Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/b011455722ee900b43e215398f54b9/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/e1f2dd4d88a44958154d42e1bd0897/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/e1f2dd4d88a44958154d42e1bd0897/.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: 4538 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 4538 => 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:4538 => 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: AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: AGAP3--BRAF HAVANA gene 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding AGAP3--BRAF HAVANA mRNA 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^ENST00000288602.11" ; Parent "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AGAP3--BRAF HAVANA gene 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding AGAP3--BRAF HAVANA mRNA 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^ENST00000335367.7" ; Parent "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GUCY1B2--NKAIN2 HAVANA gene 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding GUCY1B2--NKAIN2 HAVANA mRNA 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^ENST00000368416.5" ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: LINC00381--NKAIN2 HAVANA gene 10218 17864 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding LINC00381--NKAIN2 HAVANA mRNA 10218 17864 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "LINC00381--NKAIN2^ENST00000368416.5" ; Parent "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; 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: REXO5--TMX1 HAVANA gene 1099 21542 . + . FI_gene_label "REXO5^ENSG00000005189.20" ; ID "REXO5--TMX1^REXO5^ENSG00000005189.20" ; ccdsid "CCDS10591.1" ; exon_id "ENSE00003615038.1" ; exon_number 2 ; gene_id "REXO5--TMX1^REXO5^ENSG00000005189.20" ; gene_name REXO5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131556.5" ; havana_transcript "OTTHUMT00000254418.3" ; hgnc_id "HGNC:24661" ; level 2 ; orig_coord_info "chr16,20806954,20807091,+" ; protein_id "ENSP00000261377.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "REXO5--TMX1^ENST00000261377.11" ; transcript_name "REXO5-201" ; transcript_support_level 1 ; transcript_type protein_coding REXO5--TMX1 HAVANA mRNA 1099 21542 . + . FI_gene_label "REXO5^ENSG00000005189.20" ; ID "REXO5--TMX1^ENST00000261377.11" ; Parent "REXO5--TMX1^REXO5^ENSG00000005189.20" ; ccdsid "CCDS10591.1" ; exon_id "ENSE00003615038.1" ; exon_number 2 ; gene_id "REXO5--TMX1^REXO5^ENSG00000005189.20" ; gene_name REXO5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131556.5" ; havana_transcript "OTTHUMT00000254418.3" ; hgnc_id "HGNC:24661" ; level 2 ; orig_coord_info "chr16,20806954,20807091,+" ; protein_id "ENSP00000261377.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "REXO5--TMX1^ENST00000261377.11" ; transcript_name "REXO5-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: REXO5--TMX1 HAVANA gene 24628 34369 . + . FI_gene_label "TMX1^ENSG00000139921.13" ; ID "REXO5--TMX1^TMX1^ENSG00000139921.13" ; ccdsid "CCDS41953.1" ; exon_id "ENSE00000940750.8" ; exon_number 1 ; gene_id "REXO5--TMX1^TMX1^ENSG00000139921.13" ; gene_name TMX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171003.4" ; havana_transcript "OTTHUMT00000411206.3" ; hgnc_id "HGNC:15487" ; level 2 ; orig_coord_info "chr14,51240293,51240444,+" ; protein_id "ENSP00000393316.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "REXO5--TMX1^ENST00000457354.7" ; transcript_name "TMX1-201" ; transcript_support_level 1 ; transcript_type protein_coding REXO5--TMX1 HAVANA mRNA 24628 34369 . + . FI_gene_label "TMX1^ENSG00000139921.13" ; ID "REXO5--TMX1^ENST00000457354.7" ; Parent "REXO5--TMX1^TMX1^ENSG00000139921.13" ; ccdsid "CCDS41953.1" ; exon_id "ENSE00000940750.8" ; exon_number 1 ; gene_id "REXO5--TMX1^TMX1^ENSG00000139921.13" ; gene_name TMX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171003.4" ; havana_transcript "OTTHUMT00000411206.3" ; hgnc_id "HGNC:15487" ; level 2 ; orig_coord_info "chr14,51240293,51240444,+" ; protein_id "ENSP00000393316.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "REXO5--TMX1^ENST00000457354.7" ; transcript_name "TMX1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SMARCD3--MGAM HAVANA gene 5516 13337 . + . FI_gene_label "SMARCD3^ENSG00000082014.17" ; ID "SMARCD3--MGAM^SMARCD3^ENSG00000082014.17" ; ccdsid "CCDS34780.1" ; exon_id "ENSE00001475292.5" ; exon_number 1 ; gene_id "SMARCD3--MGAM^SMARCD3^ENSG00000082014.17" ; gene_name SMARCD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157431.7" ; havana_transcript "OTTHUMT00000348825.1" ; hgnc_id "HGNC:11108" ; level 2 ; orig_coord_info "chr7,151248485,151248562,-" ; protein_id "ENSP00000262188.8" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SMARCD3--MGAM^ENST00000262188.13" ; transcript_name "SMARCD3-201" ; transcript_support_level 1 ; transcript_type protein_coding SMARCD3--MGAM HAVANA mRNA 5516 13337 . + . FI_gene_label "SMARCD3^ENSG00000082014.17" ; ID "SMARCD3--MGAM^ENST00000262188.13" ; Parent "SMARCD3--MGAM^SMARCD3^ENSG00000082014.17" ; ccdsid "CCDS34780.1" ; exon_id "ENSE00001475292.5" ; exon_number 1 ; gene_id "SMARCD3--MGAM^SMARCD3^ENSG00000082014.17" ; gene_name SMARCD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157431.7" ; havana_transcript "OTTHUMT00000348825.1" ; hgnc_id "HGNC:11108" ; level 2 ; orig_coord_info "chr7,151248485,151248562,-" ; protein_id "ENSP00000262188.8" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SMARCD3--MGAM^ENST00000262188.13" ; transcript_name "SMARCD3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SMARCD3--MGAM HAVANA gene 16354 26854 . + . FI_gene_label "MGAM^ENSG00000257335.8" ; ID "SMARCD3--MGAM^MGAM^ENSG00000257335.8" ; exon_id "ENSE00002348689.1" ; exon_number 3 ; gene_id "SMARCD3--MGAM^MGAM^ENSG00000257335.8" ; gene_name MGAM ; gene_type protein_coding ; havana_gene "OTTHUMG00000158395.10" ; havana_transcript "OTTHUMT00000351136.3" ; hgnc_id "HGNC:7043" ; level 2 ; orig_coord_info "chr7,142005531,142005657,+" ; protein_id "ENSP00000419372.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "SMARCD3--MGAM^ENST00000465654.5" ; transcript_name "MGAM-201" ; transcript_support_level 3 ; transcript_type protein_coding SMARCD3--MGAM HAVANA mRNA 16354 26854 . + . FI_gene_label "MGAM^ENSG00000257335.8" ; ID "SMARCD3--MGAM^ENST00000465654.5" ; Parent "SMARCD3--MGAM^MGAM^ENSG00000257335.8" ; exon_id "ENSE00002348689.1" ; exon_number 3 ; gene_id "SMARCD3--MGAM^MGAM^ENSG00000257335.8" ; gene_name MGAM ; gene_type protein_coding ; havana_gene "OTTHUMG00000158395.10" ; havana_transcript "OTTHUMT00000351136.3" ; hgnc_id "HGNC:7043" ; level 2 ; orig_coord_info "chr7,142005531,142005657,+" ; protein_id "ENSP00000419372.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "SMARCD3--MGAM^ENST00000465654.5" ; transcript_name "MGAM-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: SYNE2--MTHFD1 HAVANA gene 2580 12840 . + . FI_gene_label "SYNE2^ENSG00000054654.19" ; ID "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; exon_id "ENSE00003737812.1" ; exon_number 2 ; gene_id "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; gene_name SYNE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140349.6" ; havana_transcript "OTTHUMT00000411904.2" ; hgnc_id "HGNC:17084" ; level 1 ; orig_coord_info "chr14,63909149,63909227,+" ; protein_id "ENSP00000344528.5" ; tag basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000341472.9" ; transcript_name "SYNE2-201" ; transcript_support_level 1 ; transcript_type protein_coding SYNE2--MTHFD1 HAVANA mRNA 2580 12840 . + . FI_gene_label "SYNE2^ENSG00000054654.19" ; ID "SYNE2--MTHFD1^ENST00000341472.9" ; Parent "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; exon_id "ENSE00003737812.1" ; exon_number 2 ; gene_id "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; gene_name SYNE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140349.6" ; havana_transcript "OTTHUMT00000411904.2" ; hgnc_id "HGNC:17084" ; level 1 ; orig_coord_info "chr14,63909149,63909227,+" ; protein_id "ENSP00000344528.5" ; tag basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000341472.9" ; transcript_name "SYNE2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SYNE2--MTHFD1 HAVANA gene 141022 177439 . + . FI_gene_label "MTHFD1^ENSG00000100714.17" ; ID "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; exon_id "ENSE00002279035.1" ; exon_number 1 ; gene_id "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; gene_name MTHFD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000141309.15" ; havana_transcript "OTTHUMT00000412167.3" ; hgnc_id "HGNC:7432" ; level 1 ; orig_coord_info "chr14,64388428,64388468,+" ; protein_id "ENSP00000438588.2" ; tag upstream_ATG 3_standard_supported_extension basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000545908.6" ; transcript_name "MTHFD1-201" ; transcript_support_level 2 ; transcript_type protein_coding SYNE2--MTHFD1 HAVANA mRNA 141022 177439 . + . FI_gene_label "MTHFD1^ENSG00000100714.17" ; ID "SYNE2--MTHFD1^ENST00000545908.6" ; Parent "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; exon_id "ENSE00002279035.1" ; exon_number 1 ; gene_id "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; gene_name MTHFD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000141309.15" ; havana_transcript "OTTHUMT00000412167.3" ; hgnc_id "HGNC:7432" ; level 1 ; orig_coord_info "chr14,64388428,64388468,+" ; protein_id "ENSP00000438588.2" ; tag upstream_ATG 3_standard_supported_extension basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000545908.6" ; transcript_name "MTHFD1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: 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: AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA L1 and L2 created: GUCY1B2--NKAIN2 HAVANA gene 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript GUCY1B2--NKAIN2 HAVANA RNA 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^ENST00000389600.6" ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: LINC00381--NKAIN2 HAVANA gene 1016 4365 . + . FI_gene_label "LINC00381^ENSG00000226240.2" ; ID "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; exon_id "ENSE00001743371.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2" ; havana_transcript "OTTHUMT00000045275.1" ; hgnc_id "HGNC:42708" ; level 2 ; orig_coord_info "chr13,74419173,74419228,+" ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1" ; transcript_name "LINC00381-201" ; transcript_support_level 5 ; transcript_type lncRNA LINC00381--NKAIN2 HAVANA RNA 1016 4365 . + . FI_gene_label "LINC00381^ENSG00000226240.2" ; ID "LINC00381--NKAIN2^ENST00000423629.1" ; Parent "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; exon_id "ENSE00001743371.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2" ; havana_transcript "OTTHUMT00000045275.1" ; hgnc_id "HGNC:42708" ; level 2 ; orig_coord_info "chr13,74419173,74419228,+" ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1" ; transcript_name "LINC00381-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: 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 241 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 ------------------------------ 480 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 18 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