUMT00000257821.5" ; hgnc_id "HGNC:9857" ; level 2 ; orig_coord_info "chr12,68648725,68648781,+" ; protein_id "ENSP00000250559.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000250559.14" ; transcript_name "RAP1B-201" ; transcript_support_level 1 ; transcript_type protein_coding RAP1B--SRGAP1 HAVANA mRNA 1045 26964 . + . FI_gene_label "RAP1B^ENSG00000127314.18" ; ID "RAP1B--SRGAP1^ENST00000250559.14" ; Parent "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18" ; ccdsid "CCDS8984.1" ; exon_id "ENSE00003505440.1" ; exon_number 2 ; gene_id "RAP1B--SRGAP1^RAP1B^ENSG00000127314.18" ; gene_name RAP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133660.8" ; havana_transcript "OTTHUMT00000257821.5" ; hgnc_id "HGNC:9857" ; level 2 ; orig_coord_info "chr12,68648725,68648781,+" ; protein_id "ENSP00000250559.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000250559.14" ; transcript_name "RAP1B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RAP1B--SRGAP1 HAVANA gene 29965 75316 . + . FI_gene_label "SRGAP1^ENSG00000196935.9" ; ID "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9" ; ccdsid "CCDS8967.1" ; exon_id "ENSE00002278180.2" ; exon_number 1 ; gene_id "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9" ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3" ; havana_transcript "OTTHUMT00000400896.3" ; hgnc_id "HGNC:17382" ; level 2 ; orig_coord_info "chr12,63844817,63844883,+" ; protein_id "ENSP00000347198.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000355086.8" ; transcript_name "SRGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding RAP1B--SRGAP1 HAVANA mRNA 29965 75316 . + . FI_gene_label "SRGAP1^ENSG00000196935.9" ; ID "RAP1B--SRGAP1^ENST00000355086.8" ; Parent "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9" ; ccdsid "CCDS8967.1" ; exon_id "ENSE00002278180.2" ; exon_number 1 ; gene_id "RAP1B--SRGAP1^SRGAP1^ENSG00000196935.9" ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3" ; havana_transcript "OTTHUMT00000400896.3" ; hgnc_id "HGNC:17382" ; level 2 ; orig_coord_info "chr12,63844817,63844883,+" ; protein_id "ENSP00000347198.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAP1B--SRGAP1^ENST00000355086.8" ; transcript_name "SRGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SAV1--SOS2 HAVANA gene 14032 42500 . + . FI_gene_label "SOS2^ENSG00000100485.12" ; ID "SAV1--SOS2^SOS2^ENSG00000100485.12" ; ccdsid "CCDS9697.1" ; exon_id "ENSE00002525812.2" ; exon_number 1 ; gene_id "SAV1--SOS2^SOS2^ENSG00000100485.12" ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5" ; havana_transcript "OTTHUMT00000276878.4" ; hgnc_id "HGNC:11188" ; level 2 ; orig_coord_info "chr14,50231197,50231283,-" ; protein_id "ENSP00000216373.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000216373.10" ; transcript_name "SOS2-201" ; transcript_support_level 1 ; transcript_type protein_coding SAV1--SOS2 HAVANA mRNA 14032 42500 . + . FI_gene_label "SOS2^ENSG00000100485.12" ; ID "SAV1--SOS2^ENST00000216373.10" ; Parent "SAV1--SOS2^SOS2^ENSG00000100485.12" ; ccdsid "CCDS9697.1" ; exon_id "ENSE00002525812.2" ; exon_number 1 ; gene_id "SAV1--SOS2^SOS2^ENSG00000100485.12" ; gene_name SOS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140292.5" ; havana_transcript "OTTHUMT00000276878.4" ; hgnc_id "HGNC:11188" ; level 2 ; orig_coord_info "chr14,50231197,50231283,-" ; protein_id "ENSP00000216373.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000216373.10" ; transcript_name "SOS2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SAV1--SOS2 HAVANA gene 1001 9509 . + . FI_gene_label "SAV1^ENSG00000151748.15" ; ID "SAV1--SOS2^SAV1^ENSG00000151748.15" ; ccdsid "CCDS9701.1" ; exon_id "ENSE00001246829.5" ; exon_number 1 ; gene_id "SAV1--SOS2^SAV1^ENSG00000151748.15" ; gene_name SAV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140293.8" ; havana_transcript "OTTHUMT00000276879.2" ; hgnc_id "HGNC:17795" ; level 2 ; orig_coord_info "chr14,50667874,50667967,-" ; protein_id "ENSP00000324729.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000324679.5" ; transcript_name "SAV1-201" ; transcript_support_level 1 ; transcript_type protein_coding SAV1--SOS2 HAVANA mRNA 1001 9509 . + . FI_gene_label "SAV1^ENSG00000151748.15" ; ID "SAV1--SOS2^ENST00000324679.5" ; Parent "SAV1--SOS2^SAV1^ENSG00000151748.15" ; ccdsid "CCDS9701.1" ; exon_id "ENSE00001246829.5" ; exon_number 1 ; gene_id "SAV1--SOS2^SAV1^ENSG00000151748.15" ; gene_name SAV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140293.8" ; havana_transcript "OTTHUMT00000276879.2" ; hgnc_id "HGNC:17795" ; level 2 ; orig_coord_info "chr14,50667874,50667967,-" ; protein_id "ENSP00000324729.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAV1--SOS2^ENST00000324679.5" ; transcript_name "SAV1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SRGAP1--GRIP1 HAVANA gene 1001 46352 . + . FI_gene_label "SRGAP1^ENSG00000196935.9" ; ID "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9" ; ccdsid "CCDS8967.1" ; exon_id "ENSE00002278180.2" ; exon_number 1 ; gene_id "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9" ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3" ; havana_transcript "OTTHUMT00000400896.3" ; hgnc_id "HGNC:17382" ; level 2 ; orig_coord_info "chr12,63844817,63844883,+" ; protein_id "ENSP00000347198.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRGAP1--GRIP1^ENST00000355086.8" ; transcript_name "SRGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding SRGAP1--GRIP1 HAVANA mRNA 1001 46352 . + . FI_gene_label "SRGAP1^ENSG00000196935.9" ; ID "SRGAP1--GRIP1^ENST00000355086.8" ; Parent "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9" ; ccdsid "CCDS8967.1" ; exon_id "ENSE00002278180.2" ; exon_number 1 ; gene_id "SRGAP1--GRIP1^SRGAP1^ENSG00000196935.9" ; gene_name SRGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168750.3" ; havana_transcript "OTTHUMT00000400896.3" ; hgnc_id "HGNC:17382" ; level 2 ; orig_coord_info "chr12,63844817,63844883,+" ; protein_id "ENSP00000347198.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRGAP1--GRIP1^ENST00000355086.8" ; transcript_name "SRGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SRGAP1--GRIP1 HAVANA gene 52869 85366 . + . FI_gene_label "GRIP1^ENSG00000155974.13" ; ID "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13" ; exon_id "ENSE00003912333.1" ; exon_number 1 ; gene_id "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13" ; gene_name GRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169019.7" ; hgnc_id "HGNC:18708" ; level 2 ; orig_coord_info "chr12,66678850,66678904,-" ; protein_id "ENSP00000352780.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 ; transcript_id "SRGAP1--GRIP1^ENST00000359742.9" ; transcript_name "GRIP1-201" ; transcript_support_level 5 ; transcript_type protein_coding SRGAP1--GRIP1 HAVANA mRNA 52869 85366 . + . FI_gene_label "GRIP1^ENSG00000155974.13" ; ID "SRGAP1--GRIP1^ENST00000359742.9" ; Parent "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13" ; exon_id "ENSE00003912333.1" ; exon_number 1 ; gene_id "SRGAP1--GRIP1^GRIP1^ENSG00000155974.13" ; gene_name GRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169019.7" ; hgnc_id "HGNC:18708" ; level 2 ; orig_coord_info "chr12,66678850,66678904,-" ; protein_id "ENSP00000352780.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 ; transcript_id "SRGAP1--GRIP1^ENST00000359742.9" ; transcript_name "GRIP1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TMEM243--AC020637.1 HAVANA gene 1856 8878 . + . FI_gene_label "TMEM243^ENSG00000135185.12" ; ID "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12" ; ccdsid "CCDS5602.1" ; exon_id "ENSE00001207780.5" ; exon_number 1 ; gene_id "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12" ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8" ; havana_transcript "OTTHUMT00000253377.4" ; hgnc_id "HGNC:21707" ; level 2 ; orig_coord_info "chr7,87219426,87219503,-" ; protein_id "ENSP00000257637.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM243--AC020637.1^ENST00000257637.8" ; transcript_name "TMEM243-201" ; transcript_support_level 1 ; transcript_type protein_coding TMEM243--AC020637.1 HAVANA mRNA 1856 8878 . + . FI_gene_label "TMEM243^ENSG00000135185.12" ; ID "TMEM243--AC020637.1^ENST00000257637.8" ; Parent "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12" ; ccdsid "CCDS5602.1" ; exon_id "ENSE00001207780.5" ; exon_number 1 ; gene_id "TMEM243--AC020637.1^TMEM243^ENSG00000135185.12" ; gene_name TMEM243 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130823.8" ; havana_transcript "OTTHUMT00000253377.4" ; hgnc_id "HGNC:21707" ; level 2 ; orig_coord_info "chr7,87219426,87219503,-" ; protein_id "ENSP00000257637.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM243--AC020637.1^ENST00000257637.8" ; transcript_name "TMEM243-201" ; 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: TYW1--VKORC1L1 HAVANA gene 2339 20501 . + . FI_gene_label "TYW1^ENSG00000198874.13" ; ID "TYW1--VKORC1L1^TYW1^ENSG00000198874.13" ; ccdsid "CCDS5538.1" ; exon_id "ENSE00001947681.2" ; exon_number 1 ; gene_id "TYW1--VKORC1L1^TYW1^ENSG00000198874.13" ; gene_name TYW1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129723.5" ; havana_transcript "OTTHUMT00000251932.3" ; hgnc_id "HGNC:25598" ; level 2 ; orig_coord_info "chr7,66996979,66996982,+" ; protein_id "ENSP00000352645.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000359626.10" ; transcript_name "TYW1-201" ; transcript_support_level 1 ; transcript_type protein_coding TYW1--VKORC1L1 HAVANA mRNA 2339 20501 . + . FI_gene_label "TYW1^ENSG00000198874.13" ; ID "TYW1--VKORC1L1^ENST00000359626.10" ; Parent "TYW1--VKORC1L1^TYW1^ENSG00000198874.13" ; ccdsid "CCDS5538.1" ; exon_id "ENSE00001947681.2" ; exon_number 1 ; gene_id "TYW1--VKORC1L1^TYW1^ENSG00000198874.13" ; gene_name TYW1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129723.5" ; havana_transcript "OTTHUMT00000251932.3" ; hgnc_id "HGNC:25598" ; level 2 ; orig_coord_info "chr7,66996979,66996982,+" ; protein_id "ENSP00000352645.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000359626.10" ; transcript_name "TYW1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TYW1--VKORC1L1 HAVANA gene 23507 31593 . + . FI_gene_label "VKORC1L1^ENSG00000196715.7" ; ID "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7" ; ccdsid "CCDS5529.1" ; exon_id "ENSE00003846291.1" ; exon_number 1 ; gene_id "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7" ; gene_name VKORC1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129449.5" ; havana_transcript "OTTHUMT00000251612.5" ; hgnc_id "HGNC:21492" ; level 2 ; orig_coord_info "chr7,65873372,65873565,+" ; protein_id "ENSP00000353998.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000360768.5" ; transcript_name "VKORC1L1-201" ; transcript_support_level 1 ; transcript_type protein_coding TYW1--VKORC1L1 HAVANA mRNA 23507 31593 . + . FI_gene_label "VKORC1L1^ENSG00000196715.7" ; ID "TYW1--VKORC1L1^ENST00000360768.5" ; Parent "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7" ; ccdsid "CCDS5529.1" ; exon_id "ENSE00003846291.1" ; exon_number 1 ; gene_id "TYW1--VKORC1L1^VKORC1L1^ENSG00000196715.7" ; gene_name VKORC1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129449.5" ; havana_transcript "OTTHUMT00000251612.5" ; hgnc_id "HGNC:21492" ; level 2 ; orig_coord_info "chr7,65873372,65873565,+" ; protein_id "ENSP00000353998.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TYW1--VKORC1L1^ENST00000360768.5" ; transcript_name "VKORC1L1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: VGLL4--ATG7 HAVANA gene 4453 29477 . + . FI_gene_label "VGLL4^ENSG00000144560.15" ; ID "VGLL4--ATG7^VGLL4^ENSG00000144560.15" ; ccdsid "CCDS2606.1" ; exon_id "ENSE00003614736.1" ; exon_number 2 ; gene_id "VGLL4--ATG7^VGLL4^ENSG00000144560.15" ; gene_name VGLL4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129739.21" ; havana_transcript "OTTHUMT00000251950.2" ; hgnc_id "HGNC:28966" ; level 2 ; orig_coord_info "chr3,11702971,11703034,-" ; protein_id "ENSP00000273038.3" ; tag basic CCDS ; transcript_id "VGLL4--ATG7^ENST00000273038.7" ; transcript_name "VGLL4-201" ; transcript_support_level 1 ; transcript_type protein_coding VGLL4--ATG7 HAVANA mRNA 4453 29477 . + . FI_gene_label "VGLL4^ENSG00000144560.15" ; ID "VGLL4--ATG7^ENST00000273038.7" ; Parent "VGLL4--ATG7^VGLL4^ENSG00000144560.15" ; ccdsid "CCDS2606.1" ; exon_id "ENSE00003614736.1" ; exon_number 2 ; gene_id "VGLL4--ATG7^VGLL4^ENSG00000144560.15" ; gene_name VGLL4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129739.21" ; havana_transcript "OTTHUMT00000251950.2" ; hgnc_id "HGNC:28966" ; level 2 ; orig_coord_info "chr3,11702971,11703034,-" ; protein_id "ENSP00000273038.3" ; tag basic CCDS ; transcript_id "VGLL4--ATG7^ENST00000273038.7" ; transcript_name "VGLL4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: VGLL4--ATG7 HAVANA gene 32586 67624 . + . FI_gene_label "ATG7^ENSG00000197548.12" ; ID "VGLL4--ATG7^ATG7^ENSG00000197548.12" ; ccdsid "CCDS2605.1" ; exon_id "ENSE00003638636.1" ; exon_number 2 ; gene_id "VGLL4--ATG7^ATG7^ENSG00000197548.12" ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21" ; havana_transcript "OTTHUMT00000251951.3" ; hgnc_id "HGNC:16935" ; level 2 ; orig_coord_info "chr3,11298696,11298855,+" ; protein_id "ENSP00000346437.3" ; tag basic appris_principal_1 CCDS ; transcript_id "VGLL4--ATG7^ENST00000354449.7" ; transcript_name "ATG7-201" ; transcript_support_level 1 ; transcript_type protein_coding VGLL4--ATG7 HAVANA mRNA 32586 67624 . + . FI_gene_label "ATG7^ENSG00000197548.12" ; ID "VGLL4--ATG7^ENST00000354449.7" ; Parent "VGLL4--ATG7^ATG7^ENSG00000197548.12" ; ccdsid "CCDS2605.1" ; exon_id "ENSE00003638636.1" ; exon_number 2 ; gene_id "VGLL4--ATG7^ATG7^ENSG00000197548.12" ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21" ; havana_transcript "OTTHUMT00000251951.3" ; hgnc_id "HGNC:16935" ; level 2 ; orig_coord_info "chr3,11298696,11298855,+" ; protein_id "ENSP00000346437.3" ; tag basic appris_principal_1 CCDS ; transcript_id "VGLL4--ATG7^ENST00000354449.7" ; transcript_name "ATG7-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC020637.1--TMEM243 HAVANA gene 1001 8922 . + . FI_gene_label "AC020637.1^ENSG00000258231.5" ; ID "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5" ; exon_id "ENSE00002337014.1" ; exon_number 1 ; gene_id "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5" ; gene_name "AC020637.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2" ; havana_transcript "OTTHUMT00000406685.1" ; level 1 ; orig_coord_info "chr12,58544124,58544179,+" ; tag basic exp_conf ; transcript_id "AC020637.1--TMEM243^ENST00000546977.5" ; transcript_name "AC020637.1-201" ; transcript_support_level 5 ; transcript_type lncRNA AC020637.1--TMEM243 HAVANA RNA 1001 8922 . + . FI_gene_label "AC020637.1^ENSG00000258231.5" ; ID "AC020637.1--TMEM243^ENST00000546977.5" ; Parent "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5" ; exon_id "ENSE00002337014.1" ; exon_number 1 ; gene_id "AC020637.1--TMEM243^AC020637.1^ENSG00000258231.5" ; gene_name "AC020637.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2" ; havana_transcript "OTTHUMT00000406685.1" ; level 1 ; orig_coord_info "chr12,58544124,58544179,+" ; tag basic exp_conf ; transcript_id "AC020637.1--TMEM243^ENST00000546977.5" ; transcript_name "AC020637.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: AC083805.1--EEF1AKMT3 HAVANA gene 1001 10858 . + . FI_gene_label "AC083805.1^ENSG00000245651.3" ; ID "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3" ; exon_id "ENSE00001961223.2" ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3" ; gene_name "AC083805.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11" ; havana_transcript "OTTHUMT00000409363.1" ; level 2 ; orig_coord_info "chr12,57893740,57896482,-" ; tag basic ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000499481.2" ; transcript_name "AC083805.1-202" ; transcript_support_level 1 ; transcript_type lncRNA AC083805.1--EEF1AKMT3 HAVANA RNA 1001 10858 . + . FI_gene_label "AC083805.1^ENSG00000245651.3" ; ID "AC083805.1--EEF1AKMT3^ENST00000499481.2" ; Parent "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3" ; exon_id "ENSE00001961223.2" ; exon_number 1 ; gene_id "AC083805.1--EEF1AKMT3^AC083805.1^ENSG00000245651.3" ; gene_name "AC083805.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11" ; havana_transcript "OTTHUMT00000409363.1" ; level 2 ; orig_coord_info "chr12,57893740,57896482,-" ; tag basic ; transcript_id "AC083805.1--EEF1AKMT3^ENST00000499481.2" ; transcript_name "AC083805.1-202" ; transcript_support_level 1 ; transcript_type lncRNA L1 and L2 created: AC083805.1--TSFM HAVANA gene 1001 10858 . + . FI_gene_label "AC083805.1^ENSG00000245651.3" ; ID "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3" ; exon_id "ENSE00001961223.2" ; exon_number 1 ; gene_id "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3" ; gene_name "AC083805.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11" ; havana_transcript "OTTHUMT00000409363.1" ; level 2 ; orig_coord_info "chr12,57893740,57896482,-" ; tag basic ; transcript_id "AC083805.1--TSFM^ENST00000499481.2" ; transcript_name "AC083805.1-202" ; transcript_support_level 1 ; transcript_type lncRNA AC083805.1--TSFM HAVANA RNA 1001 10858 . + . FI_gene_label "AC083805.1^ENSG00000245651.3" ; ID "AC083805.1--TSFM^ENST00000499481.2" ; Parent "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3" ; exon_id "ENSE00001961223.2" ; exon_number 1 ; gene_id "AC083805.1--TSFM^AC083805.1^ENSG00000245651.3" ; gene_name "AC083805.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170485.11" ; havana_transcript "OTTHUMT00000409363.1" ; level 2 ; orig_coord_info "chr12,57893740,57896482,-" ; tag basic ; transcript_id "AC083805.1--TSFM^ENST00000499481.2" ; transcript_name "AC083805.1-202" ; transcript_support_level 1 ; transcript_type lncRNA L1 and L2 created: AC093890.1--SOS2 HAVANA gene 1001 1540 . + . FI_gene_label "AC093890.1^ENSG00000249741.2" ; ID "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2" ; exon_id "ENSE00002087602.2" ; exon_number 1 ; gene_id "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2" ; gene_name "AC093890.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161401.2" ; havana_transcript "OTTHUMT00000364779.2" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr4,143911514,143912053,-" ; tag pseudo_consens basic ; transcript_id "AC093890.1--SOS2^ENST00000502554.2" ; transcript_name "AC093890.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene AC093890.1--SOS2 HAVANA RNA 1001 1540 . + . FI_gene_label "AC093890.1^ENSG00000249741.2" ; ID "AC093890.1--SOS2^ENST00000502554.2" ; Parent "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2" ; exon_id "ENSE00002087602.2" ; exon_number 1 ; gene_id "AC093890.1--SOS2^AC093890.1^ENSG00000249741.2" ; gene_name "AC093890.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161401.2" ; havana_transcript "OTTHUMT00000364779.2" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr4,143911514,143912053,-" ; tag pseudo_consens basic ; transcript_id "AC093890.1--SOS2^ENST00000502554.2" ; transcript_name "AC093890.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: CCNY--AL353600.1 HAVANA gene 27174 27424 . + . FI_gene_label "AL353600.1^ENSG00000273012.1" ; ID "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1" ; exon_id "ENSE00003710377.1" ; exon_number 1 ; gene_id "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1" ; gene_name "AL353600.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186206.1" ; havana_transcript "OTTHUMT00000472416.1" ; level 2 ; orig_coord_info "chr10,33341655,33341905,+" ; tag basic ; transcript_id "CCNY--AL353600.1^ENST00000608148.1" ; transcript_name "AL353600.1-201" ; transcript_support_level NA ; transcript_type lncRNA CCNY--AL353600.1 HAVANA RNA 27174 27424 . + . FI_gene_label "AL353600.1^ENSG00000273012.1" ; ID "CCNY--AL353600.1^ENST00000608148.1" ; Parent "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1" ; exon_id "ENSE00003710377.1" ; exon_number 1 ; gene_id "CCNY--AL353600.1^AL353600.1^ENSG00000273012.1" ; gene_name "AL353600.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186206.1" ; havana_transcript "OTTHUMT00000472416.1" ; level 2 ; orig_coord_info "chr10,33341655,33341905,+" ; tag basic ; transcript_id "CCNY--AL353600.1^ENST00000608148.1" ; transcript_name "AL353600.1-201" ; transcript_support_level NA ; transcript_type lncRNA L1 and L2 created: CCNY--AL353600.2 HAVANA gene 27174 30614 . + . FI_gene_label "AL353600.2^ENSG00000287278.1" ; ID "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1" ; exon_id "ENSE00003868179.1" ; exon_number 1 ; gene_id "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1" ; gene_name "AL353600.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194969.1" ; havana_transcript "OTTHUMT00000523464.1" ; level 2 ; orig_coord_info "chr10,33384891,33385325,+" ; tag basic TAGENE ; transcript_id "CCNY--AL353600.2^ENST00000654047.1" ; transcript_name "AL353600.2-201" ; transcript_type lncRNA CCNY--AL353600.2 HAVANA RNA 27174 30614 . + . FI_gene_label "AL353600.2^ENSG00000287278.1" ; ID "CCNY--AL353600.2^ENST00000654047.1" ; Parent "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1" ; exon_id "ENSE00003868179.1" ; exon_number 1 ; gene_id "CCNY--AL353600.2^AL353600.2^ENSG00000287278.1" ; gene_name "AL353600.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194969.1" ; havana_transcript "OTTHUMT00000523464.1" ; level 2 ; orig_coord_info "chr10,33384891,33385325,+" ; tag basic TAGENE ; transcript_id "CCNY--AL353600.2^ENST00000654047.1" ; transcript_name "AL353600.2-201" ; 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: TMEM243--AC020637.1 HAVANA gene 11879 19800 . + . FI_gene_label "AC020637.1^ENSG00000258231.5" ; ID "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5" ; exon_id "ENSE00002337014.1" ; exon_number 1 ; gene_id "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5" ; gene_name "AC020637.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2" ; havana_transcript "OTTHUMT00000406685.1" ; level 1 ; orig_coord_info "chr12,58544124,58544179,+" ; tag basic exp_conf ; transcript_id "TMEM243--AC020637.1^ENST00000546977.5" ; transcript_name "AC020637.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TMEM243--AC020637.1 HAVANA RNA 11879 19800 . + . FI_gene_label "AC020637.1^ENSG00000258231.5" ; ID "TMEM243--AC020637.1^ENST00000546977.5" ; Parent "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5" ; exon_id "ENSE00002337014.1" ; exon_number 1 ; gene_id "TMEM243--AC020637.1^AC020637.1^ENSG00000258231.5" ; gene_name "AC020637.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169963.2" ; havana_transcript "OTTHUMT00000406685.1" ; level 1 ; orig_coord_info "chr12,58544124,58544179,+" ; tag basic exp_conf ; transcript_id "TMEM243--AC020637.1^ENST00000546977.5" ; transcript_name "AC020637.1-201" ; transcript_support_level 5 ; transcript_type lncRNA 313 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 ------------------------------ 532 UTRs created that were missing No UTRs locations modified No supernumerary UTRs removed ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check11: all level2 locations ------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check12: all level1 locations ------------------------- We fixed 23 wrong level1 location cases ------------------------------ done in 0 seconds ------------------------------- ---------------------- Check13: remove identical isoforms ---------------------- None found ------------------------------ done in 0 seconds ------------------------------- ------ End checks (done in 0 second) ------ GFF3 file parsed