Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/cd4fdea3f270eeebb23a01a9a53631/fi_workdir/659_bCu-T1-TRNA-1_B23MHV2LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/8b9e8e42fefdc445bd42a069de83e3/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/8b9e8e42fefdc445bd42a069de83e3/.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: 7306 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 7306 => 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:7306 => 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: ADAM23--HDAC4 HAVANA gene 1001 32824 . + . FI_gene_label "ADAM23^ENSG00000114948.13" ; ID "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; ccdsid "CCDS2369.1" ; exon_id "ENSE00001950784.2" ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5" ; havana_transcript "OTTHUMT00000256431.4" ; hgnc_id "HGNC:202" ; level 2 ; orig_coord_info "chr2,206443867,206444080,+" ; protein_id "ENSP00000264377.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8" ; transcript_name "ADAM23-201" ; transcript_support_level 1 ; transcript_type protein_coding ADAM23--HDAC4 HAVANA mRNA 1001 32824 . + . FI_gene_label "ADAM23^ENSG00000114948.13" ; ID "ADAM23--HDAC4^ENST00000264377.8" ; Parent "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; ccdsid "CCDS2369.1" ; exon_id "ENSE00001950784.2" ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5" ; havana_transcript "OTTHUMT00000256431.4" ; hgnc_id "HGNC:202" ; level 2 ; orig_coord_info "chr2,206443867,206444080,+" ; protein_id "ENSP00000264377.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8" ; transcript_name "ADAM23-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ADAM23--HDAC4 HAVANA gene 36530 81643 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding ADAM23--HDAC4 HAVANA mRNA 36530 81643 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "ADAM23--HDAC4^ENST00000345617.7" ; Parent "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AL845331.2--AFF3 ENSEMBL gene 10488 55391 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "AL845331.2--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "AL845331.2--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "AL845331.2--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding AL845331.2--AFF3 ENSEMBL mRNA 10488 55391 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "AL845331.2--AFF3^ENST00000317233.8" ; Parent "AL845331.2--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "AL845331.2--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "AL845331.2--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: ALK--SNF8P1 HAVANA gene 1001 36005 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "ALK--SNF8P1^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "ALK--SNF8P1^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ALK--SNF8P1^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding ALK--SNF8P1 HAVANA mRNA 1001 36005 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "ALK--SNF8P1^ENST00000389048.8" ; Parent "ALK--SNF8P1^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "ALK--SNF8P1^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ALK--SNF8P1^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ALK--SPHKAP HAVANA gene 39067 56138 . + . FI_gene_label "SPHKAP^ENSG00000153820.13" ; ID "ALK--SPHKAP^SPHKAP^ENSG00000153820.13" ; ccdsid "CCDS33389.1" ; exon_id "ENSE00001933406.1" ; exon_number 1 ; gene_id "ALK--SPHKAP^SPHKAP^ENSG00000153820.13" ; gene_name SPHKAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000153584.2" ; havana_transcript "OTTHUMT00000331749.1" ; hgnc_id "HGNC:30619" ; level 2 ; orig_coord_info "chr2,228181567,228181598,-" ; protein_id "ENSP00000339886.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "ALK--SPHKAP^ENST00000344657.5" ; transcript_name "SPHKAP-201" ; transcript_support_level 1 ; transcript_type protein_coding ALK--SPHKAP HAVANA mRNA 39067 56138 . + . FI_gene_label "SPHKAP^ENSG00000153820.13" ; ID "ALK--SPHKAP^ENST00000344657.5" ; Parent "ALK--SPHKAP^SPHKAP^ENSG00000153820.13" ; ccdsid "CCDS33389.1" ; exon_id "ENSE00001933406.1" ; exon_number 1 ; gene_id "ALK--SPHKAP^SPHKAP^ENSG00000153820.13" ; gene_name SPHKAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000153584.2" ; havana_transcript "OTTHUMT00000331749.1" ; hgnc_id "HGNC:30619" ; level 2 ; orig_coord_info "chr2,228181567,228181598,-" ; protein_id "ENSP00000339886.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "ALK--SPHKAP^ENST00000344657.5" ; transcript_name "SPHKAP-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ALK--SPHKAP HAVANA gene 1001 36005 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "ALK--SPHKAP^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "ALK--SPHKAP^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ALK--SPHKAP^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding ALK--SPHKAP HAVANA mRNA 1001 36005 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "ALK--SPHKAP^ENST00000389048.8" ; Parent "ALK--SPHKAP^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "ALK--SPHKAP^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ALK--SPHKAP^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BMS1P23--AFF3 ENSEMBL gene 12133 57036 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "BMS1P23--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "BMS1P23--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P23--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding BMS1P23--AFF3 ENSEMBL mRNA 12133 57036 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "BMS1P23--AFF3^ENST00000317233.8" ; Parent "BMS1P23--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "BMS1P23--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P23--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: HDAC4--KCNS3 HAVANA gene 50640 56863 . + . FI_gene_label "KCNS3^ENSG00000170745.12" ; ID "HDAC4--KCNS3^KCNS3^ENSG00000170745.12" ; ccdsid "CCDS1692.1" ; exon_id "ENSE00001166371.7" ; exon_number 3 ; gene_id "HDAC4--KCNS3^KCNS3^ENSG00000170745.12" ; gene_name KCNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044150.7" ; havana_transcript "OTTHUMT00000241660.2" ; hgnc_id "HGNC:6302" ; level 2 ; orig_coord_info "chr2,17931009,17932481,+" ; protein_id "ENSP00000305824.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HDAC4--KCNS3^ENST00000304101.9" ; transcript_name "KCNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding HDAC4--KCNS3 HAVANA mRNA 50640 56863 . + . FI_gene_label "KCNS3^ENSG00000170745.12" ; ID "HDAC4--KCNS3^ENST00000304101.9" ; Parent "HDAC4--KCNS3^KCNS3^ENSG00000170745.12" ; ccdsid "CCDS1692.1" ; exon_id "ENSE00001166371.7" ; exon_number 3 ; gene_id "HDAC4--KCNS3^KCNS3^ENSG00000170745.12" ; gene_name KCNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044150.7" ; havana_transcript "OTTHUMT00000241660.2" ; hgnc_id "HGNC:6302" ; level 2 ; orig_coord_info "chr2,17931009,17932481,+" ; protein_id "ENSP00000305824.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HDAC4--KCNS3^ENST00000304101.9" ; transcript_name "KCNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: HDAC4--KCNS3 HAVANA gene 1706 46819 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "HDAC4--KCNS3^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "HDAC4--KCNS3^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "HDAC4--KCNS3^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding HDAC4--KCNS3 HAVANA mRNA 1706 46819 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "HDAC4--KCNS3^ENST00000345617.7" ; Parent "HDAC4--KCNS3^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "HDAC4--KCNS3^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "HDAC4--KCNS3^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: IRAG1--ZNF143 HAVANA gene 33464 53054 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding IRAG1--ZNF143 HAVANA mRNA 33464 53054 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "IRAG1--ZNF143^ENST00000299606.6" ; Parent "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: IRAG1--ZNF143 HAVANA gene 1237 29755 . + . FI_gene_label "IRAG1^ENSG00000072952.19" ; ID "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; ccdsid "CCDS55746.1" ; exon_id "ENSE00002197128.1" ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7" ; havana_transcript "OTTHUMT00000386137.2" ; hgnc_id "HGNC:7237" ; level 2 ; orig_coord_info "chr11,10693536,10693602,-" ; protein_id "ENSP00000412130.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6" ; transcript_name "IRAG1-201" ; transcript_support_level 2 ; transcript_type protein_coding IRAG1--ZNF143 HAVANA mRNA 1237 29755 . + . FI_gene_label "IRAG1^ENSG00000072952.19" ; ID "IRAG1--ZNF143^ENST00000423302.6" ; Parent "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; ccdsid "CCDS55746.1" ; exon_id "ENSE00002197128.1" ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7" ; havana_transcript "OTTHUMT00000386137.2" ; hgnc_id "HGNC:7237" ; level 2 ; orig_coord_info "chr11,10693536,10693602,-" ; protein_id "ENSP00000412130.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6" ; transcript_name "IRAG1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: NAV2--NELL1 HAVANA gene 60558 91777 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NAV2--NELL1^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding NAV2--NELL1 HAVANA mRNA 60558 91777 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NAV2--NELL1^ENST00000298925.9" ; Parent "NAV2--NELL1^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: NAV2--NELL1 HAVANA gene 2305 57537 . + . FI_gene_label "NAV2^ENSG00000166833.22" ; ID "NAV2--NELL1^NAV2^ENSG00000166833.22" ; ccdsid "CCDS7850.1" ; exon_id "ENSE00003846126.1" ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22" ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7" ; havana_transcript "OTTHUMT00000324114.1" ; hgnc_id "HGNC:15997" ; level 2 ; orig_coord_info "chr11,19713696,19713962,+" ; protein_id "ENSP00000309577.6" ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9" ; transcript_name "NAV2-201" ; transcript_support_level 1 ; transcript_type protein_coding NAV2--NELL1 HAVANA mRNA 2305 57537 . + . FI_gene_label "NAV2^ENSG00000166833.22" ; ID "NAV2--NELL1^ENST00000349880.9" ; Parent "NAV2--NELL1^NAV2^ENSG00000166833.22" ; ccdsid "CCDS7850.1" ; exon_id "ENSE00003846126.1" ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22" ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7" ; havana_transcript "OTTHUMT00000324114.1" ; hgnc_id "HGNC:15997" ; level 2 ; orig_coord_info "chr11,19713696,19713962,+" ; protein_id "ENSP00000309577.6" ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9" ; transcript_name "NAV2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NELL1--INSC HAVANA gene 1021 32240 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NELL1--INSC^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding NELL1--INSC HAVANA mRNA 1021 32240 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NELL1--INSC^ENST00000298925.9" ; Parent "NELL1--INSC^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: NELL1--INSC HAVANA gene 35246 55096 . + . FI_gene_label "INSC^ENSG00000188487.12" ; ID "NELL1--INSC^INSC^ENSG00000188487.12" ; ccdsid "CCDS41621.1" ; exon_id "ENSE00001538117.1" ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12" ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3" ; havana_transcript "OTTHUMT00000386590.1" ; hgnc_id "HGNC:33116" ; level 2 ; orig_coord_info "chr11,15112470,15112565,+" ; protein_id "ENSP00000368872.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7" ; transcript_name "INSC-201" ; transcript_support_level 1 ; transcript_type protein_coding NELL1--INSC HAVANA mRNA 35246 55096 . + . FI_gene_label "INSC^ENSG00000188487.12" ; ID "NELL1--INSC^ENST00000379554.7" ; Parent "NELL1--INSC^INSC^ENSG00000188487.12" ; ccdsid "CCDS41621.1" ; exon_id "ENSE00001538117.1" ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12" ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3" ; havana_transcript "OTTHUMT00000386590.1" ; hgnc_id "HGNC:33116" ; level 2 ; orig_coord_info "chr11,15112470,15112565,+" ; protein_id "ENSP00000368872.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7" ; transcript_name "INSC-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHA13 HAVANA gene 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA10--PCDHA13 HAVANA mRNA 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^ENST00000289272.3" ; Parent "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHA13 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding PCDHA10--PCDHA13 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^ENST00000562220.2" ; Parent "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHAC1 HAVANA gene 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA10--PCDHAC1 HAVANA mRNA 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHAC1 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding PCDHA10--PCDHAC1 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHAC2 HAVANA gene 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA10--PCDHAC2 HAVANA mRNA 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA10--PCDHAC2 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding PCDHA10--PCDHAC2 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PPFIBP2--PARVA HAVANA gene 1702 37120 . + . FI_gene_label "PPFIBP2^ENSG00000166387.13" ; ID "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; ccdsid "CCDS31419.1" ; exon_id "ENSE00001278528.6" ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10" ; havana_transcript "OTTHUMT00000385345.3" ; hgnc_id "HGNC:9250" ; level 2 ; orig_coord_info "chr11,7549476,7549539,+" ; protein_id "ENSP00000299492.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9" ; transcript_name "PPFIBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding PPFIBP2--PARVA HAVANA mRNA 1702 37120 . + . FI_gene_label "PPFIBP2^ENSG00000166387.13" ; ID "PPFIBP2--PARVA^ENST00000299492.9" ; Parent "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; ccdsid "CCDS31419.1" ; exon_id "ENSE00001278528.6" ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10" ; havana_transcript "OTTHUMT00000385345.3" ; hgnc_id "HGNC:9250" ; level 2 ; orig_coord_info "chr11,7549476,7549539,+" ; protein_id "ENSP00000299492.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9" ; transcript_name "PPFIBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PPFIBP2--PARVA HAVANA gene 42627 67717 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding PPFIBP2--PARVA HAVANA mRNA 42627 67717 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PPFIBP2--PARVA^ENST00000334956.15" ; Parent "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RHOG--SBF2 HAVANA gene 8810 67621 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "RHOG--SBF2^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "RHOG--SBF2^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "RHOG--SBF2^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding RHOG--SBF2 HAVANA mRNA 8810 67621 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "RHOG--SBF2^ENST00000256190.13" ; Parent "RHOG--SBF2^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "RHOG--SBF2^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "RHOG--SBF2^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RHOG--SBF2 HAVANA gene 1001 5809 . + . FI_gene_label "RHOG^ENSG00000177105.10" ; ID "RHOG--SBF2^RHOG^ENSG00000177105.10" ; ccdsid "CCDS7748.1" ; exon_id "ENSE00001393048.2" ; exon_number 2 ; gene_id "RHOG--SBF2^RHOG^ENSG00000177105.10" ; gene_name RHOG ; gene_type protein_coding ; havana_gene "OTTHUMG00000012287.4" ; havana_transcript "OTTHUMT00000034125.3" ; hgnc_id "HGNC:672" ; level 2 ; orig_coord_info "chr11,3827566,3828138,-" ; protein_id "ENSP00000339467.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RHOG--SBF2^ENST00000351018.5" ; transcript_name "RHOG-201" ; transcript_support_level 1 ; transcript_type protein_coding RHOG--SBF2 HAVANA mRNA 1001 5809 . + . FI_gene_label "RHOG^ENSG00000177105.10" ; ID "RHOG--SBF2^ENST00000351018.5" ; Parent "RHOG--SBF2^RHOG^ENSG00000177105.10" ; ccdsid "CCDS7748.1" ; exon_id "ENSE00001393048.2" ; exon_number 2 ; gene_id "RHOG--SBF2^RHOG^ENSG00000177105.10" ; gene_name RHOG ; gene_type protein_coding ; havana_gene "OTTHUMG00000012287.4" ; havana_transcript "OTTHUMT00000034125.3" ; hgnc_id "HGNC:672" ; level 2 ; orig_coord_info "chr11,3827566,3828138,-" ; protein_id "ENSP00000339467.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RHOG--SBF2^ENST00000351018.5" ; transcript_name "RHOG-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SBF2--AC009869.1 HAVANA gene 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--AC009869.1^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--AC009869.1^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC009869.1^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding SBF2--AC009869.1 HAVANA mRNA 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--AC009869.1^ENST00000256190.13" ; Parent "SBF2--AC009869.1^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--AC009869.1^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC009869.1^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SBF2--AC087379.1 HAVANA gene 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--AC087379.1^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--AC087379.1^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC087379.1^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding SBF2--AC087379.1 HAVANA mRNA 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--AC087379.1^ENST00000256190.13" ; Parent "SBF2--AC087379.1^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--AC087379.1^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC087379.1^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TBP--ATXN3 HAVANA gene 1078 10356 . + . FI_gene_label "TBP^ENSG00000112592.14" ; ID "TBP--ATXN3^TBP^ENSG00000112592.14" ; ccdsid "CCDS5315.1" ; exon_id "ENSE00000854356.1" ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14" ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6" ; havana_transcript "OTTHUMT00000043271.2" ; hgnc_id "HGNC:11588" ; level 2 ; orig_coord_info "chr6,170557030,170557083,+" ; protein_id "ENSP00000230354.5" ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10" ; transcript_name "TBP-201" ; transcript_support_level 1 ; transcript_type protein_coding TBP--ATXN3 HAVANA mRNA 1078 10356 . + . FI_gene_label "TBP^ENSG00000112592.14" ; ID "TBP--ATXN3^ENST00000230354.10" ; Parent "TBP--ATXN3^TBP^ENSG00000112592.14" ; ccdsid "CCDS5315.1" ; exon_id "ENSE00000854356.1" ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14" ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6" ; havana_transcript "OTTHUMT00000043271.2" ; hgnc_id "HGNC:11588" ; level 2 ; orig_coord_info "chr6,170557030,170557083,+" ; protein_id "ENSP00000230354.5" ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10" ; transcript_name "TBP-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TBP--ATXN3 HAVANA gene 13368 28517 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding TBP--ATXN3 HAVANA mRNA 13368 28517 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "TBP--ATXN3^ENST00000340660.10" ; Parent "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TNS1--ALK HAVANA gene 8232 56093 . + . FI_gene_label "TNS1^ENSG00000079308.19" ; ID "TNS1--ALK^TNS1^ENSG00000079308.19" ; ccdsid "CCDS2407.1" ; exon_id "ENSE00003622889.1" ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19" ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10" ; havana_transcript "OTTHUMT00000256672.2" ; hgnc_id "HGNC:11973" ; level 2 ; orig_coord_info "chr2,217897798,217897965,-" ; protein_id "ENSP00000171887.4" ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8" ; transcript_name "TNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding TNS1--ALK HAVANA mRNA 8232 56093 . + . FI_gene_label "TNS1^ENSG00000079308.19" ; ID "TNS1--ALK^ENST00000171887.8" ; Parent "TNS1--ALK^TNS1^ENSG00000079308.19" ; ccdsid "CCDS2407.1" ; exon_id "ENSE00003622889.1" ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19" ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10" ; havana_transcript "OTTHUMT00000256672.2" ; hgnc_id "HGNC:11973" ; level 2 ; orig_coord_info "chr2,217897798,217897965,-" ; protein_id "ENSP00000171887.4" ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8" ; transcript_name "TNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TNS1--ALK HAVANA gene 59295 94299 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "TNS1--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding TNS1--ALK HAVANA mRNA 59295 94299 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "TNS1--ALK^ENST00000389048.8" ; Parent "TNS1--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TRPC2--WEE1 HAVANA gene 21081 33282 . + . FI_gene_label "WEE1^ENSG00000166483.12" ; ID "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; ccdsid "CCDS44536.1" ; exon_id "ENSE00003609415.1" ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4" ; havana_transcript "OTTHUMT00000386758.2" ; hgnc_id "HGNC:12761" ; level 2 ; orig_coord_info "chr11,9575954,9576093,+" ; protein_id "ENSP00000299613.5" ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10" ; transcript_name "WEE1-201" ; transcript_support_level 2 ; transcript_type protein_coding TRPC2--WEE1 HAVANA mRNA 21081 33282 . + . FI_gene_label "WEE1^ENSG00000166483.12" ; ID "TRPC2--WEE1^ENST00000299613.10" ; Parent "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; ccdsid "CCDS44536.1" ; exon_id "ENSE00003609415.1" ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4" ; havana_transcript "OTTHUMT00000386758.2" ; hgnc_id "HGNC:12761" ; level 2 ; orig_coord_info "chr11,9575954,9576093,+" ; protein_id "ENSP00000299613.5" ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10" ; transcript_name "WEE1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: ZNF143--LINC02751 HAVANA gene 1705 21295 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "ZNF143--LINC02751^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "ZNF143--LINC02751^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "ZNF143--LINC02751^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding ZNF143--LINC02751 HAVANA mRNA 1705 21295 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "ZNF143--LINC02751^ENST00000299606.6" ; Parent "ZNF143--LINC02751^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "ZNF143--LINC02751^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "ZNF143--LINC02751^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: AL845331.2--AFF3 HAVANA gene 1001 6028 . + . FI_gene_label "AL845331.2^ENSG00000261522.5" ; ID "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5" ; exon_id "ENSE00002584959.1" ; exon_number 1 ; gene_id "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5" ; gene_name "AL845331.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175551.1" ; havana_transcript "OTTHUMT00000430470.1" ; level 2 ; orig_coord_info "chr2,94587081,94587183,-" ; tag basic ; transcript_id "AL845331.2--AFF3^ENST00000562821.5" ; transcript_name "AL845331.2-201" ; transcript_support_level 2 ; transcript_type processed_transcript AL845331.2--AFF3 HAVANA RNA 1001 6028 . + . FI_gene_label "AL845331.2^ENSG00000261522.5" ; ID "AL845331.2--AFF3^ENST00000562821.5" ; Parent "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5" ; exon_id "ENSE00002584959.1" ; exon_number 1 ; gene_id "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5" ; gene_name "AL845331.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175551.1" ; havana_transcript "OTTHUMT00000430470.1" ; level 2 ; orig_coord_info "chr2,94587081,94587183,-" ; tag basic ; transcript_id "AL845331.2--AFF3^ENST00000562821.5" ; transcript_name "AL845331.2-201" ; transcript_support_level 2 ; transcript_type processed_transcript L1 and L2 created: ALK--SNF8P1 HAVANA gene 39006 40101 . + . FI_gene_label "SNF8P1^ENSG00000203387.2" ; ID "ALK--SNF8P1^SNF8P1^ENSG00000203387.2" ; exon_id "ENSE00001730959.1" ; exon_number 1 ; gene_id "ALK--SNF8P1^SNF8P1^ENSG00000203387.2" ; gene_name SNF8P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153587.2" ; havana_transcript "OTTHUMT00000331756.2" ; hgnc_id "HGNC:54702" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr2,228352120,228353215,-" ; tag pseudo_consens basic ; transcript_id "ALK--SNF8P1^ENST00000428788.1" ; transcript_name "SNF8P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene ALK--SNF8P1 HAVANA RNA 39006 40101 . + . FI_gene_label "SNF8P1^ENSG00000203387.2" ; ID "ALK--SNF8P1^ENST00000428788.1" ; Parent "ALK--SNF8P1^SNF8P1^ENSG00000203387.2" ; exon_id "ENSE00001730959.1" ; exon_number 1 ; gene_id "ALK--SNF8P1^SNF8P1^ENSG00000203387.2" ; gene_name SNF8P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153587.2" ; havana_transcript "OTTHUMT00000331756.2" ; hgnc_id "HGNC:54702" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr2,228352120,228353215,-" ; tag pseudo_consens basic ; transcript_id "ALK--SNF8P1^ENST00000428788.1" ; transcript_name "SNF8P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: BMS1P23--AFF3 HAVANA gene 2071 7422 . + . FI_gene_label "BMS1P23^ENSG00000286156.1" ; ID "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1" ; exon_id "ENSE00003847039.1" ; exon_number 1 ; gene_id "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1" ; gene_name BMS1P23 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193495.2" ; havana_transcript "OTTHUMT00000502279.1" ; hgnc_id "HGNC:55088" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr2,94203214,94203287,-" ; tag basic ; transcript_id "BMS1P23--AFF3^ENST00000651108.1" ; transcript_name "BMS1P23-201" ; transcript_type transcribed_unprocessed_pseudogene BMS1P23--AFF3 HAVANA RNA 2071 7422 . + . FI_gene_label "BMS1P23^ENSG00000286156.1" ; ID "BMS1P23--AFF3^ENST00000651108.1" ; Parent "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1" ; exon_id "ENSE00003847039.1" ; exon_number 1 ; gene_id "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1" ; gene_name BMS1P23 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193495.2" ; havana_transcript "OTTHUMT00000502279.1" ; hgnc_id "HGNC:55088" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr2,94203214,94203287,-" ; tag basic ; transcript_id "BMS1P23--AFF3^ENST00000651108.1" ; transcript_name "BMS1P23-201" ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: SBF2--AC009869.1 HAVANA gene 62814 67704 . + . FI_gene_label "AC009869.1^ENSG00000286960.1" ; ID "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1" ; exon_id "ENSE00003867542.1" ; exon_number 1 ; gene_id "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1" ; gene_name "AC009869.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195097.1" ; havana_transcript "OTTHUMT00000524440.1" ; level 2 ; orig_coord_info "chr11,15864452,15866497,+" ; tag basic TAGENE ; transcript_id "SBF2--AC009869.1^ENST00000659436.1" ; transcript_name "AC009869.1-201" ; transcript_type lncRNA SBF2--AC009869.1 HAVANA RNA 62814 67704 . + . FI_gene_label "AC009869.1^ENSG00000286960.1" ; ID "SBF2--AC009869.1^ENST00000659436.1" ; Parent "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1" ; exon_id "ENSE00003867542.1" ; exon_number 1 ; gene_id "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1" ; gene_name "AC009869.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195097.1" ; havana_transcript "OTTHUMT00000524440.1" ; level 2 ; orig_coord_info "chr11,15864452,15866497,+" ; tag basic TAGENE ; transcript_id "SBF2--AC009869.1^ENST00000659436.1" ; transcript_name "AC009869.1-201" ; transcript_type lncRNA L1 and L2 created: SBF2--AC087379.1 HAVANA gene 62814 71750 . + . FI_gene_label "AC087379.1^ENSG00000254645.2" ; ID "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2" ; exon_id "ENSE00002159676.1" ; exon_number 1 ; gene_id "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2" ; gene_name "AC087379.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166009.2" ; havana_transcript "OTTHUMT00000387434.1" ; level 2 ; orig_coord_info "chr11,15758712,15758898,-" ; tag basic ; transcript_id "SBF2--AC087379.1^ENST00000524613.1" ; transcript_name "AC087379.1-201" ; transcript_support_level 5 ; transcript_type lncRNA SBF2--AC087379.1 HAVANA RNA 62814 71750 . + . FI_gene_label "AC087379.1^ENSG00000254645.2" ; ID "SBF2--AC087379.1^ENST00000524613.1" ; Parent "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2" ; exon_id "ENSE00002159676.1" ; exon_number 1 ; gene_id "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2" ; gene_name "AC087379.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166009.2" ; havana_transcript "OTTHUMT00000387434.1" ; level 2 ; orig_coord_info "chr11,15758712,15758898,-" ; tag basic ; transcript_id "SBF2--AC087379.1^ENST00000524613.1" ; transcript_name "AC087379.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TRPC2--WEE1 HAVANA gene 1001 17053 . + . FI_gene_label "TRPC2^ENSG00000182048.11" ; ID "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; exon_id "ENSE00001745449.1" ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2" ; havana_transcript "OTTHUMT00000032350.2" ; hgnc_id "HGNC:12334" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3609901,3609989,+" ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6" ; transcript_name "TRPC2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene TRPC2--WEE1 HAVANA RNA 1001 17053 . + . FI_gene_label "TRPC2^ENSG00000182048.11" ; ID "TRPC2--WEE1^ENST00000451043.6" ; Parent "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; exon_id "ENSE00001745449.1" ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2" ; havana_transcript "OTTHUMT00000032350.2" ; hgnc_id "HGNC:12334" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3609901,3609989,+" ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6" ; transcript_name "TRPC2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: ZNF143--LINC02751 HAVANA gene 24539 29168 . + . FI_gene_label "LINC02751^ENSG00000254946.2" ; ID "ZNF143--LINC02751^LINC02751^ENSG00000254946.2" ; exon_id "ENSE00002192715.1" ; exon_number 1 ; gene_id "ZNF143--LINC02751^LINC02751^ENSG00000254946.2" ; gene_name LINC02751 ; gene_type lncRNA ; havana_gene "OTTHUMG00000165839.3" ; havana_transcript "OTTHUMT00000386597.1" ; hgnc_id "HGNC:54271" ; level 2 ; orig_coord_info "chr11,15552855,15552913,+" ; tag dotter_confirmed basic ; transcript_id "ZNF143--LINC02751^ENST00000527770.1" ; transcript_name "LINC02751-201" ; transcript_support_level 4 ; transcript_type lncRNA ZNF143--LINC02751 HAVANA RNA 24539 29168 . + . FI_gene_label "LINC02751^ENSG00000254946.2" ; ID "ZNF143--LINC02751^ENST00000527770.1" ; Parent "ZNF143--LINC02751^LINC02751^ENSG00000254946.2" ; exon_id "ENSE00002192715.1" ; exon_number 1 ; gene_id "ZNF143--LINC02751^LINC02751^ENSG00000254946.2" ; gene_name LINC02751 ; gene_type lncRNA ; havana_gene "OTTHUMG00000165839.3" ; havana_transcript "OTTHUMT00000386597.1" ; hgnc_id "HGNC:54271" ; level 2 ; orig_coord_info "chr11,15552855,15552913,+" ; tag dotter_confirmed basic ; transcript_id "ZNF143--LINC02751^ENST00000527770.1" ; transcript_name "LINC02751-201" ; transcript_support_level 4 ; transcript_type lncRNA 433 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 ------------------------------ 827 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 26 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