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: 4572 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 4572 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => exon CDS * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:4572 => 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: ACTBP6--ACTB HAVANA gene 6203 10583 . + . FI_gene_label "ACTB^ENSG00000075624.17" ; ID "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; exon_id "ENSE00003542066.1" ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12" ; havana_transcript "OTTHUMT00000324028.2" ; hgnc_id "HGNC:132" ; level 2 ; orig_coord_info "chr7,5529535,5529657,-" ; protein_id "ENSP00000401032.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1" ; transcript_name "ACTB-201" ; transcript_support_level 4 ; transcript_type protein_coding ACTBP6--ACTB HAVANA mRNA 6203 10583 . + . FI_gene_label "ACTB^ENSG00000075624.17" ; ID "ACTBP6--ACTB^ENST00000414620.1" ; Parent "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; exon_id "ENSE00003542066.1" ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12" ; havana_transcript "OTTHUMT00000324028.2" ; hgnc_id "HGNC:132" ; level 2 ; orig_coord_info "chr7,5529535,5529657,-" ; protein_id "ENSP00000401032.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1" ; transcript_name "ACTB-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: AGO2--TRAPPC9 HAVANA gene 1001 34934 . + . FI_gene_label "AGO2^ENSG00000123908.12" ; ID "AGO2--TRAPPC9^AGO2^ENSG00000123908.12" ; ccdsid "CCDS6380.1" ; exon_id "ENSE00002115766.2" ; exon_number 1 ; gene_id "AGO2--TRAPPC9^AGO2^ENSG00000123908.12" ; gene_name AGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164232.7" ; havana_transcript "OTTHUMT00000377866.6" ; hgnc_id "HGNC:3263" ; level 2 ; orig_coord_info "chr8,140635485,140635506,-" ; protein_id "ENSP00000220592.5" ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000220592.10" ; transcript_name "AGO2-201" ; transcript_support_level 1 ; transcript_type protein_coding AGO2--TRAPPC9 HAVANA mRNA 1001 34934 . + . FI_gene_label "AGO2^ENSG00000123908.12" ; ID "AGO2--TRAPPC9^ENST00000220592.10" ; Parent "AGO2--TRAPPC9^AGO2^ENSG00000123908.12" ; ccdsid "CCDS6380.1" ; exon_id "ENSE00002115766.2" ; exon_number 1 ; gene_id "AGO2--TRAPPC9^AGO2^ENSG00000123908.12" ; gene_name AGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164232.7" ; havana_transcript "OTTHUMT00000377866.6" ; hgnc_id "HGNC:3263" ; level 2 ; orig_coord_info "chr8,140635485,140635506,-" ; protein_id "ENSP00000220592.5" ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000220592.10" ; transcript_name "AGO2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AGO2--TRAPPC9 HAVANA gene 38770 79875 . + . FI_gene_label "TRAPPC9^ENSG00000167632.18" ; ID "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; ccdsid "CCDS55278.1" ; exon_id "ENSE00003610885.1" ; exon_number 2 ; gene_id "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10" ; havana_transcript "OTTHUMT00000497841.1" ; hgnc_id "HGNC:30832" ; level 2 ; orig_coord_info "chr8,140450790,140451373,-" ; protein_id "ENSP00000405060.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000438773.4" ; transcript_name "TRAPPC9-201" ; transcript_support_level 1 ; transcript_type protein_coding AGO2--TRAPPC9 HAVANA mRNA 38770 79875 . + . FI_gene_label "TRAPPC9^ENSG00000167632.18" ; ID "AGO2--TRAPPC9^ENST00000438773.4" ; Parent "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; ccdsid "CCDS55278.1" ; exon_id "ENSE00003610885.1" ; exon_number 2 ; gene_id "AGO2--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10" ; havana_transcript "OTTHUMT00000497841.1" ; hgnc_id "HGNC:30832" ; level 2 ; orig_coord_info "chr8,140450790,140451373,-" ; protein_id "ENSP00000405060.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGO2--TRAPPC9^ENST00000438773.4" ; transcript_name "TRAPPC9-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CCL28--RN7SL1 HAVANA gene 1001 7684 . + . FI_gene_label "CCL28^ENSG00000151882.11" ; ID "CCL28--RN7SL1^CCL28^ENSG00000151882.11" ; ccdsid "CCDS3944.1" ; exon_id "ENSE00001489205.3" ; exon_number 1 ; gene_id "CCL28--RN7SL1^CCL28^ENSG00000151882.11" ; gene_name CCL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094811.3" ; havana_transcript "OTTHUMT00000211631.2" ; hgnc_id "HGNC:17700" ; level 2 ; orig_coord_info "chr5,43412253,43412316,-" ; protein_id "ENSP00000354416.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCL28--RN7SL1^ENST00000361115.4" ; transcript_name "CCL28-201" ; transcript_support_level 1 ; transcript_type protein_coding CCL28--RN7SL1 HAVANA mRNA 1001 7684 . + . FI_gene_label "CCL28^ENSG00000151882.11" ; ID "CCL28--RN7SL1^ENST00000361115.4" ; Parent "CCL28--RN7SL1^CCL28^ENSG00000151882.11" ; ccdsid "CCDS3944.1" ; exon_id "ENSE00001489205.3" ; exon_number 1 ; gene_id "CCL28--RN7SL1^CCL28^ENSG00000151882.11" ; gene_name CCL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094811.3" ; havana_transcript "OTTHUMT00000211631.2" ; hgnc_id "HGNC:17700" ; level 2 ; orig_coord_info "chr5,43412253,43412316,-" ; protein_id "ENSP00000354416.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCL28--RN7SL1^ENST00000361115.4" ; transcript_name "CCL28-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CERS6--ABCB11 HAVANA gene 1024 17424 . + . FI_gene_label "CERS6^ENSG00000172292.15" ; ID "CERS6--ABCB11^CERS6^ENSG00000172292.15" ; ccdsid "CCDS2228.1" ; exon_id "ENSE00002561332.2" ; exon_number 1 ; gene_id "CERS6--ABCB11^CERS6^ENSG00000172292.15" ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4" ; havana_transcript "OTTHUMT00000255235.3" ; hgnc_id "HGNC:23826" ; level 2 ; orig_coord_info "chr2,168456449,168456618,+" ; protein_id "ENSP00000306579.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--ABCB11^ENST00000305747.11" ; transcript_name "CERS6-201" ; transcript_support_level 2 ; transcript_type protein_coding CERS6--ABCB11 HAVANA mRNA 1024 17424 . + . FI_gene_label "CERS6^ENSG00000172292.15" ; ID "CERS6--ABCB11^ENST00000305747.11" ; Parent "CERS6--ABCB11^CERS6^ENSG00000172292.15" ; ccdsid "CCDS2228.1" ; exon_id "ENSE00002561332.2" ; exon_number 1 ; gene_id "CERS6--ABCB11^CERS6^ENSG00000172292.15" ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4" ; havana_transcript "OTTHUMT00000255235.3" ; hgnc_id "HGNC:23826" ; level 2 ; orig_coord_info "chr2,168456449,168456618,+" ; protein_id "ENSP00000306579.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--ABCB11^ENST00000305747.11" ; transcript_name "CERS6-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CERS6--ABCB11 HAVANA gene 34796 51471 . + . FI_gene_label "ABCB11^ENSG00000073734.10" ; ID "CERS6--ABCB11^ABCB11^ENSG00000073734.10" ; exon_id "ENSE00001803468.1" ; exon_number 1 ; gene_id "CERS6--ABCB11^ABCB11^ENSG00000073734.10" ; gene_name ABCB11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154039.5" ; havana_transcript "OTTHUMT00000333618.2" ; hgnc_id "HGNC:42" ; level 2 ; orig_coord_info "chr2,168971847,168972032,-" ; protein_id "ENSP00000416058.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CERS6--ABCB11^ENST00000439188.1" ; transcript_name "ABCB11-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay CERS6--ABCB11 HAVANA mRNA 34796 51471 . + . FI_gene_label "ABCB11^ENSG00000073734.10" ; ID "CERS6--ABCB11^ENST00000439188.1" ; Parent "CERS6--ABCB11^ABCB11^ENSG00000073734.10" ; exon_id "ENSE00001803468.1" ; exon_number 1 ; gene_id "CERS6--ABCB11^ABCB11^ENSG00000073734.10" ; gene_name ABCB11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154039.5" ; havana_transcript "OTTHUMT00000333618.2" ; hgnc_id "HGNC:42" ; level 2 ; orig_coord_info "chr2,168971847,168972032,-" ; protein_id "ENSP00000416058.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CERS6--ABCB11^ENST00000439188.1" ; transcript_name "ABCB11-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay L1 and L2 created: CERS6--DHRS9 HAVANA gene 1024 17424 . + . FI_gene_label "CERS6^ENSG00000172292.15" ; ID "CERS6--DHRS9^CERS6^ENSG00000172292.15" ; ccdsid "CCDS2228.1" ; exon_id "ENSE00002561332.2" ; exon_number 1 ; gene_id "CERS6--DHRS9^CERS6^ENSG00000172292.15" ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4" ; havana_transcript "OTTHUMT00000255235.3" ; hgnc_id "HGNC:23826" ; level 2 ; orig_coord_info "chr2,168456449,168456618,+" ; protein_id "ENSP00000306579.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--DHRS9^ENST00000305747.11" ; transcript_name "CERS6-201" ; transcript_support_level 2 ; transcript_type protein_coding CERS6--DHRS9 HAVANA mRNA 1024 17424 . + . FI_gene_label "CERS6^ENSG00000172292.15" ; ID "CERS6--DHRS9^ENST00000305747.11" ; Parent "CERS6--DHRS9^CERS6^ENSG00000172292.15" ; ccdsid "CCDS2228.1" ; exon_id "ENSE00002561332.2" ; exon_number 1 ; gene_id "CERS6--DHRS9^CERS6^ENSG00000172292.15" ; gene_name CERS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132183.4" ; havana_transcript "OTTHUMT00000255235.3" ; hgnc_id "HGNC:23826" ; level 2 ; orig_coord_info "chr2,168456449,168456618,+" ; protein_id "ENSP00000306579.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CERS6--DHRS9^ENST00000305747.11" ; transcript_name "CERS6-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CERS6--DHRS9 HAVANA gene 22353 33271 . + . FI_gene_label "DHRS9^ENSG00000073737.17" ; ID "CERS6--DHRS9^DHRS9^ENSG00000073737.17" ; ccdsid "CCDS2231.1" ; exon_id "ENSE00003585749.1" ; exon_number 3 ; gene_id "CERS6--DHRS9^DHRS9^ENSG00000073737.17" ; gene_name DHRS9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132180.9" ; havana_transcript "OTTHUMT00000255232.1" ; hgnc_id "HGNC:16888" ; level 2 ; orig_coord_info "chr2,169081582,169081894,+" ; protein_id "ENSP00000350154.2" ; tag basic appris_principal_2 CCDS ; transcript_id "CERS6--DHRS9^ENST00000357546.6" ; transcript_name "DHRS9-201" ; transcript_support_level 1 ; transcript_type protein_coding CERS6--DHRS9 HAVANA mRNA 22353 33271 . + . FI_gene_label "DHRS9^ENSG00000073737.17" ; ID "CERS6--DHRS9^ENST00000357546.6" ; Parent "CERS6--DHRS9^DHRS9^ENSG00000073737.17" ; ccdsid "CCDS2231.1" ; exon_id "ENSE00003585749.1" ; exon_number 3 ; gene_id "CERS6--DHRS9^DHRS9^ENSG00000073737.17" ; gene_name DHRS9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132180.9" ; havana_transcript "OTTHUMT00000255232.1" ; hgnc_id "HGNC:16888" ; level 2 ; orig_coord_info "chr2,169081582,169081894,+" ; protein_id "ENSP00000350154.2" ; tag basic appris_principal_2 CCDS ; transcript_id "CERS6--DHRS9^ENST00000357546.6" ; transcript_name "DHRS9-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CPNE4--ACP3 HAVANA gene 32505 45388 . + . FI_gene_label "ACP3^ENSG00000014257.16" ; ID "CPNE4--ACP3^ACP3^ENSG00000014257.16" ; ccdsid "CCDS3073.1" ; exon_id "ENSE00001922674.1" ; exon_number 1 ; gene_id "CPNE4--ACP3^ACP3^ENSG00000014257.16" ; gene_name ACP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159650.6" ; havana_transcript "OTTHUMT00000356699.3" ; hgnc_id "HGNC:125" ; level 2 ; orig_coord_info "chr3,132317457,132317576,+" ; protein_id "ENSP00000337471.5" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CPNE4--ACP3^ENST00000336375.10" ; transcript_name "ACP3-201" ; transcript_support_level 1 ; transcript_type protein_coding CPNE4--ACP3 HAVANA mRNA 32505 45388 . + . FI_gene_label "ACP3^ENSG00000014257.16" ; ID "CPNE4--ACP3^ENST00000336375.10" ; Parent "CPNE4--ACP3^ACP3^ENSG00000014257.16" ; ccdsid "CCDS3073.1" ; exon_id "ENSE00001922674.1" ; exon_number 1 ; gene_id "CPNE4--ACP3^ACP3^ENSG00000014257.16" ; gene_name ACP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159650.6" ; havana_transcript "OTTHUMT00000356699.3" ; hgnc_id "HGNC:125" ; level 2 ; orig_coord_info "chr3,132317457,132317576,+" ; protein_id "ENSP00000337471.5" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CPNE4--ACP3^ENST00000336375.10" ; transcript_name "ACP3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CPNE4--ACP3 ENSEMBL gene 6503 29459 . + . FI_gene_label "CPNE4^ENSG00000196353.11" ; ID "CPNE4--ACP3^CPNE4^ENSG00000196353.11" ; ccdsid "CCDS3072.1" ; exon_id "ENSE00003536115.1" ; exon_number 2 ; gene_id "CPNE4--ACP3^CPNE4^ENSG00000196353.11" ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14" ; hgnc_id "HGNC:2317" ; level 3 ; orig_coord_info "chr3,131905264,131905443,-" ; protein_id "ENSP00000411904.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ACP3^ENST00000429747.5" ; transcript_name "CPNE4-201" ; transcript_support_level 1 ; transcript_type protein_coding CPNE4--ACP3 ENSEMBL mRNA 6503 29459 . + . FI_gene_label "CPNE4^ENSG00000196353.11" ; ID "CPNE4--ACP3^ENST00000429747.5" ; Parent "CPNE4--ACP3^CPNE4^ENSG00000196353.11" ; ccdsid "CCDS3072.1" ; exon_id "ENSE00003536115.1" ; exon_number 2 ; gene_id "CPNE4--ACP3^CPNE4^ENSG00000196353.11" ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14" ; hgnc_id "HGNC:2317" ; level 3 ; orig_coord_info "chr3,131905264,131905443,-" ; protein_id "ENSP00000411904.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ACP3^ENST00000429747.5" ; transcript_name "CPNE4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GPR39--AC010974.2 HAVANA gene 1001 7766 . + . FI_gene_label "GPR39^ENSG00000183840.7" ; ID "GPR39--AC010974.2^GPR39^ENSG00000183840.7" ; ccdsid "CCDS2170.1" ; exon_id "ENSE00001315513.3" ; exon_number 1 ; gene_id "GPR39--AC010974.2^GPR39^ENSG00000183840.7" ; gene_name GPR39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131679.3" ; havana_transcript "OTTHUMT00000254582.2" ; hgnc_id "HGNC:4496" ; level 2 ; orig_coord_info "chr2,132417043,132417898,+" ; protein_id "ENSP00000327417.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPR39--AC010974.2^ENST00000329321.4" ; transcript_name "GPR39-201" ; transcript_support_level 1 ; transcript_type protein_coding GPR39--AC010974.2 HAVANA mRNA 1001 7766 . + . FI_gene_label "GPR39^ENSG00000183840.7" ; ID "GPR39--AC010974.2^ENST00000329321.4" ; Parent "GPR39--AC010974.2^GPR39^ENSG00000183840.7" ; ccdsid "CCDS2170.1" ; exon_id "ENSE00001315513.3" ; exon_number 1 ; gene_id "GPR39--AC010974.2^GPR39^ENSG00000183840.7" ; gene_name GPR39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131679.3" ; havana_transcript "OTTHUMT00000254582.2" ; hgnc_id "HGNC:4496" ; level 2 ; orig_coord_info "chr2,132417043,132417898,+" ; protein_id "ENSP00000327417.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPR39--AC010974.2^ENST00000329321.4" ; transcript_name "GPR39-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: LINC00665--WDR62 HAVANA gene 25529 56982 . + . FI_gene_label "WDR62^ENSG00000075702.19" ; ID "LINC00665--WDR62^WDR62^ENSG00000075702.19" ; ccdsid "CCDS33001.1" ; exon_id "ENSE00002287575.1" ; exon_number 1 ; gene_id "LINC00665--WDR62^WDR62^ENSG00000075702.19" ; gene_name WDR62 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048139.9" ; havana_transcript "OTTHUMT00000457436.1" ; hgnc_id "HGNC:24502" ; level 2 ; orig_coord_info "chr19,36054972,36055148,+" ; protein_id "ENSP00000270301.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "LINC00665--WDR62^ENST00000270301.12" ; transcript_name "WDR62-201" ; transcript_support_level 5 ; transcript_type protein_coding LINC00665--WDR62 HAVANA mRNA 25529 56982 . + . FI_gene_label "WDR62^ENSG00000075702.19" ; ID "LINC00665--WDR62^ENST00000270301.12" ; Parent "LINC00665--WDR62^WDR62^ENSG00000075702.19" ; ccdsid "CCDS33001.1" ; exon_id "ENSE00002287575.1" ; exon_number 1 ; gene_id "LINC00665--WDR62^WDR62^ENSG00000075702.19" ; gene_name WDR62 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048139.9" ; havana_transcript "OTTHUMT00000457436.1" ; hgnc_id "HGNC:24502" ; level 2 ; orig_coord_info "chr19,36054972,36055148,+" ; protein_id "ENSP00000270301.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "LINC00665--WDR62^ENST00000270301.12" ; transcript_name "WDR62-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: MAL2--DIPK1A HAVANA gene 13031 20286 . + . FI_gene_label "DIPK1A^ENSG00000154511.12" ; ID "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12" ; ccdsid "CCDS44173.1" ; exon_id "ENSE00001882462.2" ; exon_number 1 ; gene_id "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12" ; gene_name DIPK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000010894.3" ; havana_transcript "OTTHUMT00000030046.3" ; hgnc_id "HGNC:32213" ; level 2 ; orig_coord_info "chr1,92961376,92961429,-" ; protein_id "ENSP00000359333.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAL2--DIPK1A^ENST00000370310.5" ; transcript_name "DIPK1A-201" ; transcript_support_level 2 ; transcript_type protein_coding MAL2--DIPK1A HAVANA mRNA 13031 20286 . + . FI_gene_label "DIPK1A^ENSG00000154511.12" ; ID "MAL2--DIPK1A^ENST00000370310.5" ; Parent "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12" ; ccdsid "CCDS44173.1" ; exon_id "ENSE00001882462.2" ; exon_number 1 ; gene_id "MAL2--DIPK1A^DIPK1A^ENSG00000154511.12" ; gene_name DIPK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000010894.3" ; havana_transcript "OTTHUMT00000030046.3" ; hgnc_id "HGNC:32213" ; level 2 ; orig_coord_info "chr1,92961376,92961429,-" ; protein_id "ENSP00000359333.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAL2--DIPK1A^ENST00000370310.5" ; transcript_name "DIPK1A-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: MAL2--DIPK1A HAVANA gene 1001 7825 . + . FI_gene_label "MAL2^ENSG00000147676.14" ; ID "MAL2--DIPK1A^MAL2^ENSG00000147676.14" ; exon_id "ENSE00003500807.1" ; exon_number 3 ; gene_id "MAL2--DIPK1A^MAL2^ENSG00000147676.14" ; gene_name MAL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164973.5" ; havana_transcript "OTTHUMT00000383353.2" ; hgnc_id "HGNC:13634" ; level 2 ; orig_coord_info "chr8,119221659,119221757,+" ; protein_id "ENSP00000483044.1" ; tag alternative_5_UTR basic ; transcript_id "MAL2--DIPK1A^ENST00000522112.6" ; transcript_name "MAL2-201" ; transcript_support_level 4 ; transcript_type protein_coding MAL2--DIPK1A HAVANA mRNA 1001 7825 . + . FI_gene_label "MAL2^ENSG00000147676.14" ; ID "MAL2--DIPK1A^ENST00000522112.6" ; Parent "MAL2--DIPK1A^MAL2^ENSG00000147676.14" ; exon_id "ENSE00003500807.1" ; exon_number 3 ; gene_id "MAL2--DIPK1A^MAL2^ENSG00000147676.14" ; gene_name MAL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164973.5" ; havana_transcript "OTTHUMT00000383353.2" ; hgnc_id "HGNC:13634" ; level 2 ; orig_coord_info "chr8,119221659,119221757,+" ; protein_id "ENSP00000483044.1" ; tag alternative_5_UTR basic ; transcript_id "MAL2--DIPK1A^ENST00000522112.6" ; transcript_name "MAL2-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: PHF8--CBX1P4 HAVANA gene 4110 26409 . + . FI_gene_label "PHF8^ENSG00000172943.20" ; ID "PHF8--CBX1P4^PHF8^ENSG00000172943.20" ; ccdsid "CCDS55419.1" ; exon_id "ENSE00003602569.1" ; exon_number 2 ; gene_id "PHF8--CBX1P4^PHF8^ENSG00000172943.20" ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4" ; havana_transcript "OTTHUMT00000056785.2" ; hgnc_id "HGNC:20672" ; level 1 ; orig_coord_info "chrX,54042631,54042728,-" ; protein_id "ENSP00000319473.8" ; tag basic exp_conf CCDS ; transcript_id "PHF8--CBX1P4^ENST00000322659.12" ; transcript_name "PHF8-201" ; transcript_support_level 1 ; transcript_type protein_coding PHF8--CBX1P4 HAVANA mRNA 4110 26409 . + . FI_gene_label "PHF8^ENSG00000172943.20" ; ID "PHF8--CBX1P4^ENST00000322659.12" ; Parent "PHF8--CBX1P4^PHF8^ENSG00000172943.20" ; ccdsid "CCDS55419.1" ; exon_id "ENSE00003602569.1" ; exon_number 2 ; gene_id "PHF8--CBX1P4^PHF8^ENSG00000172943.20" ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4" ; havana_transcript "OTTHUMT00000056785.2" ; hgnc_id "HGNC:20672" ; level 1 ; orig_coord_info "chrX,54042631,54042728,-" ; protein_id "ENSP00000319473.8" ; tag basic exp_conf CCDS ; transcript_id "PHF8--CBX1P4^ENST00000322659.12" ; transcript_name "PHF8-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PHF8--REPS2 HAVANA gene 35093 62864 . + . FI_gene_label "REPS2^ENSG00000169891.18" ; ID "PHF8--REPS2^REPS2^ENSG00000169891.18" ; ccdsid "CCDS43919.1" ; exon_id "ENSE00001956325.1" ; exon_number 1 ; gene_id "PHF8--REPS2^REPS2^ENSG00000169891.18" ; gene_name REPS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021199.4" ; havana_transcript "OTTHUMT00000055924.3" ; hgnc_id "HGNC:9963" ; level 2 ; orig_coord_info "chrX,16946862,16947134,+" ; protein_id "ENSP00000306033.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "PHF8--REPS2^ENST00000303843.7" ; transcript_name "REPS2-201" ; transcript_support_level 1 ; transcript_type protein_coding PHF8--REPS2 HAVANA mRNA 35093 62864 . + . FI_gene_label "REPS2^ENSG00000169891.18" ; ID "PHF8--REPS2^ENST00000303843.7" ; Parent "PHF8--REPS2^REPS2^ENSG00000169891.18" ; ccdsid "CCDS43919.1" ; exon_id "ENSE00001956325.1" ; exon_number 1 ; gene_id "PHF8--REPS2^REPS2^ENSG00000169891.18" ; gene_name REPS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021199.4" ; havana_transcript "OTTHUMT00000055924.3" ; hgnc_id "HGNC:9963" ; level 2 ; orig_coord_info "chrX,16946862,16947134,+" ; protein_id "ENSP00000306033.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "PHF8--REPS2^ENST00000303843.7" ; transcript_name "REPS2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PHF8--REPS2 HAVANA gene 4110 26409 . + . FI_gene_label "PHF8^ENSG00000172943.20" ; ID "PHF8--REPS2^PHF8^ENSG00000172943.20" ; ccdsid "CCDS55419.1" ; exon_id "ENSE00003602569.1" ; exon_number 2 ; gene_id "PHF8--REPS2^PHF8^ENSG00000172943.20" ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4" ; havana_transcript "OTTHUMT00000056785.2" ; hgnc_id "HGNC:20672" ; level 1 ; orig_coord_info "chrX,54042631,54042728,-" ; protein_id "ENSP00000319473.8" ; tag basic exp_conf CCDS ; transcript_id "PHF8--REPS2^ENST00000322659.12" ; transcript_name "PHF8-201" ; transcript_support_level 1 ; transcript_type protein_coding PHF8--REPS2 HAVANA mRNA 4110 26409 . + . FI_gene_label "PHF8^ENSG00000172943.20" ; ID "PHF8--REPS2^ENST00000322659.12" ; Parent "PHF8--REPS2^PHF8^ENSG00000172943.20" ; ccdsid "CCDS55419.1" ; exon_id "ENSE00003602569.1" ; exon_number 2 ; gene_id "PHF8--REPS2^PHF8^ENSG00000172943.20" ; gene_name PHF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021622.4" ; havana_transcript "OTTHUMT00000056785.2" ; hgnc_id "HGNC:20672" ; level 1 ; orig_coord_info "chrX,54042631,54042728,-" ; protein_id "ENSP00000319473.8" ; tag basic exp_conf CCDS ; transcript_id "PHF8--REPS2^ENST00000322659.12" ; transcript_name "PHF8-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TTBK2--SH2D3A HAVANA gene 36731 47573 . + . FI_gene_label "SH2D3A^ENSG00000125731.13" ; ID "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13" ; ccdsid "CCDS12173.1" ; exon_id "ENSE00003633486.1" ; exon_number 2 ; gene_id "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13" ; gene_name SH2D3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000181868.3" ; havana_transcript "OTTHUMT00000458016.2" ; hgnc_id "HGNC:16885" ; level 2 ; orig_coord_info "chr19,6763680,6763748,-" ; protein_id "ENSP00000245908.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000245908.11" ; transcript_name "SH2D3A-201" ; transcript_support_level 1 ; transcript_type protein_coding TTBK2--SH2D3A HAVANA mRNA 36731 47573 . + . FI_gene_label "SH2D3A^ENSG00000125731.13" ; ID "TTBK2--SH2D3A^ENST00000245908.11" ; Parent "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13" ; ccdsid "CCDS12173.1" ; exon_id "ENSE00003633486.1" ; exon_number 2 ; gene_id "TTBK2--SH2D3A^SH2D3A^ENSG00000125731.13" ; gene_name SH2D3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000181868.3" ; havana_transcript "OTTHUMT00000458016.2" ; hgnc_id "HGNC:16885" ; level 2 ; orig_coord_info "chr19,6763680,6763748,-" ; protein_id "ENSP00000245908.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000245908.11" ; transcript_name "SH2D3A-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TTBK2--SH2D3A HAVANA gene 1032 33702 . + . FI_gene_label "TTBK2^ENSG00000128881.17" ; ID "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17" ; ccdsid "CCDS42029.1" ; exon_id "ENSE00003688715.1" ; exon_number 2 ; gene_id "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17" ; gene_name TTBK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175802.5" ; havana_transcript "OTTHUMT00000431106.3" ; hgnc_id "HGNC:19141" ; level 2 ; orig_coord_info "chr15,42878549,42878617,-" ; protein_id "ENSP00000267890.6" ; tag basic MANE_Select CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000267890.11" ; transcript_name "TTBK2-201" ; transcript_support_level 5 ; transcript_type protein_coding TTBK2--SH2D3A HAVANA mRNA 1032 33702 . + . FI_gene_label "TTBK2^ENSG00000128881.17" ; ID "TTBK2--SH2D3A^ENST00000267890.11" ; Parent "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17" ; ccdsid "CCDS42029.1" ; exon_id "ENSE00003688715.1" ; exon_number 2 ; gene_id "TTBK2--SH2D3A^TTBK2^ENSG00000128881.17" ; gene_name TTBK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175802.5" ; havana_transcript "OTTHUMT00000431106.3" ; hgnc_id "HGNC:19141" ; level 2 ; orig_coord_info "chr15,42878549,42878617,-" ; protein_id "ENSP00000267890.6" ; tag basic MANE_Select CCDS ; transcript_id "TTBK2--SH2D3A^ENST00000267890.11" ; transcript_name "TTBK2-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TTC6--MIPOL1 ENSEMBL gene 25637 41624 . + . FI_gene_label "TTC6^ENSG00000139865.16" ; ID "TTC6--MIPOL1^TTC6^ENSG00000139865.16" ; exon_id "ENSE00003549424.1" ; exon_number 2 ; gene_id "TTC6--MIPOL1^TTC6^ENSG00000139865.16" ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8" ; hgnc_id "HGNC:19739" ; level 3 ; orig_coord_info "chr14,37796310,37796370,+" ; protein_id "ENSP00000267368.7" ; tag basic ; transcript_id "TTC6--MIPOL1^ENST00000267368.11" ; transcript_name "TTC6-201" ; transcript_support_level 5 ; transcript_type protein_coding TTC6--MIPOL1 ENSEMBL mRNA 25637 41624 . + . FI_gene_label "TTC6^ENSG00000139865.16" ; ID "TTC6--MIPOL1^ENST00000267368.11" ; Parent "TTC6--MIPOL1^TTC6^ENSG00000139865.16" ; exon_id "ENSE00003549424.1" ; exon_number 2 ; gene_id "TTC6--MIPOL1^TTC6^ENSG00000139865.16" ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8" ; hgnc_id "HGNC:19739" ; level 3 ; orig_coord_info "chr14,37796310,37796370,+" ; protein_id "ENSP00000267368.7" ; tag basic ; transcript_id "TTC6--MIPOL1^ENST00000267368.11" ; transcript_name "TTC6-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TTC6--MIPOL1 HAVANA gene 55184 98633 . + . FI_gene_label "MIPOL1^ENSG00000151338.18" ; ID "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18" ; ccdsid "CCDS9664.1" ; exon_id "ENSE00003679602.1" ; exon_number 4 ; gene_id "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18" ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3" ; havana_transcript "OTTHUMT00000276734.1" ; hgnc_id "HGNC:21460" ; level 2 ; orig_coord_info "chr14,37247889,37247907,+" ; protein_id "ENSP00000333539.7" ; tag basic appris_principal_2 CCDS ; transcript_id "TTC6--MIPOL1^ENST00000327441.11" ; transcript_name "MIPOL1-201" ; transcript_support_level 1 ; transcript_type protein_coding TTC6--MIPOL1 HAVANA mRNA 55184 98633 . + . FI_gene_label "MIPOL1^ENSG00000151338.18" ; ID "TTC6--MIPOL1^ENST00000327441.11" ; Parent "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18" ; ccdsid "CCDS9664.1" ; exon_id "ENSE00003679602.1" ; exon_number 4 ; gene_id "TTC6--MIPOL1^MIPOL1^ENSG00000151338.18" ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3" ; havana_transcript "OTTHUMT00000276734.1" ; hgnc_id "HGNC:21460" ; level 2 ; orig_coord_info "chr14,37247889,37247907,+" ; protein_id "ENSP00000333539.7" ; tag basic appris_principal_2 CCDS ; transcript_id "TTC6--MIPOL1^ENST00000327441.11" ; transcript_name "MIPOL1-201" ; 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: WDR92--PPP3R1 HAVANA gene 18563 27322 . + . FI_gene_label "PPP3R1^ENSG00000221823.11" ; ID "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11" ; ccdsid "CCDS46310.1" ; exon_id "ENSE00001191356.5" ; exon_number 1 ; gene_id "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11" ; gene_name PPP3R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129561.9" ; havana_transcript "OTTHUMT00000326765.5" ; hgnc_id "HGNC:9317" ; level 2 ; orig_coord_info "chr2,68252125,68252127,-" ; protein_id "ENSP00000234310.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000234310.8" ; transcript_name "PPP3R1-201" ; transcript_support_level 1 ; transcript_type protein_coding WDR92--PPP3R1 HAVANA mRNA 18563 27322 . + . FI_gene_label "PPP3R1^ENSG00000221823.11" ; ID "WDR92--PPP3R1^ENST00000234310.8" ; Parent "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11" ; ccdsid "CCDS46310.1" ; exon_id "ENSE00001191356.5" ; exon_number 1 ; gene_id "WDR92--PPP3R1^PPP3R1^ENSG00000221823.11" ; gene_name PPP3R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129561.9" ; havana_transcript "OTTHUMT00000326765.5" ; hgnc_id "HGNC:9317" ; level 2 ; orig_coord_info "chr2,68252125,68252127,-" ; protein_id "ENSP00000234310.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000234310.8" ; transcript_name "PPP3R1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: WDR92--PPP3R1 HAVANA gene 1023 12125 . + . FI_gene_label "WDR92^ENSG00000243667.7" ; ID "WDR92--PPP3R1^WDR92^ENSG00000243667.7" ; ccdsid "CCDS1884.1" ; exon_id "ENSE00001738493.3" ; exon_number 1 ; gene_id "WDR92--PPP3R1^WDR92^ENSG00000243667.7" ; gene_name WDR92 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152561.6" ; havana_transcript "OTTHUMT00000251754.4" ; hgnc_id "HGNC:25176" ; level 2 ; orig_coord_info "chr2,68157261,68157443,-" ; protein_id "ENSP00000295121.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000295121.11" ; transcript_name "WDR92-201" ; transcript_support_level 1 ; transcript_type protein_coding WDR92--PPP3R1 HAVANA mRNA 1023 12125 . + . FI_gene_label "WDR92^ENSG00000243667.7" ; ID "WDR92--PPP3R1^ENST00000295121.11" ; Parent "WDR92--PPP3R1^WDR92^ENSG00000243667.7" ; ccdsid "CCDS1884.1" ; exon_id "ENSE00001738493.3" ; exon_number 1 ; gene_id "WDR92--PPP3R1^WDR92^ENSG00000243667.7" ; gene_name WDR92 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152561.6" ; havana_transcript "OTTHUMT00000251754.4" ; hgnc_id "HGNC:25176" ; level 2 ; orig_coord_info "chr2,68157261,68157443,-" ; protein_id "ENSP00000295121.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR92--PPP3R1^ENST00000295121.11" ; transcript_name "WDR92-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ZNF875--ZNF793 HAVANA gene 10040 20910 . + . FI_gene_label "ZNF875^ENSG00000181666.18" ; ID "ZNF875--ZNF793^ZNF875^ENSG00000181666.18" ; ccdsid "CCDS12502.1" ; exon_id "ENSE00001337429.2" ; exon_number 3 ; gene_id "ZNF875--ZNF793^ZNF875^ENSG00000181666.18" ; gene_name ZNF875 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181937.8" ; havana_transcript "OTTHUMT00000458375.1" ; hgnc_id "HGNC:4928" ; level 2 ; orig_coord_info "chr19,37344685,37344774,+" ; protein_id "ENSP00000315505.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000324411.8" ; transcript_name "ZNF875-201" ; transcript_support_level 1 ; transcript_type protein_coding ZNF875--ZNF793 HAVANA mRNA 10040 20910 . + . FI_gene_label "ZNF875^ENSG00000181666.18" ; ID "ZNF875--ZNF793^ENST00000324411.8" ; Parent "ZNF875--ZNF793^ZNF875^ENSG00000181666.18" ; ccdsid "CCDS12502.1" ; exon_id "ENSE00001337429.2" ; exon_number 3 ; gene_id "ZNF875--ZNF793^ZNF875^ENSG00000181666.18" ; gene_name ZNF875 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181937.8" ; havana_transcript "OTTHUMT00000458375.1" ; hgnc_id "HGNC:4928" ; level 2 ; orig_coord_info "chr19,37344685,37344774,+" ; protein_id "ENSP00000315505.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000324411.8" ; transcript_name "ZNF875-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ZNF875--ZNF793 ENSEMBL gene 29565 41594 . + . FI_gene_label "ZNF793^ENSG00000188227.13" ; ID "ZNF875--ZNF793^ZNF793^ENSG00000188227.13" ; ccdsid "CCDS46062.1" ; exon_id "ENSE00001806128.1" ; exon_number 1 ; gene_id "ZNF875--ZNF793^ZNF793^ENSG00000188227.13" ; gene_name ZNF793 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182003.5" ; hgnc_id "HGNC:33115" ; level 3 ; orig_coord_info "chr19,37523440,37523454,+" ; protein_id "ENSP00000396402.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000445217.5" ; transcript_name "ZNF793-201" ; transcript_support_level 5 ; transcript_type protein_coding ZNF875--ZNF793 ENSEMBL mRNA 29565 41594 . + . FI_gene_label "ZNF793^ENSG00000188227.13" ; ID "ZNF875--ZNF793^ENST00000445217.5" ; Parent "ZNF875--ZNF793^ZNF793^ENSG00000188227.13" ; ccdsid "CCDS46062.1" ; exon_id "ENSE00001806128.1" ; exon_number 1 ; gene_id "ZNF875--ZNF793^ZNF793^ENSG00000188227.13" ; gene_name ZNF793 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182003.5" ; hgnc_id "HGNC:33115" ; level 3 ; orig_coord_info "chr19,37523440,37523454,+" ; protein_id "ENSP00000396402.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF875--ZNF793^ENST00000445217.5" ; transcript_name "ZNF793-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: ACTBP6--ACTB HAVANA gene 1001 2090 . + . FI_gene_label "ACTBP6^ENSG00000203413.3" ; ID "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; exon_id "ENSE00002116857.1" ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2" ; havana_transcript "OTTHUMT00000379462.2" ; hgnc_id "HGNC:139" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,84948585,84949674,+" ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1" ; transcript_name "ACTBP6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene ACTBP6--ACTB HAVANA RNA 1001 2090 . + . FI_gene_label "ACTBP6^ENSG00000203413.3" ; ID "ACTBP6--ACTB^ENST00000520036.1" ; Parent "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; exon_id "ENSE00002116857.1" ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2" ; havana_transcript "OTTHUMT00000379462.2" ; hgnc_id "HGNC:139" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,84948585,84949674,+" ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1" ; transcript_name "ACTBP6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: CCL28--RN7SL1 ENSEMBL gene 12525 12823 . + . FI_gene_label "RN7SL1^ENSG00000276168.1" ; ID "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1" ; exon_id "ENSE00003741348.1" ; exon_number 1 ; gene_id "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1" ; gene_name RN7SL1 ; gene_type misc_RNA ; hgnc_id "HGNC:10038" ; level 3 ; orig_coord_info "chr14,49586580,49586878,+" ; tag basic ; transcript_id "CCL28--RN7SL1^ENST00000618786.1" ; transcript_name "RN7SL1-201" ; transcript_support_level NA ; transcript_type misc_RNA CCL28--RN7SL1 ENSEMBL RNA 12525 12823 . + . FI_gene_label "RN7SL1^ENSG00000276168.1" ; ID "CCL28--RN7SL1^ENST00000618786.1" ; Parent "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1" ; exon_id "ENSE00003741348.1" ; exon_number 1 ; gene_id "CCL28--RN7SL1^RN7SL1^ENSG00000276168.1" ; gene_name RN7SL1 ; gene_type misc_RNA ; hgnc_id "HGNC:10038" ; level 3 ; orig_coord_info "chr14,49586580,49586878,+" ; tag basic ; transcript_id "CCL28--RN7SL1^ENST00000618786.1" ; transcript_name "RN7SL1-201" ; transcript_support_level NA ; transcript_type misc_RNA L1 and L2 created: GPR39--AC010974.2 HAVANA gene 10767 14791 . + . FI_gene_label "AC010974.2^ENSG00000286068.1" ; ID "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1" ; exon_id "ENSE00003850879.1" ; exon_number 1 ; gene_id "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1" ; gene_name "AC010974.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192755.1" ; havana_transcript "OTTHUMT00000499024.1" ; level 2 ; orig_coord_info "chr2,132685224,132685548,+" ; tag basic ; transcript_id "GPR39--AC010974.2^ENST00000651100.1" ; transcript_name "AC010974.2-201" ; transcript_type lncRNA GPR39--AC010974.2 HAVANA RNA 10767 14791 . + . FI_gene_label "AC010974.2^ENSG00000286068.1" ; ID "GPR39--AC010974.2^ENST00000651100.1" ; Parent "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1" ; exon_id "ENSE00003850879.1" ; exon_number 1 ; gene_id "GPR39--AC010974.2^AC010974.2^ENSG00000286068.1" ; gene_name "AC010974.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192755.1" ; havana_transcript "OTTHUMT00000499024.1" ; level 2 ; orig_coord_info "chr2,132685224,132685548,+" ; tag basic ; transcript_id "GPR39--AC010974.2^ENST00000651100.1" ; transcript_name "AC010974.2-201" ; transcript_type lncRNA L1 and L2 created: LINC00665--WDR62 HAVANA gene 1037 15549 . + . FI_gene_label "LINC00665^ENSG00000232677.9" ; ID "LINC00665--WDR62^LINC00665^ENSG00000232677.9" ; exon_id "ENSE00003882974.1" ; exon_number 1 ; gene_id "LINC00665--WDR62^LINC00665^ENSG00000232677.9" ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6" ; havana_transcript "OTTHUMT00000109548.1" ; hgnc_id "HGNC:44323" ; level 1 ; orig_coord_info "chr19,36331447,36331734,-" ; tag exp_conf ; transcript_id "LINC00665--WDR62^ENST00000412740.7" ; transcript_name "LINC00665-201" ; transcript_support_level 3 ; transcript_type lncRNA LINC00665--WDR62 HAVANA RNA 1037 15549 . + . FI_gene_label "LINC00665^ENSG00000232677.9" ; ID "LINC00665--WDR62^ENST00000412740.7" ; Parent "LINC00665--WDR62^LINC00665^ENSG00000232677.9" ; exon_id "ENSE00003882974.1" ; exon_number 1 ; gene_id "LINC00665--WDR62^LINC00665^ENSG00000232677.9" ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6" ; havana_transcript "OTTHUMT00000109548.1" ; hgnc_id "HGNC:44323" ; level 1 ; orig_coord_info "chr19,36331447,36331734,-" ; tag exp_conf ; transcript_id "LINC00665--WDR62^ENST00000412740.7" ; transcript_name "LINC00665-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: PHF8--CBX1P4 HAVANA gene 34889 35345 . + . FI_gene_label "CBX1P4^ENSG00000214321.3" ; ID "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3" ; exon_id "ENSE00001785430.1" ; exon_number 1 ; gene_id "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3" ; gene_name CBX1P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021201.1" ; havana_transcript "OTTHUMT00000055929.1" ; hgnc_id "HGNC:38658" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,17282637,17283093,+" ; tag pseudo_consens basic ; transcript_id "PHF8--CBX1P4^ENST00000439415.1" ; transcript_name "CBX1P4-201" ; transcript_support_level NA ; transcript_type processed_pseudogene PHF8--CBX1P4 HAVANA RNA 34889 35345 . + . FI_gene_label "CBX1P4^ENSG00000214321.3" ; ID "PHF8--CBX1P4^ENST00000439415.1" ; Parent "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3" ; exon_id "ENSE00001785430.1" ; exon_number 1 ; gene_id "PHF8--CBX1P4^CBX1P4^ENSG00000214321.3" ; gene_name CBX1P4 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021201.1" ; havana_transcript "OTTHUMT00000055929.1" ; hgnc_id "HGNC:38658" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,17282637,17283093,+" ; tag pseudo_consens basic ; transcript_id "PHF8--CBX1P4^ENST00000439415.1" ; transcript_name "CBX1P4-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript 352 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 ------------------------------ 777 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 28 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