Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/4db70daa6c85f903da1a5bd4298871/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/08dafc3210e5fda7b1702132a7d3dc/fi_workdir/tih_rna_sample_00583_B23MVV7LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/4db70daa6c85f903da1a5bd4298871/.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: 3979 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3979 => 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:3979 => 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: CASK--BANF2 HAVANA gene 55697 61995 . + . FI_gene_label "BANF2^ENSG00000125888.15" ; ID "CASK--BANF2^BANF2^ENSG00000125888.15" ; ccdsid "CCDS13129.1" ; exon_id "ENSE00003800248.1" ; exon_number 3 ; gene_id "CASK--BANF2^BANF2^ENSG00000125888.15" ; gene_name BANF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031949.8" ; havana_transcript "OTTHUMT00000102261.2" ; hgnc_id "HGNC:16172" ; level 2 ; orig_coord_info "chr20,17725026,17725151,+" ; protein_id "ENSP00000246090.5" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "CASK--BANF2^ENST00000246090.6" ; transcript_name "BANF2-201" ; transcript_support_level 1 ; transcript_type protein_coding CASK--BANF2 HAVANA mRNA 55697 61995 . + . FI_gene_label "BANF2^ENSG00000125888.15" ; ID "CASK--BANF2^ENST00000246090.6" ; Parent "CASK--BANF2^BANF2^ENSG00000125888.15" ; ccdsid "CCDS13129.1" ; exon_id "ENSE00003800248.1" ; exon_number 3 ; gene_id "CASK--BANF2^BANF2^ENSG00000125888.15" ; gene_name BANF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031949.8" ; havana_transcript "OTTHUMT00000102261.2" ; hgnc_id "HGNC:16172" ; level 2 ; orig_coord_info "chr20,17725026,17725151,+" ; protein_id "ENSP00000246090.5" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "CASK--BANF2^ENST00000246090.6" ; transcript_name "BANF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CASK--BANF2 HAVANA gene 1126 47017 . + . FI_gene_label "CASK^ENSG00000147044.23" ; ID "CASK--BANF2^CASK^ENSG00000147044.23" ; exon_id "ENSE00001476451.3" ; exon_number 1 ; gene_id "CASK--BANF2^CASK^ENSG00000147044.23" ; gene_name CASK ; gene_type protein_coding ; havana_gene "OTTHUMG00000021378.10" ; havana_transcript "OTTHUMT00000056279.3" ; hgnc_id "HGNC:1497" ; level 2 ; orig_coord_info "chrX,41922930,41922988,-" ; protein_id "ENSP00000367396.2" ; tag not_organism_supported basic ; transcript_id "CASK--BANF2^ENST00000378154.3" ; transcript_name "CASK-201" ; transcript_support_level 5 ; transcript_type protein_coding CASK--BANF2 HAVANA mRNA 1126 47017 . + . FI_gene_label "CASK^ENSG00000147044.23" ; ID "CASK--BANF2^ENST00000378154.3" ; Parent "CASK--BANF2^CASK^ENSG00000147044.23" ; exon_id "ENSE00001476451.3" ; exon_number 1 ; gene_id "CASK--BANF2^CASK^ENSG00000147044.23" ; gene_name CASK ; gene_type protein_coding ; havana_gene "OTTHUMG00000021378.10" ; havana_transcript "OTTHUMT00000056279.3" ; hgnc_id "HGNC:1497" ; level 2 ; orig_coord_info "chrX,41922930,41922988,-" ; protein_id "ENSP00000367396.2" ; tag not_organism_supported basic ; transcript_id "CASK--BANF2^ENST00000378154.3" ; transcript_name "CASK-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: CASK--RRBP1 ENSEMBL gene 57004 79275 . + . FI_gene_label "RRBP1^ENSG00000125844.16" ; ID "CASK--RRBP1^RRBP1^ENSG00000125844.16" ; exon_id "ENSE00000859255.1" ; exon_number 1 ; gene_id "CASK--RRBP1^RRBP1^ENSG00000125844.16" ; gene_name RRBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031945.13" ; hgnc_id "HGNC:10448" ; level 3 ; orig_coord_info "chr20,17658596,17660507,-" ; protein_id "ENSP00000246043.4" ; tag basic appris_principal_2 ; transcript_id "CASK--RRBP1^ENST00000246043.8" ; transcript_name "RRBP1-201" ; transcript_support_level 1 ; transcript_type protein_coding CASK--RRBP1 ENSEMBL mRNA 57004 79275 . + . FI_gene_label "RRBP1^ENSG00000125844.16" ; ID "CASK--RRBP1^ENST00000246043.8" ; Parent "CASK--RRBP1^RRBP1^ENSG00000125844.16" ; exon_id "ENSE00000859255.1" ; exon_number 1 ; gene_id "CASK--RRBP1^RRBP1^ENSG00000125844.16" ; gene_name RRBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031945.13" ; hgnc_id "HGNC:10448" ; level 3 ; orig_coord_info "chr20,17658596,17660507,-" ; protein_id "ENSP00000246043.4" ; tag basic appris_principal_2 ; transcript_id "CASK--RRBP1^ENST00000246043.8" ; transcript_name "RRBP1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CASK--RRBP1 HAVANA gene 1126 47017 . + . FI_gene_label "CASK^ENSG00000147044.23" ; ID "CASK--RRBP1^CASK^ENSG00000147044.23" ; exon_id "ENSE00001476451.3" ; exon_number 1 ; gene_id "CASK--RRBP1^CASK^ENSG00000147044.23" ; gene_name CASK ; gene_type protein_coding ; havana_gene "OTTHUMG00000021378.10" ; havana_transcript "OTTHUMT00000056279.3" ; hgnc_id "HGNC:1497" ; level 2 ; orig_coord_info "chrX,41922930,41922988,-" ; protein_id "ENSP00000367396.2" ; tag not_organism_supported basic ; transcript_id "CASK--RRBP1^ENST00000378154.3" ; transcript_name "CASK-201" ; transcript_support_level 5 ; transcript_type protein_coding CASK--RRBP1 HAVANA mRNA 1126 47017 . + . FI_gene_label "CASK^ENSG00000147044.23" ; ID "CASK--RRBP1^ENST00000378154.3" ; Parent "CASK--RRBP1^CASK^ENSG00000147044.23" ; exon_id "ENSE00001476451.3" ; exon_number 1 ; gene_id "CASK--RRBP1^CASK^ENSG00000147044.23" ; gene_name CASK ; gene_type protein_coding ; havana_gene "OTTHUMG00000021378.10" ; havana_transcript "OTTHUMT00000056279.3" ; hgnc_id "HGNC:1497" ; level 2 ; orig_coord_info "chrX,41922930,41922988,-" ; protein_id "ENSP00000367396.2" ; tag not_organism_supported basic ; transcript_id "CASK--RRBP1^ENST00000378154.3" ; transcript_name "CASK-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: GRHL2--NCALD HAVANA gene 36944 52553 . + . FI_gene_label "NCALD^ENSG00000104490.18" ; ID "GRHL2--NCALD^NCALD^ENSG00000104490.18" ; ccdsid "CCDS6292.1" ; exon_id "ENSE00001161961.1" ; exon_number 2 ; gene_id "GRHL2--NCALD^NCALD^ENSG00000104490.18" ; gene_name NCALD ; gene_type protein_coding ; havana_gene "OTTHUMG00000164876.8" ; havana_transcript "OTTHUMT00000380727.2" ; hgnc_id "HGNC:7655" ; level 2 ; orig_coord_info "chr8,101719252,101719629,-" ; protein_id "ENSP00000220931.6" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRHL2--NCALD^ENST00000220931.11" ; transcript_name "NCALD-201" ; transcript_support_level 1 ; transcript_type protein_coding GRHL2--NCALD HAVANA mRNA 36944 52553 . + . FI_gene_label "NCALD^ENSG00000104490.18" ; ID "GRHL2--NCALD^ENST00000220931.11" ; Parent "GRHL2--NCALD^NCALD^ENSG00000104490.18" ; ccdsid "CCDS6292.1" ; exon_id "ENSE00001161961.1" ; exon_number 2 ; gene_id "GRHL2--NCALD^NCALD^ENSG00000104490.18" ; gene_name NCALD ; gene_type protein_coding ; havana_gene "OTTHUMG00000164876.8" ; havana_transcript "OTTHUMT00000380727.2" ; hgnc_id "HGNC:7655" ; level 2 ; orig_coord_info "chr8,101719252,101719629,-" ; protein_id "ENSP00000220931.6" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRHL2--NCALD^ENST00000220931.11" ; transcript_name "NCALD-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GRHL2--NCALD HAVANA gene 1320 18721 . + . FI_gene_label "GRHL2^ENSG00000083307.12" ; ID "GRHL2--NCALD^GRHL2^ENSG00000083307.12" ; ccdsid "CCDS83312.1" ; exon_id "ENSE00003671771.1" ; exon_number 2 ; gene_id "GRHL2--NCALD^GRHL2^ENSG00000083307.12" ; gene_name GRHL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149915.5" ; havana_transcript "OTTHUMT00000313883.1" ; hgnc_id "HGNC:2799" ; level 2 ; orig_coord_info "chr8,101543269,101543436,+" ; protein_id "ENSP00000379260.1" ; tag basic CCDS ; transcript_id "GRHL2--NCALD^ENST00000395927.1" ; transcript_name "GRHL2-201" ; transcript_support_level 2 ; transcript_type protein_coding GRHL2--NCALD HAVANA mRNA 1320 18721 . + . FI_gene_label "GRHL2^ENSG00000083307.12" ; ID "GRHL2--NCALD^ENST00000395927.1" ; Parent "GRHL2--NCALD^GRHL2^ENSG00000083307.12" ; ccdsid "CCDS83312.1" ; exon_id "ENSE00003671771.1" ; exon_number 2 ; gene_id "GRHL2--NCALD^GRHL2^ENSG00000083307.12" ; gene_name GRHL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149915.5" ; havana_transcript "OTTHUMT00000313883.1" ; hgnc_id "HGNC:2799" ; level 2 ; orig_coord_info "chr8,101543269,101543436,+" ; protein_id "ENSP00000379260.1" ; tag basic CCDS ; transcript_id "GRHL2--NCALD^ENST00000395927.1" ; transcript_name "GRHL2-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHA13 HAVANA gene 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA3--PCDHA13 HAVANA mRNA 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^ENST00000289272.3" ; Parent "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHA13 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA3--PCDHA13 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^ENST00000532566.3" ; Parent "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHAC1 HAVANA gene 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA3--PCDHAC1 HAVANA mRNA 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHAC1 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA3--PCDHAC1 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHAC2 HAVANA gene 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA3--PCDHAC2 HAVANA mRNA 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA3--PCDHAC2 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA3--PCDHAC2 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: SNX16--TRPS1 HAVANA gene 18595 35247 . + . FI_gene_label "TRPS1^ENSG00000104447.13" ; ID "SNX16--TRPS1^TRPS1^ENSG00000104447.13" ; ccdsid "CCDS83316.1" ; exon_id "ENSE00003549754.1" ; exon_number 2 ; gene_id "SNX16--TRPS1^TRPS1^ENSG00000104447.13" ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6" ; havana_transcript "OTTHUMT00000286436.3" ; hgnc_id "HGNC:12340" ; level 2 ; orig_coord_info "chr8,115619132,115620058,-" ; protein_id "ENSP00000220888.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "SNX16--TRPS1^ENST00000220888.9" ; transcript_name "TRPS1-201" ; transcript_support_level 1 ; transcript_type protein_coding SNX16--TRPS1 HAVANA mRNA 18595 35247 . + . FI_gene_label "TRPS1^ENSG00000104447.13" ; ID "SNX16--TRPS1^ENST00000220888.9" ; Parent "SNX16--TRPS1^TRPS1^ENSG00000104447.13" ; ccdsid "CCDS83316.1" ; exon_id "ENSE00003549754.1" ; exon_number 2 ; gene_id "SNX16--TRPS1^TRPS1^ENSG00000104447.13" ; gene_name TRPS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142829.6" ; havana_transcript "OTTHUMT00000286436.3" ; hgnc_id "HGNC:12340" ; level 2 ; orig_coord_info "chr8,115619132,115620058,-" ; protein_id "ENSP00000220888.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "SNX16--TRPS1^ENST00000220888.9" ; transcript_name "TRPS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SNX16--TRPS1 HAVANA gene 1682 12633 . + . FI_gene_label "SNX16^ENSG00000104497.14" ; ID "SNX16--TRPS1^SNX16^ENSG00000104497.14" ; ccdsid "CCDS6234.1" ; exon_id "ENSE00001211854.1" ; exon_number 2 ; gene_id "SNX16--TRPS1^SNX16^ENSG00000104497.14" ; gene_name SNX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164727.5" ; havana_transcript "OTTHUMT00000379929.2" ; hgnc_id "HGNC:14980" ; level 2 ; orig_coord_info "chr8,81839612,81839986,-" ; protein_id "ENSP00000322652.4" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SNX16--TRPS1^ENST00000345957.9" ; transcript_name "SNX16-201" ; transcript_support_level 1 ; transcript_type protein_coding SNX16--TRPS1 HAVANA mRNA 1682 12633 . + . FI_gene_label "SNX16^ENSG00000104497.14" ; ID "SNX16--TRPS1^ENST00000345957.9" ; Parent "SNX16--TRPS1^SNX16^ENSG00000104497.14" ; ccdsid "CCDS6234.1" ; exon_id "ENSE00001211854.1" ; exon_number 2 ; gene_id "SNX16--TRPS1^SNX16^ENSG00000104497.14" ; gene_name SNX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164727.5" ; havana_transcript "OTTHUMT00000379929.2" ; hgnc_id "HGNC:14980" ; level 2 ; orig_coord_info "chr8,81839612,81839986,-" ; protein_id "ENSP00000322652.4" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SNX16--TRPS1^ENST00000345957.9" ; transcript_name "SNX16-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SSH2--AC022816.1 HAVANA gene 1125 32617 . + . FI_gene_label "SSH2^ENSG00000141298.19" ; ID "SSH2--AC022816.1^SSH2^ENSG00000141298.19" ; ccdsid "CCDS11253.1" ; exon_id "ENSE00001878927.1" ; exon_number 1 ; gene_id "SSH2--AC022816.1^SSH2^ENSG00000141298.19" ; gene_name SSH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132752.8" ; havana_transcript "OTTHUMT00000256116.1" ; hgnc_id "HGNC:30580" ; level 2 ; orig_coord_info "chr17,29929938,29930000,-" ; protein_id "ENSP00000269033.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SSH2--AC022816.1^ENST00000269033.7" ; transcript_name "SSH2-201" ; transcript_support_level 1 ; transcript_type protein_coding SSH2--AC022816.1 HAVANA mRNA 1125 32617 . + . FI_gene_label "SSH2^ENSG00000141298.19" ; ID "SSH2--AC022816.1^ENST00000269033.7" ; Parent "SSH2--AC022816.1^SSH2^ENSG00000141298.19" ; ccdsid "CCDS11253.1" ; exon_id "ENSE00001878927.1" ; exon_number 1 ; gene_id "SSH2--AC022816.1^SSH2^ENSG00000141298.19" ; gene_name SSH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132752.8" ; havana_transcript "OTTHUMT00000256116.1" ; hgnc_id "HGNC:30580" ; level 2 ; orig_coord_info "chr17,29929938,29930000,-" ; protein_id "ENSP00000269033.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SSH2--AC022816.1^ENST00000269033.7" ; transcript_name "SSH2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SSH2--RPS18P12 HAVANA gene 1125 32617 . + . FI_gene_label "SSH2^ENSG00000141298.19" ; ID "SSH2--RPS18P12^SSH2^ENSG00000141298.19" ; ccdsid "CCDS11253.1" ; exon_id "ENSE00001878927.1" ; exon_number 1 ; gene_id "SSH2--RPS18P12^SSH2^ENSG00000141298.19" ; gene_name SSH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132752.8" ; havana_transcript "OTTHUMT00000256116.1" ; hgnc_id "HGNC:30580" ; level 2 ; orig_coord_info "chr17,29929938,29930000,-" ; protein_id "ENSP00000269033.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SSH2--RPS18P12^ENST00000269033.7" ; transcript_name "SSH2-201" ; transcript_support_level 1 ; transcript_type protein_coding SSH2--RPS18P12 HAVANA mRNA 1125 32617 . + . FI_gene_label "SSH2^ENSG00000141298.19" ; ID "SSH2--RPS18P12^ENST00000269033.7" ; Parent "SSH2--RPS18P12^SSH2^ENSG00000141298.19" ; ccdsid "CCDS11253.1" ; exon_id "ENSE00001878927.1" ; exon_number 1 ; gene_id "SSH2--RPS18P12^SSH2^ENSG00000141298.19" ; gene_name SSH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132752.8" ; havana_transcript "OTTHUMT00000256116.1" ; hgnc_id "HGNC:30580" ; level 2 ; orig_coord_info "chr17,29929938,29930000,-" ; protein_id "ENSP00000269033.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SSH2--RPS18P12^ENST00000269033.7" ; transcript_name "SSH2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: 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: ZNF703--MTSS1 HAVANA gene 8439 31975 . + . FI_gene_label "MTSS1^ENSG00000170873.19" ; ID "ZNF703--MTSS1^MTSS1^ENSG00000170873.19" ; ccdsid "CCDS64969.1" ; exon_id "ENSE00002313690.1" ; exon_number 1 ; gene_id "ZNF703--MTSS1^MTSS1^ENSG00000170873.19" ; gene_name MTSS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048189.5" ; havana_transcript "OTTHUMT00000381615.1" ; hgnc_id "HGNC:20443" ; level 2 ; orig_coord_info "chr8,124727884,124727955,-" ; protein_id "ENSP00000322804.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "ZNF703--MTSS1^ENST00000325064.9" ; transcript_name "MTSS1-201" ; transcript_support_level 2 ; transcript_type protein_coding ZNF703--MTSS1 HAVANA mRNA 8439 31975 . + . FI_gene_label "MTSS1^ENSG00000170873.19" ; ID "ZNF703--MTSS1^ENST00000325064.9" ; Parent "ZNF703--MTSS1^MTSS1^ENSG00000170873.19" ; ccdsid "CCDS64969.1" ; exon_id "ENSE00002313690.1" ; exon_number 1 ; gene_id "ZNF703--MTSS1^MTSS1^ENSG00000170873.19" ; gene_name MTSS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048189.5" ; havana_transcript "OTTHUMT00000381615.1" ; hgnc_id "HGNC:20443" ; level 2 ; orig_coord_info "chr8,124727884,124727955,-" ; protein_id "ENSP00000322804.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "ZNF703--MTSS1^ENST00000325064.9" ; transcript_name "MTSS1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: ZNF703--MTSS1 HAVANA gene 1001 5238 . + . FI_gene_label "ZNF703^ENSG00000183779.7" ; ID "ZNF703--MTSS1^ZNF703^ENSG00000183779.7" ; ccdsid "CCDS6094.1" ; exon_id "ENSE00002102574.2" ; exon_number 1 ; gene_id "ZNF703--MTSS1^ZNF703^ENSG00000183779.7" ; gene_name ZNF703 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164001.4" ; havana_transcript "OTTHUMT00000376683.4" ; hgnc_id "HGNC:25883" ; level 2 ; orig_coord_info "chr8,37695980,37696222,+" ; protein_id "ENSP00000332325.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF703--MTSS1^ENST00000331569.6" ; transcript_name "ZNF703-201" ; transcript_support_level 1 ; transcript_type protein_coding ZNF703--MTSS1 HAVANA mRNA 1001 5238 . + . FI_gene_label "ZNF703^ENSG00000183779.7" ; ID "ZNF703--MTSS1^ENST00000331569.6" ; Parent "ZNF703--MTSS1^ZNF703^ENSG00000183779.7" ; ccdsid "CCDS6094.1" ; exon_id "ENSE00002102574.2" ; exon_number 1 ; gene_id "ZNF703--MTSS1^ZNF703^ENSG00000183779.7" ; gene_name ZNF703 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164001.4" ; havana_transcript "OTTHUMT00000376683.4" ; hgnc_id "HGNC:25883" ; level 2 ; orig_coord_info "chr8,37695980,37696222,+" ; protein_id "ENSP00000332325.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF703--MTSS1^ENST00000331569.6" ; transcript_name "ZNF703-201" ; 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: SSH2--AC022816.1 HAVANA gene 35618 40421 . + . FI_gene_label "AC022816.1^ENSG00000230647.2" ; ID "SSH2--AC022816.1^AC022816.1^ENSG00000230647.2" ; exon_id "ENSE00001720153.1" ; exon_number 1 ; gene_id "SSH2--AC022816.1^AC022816.1^ENSG00000230647.2" ; gene_name "AC022816.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000058811.2" ; havana_transcript "OTTHUMT00000130000.1" ; level 2 ; orig_coord_info "chr17,14374139,14374228,+" ; tag dotter_confirmed low_sequence_quality basic ; transcript_id "SSH2--AC022816.1^ENST00000436469.1" ; transcript_name "AC022816.1-201" ; transcript_support_level 5 ; transcript_type lncRNA SSH2--AC022816.1 HAVANA RNA 35618 40421 . + . FI_gene_label "AC022816.1^ENSG00000230647.2" ; ID "SSH2--AC022816.1^ENST00000436469.1" ; Parent "SSH2--AC022816.1^AC022816.1^ENSG00000230647.2" ; exon_id "ENSE00001720153.1" ; exon_number 1 ; gene_id "SSH2--AC022816.1^AC022816.1^ENSG00000230647.2" ; gene_name "AC022816.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000058811.2" ; havana_transcript "OTTHUMT00000130000.1" ; level 2 ; orig_coord_info "chr17,14374139,14374228,+" ; tag dotter_confirmed low_sequence_quality basic ; transcript_id "SSH2--AC022816.1^ENST00000436469.1" ; transcript_name "AC022816.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: SSH2--RPS18P12 HAVANA gene 35618 36076 . + . FI_gene_label "RPS18P12^ENSG00000230897.1" ; ID "SSH2--RPS18P12^RPS18P12^ENSG00000230897.1" ; exon_id "ENSE00002342387.1" ; exon_number 1 ; gene_id "SSH2--RPS18P12^RPS18P12^ENSG00000230897.1" ; gene_name RPS18P12 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000058815.1" ; havana_transcript "OTTHUMT00000130005.1" ; hgnc_id "HGNC:35967" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,14705076,14705534,-" ; tag pseudo_consens basic ; transcript_id "SSH2--RPS18P12^ENST00000412454.1" ; transcript_name "RPS18P12-201" ; transcript_support_level NA ; transcript_type processed_pseudogene SSH2--RPS18P12 HAVANA RNA 35618 36076 . + . FI_gene_label "RPS18P12^ENSG00000230897.1" ; ID "SSH2--RPS18P12^ENST00000412454.1" ; Parent "SSH2--RPS18P12^RPS18P12^ENSG00000230897.1" ; exon_id "ENSE00002342387.1" ; exon_number 1 ; gene_id "SSH2--RPS18P12^RPS18P12^ENSG00000230897.1" ; gene_name RPS18P12 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000058815.1" ; havana_transcript "OTTHUMT00000130005.1" ; hgnc_id "HGNC:35967" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,14705076,14705534,-" ; tag pseudo_consens basic ; transcript_id "SSH2--RPS18P12^ENST00000412454.1" ; transcript_name "RPS18P12-201" ; transcript_support_level NA ; transcript_type processed_pseudogene 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 265 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 ------------------------------ 521 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 1 seconds ------------------------------- ------------------------ Check12: all level1 locations ------------------------- We fixed 20 wrong level1 location cases ------------------------------ done in 0 seconds ------------------------------- ---------------------- Check13: remove identical isoforms ---------------------- None found ------------------------------ done in 0 seconds ------------------------------- ------ End checks (done in 1 second) ------ GFF3 file parsed