Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/76dd605bcd62419e3e8a053208398e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/e55b734f6a6e40466a487c11627498/fi_workdir/tih_rna_sample_00572_B23MVV7LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/76dd605bcd62419e3e8a053208398e/.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: 1697 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 1697 => 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:1697 => 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: AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding 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: C1QTNF3--AMACR HAVANA gene 1001 8952 . + . FI_gene_label "C1QTNF3^ENSG00000082196.21" ; ID "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21" ; ccdsid "CCDS3904.1" ; exon_id "ENSE00001898423.1" ; exon_number 1 ; gene_id "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21" ; gene_name C1QTNF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090735.5" ; havana_transcript "OTTHUMT00000207469.1" ; hgnc_id "HGNC:14326" ; level 2 ; orig_coord_info "chr5,34043042,34043125,-" ; protein_id "ENSP00000231338.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000231338.7" ; transcript_name "C1QTNF3-201" ; transcript_support_level 1 ; transcript_type protein_coding C1QTNF3--AMACR HAVANA mRNA 1001 8952 . + . FI_gene_label "C1QTNF3^ENSG00000082196.21" ; ID "C1QTNF3--AMACR^ENST00000231338.7" ; Parent "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21" ; ccdsid "CCDS3904.1" ; exon_id "ENSE00001898423.1" ; exon_number 1 ; gene_id "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21" ; gene_name C1QTNF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090735.5" ; havana_transcript "OTTHUMT00000207469.1" ; hgnc_id "HGNC:14326" ; level 2 ; orig_coord_info "chr5,34043042,34043125,-" ; protein_id "ENSP00000231338.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000231338.7" ; transcript_name "C1QTNF3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: C1QTNF3--AMACR HAVANA gene 13602 24394 . + . FI_gene_label "AMACR^ENSG00000242110.8" ; ID "C1QTNF3--AMACR^AMACR^ENSG00000242110.8" ; ccdsid "CCDS3902.1" ; exon_id "ENSE00001953485.2" ; exon_number 1 ; gene_id "C1QTNF3--AMACR^AMACR^ENSG00000242110.8" ; gene_name AMACR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090734.3" ; havana_transcript "OTTHUMT00000207467.2" ; hgnc_id "HGNC:451" ; level 2 ; orig_coord_info "chr5,34007773,34008019,-" ; protein_id "ENSP00000334424.6" ; tag basic MANE_Select CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000335606.11" ; transcript_name "AMACR-201" ; transcript_support_level 1 ; transcript_type protein_coding C1QTNF3--AMACR HAVANA mRNA 13602 24394 . + . FI_gene_label "AMACR^ENSG00000242110.8" ; ID "C1QTNF3--AMACR^ENST00000335606.11" ; Parent "C1QTNF3--AMACR^AMACR^ENSG00000242110.8" ; ccdsid "CCDS3902.1" ; exon_id "ENSE00001953485.2" ; exon_number 1 ; gene_id "C1QTNF3--AMACR^AMACR^ENSG00000242110.8" ; gene_name AMACR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090734.3" ; havana_transcript "OTTHUMT00000207467.2" ; hgnc_id "HGNC:451" ; level 2 ; orig_coord_info "chr5,34007773,34008019,-" ; protein_id "ENSP00000334424.6" ; tag basic MANE_Select CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000335606.11" ; transcript_name "AMACR-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: LYSMD4--AC084855.1 ENSEMBL gene 1118 6720 . + . FI_gene_label "LYSMD4^ENSG00000183060.15" ; ID "LYSMD4--AC084855.1^LYSMD4^ENSG00000183060.15" ; ccdsid "CCDS66876.1" ; exon_id "ENSE00003628427.2" ; exon_number 5 ; gene_id "LYSMD4--AC084855.1^LYSMD4^ENSG00000183060.15" ; gene_name LYSMD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149853.5" ; hgnc_id "HGNC:26571" ; level 3 ; orig_coord_info "chr15,99729126,99729635,-" ; protein_id "ENSP00000333008.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "LYSMD4--AC084855.1^ENST00000332728.8" ; transcript_name "LYSMD4-201" ; transcript_support_level 4 ; transcript_type protein_coding LYSMD4--AC084855.1 ENSEMBL mRNA 1118 6720 . + . FI_gene_label "LYSMD4^ENSG00000183060.15" ; ID "LYSMD4--AC084855.1^ENST00000332728.8" ; Parent "LYSMD4--AC084855.1^LYSMD4^ENSG00000183060.15" ; ccdsid "CCDS66876.1" ; exon_id "ENSE00003628427.2" ; exon_number 5 ; gene_id "LYSMD4--AC084855.1^LYSMD4^ENSG00000183060.15" ; gene_name LYSMD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149853.5" ; hgnc_id "HGNC:26571" ; level 3 ; orig_coord_info "chr15,99729126,99729635,-" ; protein_id "ENSP00000333008.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "LYSMD4--AC084855.1^ENST00000332728.8" ; transcript_name "LYSMD4-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: LYSMD4--AC090825.1 ENSEMBL gene 1118 6720 . + . FI_gene_label "LYSMD4^ENSG00000183060.15" ; ID "LYSMD4--AC090825.1^LYSMD4^ENSG00000183060.15" ; ccdsid "CCDS66876.1" ; exon_id "ENSE00003628427.2" ; exon_number 5 ; gene_id "LYSMD4--AC090825.1^LYSMD4^ENSG00000183060.15" ; gene_name LYSMD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149853.5" ; hgnc_id "HGNC:26571" ; level 3 ; orig_coord_info "chr15,99729126,99729635,-" ; protein_id "ENSP00000333008.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "LYSMD4--AC090825.1^ENST00000332728.8" ; transcript_name "LYSMD4-201" ; transcript_support_level 4 ; transcript_type protein_coding LYSMD4--AC090825.1 ENSEMBL mRNA 1118 6720 . + . FI_gene_label "LYSMD4^ENSG00000183060.15" ; ID "LYSMD4--AC090825.1^ENST00000332728.8" ; Parent "LYSMD4--AC090825.1^LYSMD4^ENSG00000183060.15" ; ccdsid "CCDS66876.1" ; exon_id "ENSE00003628427.2" ; exon_number 5 ; gene_id "LYSMD4--AC090825.1^LYSMD4^ENSG00000183060.15" ; gene_name LYSMD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149853.5" ; hgnc_id "HGNC:26571" ; level 3 ; orig_coord_info "chr15,99729126,99729635,-" ; protein_id "ENSP00000333008.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "LYSMD4--AC090825.1^ENST00000332728.8" ; transcript_name "LYSMD4-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: NOTCH2--AL157904.1 HAVANA gene 8089 55985 . + . FI_gene_label "NOTCH2^ENSG00000134250.20" ; ID "NOTCH2--AL157904.1^NOTCH2^ENSG00000134250.20" ; ccdsid "CCDS908.1" ; exon_id "ENSE00003518443.2" ; exon_number 1 ; gene_id "NOTCH2--AL157904.1^NOTCH2^ENSG00000134250.20" ; gene_name NOTCH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012177.8" ; havana_transcript "OTTHUMT00000033679.3" ; hgnc_id "HGNC:7882" ; level 2 ; orig_coord_info "chr1,120069334,120069406,-" ; protein_id "ENSP00000256646.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOTCH2--AL157904.1^ENST00000256646.7" ; transcript_name "NOTCH2-201" ; transcript_support_level 1 ; transcript_type protein_coding NOTCH2--AL157904.1 HAVANA mRNA 8089 55985 . + . FI_gene_label "NOTCH2^ENSG00000134250.20" ; ID "NOTCH2--AL157904.1^ENST00000256646.7" ; Parent "NOTCH2--AL157904.1^NOTCH2^ENSG00000134250.20" ; ccdsid "CCDS908.1" ; exon_id "ENSE00003518443.2" ; exon_number 1 ; gene_id "NOTCH2--AL157904.1^NOTCH2^ENSG00000134250.20" ; gene_name NOTCH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012177.8" ; havana_transcript "OTTHUMT00000033679.3" ; hgnc_id "HGNC:7882" ; level 2 ; orig_coord_info "chr1,120069334,120069406,-" ; protein_id "ENSP00000256646.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOTCH2--AL157904.1^ENST00000256646.7" ; transcript_name "NOTCH2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NOTCH2--FTH1P22 HAVANA gene 8089 55985 . + . FI_gene_label "NOTCH2^ENSG00000134250.20" ; ID "NOTCH2--FTH1P22^NOTCH2^ENSG00000134250.20" ; ccdsid "CCDS908.1" ; exon_id "ENSE00003518443.2" ; exon_number 1 ; gene_id "NOTCH2--FTH1P22^NOTCH2^ENSG00000134250.20" ; gene_name NOTCH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012177.8" ; havana_transcript "OTTHUMT00000033679.3" ; hgnc_id "HGNC:7882" ; level 2 ; orig_coord_info "chr1,120069334,120069406,-" ; protein_id "ENSP00000256646.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOTCH2--FTH1P22^ENST00000256646.7" ; transcript_name "NOTCH2-201" ; transcript_support_level 1 ; transcript_type protein_coding NOTCH2--FTH1P22 HAVANA mRNA 8089 55985 . + . FI_gene_label "NOTCH2^ENSG00000134250.20" ; ID "NOTCH2--FTH1P22^ENST00000256646.7" ; Parent "NOTCH2--FTH1P22^NOTCH2^ENSG00000134250.20" ; ccdsid "CCDS908.1" ; exon_id "ENSE00003518443.2" ; exon_number 1 ; gene_id "NOTCH2--FTH1P22^NOTCH2^ENSG00000134250.20" ; gene_name NOTCH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012177.8" ; havana_transcript "OTTHUMT00000033679.3" ; hgnc_id "HGNC:7882" ; level 2 ; orig_coord_info "chr1,120069334,120069406,-" ; protein_id "ENSP00000256646.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOTCH2--FTH1P22^ENST00000256646.7" ; transcript_name "NOTCH2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PARG--BMS1 HAVANA gene 27761 52028 . + . FI_gene_label "BMS1^ENSG00000165733.8" ; ID "PARG--BMS1^BMS1^ENSG00000165733.8" ; ccdsid "CCDS7199.1" ; exon_id "ENSE00002486183.1" ; exon_number 2 ; gene_id "PARG--BMS1^BMS1^ENSG00000165733.8" ; gene_name BMS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018020.3" ; havana_transcript "OTTHUMT00000047690.3" ; hgnc_id "HGNC:23505" ; level 2 ; orig_coord_info "chr10,42784395,42784570,+" ; protein_id "ENSP00000363642.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PARG--BMS1^ENST00000374518.6" ; transcript_name "BMS1-201" ; transcript_support_level 1 ; transcript_type protein_coding PARG--BMS1 HAVANA mRNA 27761 52028 . + . FI_gene_label "BMS1^ENSG00000165733.8" ; ID "PARG--BMS1^ENST00000374518.6" ; Parent "PARG--BMS1^BMS1^ENSG00000165733.8" ; ccdsid "CCDS7199.1" ; exon_id "ENSE00002486183.1" ; exon_number 2 ; gene_id "PARG--BMS1^BMS1^ENSG00000165733.8" ; gene_name BMS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018020.3" ; havana_transcript "OTTHUMT00000047690.3" ; hgnc_id "HGNC:23505" ; level 2 ; orig_coord_info "chr10,42784395,42784570,+" ; protein_id "ENSP00000363642.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PARG--BMS1^ENST00000374518.6" ; transcript_name "BMS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PARG--BMS1 HAVANA gene 1001 24760 . + . FI_gene_label "PARG^ENSG00000227345.9" ; ID "PARG--BMS1^PARG^ENSG00000227345.9" ; ccdsid "CCDS73130.1" ; exon_id "ENSE00003720657.1" ; exon_number 2 ; gene_id "PARG--BMS1^PARG^ENSG00000227345.9" ; gene_name PARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000018201.3" ; havana_transcript "OTTHUMT00000048011.3" ; hgnc_id "HGNC:8605" ; level 2 ; orig_coord_info "chr10,49941509,49941725,-" ; protein_id "ENSP00000384408.3" ; tag basic appris_principal_1 CCDS ; transcript_id "PARG--BMS1^ENST00000402038.7" ; transcript_name "PARG-201" ; transcript_support_level 1 ; transcript_type protein_coding PARG--BMS1 HAVANA mRNA 1001 24760 . + . FI_gene_label "PARG^ENSG00000227345.9" ; ID "PARG--BMS1^ENST00000402038.7" ; Parent "PARG--BMS1^PARG^ENSG00000227345.9" ; ccdsid "CCDS73130.1" ; exon_id "ENSE00003720657.1" ; exon_number 2 ; gene_id "PARG--BMS1^PARG^ENSG00000227345.9" ; gene_name PARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000018201.3" ; havana_transcript "OTTHUMT00000048011.3" ; hgnc_id "HGNC:8605" ; level 2 ; orig_coord_info "chr10,49941509,49941725,-" ; protein_id "ENSP00000384408.3" ; tag basic appris_principal_1 CCDS ; transcript_id "PARG--BMS1^ENST00000402038.7" ; transcript_name "PARG-201" ; transcript_support_level 1 ; 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: 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: AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA 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: LYSMD4--AC084855.1 HAVANA gene 14032 16495 . + . FI_gene_label "AC084855.1^ENSG00000254744.3" ; ID "LYSMD4--AC084855.1^AC084855.1^ENSG00000254744.3" ; exon_id "ENSE00002157584.2" ; exon_number 1 ; gene_id "LYSMD4--AC084855.1^AC084855.1^ENSG00000254744.3" ; gene_name "AC084855.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165445.4" ; havana_transcript "OTTHUMT00000384139.3" ; level 2 ; orig_coord_info "chr15,99970215,99970355,+" ; tag basic ; transcript_id "LYSMD4--AC084855.1^ENST00000528696.3" ; transcript_name "AC084855.1-201" ; transcript_support_level 2 ; transcript_type lncRNA LYSMD4--AC084855.1 HAVANA RNA 14032 16495 . + . FI_gene_label "AC084855.1^ENSG00000254744.3" ; ID "LYSMD4--AC084855.1^ENST00000528696.3" ; Parent "LYSMD4--AC084855.1^AC084855.1^ENSG00000254744.3" ; exon_id "ENSE00002157584.2" ; exon_number 1 ; gene_id "LYSMD4--AC084855.1^AC084855.1^ENSG00000254744.3" ; gene_name "AC084855.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165445.4" ; havana_transcript "OTTHUMT00000384139.3" ; level 2 ; orig_coord_info "chr15,99970215,99970355,+" ; tag basic ; transcript_id "LYSMD4--AC084855.1^ENST00000528696.3" ; transcript_name "AC084855.1-201" ; transcript_support_level 2 ; transcript_type lncRNA L1 and L2 created: LYSMD4--AC090825.1 HAVANA gene 16067 25108 . + . FI_gene_label "AC090825.1^ENSG00000259363.6" ; ID "LYSMD4--AC090825.1^AC090825.1^ENSG00000259363.6" ; exon_id "ENSE00003884497.1" ; exon_number 1 ; gene_id "LYSMD4--AC090825.1^AC090825.1^ENSG00000259363.6" ; gene_name "AC090825.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172118.19" ; havana_transcript "OTTHUMT00000520491.1" ; level 2 ; orig_coord_info "chr15,99807828,99808302,+" ; tag TAGENE ; transcript_id "LYSMD4--AC090825.1^ENST00000558188.2" ; transcript_name "AC090825.1-211" ; transcript_support_level 3 ; transcript_type lncRNA LYSMD4--AC090825.1 HAVANA RNA 16067 25108 . + . FI_gene_label "AC090825.1^ENSG00000259363.6" ; ID "LYSMD4--AC090825.1^ENST00000558188.2" ; Parent "LYSMD4--AC090825.1^AC090825.1^ENSG00000259363.6" ; exon_id "ENSE00003884497.1" ; exon_number 1 ; gene_id "LYSMD4--AC090825.1^AC090825.1^ENSG00000259363.6" ; gene_name "AC090825.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172118.19" ; havana_transcript "OTTHUMT00000520491.1" ; level 2 ; orig_coord_info "chr15,99807828,99808302,+" ; tag TAGENE ; transcript_id "LYSMD4--AC090825.1^ENST00000558188.2" ; transcript_name "AC090825.1-211" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: NOTCH2--AL157904.1 HAVANA gene 58986 59368 . + . FI_gene_label "AL157904.1^ENSG00000272715.1" ; ID "NOTCH2--AL157904.1^AL157904.1^ENSG00000272715.1" ; exon_id "ENSE00003705346.1" ; exon_number 1 ; gene_id "NOTCH2--AL157904.1^AL157904.1^ENSG00000272715.1" ; gene_name "AL157904.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186394.1" ; havana_transcript "OTTHUMT00000473087.1" ; level 2 ; orig_coord_info "chr1,116909149,116909531,-" ; tag basic ; transcript_id "NOTCH2--AL157904.1^ENST00000610171.1" ; transcript_name "AL157904.1-201" ; transcript_support_level NA ; transcript_type lncRNA NOTCH2--AL157904.1 HAVANA RNA 58986 59368 . + . FI_gene_label "AL157904.1^ENSG00000272715.1" ; ID "NOTCH2--AL157904.1^ENST00000610171.1" ; Parent "NOTCH2--AL157904.1^AL157904.1^ENSG00000272715.1" ; exon_id "ENSE00003705346.1" ; exon_number 1 ; gene_id "NOTCH2--AL157904.1^AL157904.1^ENSG00000272715.1" ; gene_name "AL157904.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186394.1" ; havana_transcript "OTTHUMT00000473087.1" ; level 2 ; orig_coord_info "chr1,116909149,116909531,-" ; tag basic ; transcript_id "NOTCH2--AL157904.1^ENST00000610171.1" ; transcript_name "AL157904.1-201" ; transcript_support_level NA ; transcript_type lncRNA L1 and L2 created: NOTCH2--FTH1P22 HAVANA gene 58986 59505 . + . FI_gene_label "FTH1P22^ENSG00000225079.2" ; ID "NOTCH2--FTH1P22^FTH1P22^ENSG00000225079.2" ; exon_id "ENSE00001679061.2" ; exon_number 1 ; gene_id "NOTCH2--FTH1P22^FTH1P22^ENSG00000225079.2" ; gene_name FTH1P22 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000022797.2" ; havana_transcript "OTTHUMT00000059114.2" ; hgnc_id "HGNC:37640" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,116775104,116775623,-" ; tag pseudo_consens basic ; transcript_id "NOTCH2--FTH1P22^ENST00000456305.2" ; transcript_name "FTH1P22-201" ; transcript_support_level NA ; transcript_type processed_pseudogene NOTCH2--FTH1P22 HAVANA RNA 58986 59505 . + . FI_gene_label "FTH1P22^ENSG00000225079.2" ; ID "NOTCH2--FTH1P22^ENST00000456305.2" ; Parent "NOTCH2--FTH1P22^FTH1P22^ENSG00000225079.2" ; exon_id "ENSE00001679061.2" ; exon_number 1 ; gene_id "NOTCH2--FTH1P22^FTH1P22^ENSG00000225079.2" ; gene_name FTH1P22 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000022797.2" ; havana_transcript "OTTHUMT00000059114.2" ; hgnc_id "HGNC:37640" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,116775104,116775623,-" ; tag pseudo_consens basic ; transcript_id "NOTCH2--FTH1P22^ENST00000456305.2" ; transcript_name "FTH1P22-201" ; 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 179 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 ------------------------------ 317 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 16 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