Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/0404fdfe47e04792b69dc790bda698/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/ead37e96e44133d7089b7e60be801c/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/0404fdfe47e04792b69dc790bda698/.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: 3298 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3298 => 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:3298 => 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: DTX2--PTPN12 HAVANA gene 23984 48846 . + . FI_gene_label "PTPN12^ENSG00000127947.16" ; ID "DTX2--PTPN12^PTPN12^ENSG00000127947.16" ; ccdsid "CCDS5592.1" ; exon_id "ENSE00001819992.2" ; exon_number 1 ; gene_id "DTX2--PTPN12^PTPN12^ENSG00000127947.16" ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10" ; havana_transcript "OTTHUMT00000253183.4" ; hgnc_id "HGNC:9645" ; level 2 ; orig_coord_info "chr7,77537547,77537645,+" ; protein_id "ENSP00000248594.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DTX2--PTPN12^ENST00000248594.11" ; transcript_name "PTPN12-201" ; transcript_support_level 1 ; transcript_type protein_coding DTX2--PTPN12 HAVANA mRNA 23984 48846 . + . FI_gene_label "PTPN12^ENSG00000127947.16" ; ID "DTX2--PTPN12^ENST00000248594.11" ; Parent "DTX2--PTPN12^PTPN12^ENSG00000127947.16" ; ccdsid "CCDS5592.1" ; exon_id "ENSE00001819992.2" ; exon_number 1 ; gene_id "DTX2--PTPN12^PTPN12^ENSG00000127947.16" ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10" ; havana_transcript "OTTHUMT00000253183.4" ; hgnc_id "HGNC:9645" ; level 2 ; orig_coord_info "chr7,77537547,77537645,+" ; protein_id "ENSP00000248594.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DTX2--PTPN12^ENST00000248594.11" ; transcript_name "PTPN12-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: DTX2--PTPN12 HAVANA gene 1026 20979 . + . FI_gene_label "DTX2^ENSG00000091073.19" ; ID "DTX2--PTPN12^DTX2^ENSG00000091073.19" ; ccdsid "CCDS5587.1" ; exon_id "ENSE00003639247.1" ; exon_number 4 ; gene_id "DTX2--PTPN12^DTX2^ENSG00000091073.19" ; gene_name DTX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162594.3" ; havana_transcript "OTTHUMT00000253104.2" ; hgnc_id "HGNC:15973" ; level 2 ; orig_coord_info "chr7,76480510,76480777,+" ; protein_id "ENSP00000322885.5" ; tag basic appris_principal_4 CCDS ; transcript_id "DTX2--PTPN12^ENST00000324432.9" ; transcript_name "DTX2-201" ; transcript_support_level 1 ; transcript_type protein_coding DTX2--PTPN12 HAVANA mRNA 1026 20979 . + . FI_gene_label "DTX2^ENSG00000091073.19" ; ID "DTX2--PTPN12^ENST00000324432.9" ; Parent "DTX2--PTPN12^DTX2^ENSG00000091073.19" ; ccdsid "CCDS5587.1" ; exon_id "ENSE00003639247.1" ; exon_number 4 ; gene_id "DTX2--PTPN12^DTX2^ENSG00000091073.19" ; gene_name DTX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162594.3" ; havana_transcript "OTTHUMT00000253104.2" ; hgnc_id "HGNC:15973" ; level 2 ; orig_coord_info "chr7,76480510,76480777,+" ; protein_id "ENSP00000322885.5" ; tag basic appris_principal_4 CCDS ; transcript_id "DTX2--PTPN12^ENST00000324432.9" ; transcript_name "DTX2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PTPN12--MAGI2 HAVANA gene 1001 25863 . + . FI_gene_label "PTPN12^ENSG00000127947.16" ; ID "PTPN12--MAGI2^PTPN12^ENSG00000127947.16" ; ccdsid "CCDS5592.1" ; exon_id "ENSE00001819992.2" ; exon_number 1 ; gene_id "PTPN12--MAGI2^PTPN12^ENSG00000127947.16" ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10" ; havana_transcript "OTTHUMT00000253183.4" ; hgnc_id "HGNC:9645" ; level 2 ; orig_coord_info "chr7,77537547,77537645,+" ; protein_id "ENSP00000248594.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000248594.11" ; transcript_name "PTPN12-201" ; transcript_support_level 1 ; transcript_type protein_coding PTPN12--MAGI2 HAVANA mRNA 1001 25863 . + . FI_gene_label "PTPN12^ENSG00000127947.16" ; ID "PTPN12--MAGI2^ENST00000248594.11" ; Parent "PTPN12--MAGI2^PTPN12^ENSG00000127947.16" ; ccdsid "CCDS5592.1" ; exon_id "ENSE00001819992.2" ; exon_number 1 ; gene_id "PTPN12--MAGI2^PTPN12^ENSG00000127947.16" ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10" ; havana_transcript "OTTHUMT00000253183.4" ; hgnc_id "HGNC:9645" ; level 2 ; orig_coord_info "chr7,77537547,77537645,+" ; protein_id "ENSP00000248594.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000248594.11" ; transcript_name "PTPN12-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PTPN12--MAGI2 HAVANA gene 28864 111262 . + . FI_gene_label "MAGI2^ENSG00000187391.22" ; ID "PTPN12--MAGI2^MAGI2^ENSG00000187391.22" ; ccdsid "CCDS5594.1" ; exon_id "ENSE00001597225.2" ; exon_number 1 ; gene_id "PTPN12--MAGI2^MAGI2^ENSG00000187391.22" ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19" ; havana_transcript "OTTHUMT00000253197.5" ; hgnc_id "HGNC:18957" ; level 2 ; orig_coord_info "chr7,79453020,79453320,-" ; protein_id "ENSP00000346151.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000354212.9" ; transcript_name "MAGI2-201" ; transcript_support_level 1 ; transcript_type protein_coding PTPN12--MAGI2 HAVANA mRNA 28864 111262 . + . FI_gene_label "MAGI2^ENSG00000187391.22" ; ID "PTPN12--MAGI2^ENST00000354212.9" ; Parent "PTPN12--MAGI2^MAGI2^ENSG00000187391.22" ; ccdsid "CCDS5594.1" ; exon_id "ENSE00001597225.2" ; exon_number 1 ; gene_id "PTPN12--MAGI2^MAGI2^ENSG00000187391.22" ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19" ; havana_transcript "OTTHUMT00000253197.5" ; hgnc_id "HGNC:18957" ; level 2 ; orig_coord_info "chr7,79453020,79453320,-" ; protein_id "ENSP00000346151.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000354212.9" ; transcript_name "MAGI2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SRRM1--CLIC4 HAVANA gene 5570 25576 . + . FI_gene_label "SRRM1^ENSG00000133226.17" ; ID "SRRM1--CLIC4^SRRM1^ENSG00000133226.17" ; ccdsid "CCDS255.1" ; exon_id "ENSE00002225700.3" ; exon_number 1 ; gene_id "SRRM1--CLIC4^SRRM1^ENSG00000133226.17" ; gene_name SRRM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003320.5" ; havana_transcript "OTTHUMT00000009292.3" ; hgnc_id "HGNC:16638" ; level 2 ; orig_coord_info "chr1,24643327,24643347,+" ; protein_id "ENSP00000326261.8" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000323848.14" ; transcript_name "SRRM1-201" ; transcript_support_level 1 ; transcript_type protein_coding SRRM1--CLIC4 HAVANA mRNA 5570 25576 . + . FI_gene_label "SRRM1^ENSG00000133226.17" ; ID "SRRM1--CLIC4^ENST00000323848.14" ; Parent "SRRM1--CLIC4^SRRM1^ENSG00000133226.17" ; ccdsid "CCDS255.1" ; exon_id "ENSE00002225700.3" ; exon_number 1 ; gene_id "SRRM1--CLIC4^SRRM1^ENSG00000133226.17" ; gene_name SRRM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003320.5" ; havana_transcript "OTTHUMT00000009292.3" ; hgnc_id "HGNC:16638" ; level 2 ; orig_coord_info "chr1,24643327,24643347,+" ; protein_id "ENSP00000326261.8" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000323848.14" ; transcript_name "SRRM1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SRRM1--CLIC4 HAVANA gene 28642 38774 . + . FI_gene_label "CLIC4^ENSG00000169504.15" ; ID "SRRM1--CLIC4^CLIC4^ENSG00000169504.15" ; ccdsid "CCDS256.1" ; exon_id "ENSE00001463371.4" ; exon_number 1 ; gene_id "SRRM1--CLIC4^CLIC4^ENSG00000169504.15" ; gene_name CLIC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003327.5" ; havana_transcript "OTTHUMT00000009332.2" ; hgnc_id "HGNC:13518" ; level 2 ; orig_coord_info "chr1,24745554,24745625,+" ; protein_id "ENSP00000363500.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000374379.9" ; transcript_name "CLIC4-201" ; transcript_support_level 1 ; transcript_type protein_coding SRRM1--CLIC4 HAVANA mRNA 28642 38774 . + . FI_gene_label "CLIC4^ENSG00000169504.15" ; ID "SRRM1--CLIC4^ENST00000374379.9" ; Parent "SRRM1--CLIC4^CLIC4^ENSG00000169504.15" ; ccdsid "CCDS256.1" ; exon_id "ENSE00001463371.4" ; exon_number 1 ; gene_id "SRRM1--CLIC4^CLIC4^ENSG00000169504.15" ; gene_name CLIC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003327.5" ; havana_transcript "OTTHUMT00000009332.2" ; hgnc_id "HGNC:13518" ; level 2 ; orig_coord_info "chr1,24745554,24745625,+" ; protein_id "ENSP00000363500.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000374379.9" ; transcript_name "CLIC4-201" ; 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: TOPORS--AL162725.2 HAVANA gene 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--AL162725.2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding TOPORS--AL162725.2 HAVANA mRNA 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--AL162725.2^ENST00000360538.7" ; Parent "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--AL162725.2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TOPORS--BNC2 HAVANA gene 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--BNC2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--BNC2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--BNC2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding TOPORS--BNC2 HAVANA mRNA 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--BNC2^ENST00000360538.7" ; Parent "TOPORS--BNC2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--BNC2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--BNC2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TOPORS--BNC2 HAVANA gene 11330 21161 . + . FI_gene_label "BNC2^ENSG00000173068.18" ; ID "TOPORS--BNC2^BNC2^ENSG00000173068.18" ; exon_id "ENSE00003666105.1" ; exon_number 2 ; gene_id "TOPORS--BNC2^BNC2^ENSG00000173068.18" ; gene_name BNC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019593.13" ; havana_transcript "OTTHUMT00000476395.2" ; hgnc_id "HGNC:30988" ; level 2 ; orig_coord_info "chr9,16727797,16727892,-" ; protein_id "ENSP00000370041.3" ; tag mRNA_end_NF cds_end_NF ; transcript_id "TOPORS--BNC2^ENST00000380666.6" ; transcript_name "BNC2-201" ; transcript_support_level 5 ; transcript_type protein_coding TOPORS--BNC2 HAVANA mRNA 11330 21161 . + . FI_gene_label "BNC2^ENSG00000173068.18" ; ID "TOPORS--BNC2^ENST00000380666.6" ; Parent "TOPORS--BNC2^BNC2^ENSG00000173068.18" ; exon_id "ENSE00003666105.1" ; exon_number 2 ; gene_id "TOPORS--BNC2^BNC2^ENSG00000173068.18" ; gene_name BNC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019593.13" ; havana_transcript "OTTHUMT00000476395.2" ; hgnc_id "HGNC:30988" ; level 2 ; orig_coord_info "chr9,16727797,16727892,-" ; protein_id "ENSP00000370041.3" ; tag mRNA_end_NF cds_end_NF ; transcript_id "TOPORS--BNC2^ENST00000380666.6" ; transcript_name "BNC2-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TOPORS--LINGO2 ENSEMBL gene 10133 20603 . + . FI_gene_label "LINGO2^ENSG00000174482.10" ; ID "TOPORS--LINGO2^LINGO2^ENSG00000174482.10" ; ccdsid "CCDS6524.1" ; exon_id "ENSE00001200037.5" ; exon_number 6 ; gene_id "TOPORS--LINGO2^LINGO2^ENSG00000174482.10" ; gene_name LINGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019721.2" ; hgnc_id "HGNC:21207" ; level 3 ; orig_coord_info "chr9,27948854,27950671,-" ; protein_id "ENSP00000310126.3" ; tag basic appris_principal_1 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000308675.5" ; transcript_name "LINGO2-201" ; transcript_support_level 5 ; transcript_type protein_coding TOPORS--LINGO2 ENSEMBL mRNA 10133 20603 . + . FI_gene_label "LINGO2^ENSG00000174482.10" ; ID "TOPORS--LINGO2^ENST00000308675.5" ; Parent "TOPORS--LINGO2^LINGO2^ENSG00000174482.10" ; ccdsid "CCDS6524.1" ; exon_id "ENSE00001200037.5" ; exon_number 6 ; gene_id "TOPORS--LINGO2^LINGO2^ENSG00000174482.10" ; gene_name LINGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019721.2" ; hgnc_id "HGNC:21207" ; level 3 ; orig_coord_info "chr9,27948854,27950671,-" ; protein_id "ENSP00000310126.3" ; tag basic appris_principal_1 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000308675.5" ; transcript_name "LINGO2-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TOPORS--LINGO2 HAVANA gene 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--LINGO2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--LINGO2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding TOPORS--LINGO2 HAVANA mRNA 1001 7131 . + . FI_gene_label "TOPORS^ENSG00000197579.8" ; ID "TOPORS--LINGO2^ENST00000360538.7" ; Parent "TOPORS--LINGO2^TOPORS^ENSG00000197579.8" ; ccdsid "CCDS6527.1" ; exon_id "ENSE00003844059.1" ; exon_number 1 ; gene_id "TOPORS--LINGO2^TOPORS^ENSG00000197579.8" ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2" ; havana_transcript "OTTHUMT00000052007.2" ; hgnc_id "HGNC:21653" ; level 2 ; orig_coord_info "chr9,32552434,32552436,-" ; protein_id "ENSP00000353735.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000360538.7" ; transcript_name "TOPORS-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TSBP1--NOTCH4 HAVANA gene 1006 24941 . + . FI_gene_label "TSBP1^ENSG00000204296.12" ; ID "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12" ; exon_id "ENSE00001877826.1" ; exon_number 1 ; gene_id "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12" ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5" ; havana_transcript "OTTHUMT00000076177.2" ; hgnc_id "HGNC:13922" ; level 2 ; orig_coord_info "chr6,32371694,32371706,-" ; protein_id "ENSP00000364155.4" ; tag basic appris_alternative_2 ; transcript_id "TSBP1--NOTCH4^ENST00000375015.8" ; transcript_name "TSBP1-201" ; transcript_support_level 5 ; transcript_type protein_coding TSBP1--NOTCH4 HAVANA mRNA 1006 24941 . + . FI_gene_label "TSBP1^ENSG00000204296.12" ; ID "TSBP1--NOTCH4^ENST00000375015.8" ; Parent "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12" ; exon_id "ENSE00001877826.1" ; exon_number 1 ; gene_id "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12" ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5" ; havana_transcript "OTTHUMT00000076177.2" ; hgnc_id "HGNC:13922" ; level 2 ; orig_coord_info "chr6,32371694,32371706,-" ; protein_id "ENSP00000364155.4" ; tag basic appris_alternative_2 ; transcript_id "TSBP1--NOTCH4^ENST00000375015.8" ; transcript_name "TSBP1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TSBP1--NOTCH4 HAVANA gene 29086 51058 . + . FI_gene_label "NOTCH4^ENSG00000204301.6" ; ID "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6" ; ccdsid "CCDS34420.1" ; exon_id "ENSE00001658736.1" ; exon_number 1 ; gene_id "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6" ; gene_name NOTCH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031044.2" ; havana_transcript "OTTHUMT00000076045.2" ; hgnc_id "HGNC:7884" ; level 2 ; orig_coord_info "chr6,32223856,32223928,-" ; protein_id "ENSP00000364163.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSBP1--NOTCH4^ENST00000375023.3" ; transcript_name "NOTCH4-201" ; transcript_support_level 1 ; transcript_type protein_coding TSBP1--NOTCH4 HAVANA mRNA 29086 51058 . + . FI_gene_label "NOTCH4^ENSG00000204301.6" ; ID "TSBP1--NOTCH4^ENST00000375023.3" ; Parent "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6" ; ccdsid "CCDS34420.1" ; exon_id "ENSE00001658736.1" ; exon_number 1 ; gene_id "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6" ; gene_name NOTCH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031044.2" ; havana_transcript "OTTHUMT00000076045.2" ; hgnc_id "HGNC:7884" ; level 2 ; orig_coord_info "chr6,32223856,32223928,-" ; protein_id "ENSP00000364163.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSBP1--NOTCH4^ENST00000375023.3" ; transcript_name "NOTCH4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TSBP1--TSBP1-AS1 HAVANA gene 1006 24941 . + . FI_gene_label "TSBP1^ENSG00000204296.12" ; ID "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12" ; exon_id "ENSE00001877826.1" ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12" ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5" ; havana_transcript "OTTHUMT00000076177.2" ; hgnc_id "HGNC:13922" ; level 2 ; orig_coord_info "chr6,32371694,32371706,-" ; protein_id "ENSP00000364155.4" ; tag basic appris_alternative_2 ; transcript_id "TSBP1--TSBP1-AS1^ENST00000375015.8" ; transcript_name "TSBP1-201" ; transcript_support_level 5 ; transcript_type protein_coding TSBP1--TSBP1-AS1 HAVANA mRNA 1006 24941 . + . FI_gene_label "TSBP1^ENSG00000204296.12" ; ID "TSBP1--TSBP1-AS1^ENST00000375015.8" ; Parent "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12" ; exon_id "ENSE00001877826.1" ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12" ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5" ; havana_transcript "OTTHUMT00000076177.2" ; hgnc_id "HGNC:13922" ; level 2 ; orig_coord_info "chr6,32371694,32371706,-" ; protein_id "ENSP00000364155.4" ; tag basic appris_alternative_2 ; transcript_id "TSBP1--TSBP1-AS1^ENST00000375015.8" ; transcript_name "TSBP1-201" ; transcript_support_level 5 ; 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: FRG1DP--5_8S_rRNA HAVANA gene 1001 9531 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene FRG1DP--5_8S_rRNA HAVANA RNA 1001 9531 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "FRG1DP--5_8S_rRNA^ENST00000635586.1" ; Parent "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene L1 and L2 created: FRG1DP--5_8S_rRNA ENSEMBL gene 12532 12682 . + . FI_gene_label "5_8S_rRNA^ENSG00000283274.1" ; ID "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; exon_id "ENSE00003799578.1" ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+" ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000636054.1" ; transcript_name "5_8S_rRNA.7-201" ; transcript_support_level NA ; transcript_type rRNA FRG1DP--5_8S_rRNA ENSEMBL RNA 12532 12682 . + . FI_gene_label "5_8S_rRNA^ENSG00000283274.1" ; ID "FRG1DP--5_8S_rRNA^ENST00000636054.1" ; Parent "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; exon_id "ENSE00003799578.1" ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+" ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000636054.1" ; transcript_name "5_8S_rRNA.7-201" ; transcript_support_level NA ; transcript_type rRNA L1 and L2 created: FRG1DP--MLLT10P1 HAVANA gene 12532 12793 . + . FI_gene_label "MLLT10P1^ENSG00000238151.1" ; ID "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1" ; exon_id "ENSE00001734098.1" ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1" ; gene_name MLLT10P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032156.1" ; havana_transcript "OTTHUMT00000078493.1" ; hgnc_id "HGNC:15794" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr20,30403123,30403384,-" ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000418346.1" ; transcript_name "MLLT10P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene FRG1DP--MLLT10P1 HAVANA RNA 12532 12793 . + . FI_gene_label "MLLT10P1^ENSG00000238151.1" ; ID "FRG1DP--MLLT10P1^ENST00000418346.1" ; Parent "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1" ; exon_id "ENSE00001734098.1" ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1" ; gene_name MLLT10P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032156.1" ; havana_transcript "OTTHUMT00000078493.1" ; hgnc_id "HGNC:15794" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr20,30403123,30403384,-" ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000418346.1" ; transcript_name "MLLT10P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: FRG1DP--MLLT10P1 HAVANA gene 1001 9531 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene FRG1DP--MLLT10P1 HAVANA RNA 1001 9531 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "FRG1DP--MLLT10P1^ENST00000635586.1" ; Parent "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_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 L1 and L2 created: TOPORS--AL162725.2 HAVANA gene 17485 24869 . + . FI_gene_label "AL162725.2^ENSG00000237153.4" ; ID "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4" ; exon_id "ENSE00003809911.2" ; exon_number 1 ; gene_id "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4" ; gene_name "AL162725.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000019594.5" ; havana_transcript "OTTHUMT00000051787.4" ; level 2 ; orig_coord_info "chr9,17018520,17018789,+" ; tag CAGE_supported_TSS TAGENE ; transcript_id "TOPORS--AL162725.2^ENST00000430545.4" ; transcript_name "AL162725.2-202" ; transcript_support_level 5 ; transcript_type lncRNA TOPORS--AL162725.2 HAVANA RNA 17485 24869 . + . FI_gene_label "AL162725.2^ENSG00000237153.4" ; ID "TOPORS--AL162725.2^ENST00000430545.4" ; Parent "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4" ; exon_id "ENSE00003809911.2" ; exon_number 1 ; gene_id "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4" ; gene_name "AL162725.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000019594.5" ; havana_transcript "OTTHUMT00000051787.4" ; level 2 ; orig_coord_info "chr9,17018520,17018789,+" ; tag CAGE_supported_TSS TAGENE ; transcript_id "TOPORS--AL162725.2^ENST00000430545.4" ; transcript_name "AL162725.2-202" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TSBP1--TSBP1-AS1 HAVANA gene 30157 34671 . + . FI_gene_label "TSBP1-AS1^ENSG00000225914.3" ; ID "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3" ; exon_id "ENSE00001680220.1" ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3" ; gene_name "TSBP1-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000031217.4" ; havana_transcript "OTTHUMT00000316882.2" ; hgnc_id "HGNC:39756" ; level 1 ; orig_coord_info "chr6,32255711,32255941,+" ; tag exp_conf ; transcript_id "TSBP1--TSBP1-AS1^ENST00000425033.1" ; transcript_name "TSBP1-AS1-203" ; transcript_support_level 2 ; transcript_type lncRNA TSBP1--TSBP1-AS1 HAVANA RNA 30157 34671 . + . FI_gene_label "TSBP1-AS1^ENSG00000225914.3" ; ID "TSBP1--TSBP1-AS1^ENST00000425033.1" ; Parent "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3" ; exon_id "ENSE00001680220.1" ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3" ; gene_name "TSBP1-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000031217.4" ; havana_transcript "OTTHUMT00000316882.2" ; hgnc_id "HGNC:39756" ; level 1 ; orig_coord_info "chr6,32255711,32255941,+" ; tag exp_conf ; transcript_id "TSBP1--TSBP1-AS1^ENST00000425033.1" ; transcript_name "TSBP1-AS1-203" ; transcript_support_level 2 ; transcript_type lncRNA 260 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 ------------------------------ 438 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 15 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