Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/4470cf5f35d6936be3232d643d81dc/fi_workdir/659_bua-T1-TRNA-1_B23MHV2LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/2aab80a40f7709497dbee04ef6102c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/2aab80a40f7709497dbee04ef6102c/.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: 4237 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 4237 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => CDS exon * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:4237 => 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 2 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: AC013268.1--MALL HAVANA gene 16390 22812 . + . FI_gene_label "MALL^ENSG00000144063.4" ; ID "AC013268.1--MALL^MALL^ENSG00000144063.4" ; ccdsid "CCDS2085.1" ; exon_id "ENSE00001129113.3" ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4" ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3" ; havana_transcript "OTTHUMT00000253921.2" ; hgnc_id "HGNC:6818" ; level 2 ; orig_coord_info "chr2,110115688,110115792,-" ; protein_id "ENSP00000272462.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3" ; transcript_name "MALL-201" ; transcript_support_level 1 ; transcript_type protein_coding AC013268.1--MALL HAVANA mRNA 16390 22812 . + . FI_gene_label "MALL^ENSG00000144063.4" ; ID "AC013268.1--MALL^ENST00000272462.3" ; Parent "AC013268.1--MALL^MALL^ENSG00000144063.4" ; ccdsid "CCDS2085.1" ; exon_id "ENSE00001129113.3" ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4" ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3" ; havana_transcript "OTTHUMT00000253921.2" ; hgnc_id "HGNC:6818" ; level 2 ; orig_coord_info "chr2,110115688,110115792,-" ; protein_id "ENSP00000272462.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3" ; transcript_name "MALL-201" ; transcript_support_level 1 ; transcript_type protein_coding 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: ADAMTS2--RARS1 HAVANA gene 32835 48962 . + . FI_gene_label "RARS1^ENSG00000113643.9" ; ID "ADAMTS2--RARS1^RARS1^ENSG00000113643.9" ; ccdsid "CCDS4367.1" ; exon_id "ENSE00001148323.6" ; exon_number 1 ; gene_id "ADAMTS2--RARS1^RARS1^ENSG00000113643.9" ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4" ; havana_transcript "OTTHUMT00000252794.3" ; hgnc_id "HGNC:9870" ; level 2 ; orig_coord_info "chr5,168486499,168486543,+" ; protein_id "ENSP00000231572.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000231572.8" ; transcript_name "RARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding ADAMTS2--RARS1 HAVANA mRNA 32835 48962 . + . FI_gene_label "RARS1^ENSG00000113643.9" ; ID "ADAMTS2--RARS1^ENST00000231572.8" ; Parent "ADAMTS2--RARS1^RARS1^ENSG00000113643.9" ; ccdsid "CCDS4367.1" ; exon_id "ENSE00001148323.6" ; exon_number 1 ; gene_id "ADAMTS2--RARS1^RARS1^ENSG00000113643.9" ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4" ; havana_transcript "OTTHUMT00000252794.3" ; hgnc_id "HGNC:9870" ; level 2 ; orig_coord_info "chr5,168486499,168486543,+" ; protein_id "ENSP00000231572.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000231572.8" ; transcript_name "RARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ADAMTS2--RARS1 HAVANA gene 1001 29814 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding ADAMTS2--RARS1 HAVANA mRNA 1001 29814 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "ADAMTS2--RARS1^ENST00000251582.12" ; Parent "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AVL9--RNU6-1085P HAVANA gene 1064 30635 . + . FI_gene_label "AVL9^ENSG00000105778.19" ; ID "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19" ; ccdsid "CCDS34613.1" ; exon_id "ENSE00001944463.1" ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19" ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2" ; havana_transcript "OTTHUMT00000328643.2" ; hgnc_id "HGNC:28994" ; level 2 ; orig_coord_info "chr7,32495710,32495802,+" ; protein_id "ENSP00000315568.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--RNU6-1085P^ENST00000318709.9" ; transcript_name "AVL9-201" ; transcript_support_level 2 ; transcript_type protein_coding AVL9--RNU6-1085P HAVANA mRNA 1064 30635 . + . FI_gene_label "AVL9^ENSG00000105778.19" ; ID "AVL9--RNU6-1085P^ENST00000318709.9" ; Parent "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19" ; ccdsid "CCDS34613.1" ; exon_id "ENSE00001944463.1" ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19" ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2" ; havana_transcript "OTTHUMT00000328643.2" ; hgnc_id "HGNC:28994" ; level 2 ; orig_coord_info "chr7,32495710,32495802,+" ; protein_id "ENSP00000315568.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--RNU6-1085P^ENST00000318709.9" ; transcript_name "AVL9-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: AVL9--SEPTIN7 HAVANA gene 1064 30635 . + . FI_gene_label "AVL9^ENSG00000105778.19" ; ID "AVL9--SEPTIN7^AVL9^ENSG00000105778.19" ; ccdsid "CCDS34613.1" ; exon_id "ENSE00001944463.1" ; exon_number 1 ; gene_id "AVL9--SEPTIN7^AVL9^ENSG00000105778.19" ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2" ; havana_transcript "OTTHUMT00000328643.2" ; hgnc_id "HGNC:28994" ; level 2 ; orig_coord_info "chr7,32495710,32495802,+" ; protein_id "ENSP00000315568.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--SEPTIN7^ENST00000318709.9" ; transcript_name "AVL9-201" ; transcript_support_level 2 ; transcript_type protein_coding AVL9--SEPTIN7 HAVANA mRNA 1064 30635 . + . FI_gene_label "AVL9^ENSG00000105778.19" ; ID "AVL9--SEPTIN7^ENST00000318709.9" ; Parent "AVL9--SEPTIN7^AVL9^ENSG00000105778.19" ; ccdsid "CCDS34613.1" ; exon_id "ENSE00001944463.1" ; exon_number 1 ; gene_id "AVL9--SEPTIN7^AVL9^ENSG00000105778.19" ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2" ; havana_transcript "OTTHUMT00000328643.2" ; hgnc_id "HGNC:28994" ; level 2 ; orig_coord_info "chr7,32495710,32495802,+" ; protein_id "ENSP00000315568.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--SEPTIN7^ENST00000318709.9" ; transcript_name "AVL9-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: AVL9--SEPTIN7 ENSEMBL gene 33690 63614 . + . FI_gene_label "SEPTIN7^ENSG00000122545.20" ; ID "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20" ; exon_id "ENSE00003749079.1" ; exon_number 1 ; gene_id "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20" ; gene_name SEPTIN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155063.6" ; hgnc_id "HGNC:1717" ; level 3 ; orig_coord_info "chr7,35801210,35801270,+" ; protein_id "ENSP00000344868.7" ; tag basic appris_alternative_1 ; transcript_id "AVL9--SEPTIN7^ENST00000350320.10" ; transcript_name "SEPTIN7-201" ; transcript_support_level 5 ; transcript_type protein_coding AVL9--SEPTIN7 ENSEMBL mRNA 33690 63614 . + . FI_gene_label "SEPTIN7^ENSG00000122545.20" ; ID "AVL9--SEPTIN7^ENST00000350320.10" ; Parent "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20" ; exon_id "ENSE00003749079.1" ; exon_number 1 ; gene_id "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20" ; gene_name SEPTIN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155063.6" ; hgnc_id "HGNC:1717" ; level 3 ; orig_coord_info "chr7,35801210,35801270,+" ; protein_id "ENSP00000344868.7" ; tag basic appris_alternative_1 ; transcript_id "AVL9--SEPTIN7^ENST00000350320.10" ; transcript_name "SEPTIN7-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: CRACD--THEGL HAVANA gene 2941 23980 . + . FI_gene_label "CRACD^ENSG00000109265.14" ; ID "CRACD--THEGL^CRACD^ENSG00000109265.14" ; ccdsid "CCDS43230.1" ; exon_id "ENSE00003562187.1" ; exon_number 4 ; gene_id "CRACD--THEGL^CRACD^ENSG00000109265.14" ; gene_name CRACD ; gene_type protein_coding ; havana_gene "OTTHUMG00000160749.7" ; havana_transcript "OTTHUMT00000362097.3" ; hgnc_id "HGNC:29219" ; level 2 ; orig_coord_info "chr4,56298230,56298349,+" ; protein_id "ENSP00000264229.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRACD--THEGL^ENST00000264229.11" ; transcript_name "CRACD-201" ; transcript_support_level 2 ; transcript_type protein_coding CRACD--THEGL HAVANA mRNA 2941 23980 . + . FI_gene_label "CRACD^ENSG00000109265.14" ; ID "CRACD--THEGL^ENST00000264229.11" ; Parent "CRACD--THEGL^CRACD^ENSG00000109265.14" ; ccdsid "CCDS43230.1" ; exon_id "ENSE00003562187.1" ; exon_number 4 ; gene_id "CRACD--THEGL^CRACD^ENSG00000109265.14" ; gene_name CRACD ; gene_type protein_coding ; havana_gene "OTTHUMG00000160749.7" ; havana_transcript "OTTHUMT00000362097.3" ; hgnc_id "HGNC:29219" ; level 2 ; orig_coord_info "chr4,56298230,56298349,+" ; protein_id "ENSP00000264229.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRACD--THEGL^ENST00000264229.11" ; transcript_name "CRACD-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CRACD--THEGL HAVANA gene 26981 37776 . + . FI_gene_label "THEGL^ENSG00000249693.3" ; ID "CRACD--THEGL^THEGL^ENSG00000249693.3" ; ccdsid "CCDS58899.1" ; exon_id "ENSE00002081975.2" ; exon_number 1 ; gene_id "CRACD--THEGL^THEGL^ENSG00000249693.3" ; gene_name THEGL ; gene_type protein_coding ; havana_gene "OTTHUMG00000160770.3" ; havana_transcript "OTTHUMT00000362201.3" ; hgnc_id "HGNC:43771" ; level 1 ; orig_coord_info "chr4,56530677,56531169,+" ; protein_id "ENSP00000456850.1" ; tag not_organism_supported basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "CRACD--THEGL^ENST00000512175.3" ; transcript_name "THEGL-202" ; transcript_support_level 5 ; transcript_type protein_coding CRACD--THEGL HAVANA mRNA 26981 37776 . + . FI_gene_label "THEGL^ENSG00000249693.3" ; ID "CRACD--THEGL^ENST00000512175.3" ; Parent "CRACD--THEGL^THEGL^ENSG00000249693.3" ; ccdsid "CCDS58899.1" ; exon_id "ENSE00002081975.2" ; exon_number 1 ; gene_id "CRACD--THEGL^THEGL^ENSG00000249693.3" ; gene_name THEGL ; gene_type protein_coding ; havana_gene "OTTHUMG00000160770.3" ; havana_transcript "OTTHUMT00000362201.3" ; hgnc_id "HGNC:43771" ; level 1 ; orig_coord_info "chr4,56530677,56531169,+" ; protein_id "ENSP00000456850.1" ; tag not_organism_supported basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "CRACD--THEGL^ENST00000512175.3" ; transcript_name "THEGL-202" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: ERBIN--ARHGAP26 HAVANA gene 38475 91117 . + . FI_gene_label "ARHGAP26^ENSG00000145819.18" ; ID "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18" ; ccdsid "CCDS4277.1" ; exon_id "ENSE00001921830.2" ; exon_number 1 ; gene_id "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18" ; gene_name ARHGAP26 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059705.15" ; havana_transcript "OTTHUMT00000496686.1" ; hgnc_id "HGNC:17073" ; level 2 ; orig_coord_info "chr5,142770762,142770915,+" ; protein_id "ENSP00000274498.4" ; tag CAGE_supported_TSS basic appris_alternative_1 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000274498.9" ; transcript_name "ARHGAP26-201" ; transcript_support_level 1 ; transcript_type protein_coding ERBIN--ARHGAP26 HAVANA mRNA 38475 91117 . + . FI_gene_label "ARHGAP26^ENSG00000145819.18" ; ID "ERBIN--ARHGAP26^ENST00000274498.9" ; Parent "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18" ; ccdsid "CCDS4277.1" ; exon_id "ENSE00001921830.2" ; exon_number 1 ; gene_id "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18" ; gene_name ARHGAP26 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059705.15" ; havana_transcript "OTTHUMT00000496686.1" ; hgnc_id "HGNC:17073" ; level 2 ; orig_coord_info "chr5,142770762,142770915,+" ; protein_id "ENSP00000274498.4" ; tag CAGE_supported_TSS basic appris_alternative_1 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000274498.9" ; transcript_name "ARHGAP26-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ERBIN--ARHGAP26 HAVANA gene 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding ERBIN--ARHGAP26 HAVANA mRNA 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--ARHGAP26^ENST00000284037.10" ; Parent "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NTRK1--NUP210L ENSEMBL gene 22273 61957 . + . FI_gene_label "NUP210L^ENSG00000143552.9" ; ID "NTRK1--NUP210L^NUP210L^ENSG00000143552.9" ; ccdsid "CCDS53370.1" ; exon_id "ENSE00002224107.1" ; exon_number 1 ; gene_id "NTRK1--NUP210L^NUP210L^ENSG00000143552.9" ; gene_name NUP210L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035852.3" ; hgnc_id "HGNC:29915" ; level 3 ; orig_coord_info "chr1,154154842,154155044,-" ; protein_id "ENSP00000271854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "NTRK1--NUP210L^ENST00000271854.3" ; transcript_name "NUP210L-201" ; transcript_support_level 5 ; transcript_type protein_coding NTRK1--NUP210L ENSEMBL mRNA 22273 61957 . + . FI_gene_label "NUP210L^ENSG00000143552.9" ; ID "NTRK1--NUP210L^ENST00000271854.3" ; Parent "NTRK1--NUP210L^NUP210L^ENSG00000143552.9" ; ccdsid "CCDS53370.1" ; exon_id "ENSE00002224107.1" ; exon_number 1 ; gene_id "NTRK1--NUP210L^NUP210L^ENSG00000143552.9" ; gene_name NUP210L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035852.3" ; hgnc_id "HGNC:29915" ; level 3 ; orig_coord_info "chr1,154154842,154155044,-" ; protein_id "ENSP00000271854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "NTRK1--NUP210L^ENST00000271854.3" ; transcript_name "NUP210L-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: NTRK1--NUP210L HAVANA gene 5049 19133 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "NTRK1--NUP210L^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "NTRK1--NUP210L^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "NTRK1--NUP210L^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding NTRK1--NUP210L HAVANA mRNA 5049 19133 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "NTRK1--NUP210L^ENST00000358660.3" ; Parent "NTRK1--NUP210L^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "NTRK1--NUP210L^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "NTRK1--NUP210L^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: RARS1--WWC1 HAVANA gene 1021 17148 . + . FI_gene_label "RARS1^ENSG00000113643.9" ; ID "RARS1--WWC1^RARS1^ENSG00000113643.9" ; ccdsid "CCDS4367.1" ; exon_id "ENSE00001148323.6" ; exon_number 1 ; gene_id "RARS1--WWC1^RARS1^ENSG00000113643.9" ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4" ; havana_transcript "OTTHUMT00000252794.3" ; hgnc_id "HGNC:9870" ; level 2 ; orig_coord_info "chr5,168486499,168486543,+" ; protein_id "ENSP00000231572.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RARS1--WWC1^ENST00000231572.8" ; transcript_name "RARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding RARS1--WWC1 HAVANA mRNA 1021 17148 . + . FI_gene_label "RARS1^ENSG00000113643.9" ; ID "RARS1--WWC1^ENST00000231572.8" ; Parent "RARS1--WWC1^RARS1^ENSG00000113643.9" ; ccdsid "CCDS4367.1" ; exon_id "ENSE00001148323.6" ; exon_number 1 ; gene_id "RARS1--WWC1^RARS1^ENSG00000113643.9" ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4" ; havana_transcript "OTTHUMT00000252794.3" ; hgnc_id "HGNC:9870" ; level 2 ; orig_coord_info "chr5,168486499,168486543,+" ; protein_id "ENSP00000231572.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RARS1--WWC1^ENST00000231572.8" ; transcript_name "RARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RARS1--WWC1 HAVANA gene 20149 54097 . + . FI_gene_label "WWC1^ENSG00000113645.15" ; ID "RARS1--WWC1^WWC1^ENSG00000113645.15" ; ccdsid "CCDS4366.1" ; exon_id "ENSE00001869765.3" ; exon_number 1 ; gene_id "RARS1--WWC1^WWC1^ENSG00000113645.15" ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4" ; havana_transcript "OTTHUMT00000252791.2" ; hgnc_id "HGNC:29435" ; level 2 ; orig_coord_info "chr5,168292153,168292271,+" ; protein_id "ENSP00000265293.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RARS1--WWC1^ENST00000265293.9" ; transcript_name "WWC1-201" ; transcript_support_level 1 ; transcript_type protein_coding RARS1--WWC1 HAVANA mRNA 20149 54097 . + . FI_gene_label "WWC1^ENSG00000113645.15" ; ID "RARS1--WWC1^ENST00000265293.9" ; Parent "RARS1--WWC1^WWC1^ENSG00000113645.15" ; ccdsid "CCDS4366.1" ; exon_id "ENSE00001869765.3" ; exon_number 1 ; gene_id "RARS1--WWC1^WWC1^ENSG00000113645.15" ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4" ; havana_transcript "OTTHUMT00000252791.2" ; hgnc_id "HGNC:29435" ; level 2 ; orig_coord_info "chr5,168292153,168292271,+" ; protein_id "ENSP00000265293.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RARS1--WWC1^ENST00000265293.9" ; transcript_name "WWC1-201" ; 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: TPM3--NTRK1 HAVANA gene 2360 24514 . + . FI_gene_label "TPM3^ENSG00000143549.21" ; ID "TPM3--NTRK1^TPM3^ENSG00000143549.21" ; exon_id "ENSE00002024480.1" ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21" ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12" ; havana_transcript "OTTHUMT00000360295.1" ; hgnc_id "HGNC:12012" ; level 2 ; orig_coord_info "chr1,154191902,154192018,-" ; protein_id "ENSP00000271850.7" ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11" ; transcript_name "TPM3-201" ; transcript_support_level 5 ; transcript_type protein_coding TPM3--NTRK1 HAVANA mRNA 2360 24514 . + . FI_gene_label "TPM3^ENSG00000143549.21" ; ID "TPM3--NTRK1^ENST00000271850.11" ; Parent "TPM3--NTRK1^TPM3^ENSG00000143549.21" ; exon_id "ENSE00002024480.1" ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21" ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12" ; havana_transcript "OTTHUMT00000360295.1" ; hgnc_id "HGNC:12012" ; level 2 ; orig_coord_info "chr1,154191902,154192018,-" ; protein_id "ENSP00000271850.7" ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11" ; transcript_name "TPM3-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TPM3--NTRK1 HAVANA gene 33577 47661 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "TPM3--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding TPM3--NTRK1 HAVANA mRNA 33577 47661 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "TPM3--NTRK1^ENST00000358660.3" ; Parent "TPM3--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: TPM4--NTRK1 HAVANA gene 3909 21814 . + . FI_gene_label "TPM4^ENSG00000167460.17" ; ID "TPM4--NTRK1^TPM4^ENSG00000167460.17" ; exon_id "ENSE00003879509.1" ; exon_number 1 ; gene_id "TPM4--NTRK1^TPM4^ENSG00000167460.17" ; gene_name TPM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182134.12" ; havana_transcript "OTTHUMT00000505346.1" ; hgnc_id "HGNC:12013" ; level 2 ; orig_coord_info "chr19,16076645,16076697,+" ; protein_id "ENSP00000300933.4" ; tag mRNA_start_NF cds_start_NF RNA_Seq_supported_only ; transcript_id "TPM4--NTRK1^ENST00000300933.9" ; transcript_name "TPM4-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay TPM4--NTRK1 HAVANA mRNA 3909 21814 . + . FI_gene_label "TPM4^ENSG00000167460.17" ; ID "TPM4--NTRK1^ENST00000300933.9" ; Parent "TPM4--NTRK1^TPM4^ENSG00000167460.17" ; exon_id "ENSE00003879509.1" ; exon_number 1 ; gene_id "TPM4--NTRK1^TPM4^ENSG00000167460.17" ; gene_name TPM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182134.12" ; havana_transcript "OTTHUMT00000505346.1" ; hgnc_id "HGNC:12013" ; level 2 ; orig_coord_info "chr19,16076645,16076697,+" ; protein_id "ENSP00000300933.4" ; tag mRNA_start_NF cds_start_NF RNA_Seq_supported_only ; transcript_id "TPM4--NTRK1^ENST00000300933.9" ; transcript_name "TPM4-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay L1 and L2 created: TPM4--NTRK1 HAVANA gene 28913 42997 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "TPM4--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "TPM4--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "TPM4--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding TPM4--NTRK1 HAVANA mRNA 28913 42997 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "TPM4--NTRK1^ENST00000358660.3" ; Parent "TPM4--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "TPM4--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "TPM4--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; 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: WWC1--ADAMTS2 HAVANA gene 37950 66763 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding WWC1--ADAMTS2 HAVANA mRNA 37950 66763 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "WWC1--ADAMTS2^ENST00000251582.12" ; Parent "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: WWC1--ADAMTS2 HAVANA gene 1001 34949 . + . FI_gene_label "WWC1^ENSG00000113645.15" ; ID "WWC1--ADAMTS2^WWC1^ENSG00000113645.15" ; ccdsid "CCDS4366.1" ; exon_id "ENSE00001869765.3" ; exon_number 1 ; gene_id "WWC1--ADAMTS2^WWC1^ENSG00000113645.15" ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4" ; havana_transcript "OTTHUMT00000252791.2" ; hgnc_id "HGNC:29435" ; level 2 ; orig_coord_info "chr5,168292153,168292271,+" ; protein_id "ENSP00000265293.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000265293.9" ; transcript_name "WWC1-201" ; transcript_support_level 1 ; transcript_type protein_coding WWC1--ADAMTS2 HAVANA mRNA 1001 34949 . + . FI_gene_label "WWC1^ENSG00000113645.15" ; ID "WWC1--ADAMTS2^ENST00000265293.9" ; Parent "WWC1--ADAMTS2^WWC1^ENSG00000113645.15" ; ccdsid "CCDS4366.1" ; exon_id "ENSE00001869765.3" ; exon_number 1 ; gene_id "WWC1--ADAMTS2^WWC1^ENSG00000113645.15" ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4" ; havana_transcript "OTTHUMT00000252791.2" ; hgnc_id "HGNC:29435" ; level 2 ; orig_coord_info "chr5,168292153,168292271,+" ; protein_id "ENSP00000265293.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000265293.9" ; transcript_name "WWC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC013268.1--MALL HAVANA gene 3129 10448 . + . FI_gene_label "AC013268.1^ENSG00000186148.13" ; ID "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; exon_id "ENSE00002526923.1" ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; gene_name "AC013268.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2" ; havana_transcript "OTTHUMT00000330194.1" ; level 2 ; orig_coord_info "chr2,109936342,109938072,+" ; transcript_id "AC013268.1--MALL^ENST00000417926.5" ; transcript_name "AC013268.1-202" ; transcript_support_level 2 ; transcript_type processed_transcript AC013268.1--MALL HAVANA RNA 3129 10448 . + . FI_gene_label "AC013268.1^ENSG00000186148.13" ; ID "AC013268.1--MALL^ENST00000417926.5" ; Parent "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; exon_id "ENSE00002526923.1" ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; gene_name "AC013268.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2" ; havana_transcript "OTTHUMT00000330194.1" ; level 2 ; orig_coord_info "chr2,109936342,109938072,+" ; transcript_id "AC013268.1--MALL^ENST00000417926.5" ; transcript_name "AC013268.1-202" ; transcript_support_level 2 ; transcript_type processed_transcript 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: AVL9--RNU6-1085P ENSEMBL gene 33636 33742 . + . FI_gene_label "RNU6-1085P^ENSG00000200446.1" ; ID "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1" ; exon_id "ENSE00001807627.1" ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1" ; gene_name "RNU6-1085P" ; gene_type snRNA ; hgnc_id "HGNC:48048" ; level 3 ; orig_coord_info "chr7,35930158,35930264,-" ; tag basic ; transcript_id "AVL9--RNU6-1085P^ENST00000363576.1" ; transcript_name "RNU6-1085P-201" ; transcript_support_level NA ; transcript_type snRNA AVL9--RNU6-1085P ENSEMBL RNA 33636 33742 . + . FI_gene_label "RNU6-1085P^ENSG00000200446.1" ; ID "AVL9--RNU6-1085P^ENST00000363576.1" ; Parent "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1" ; exon_id "ENSE00001807627.1" ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1" ; gene_name "RNU6-1085P" ; gene_type snRNA ; hgnc_id "HGNC:48048" ; level 3 ; orig_coord_info "chr7,35930158,35930264,-" ; tag basic ; transcript_id "AVL9--RNU6-1085P^ENST00000363576.1" ; transcript_name "RNU6-1085P-201" ; transcript_support_level NA ; transcript_type snRNA 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 306 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 ------------------------------ 490 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 19 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