Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b682ccadbf844b961aa4dc1813606f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/b3b0bda5c86f4db19c4feacf537fa2/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b682ccadbf844b961aa4dc1813606f/.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: 3526 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3526 => 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:3526 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 1 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: AGAP1--SH3BP4 HAVANA gene 1001 37685 . + . FI_gene_label "AGAP1^ENSG00000157985.19" ; ID "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19" ; ccdsid "CCDS33408.1" ; exon_id "ENSE00003848629.1" ; exon_number 1 ; gene_id "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19" ; gene_name AGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133293.7" ; havana_transcript "OTTHUMT00000257076.3" ; hgnc_id "HGNC:16922" ; level 2 ; orig_coord_info "chr2,235494687,235494849,+" ; protein_id "ENSP00000307634.7" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000304032.13" ; transcript_name "AGAP1-201" ; transcript_support_level 5 ; transcript_type protein_coding AGAP1--SH3BP4 HAVANA mRNA 1001 37685 . + . FI_gene_label "AGAP1^ENSG00000157985.19" ; ID "AGAP1--SH3BP4^ENST00000304032.13" ; Parent "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19" ; ccdsid "CCDS33408.1" ; exon_id "ENSE00003848629.1" ; exon_number 1 ; gene_id "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19" ; gene_name AGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133293.7" ; havana_transcript "OTTHUMT00000257076.3" ; hgnc_id "HGNC:16922" ; level 2 ; orig_coord_info "chr2,235494687,235494849,+" ; protein_id "ENSP00000307634.7" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000304032.13" ; transcript_name "AGAP1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: AGAP1--SH3BP4 HAVANA gene 42885 58440 . + . FI_gene_label "SH3BP4^ENSG00000130147.16" ; ID "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16" ; ccdsid "CCDS2513.1" ; exon_id "ENSE00001589692.1" ; exon_number 3 ; gene_id "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16" ; gene_name SH3BP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133292.5" ; havana_transcript "OTTHUMT00000329764.1" ; hgnc_id "HGNC:10826" ; level 2 ; orig_coord_info "chr2,235035003,235035120,+" ; protein_id "ENSP00000340237.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000344528.8" ; transcript_name "SH3BP4-201" ; transcript_support_level 1 ; transcript_type protein_coding AGAP1--SH3BP4 HAVANA mRNA 42885 58440 . + . FI_gene_label "SH3BP4^ENSG00000130147.16" ; ID "AGAP1--SH3BP4^ENST00000344528.8" ; Parent "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16" ; ccdsid "CCDS2513.1" ; exon_id "ENSE00001589692.1" ; exon_number 3 ; gene_id "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16" ; gene_name SH3BP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133292.5" ; havana_transcript "OTTHUMT00000329764.1" ; hgnc_id "HGNC:10826" ; level 2 ; orig_coord_info "chr2,235035003,235035120,+" ; protein_id "ENSP00000340237.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000344528.8" ; transcript_name "SH3BP4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AL669831.4--SEPTIN14 HAVANA gene 8876 22423 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding AL669831.4--SEPTIN14 HAVANA mRNA 8876 22423 . + . FI_gene_label "SEPTIN14^ENSG00000154997.9" ; ID "AL669831.4--SEPTIN14^ENST00000388975.4" ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; ccdsid "CCDS5519.2" ; exon_id "ENSE00003671928.1" ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9" ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4" ; havana_transcript "OTTHUMT00000251489.3" ; hgnc_id "HGNC:33280" ; level 2 ; orig_coord_info "chr7,55861943,55861996,-" ; protein_id "ENSP00000373627.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4" ; transcript_name "SEPTIN14-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: ARMCX2--BTK HAVANA gene 9923 27240 . + . FI_gene_label "BTK^ENSG00000010671.16" ; ID "ARMCX2--BTK^BTK^ENSG00000010671.16" ; ccdsid "CCDS14482.1" ; exon_id "ENSE00003687319.1" ; exon_number 2 ; gene_id "ARMCX2--BTK^BTK^ENSG00000010671.16" ; gene_name BTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000022022.2" ; havana_transcript "OTTHUMT00000057532.2" ; hgnc_id "HGNC:1133" ; level 2 ; orig_coord_info "chrX,101375144,101375284,-" ; protein_id "ENSP00000308176.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000308731.8" ; transcript_name "BTK-201" ; transcript_support_level 1 ; transcript_type protein_coding ARMCX2--BTK HAVANA mRNA 9923 27240 . + . FI_gene_label "BTK^ENSG00000010671.16" ; ID "ARMCX2--BTK^ENST00000308731.8" ; Parent "ARMCX2--BTK^BTK^ENSG00000010671.16" ; ccdsid "CCDS14482.1" ; exon_id "ENSE00003687319.1" ; exon_number 2 ; gene_id "ARMCX2--BTK^BTK^ENSG00000010671.16" ; gene_name BTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000022022.2" ; havana_transcript "OTTHUMT00000057532.2" ; hgnc_id "HGNC:1133" ; level 2 ; orig_coord_info "chrX,101375144,101375284,-" ; protein_id "ENSP00000308176.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000308731.8" ; transcript_name "BTK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ARMCX2--BTK HAVANA gene 1007 5570 . + . FI_gene_label "ARMCX2^ENSG00000184867.14" ; ID "ARMCX2--BTK^ARMCX2^ENSG00000184867.14" ; ccdsid "CCDS14490.1" ; exon_id "ENSE00001347589.3" ; exon_number 5 ; gene_id "ARMCX2--BTK^ARMCX2^ENSG00000184867.14" ; gene_name ARMCX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022038.4" ; havana_transcript "OTTHUMT00000057586.1" ; hgnc_id "HGNC:16869" ; level 2 ; orig_coord_info "chrX,101655693,101657588,-" ; protein_id "ENSP00000331662.5" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000328766.9" ; transcript_name "ARMCX2-201" ; transcript_support_level 1 ; transcript_type protein_coding ARMCX2--BTK HAVANA mRNA 1007 5570 . + . FI_gene_label "ARMCX2^ENSG00000184867.14" ; ID "ARMCX2--BTK^ENST00000328766.9" ; Parent "ARMCX2--BTK^ARMCX2^ENSG00000184867.14" ; ccdsid "CCDS14490.1" ; exon_id "ENSE00001347589.3" ; exon_number 5 ; gene_id "ARMCX2--BTK^ARMCX2^ENSG00000184867.14" ; gene_name ARMCX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022038.4" ; havana_transcript "OTTHUMT00000057586.1" ; hgnc_id "HGNC:16869" ; level 2 ; orig_coord_info "chrX,101655693,101657588,-" ; protein_id "ENSP00000331662.5" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000328766.9" ; transcript_name "ARMCX2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCDC6--RET HAVANA gene 1001 16128 . + . FI_gene_label "CCDC6^ENSG00000108091.11" ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11" ; ccdsid "CCDS7257.1" ; exon_id "ENSE00001950758.3" ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11" ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3" ; havana_transcript "OTTHUMT00000048176.3" ; hgnc_id "HGNC:18782" ; level 2 ; orig_coord_info "chr10,59906122,59906424,-" ; protein_id "ENSP00000263102.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7" ; transcript_name "CCDC6-201" ; transcript_support_level 1 ; transcript_type protein_coding CCDC6--RET HAVANA mRNA 1001 16128 . + . FI_gene_label "CCDC6^ENSG00000108091.11" ; ID "CCDC6--RET^ENST00000263102.7" ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11" ; ccdsid "CCDS7257.1" ; exon_id "ENSE00001950758.3" ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11" ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3" ; havana_transcript "OTTHUMT00000048176.3" ; hgnc_id "HGNC:18782" ; level 2 ; orig_coord_info "chr10,59906122,59906424,-" ; protein_id "ENSP00000263102.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7" ; transcript_name "CCDC6-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCDC6--RET HAVANA gene 19134 39754 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "CCDC6--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding CCDC6--RET HAVANA mRNA 19134 39754 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "CCDC6--RET^ENST00000340058.6" ; Parent "CCDC6--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CYB5R3--NDUFA6 HAVANA gene 1001 14475 . + . FI_gene_label "CYB5R3^ENSG00000100243.21" ; ID "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21" ; ccdsid "CCDS33658.1" ; exon_id "ENSE00001892790.2" ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21" ; gene_name CYB5R3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150745.7" ; havana_transcript "OTTHUMT00000320439.2" ; hgnc_id "HGNC:2873" ; level 2 ; orig_coord_info "chr22,42649295,42649315,-" ; protein_id "ENSP00000338461.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYB5R3--NDUFA6^ENST00000352397.10" ; transcript_name "CYB5R3-201" ; transcript_support_level 1 ; transcript_type protein_coding CYB5R3--NDUFA6 HAVANA mRNA 1001 14475 . + . FI_gene_label "CYB5R3^ENSG00000100243.21" ; ID "CYB5R3--NDUFA6^ENST00000352397.10" ; Parent "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21" ; ccdsid "CCDS33658.1" ; exon_id "ENSE00001892790.2" ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21" ; gene_name CYB5R3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150745.7" ; havana_transcript "OTTHUMT00000320439.2" ; hgnc_id "HGNC:2873" ; level 2 ; orig_coord_info "chr22,42649295,42649315,-" ; protein_id "ENSP00000338461.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYB5R3--NDUFA6^ENST00000352397.10" ; transcript_name "CYB5R3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CYB5R3--NDUFA6 HAVANA gene 18755 19974 . + . FI_gene_label "NDUFA6^ENSG00000184983.11" ; ID "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11" ; exon_id "ENSE00001919192.1" ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11" ; gene_name NDUFA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151287.6" ; havana_transcript "OTTHUMT00000322090.2" ; hgnc_id "HGNC:7690" ; level 2 ; orig_coord_info "chr22,42087060,42087143,-" ; protein_id "ENSP00000473478.1" ; tag RP_supported_TIS basic ; transcript_id "CYB5R3--NDUFA6^ENST00000470753.1" ; transcript_name "NDUFA6-201" ; transcript_support_level 2 ; transcript_type protein_coding CYB5R3--NDUFA6 HAVANA mRNA 18755 19974 . + . FI_gene_label "NDUFA6^ENSG00000184983.11" ; ID "CYB5R3--NDUFA6^ENST00000470753.1" ; Parent "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11" ; exon_id "ENSE00001919192.1" ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11" ; gene_name NDUFA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151287.6" ; havana_transcript "OTTHUMT00000322090.2" ; hgnc_id "HGNC:7690" ; level 2 ; orig_coord_info "chr22,42087060,42087143,-" ; protein_id "ENSP00000473478.1" ; tag RP_supported_TIS basic ; transcript_id "CYB5R3--NDUFA6^ENST00000470753.1" ; transcript_name "NDUFA6-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: EIF3E--RSPO2 HAVANA gene 23210 53212 . + . FI_gene_label "EIF3E^ENSG00000104408.11" ; ID "EIF3E--RSPO2^EIF3E^ENSG00000104408.11" ; ccdsid "CCDS6308.1" ; exon_id "ENSE00003671921.1" ; exon_number 1 ; gene_id "EIF3E--RSPO2^EIF3E^ENSG00000104408.11" ; gene_name EIF3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000164858.7" ; havana_transcript "OTTHUMT00000380612.3" ; hgnc_id "HGNC:3277" ; level 2 ; orig_coord_info "chr8,108248613,108248702,-" ; protein_id "ENSP00000220849.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000220849.10" ; transcript_name "EIF3E-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF3E--RSPO2 HAVANA mRNA 23210 53212 . + . FI_gene_label "EIF3E^ENSG00000104408.11" ; ID "EIF3E--RSPO2^ENST00000220849.10" ; Parent "EIF3E--RSPO2^EIF3E^ENSG00000104408.11" ; ccdsid "CCDS6308.1" ; exon_id "ENSE00003671921.1" ; exon_number 1 ; gene_id "EIF3E--RSPO2^EIF3E^ENSG00000104408.11" ; gene_name EIF3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000164858.7" ; havana_transcript "OTTHUMT00000380612.3" ; hgnc_id "HGNC:3277" ; level 2 ; orig_coord_info "chr8,108248613,108248702,-" ; protein_id "ENSP00000220849.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000220849.10" ; transcript_name "EIF3E-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EIF3E--RSPO2 HAVANA gene 61623 73686 . + . FI_gene_label "RSPO2^ENSG00000147655.12" ; ID "EIF3E--RSPO2^RSPO2^ENSG00000147655.12" ; ccdsid "CCDS6307.1" ; exon_id "ENSE00001378581.2" ; exon_number 2 ; gene_id "EIF3E--RSPO2^RSPO2^ENSG00000147655.12" ; gene_name RSPO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164893.4" ; havana_transcript "OTTHUMT00000380830.2" ; hgnc_id "HGNC:28583" ; level 2 ; orig_coord_info "chr8,108082545,108082638,-" ; protein_id "ENSP00000276659.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000276659.10" ; transcript_name "RSPO2-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF3E--RSPO2 HAVANA mRNA 61623 73686 . + . FI_gene_label "RSPO2^ENSG00000147655.12" ; ID "EIF3E--RSPO2^ENST00000276659.10" ; Parent "EIF3E--RSPO2^RSPO2^ENSG00000147655.12" ; ccdsid "CCDS6307.1" ; exon_id "ENSE00001378581.2" ; exon_number 2 ; gene_id "EIF3E--RSPO2^RSPO2^ENSG00000147655.12" ; gene_name RSPO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164893.4" ; havana_transcript "OTTHUMT00000380830.2" ; hgnc_id "HGNC:28583" ; level 2 ; orig_coord_info "chr8,108082545,108082638,-" ; protein_id "ENSP00000276659.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000276659.10" ; transcript_name "RSPO2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MANBA--AC098487.1 HAVANA gene 1062 34457 . + . FI_gene_label "MANBA^ENSG00000109323.11" ; ID "MANBA--AC098487.1^MANBA^ENSG00000109323.11" ; exon_id "ENSE00002066732.1" ; exon_number 1 ; gene_id "MANBA--AC098487.1^MANBA^ENSG00000109323.11" ; gene_name MANBA ; gene_type protein_coding ; havana_gene "OTTHUMG00000131123.14" ; havana_transcript "OTTHUMT00000363561.1" ; hgnc_id "HGNC:6831" ; level 2 ; orig_coord_info "chr4,102760718,102760894,-" ; protein_id "ENSP00000427322.1" ; tag basic ; transcript_id "MANBA--AC098487.1^ENST00000505239.1" ; transcript_name "MANBA-201" ; transcript_support_level 2 ; transcript_type protein_coding MANBA--AC098487.1 HAVANA mRNA 1062 34457 . + . FI_gene_label "MANBA^ENSG00000109323.11" ; ID "MANBA--AC098487.1^ENST00000505239.1" ; Parent "MANBA--AC098487.1^MANBA^ENSG00000109323.11" ; exon_id "ENSE00002066732.1" ; exon_number 1 ; gene_id "MANBA--AC098487.1^MANBA^ENSG00000109323.11" ; gene_name MANBA ; gene_type protein_coding ; havana_gene "OTTHUMG00000131123.14" ; havana_transcript "OTTHUMT00000363561.1" ; hgnc_id "HGNC:6831" ; level 2 ; orig_coord_info "chr4,102760718,102760894,-" ; protein_id "ENSP00000427322.1" ; tag basic ; transcript_id "MANBA--AC098487.1^ENST00000505239.1" ; transcript_name "MANBA-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: SLCO1B3--SLCO1B7 ENSEMBL gene 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding SLCO1B3--SLCO1B7 ENSEMBL mRNA 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6" ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TXNRD2--GNB1L HAVANA gene 29384 41811 . + . FI_gene_label "GNB1L^ENSG00000185838.14" ; ID "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14" ; ccdsid "CCDS13768.1" ; exon_id "ENSE00001297632.2" ; exon_number 3 ; gene_id "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14" ; gene_name GNB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000150279.4" ; havana_transcript "OTTHUMT00000075202.2" ; hgnc_id "HGNC:4397" ; level 2 ; orig_coord_info "chr22,19821228,19821355,-" ; protein_id "ENSP00000331313.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000329517.11" ; transcript_name "GNB1L-201" ; transcript_support_level 1 ; transcript_type protein_coding TXNRD2--GNB1L HAVANA mRNA 29384 41811 . + . FI_gene_label "GNB1L^ENSG00000185838.14" ; ID "TXNRD2--GNB1L^ENST00000329517.11" ; Parent "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14" ; ccdsid "CCDS13768.1" ; exon_id "ENSE00001297632.2" ; exon_number 3 ; gene_id "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14" ; gene_name GNB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000150279.4" ; havana_transcript "OTTHUMT00000075202.2" ; hgnc_id "HGNC:4397" ; level 2 ; orig_coord_info "chr22,19821228,19821355,-" ; protein_id "ENSP00000331313.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000329517.11" ; transcript_name "GNB1L-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TXNRD2--GNB1L HAVANA gene 1017 16347 . + . FI_gene_label "TXNRD2^ENSG00000184470.21" ; ID "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21" ; ccdsid "CCDS63402.1" ; exon_id "ENSE00001543323.2" ; exon_number 1 ; gene_id "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21" ; gene_name TXNRD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149975.8" ; havana_transcript "OTTHUMT00000488472.1" ; hgnc_id "HGNC:18155" ; level 2 ; orig_coord_info "chr22,19941701,19941803,-" ; protein_id "ENSP00000334451.9" ; tag basic CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000334363.14" ; transcript_name "TXNRD2-201" ; transcript_support_level 1 ; transcript_type protein_coding TXNRD2--GNB1L HAVANA mRNA 1017 16347 . + . FI_gene_label "TXNRD2^ENSG00000184470.21" ; ID "TXNRD2--GNB1L^ENST00000334363.14" ; Parent "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21" ; ccdsid "CCDS63402.1" ; exon_id "ENSE00001543323.2" ; exon_number 1 ; gene_id "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21" ; gene_name TXNRD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149975.8" ; havana_transcript "OTTHUMT00000488472.1" ; hgnc_id "HGNC:18155" ; level 2 ; orig_coord_info "chr22,19941701,19941803,-" ; protein_id "ENSP00000334451.9" ; tag basic CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000334363.14" ; transcript_name "TXNRD2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: UPF1--AC011447.3 HAVANA gene 1001 23784 . + . FI_gene_label "UPF1^ENSG00000005007.13" ; ID "UPF1--AC011447.3^UPF1^ENSG00000005007.13" ; ccdsid "CCDS12386.1" ; exon_id "ENSE00001123172.8" ; exon_number 1 ; gene_id "UPF1--AC011447.3^UPF1^ENSG00000005007.13" ; gene_name UPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183025.2" ; havana_transcript "OTTHUMT00000464683.1" ; hgnc_id "HGNC:9962" ; level 2 ; orig_coord_info "chr19,18832210,18832440,+" ; protein_id "ENSP00000262803.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UPF1--AC011447.3^ENST00000262803.10" ; transcript_name "UPF1-201" ; transcript_support_level 1 ; transcript_type protein_coding UPF1--AC011447.3 HAVANA mRNA 1001 23784 . + . FI_gene_label "UPF1^ENSG00000005007.13" ; ID "UPF1--AC011447.3^ENST00000262803.10" ; Parent "UPF1--AC011447.3^UPF1^ENSG00000005007.13" ; ccdsid "CCDS12386.1" ; exon_id "ENSE00001123172.8" ; exon_number 1 ; gene_id "UPF1--AC011447.3^UPF1^ENSG00000005007.13" ; gene_name UPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183025.2" ; havana_transcript "OTTHUMT00000464683.1" ; hgnc_id "HGNC:9962" ; level 2 ; orig_coord_info "chr19,18832210,18832440,+" ; protein_id "ENSP00000262803.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UPF1--AC011447.3^ENST00000262803.10" ; transcript_name "UPF1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AL669831.4--SEPTIN14 HAVANA gene 1001 5872 . + . FI_gene_label "AL669831.4^ENSG00000230092.7" ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; exon_id "ENSE00001746491.1" ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; gene_name "AL669831.4" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3" ; havana_transcript "OTTHUMT00000448550.2" ; level 2 ; orig_coord_info "chr1,817373,817712,-" ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4" ; transcript_name "AL669831.4-201" ; transcript_support_level 5 ; transcript_type processed_transcript AL669831.4--SEPTIN14 HAVANA RNA 1001 5872 . + . FI_gene_label "AL669831.4^ENSG00000230092.7" ; ID "AL669831.4--SEPTIN14^ENST00000447500.4" ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; exon_id "ENSE00001746491.1" ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7" ; gene_name "AL669831.4" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3" ; havana_transcript "OTTHUMT00000448550.2" ; level 2 ; orig_coord_info "chr1,817373,817712,-" ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4" ; transcript_name "AL669831.4-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene L1 and L2 created: MANBA--AC098487.1 HAVANA gene 39797 42842 . + . FI_gene_label "AC098487.1^ENSG00000248161.5" ; ID "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5" ; exon_id "ENSE00002028515.1" ; exon_number 1 ; gene_id "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5" ; gene_name "AC098487.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10" ; havana_transcript "OTTHUMT00000363754.1" ; level 2 ; orig_coord_info "chr4,102431062,102431249,-" ; tag dotter_confirmed ; transcript_id "MANBA--AC098487.1^ENST00000502883.5" ; transcript_name "AC098487.1-201" ; transcript_support_level 5 ; transcript_type lncRNA MANBA--AC098487.1 HAVANA RNA 39797 42842 . + . FI_gene_label "AC098487.1^ENSG00000248161.5" ; ID "MANBA--AC098487.1^ENST00000502883.5" ; Parent "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5" ; exon_id "ENSE00002028515.1" ; exon_number 1 ; gene_id "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5" ; gene_name "AC098487.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10" ; havana_transcript "OTTHUMT00000363754.1" ; level 2 ; orig_coord_info "chr4,102431062,102431249,-" ; tag dotter_confirmed ; transcript_id "MANBA--AC098487.1^ENST00000502883.5" ; transcript_name "AC098487.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: SLCO1B3--SLCO1B7 HAVANA gene 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript SLCO1B3--SLCO1B7 HAVANA RNA 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1" ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: UPF1--AC011447.3 HAVANA gene 30125 36749 . + . FI_gene_label "AC011447.3^ENSG00000267383.7" ; ID "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7" ; exon_id "ENSE00002836707.1" ; exon_number 1 ; gene_id "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7" ; gene_name "AC011447.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000180742.4" ; havana_transcript "OTTHUMT00000452861.1" ; level 2 ; orig_coord_info "chr19,20238288,20238460,-" ; transcript_id "UPF1--AC011447.3^ENST00000585498.1" ; transcript_name "AC011447.3-204" ; transcript_support_level 2 ; transcript_type lncRNA UPF1--AC011447.3 HAVANA RNA 30125 36749 . + . FI_gene_label "AC011447.3^ENSG00000267383.7" ; ID "UPF1--AC011447.3^ENST00000585498.1" ; Parent "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7" ; exon_id "ENSE00002836707.1" ; exon_number 1 ; gene_id "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7" ; gene_name "AC011447.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000180742.4" ; havana_transcript "OTTHUMT00000452861.1" ; level 2 ; orig_coord_info "chr19,20238288,20238460,-" ; transcript_id "UPF1--AC011447.3^ENST00000585498.1" ; transcript_name "AC011447.3-204" ; transcript_support_level 2 ; transcript_type lncRNA 266 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 ------------------------------ 594 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 22 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