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: 4155 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 4155 => 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:4155 => 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: AC015712.1--KLK9 HAVANA gene 9982 13429 . + . FI_gene_label "KLK9^ENSG00000213022.6" ; ID "AC015712.1--KLK9^KLK9^ENSG00000213022.6" ; exon_id "ENSE00001320748.5" ; exon_number 1 ; gene_id "AC015712.1--KLK9^KLK9^ENSG00000213022.6" ; gene_name KLK9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183087.5" ; havana_transcript "OTTHUMT00000465036.3" ; hgnc_id "HGNC:6370" ; level 2 ; orig_coord_info "chr19,51009505,51009547,-" ; protein_id "ENSP00000443289.1" ; transcript_id "AC015712.1--KLK9^ENST00000544410.1" ; transcript_name "KLK9-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay AC015712.1--KLK9 HAVANA mRNA 9982 13429 . + . FI_gene_label "KLK9^ENSG00000213022.6" ; ID "AC015712.1--KLK9^ENST00000544410.1" ; Parent "AC015712.1--KLK9^KLK9^ENSG00000213022.6" ; exon_id "ENSE00001320748.5" ; exon_number 1 ; gene_id "AC015712.1--KLK9^KLK9^ENSG00000213022.6" ; gene_name KLK9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183087.5" ; havana_transcript "OTTHUMT00000465036.3" ; hgnc_id "HGNC:6370" ; level 2 ; orig_coord_info "chr19,51009505,51009547,-" ; protein_id "ENSP00000443289.1" ; transcript_id "AC015712.1--KLK9^ENST00000544410.1" ; transcript_name "KLK9-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay 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: ACIN1--HOMEZ HAVANA gene 1001 23157 . + . FI_gene_label "ACIN1^ENSG00000100813.14" ; ID "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14" ; ccdsid "CCDS9587.1" ; exon_id "ENSE00001031625.1" ; exon_number 1 ; gene_id "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14" ; gene_name ACIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028716.8" ; havana_transcript "OTTHUMT00000071707.3" ; hgnc_id "HGNC:17066" ; level 2 ; orig_coord_info "chr14,23094975,23095286,-" ; protein_id "ENSP00000262710.1" ; tag basic appris_principal_4 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000262710.5" ; transcript_name "ACIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding ACIN1--HOMEZ HAVANA mRNA 1001 23157 . + . FI_gene_label "ACIN1^ENSG00000100813.14" ; ID "ACIN1--HOMEZ^ENST00000262710.5" ; Parent "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14" ; ccdsid "CCDS9587.1" ; exon_id "ENSE00001031625.1" ; exon_number 1 ; gene_id "ACIN1--HOMEZ^ACIN1^ENSG00000100813.14" ; gene_name ACIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028716.8" ; havana_transcript "OTTHUMT00000071707.3" ; hgnc_id "HGNC:17066" ; level 2 ; orig_coord_info "chr14,23094975,23095286,-" ; protein_id "ENSP00000262710.1" ; tag basic appris_principal_4 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000262710.5" ; transcript_name "ACIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ACIN1--HOMEZ HAVANA gene 26161 33068 . + . FI_gene_label "HOMEZ^ENSG00000215271.9" ; ID "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9" ; ccdsid "CCDS45085.1" ; exon_id "ENSE00003478704.2" ; exon_number 1 ; gene_id "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9" ; gene_name HOMEZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000172122.9" ; havana_transcript "OTTHUMT00000416939.4" ; hgnc_id "HGNC:20164" ; level 2 ; orig_coord_info "chr14,23285913,23285952,-" ; protein_id "ENSP00000350049.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000357460.7" ; transcript_name "HOMEZ-201" ; transcript_support_level 1 ; transcript_type protein_coding ACIN1--HOMEZ HAVANA mRNA 26161 33068 . + . FI_gene_label "HOMEZ^ENSG00000215271.9" ; ID "ACIN1--HOMEZ^ENST00000357460.7" ; Parent "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9" ; ccdsid "CCDS45085.1" ; exon_id "ENSE00003478704.2" ; exon_number 1 ; gene_id "ACIN1--HOMEZ^HOMEZ^ENSG00000215271.9" ; gene_name HOMEZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000172122.9" ; havana_transcript "OTTHUMT00000416939.4" ; hgnc_id "HGNC:20164" ; level 2 ; orig_coord_info "chr14,23285913,23285952,-" ; protein_id "ENSP00000350049.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACIN1--HOMEZ^ENST00000357460.7" ; transcript_name "HOMEZ-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CLTC--VMP1 HAVANA gene 39205 57907 . + . FI_gene_label "VMP1^ENSG00000062716.13" ; ID "CLTC--VMP1^VMP1^ENSG00000062716.13" ; ccdsid "CCDS11619.1" ; exon_id "ENSE00003550286.1" ; exon_number 2 ; gene_id "CLTC--VMP1^VMP1^ENSG00000062716.13" ; gene_name VMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179882.4" ; havana_transcript "OTTHUMT00000448793.2" ; hgnc_id "HGNC:29559" ; level 2 ; orig_coord_info "chr17,59731447,59731522,+" ; protein_id "ENSP00000262291.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000262291.9" ; transcript_name "VMP1-201" ; transcript_support_level 1 ; transcript_type protein_coding CLTC--VMP1 HAVANA mRNA 39205 57907 . + . FI_gene_label "VMP1^ENSG00000062716.13" ; ID "CLTC--VMP1^ENST00000262291.9" ; Parent "CLTC--VMP1^VMP1^ENSG00000062716.13" ; ccdsid "CCDS11619.1" ; exon_id "ENSE00003550286.1" ; exon_number 2 ; gene_id "CLTC--VMP1^VMP1^ENSG00000062716.13" ; gene_name VMP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179882.4" ; havana_transcript "OTTHUMT00000448793.2" ; hgnc_id "HGNC:29559" ; level 2 ; orig_coord_info "chr17,59731447,59731522,+" ; protein_id "ENSP00000262291.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000262291.9" ; transcript_name "VMP1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CLTC--VMP1 HAVANA gene 1207 35742 . + . FI_gene_label "CLTC^ENSG00000141367.12" ; ID "CLTC--VMP1^CLTC^ENSG00000141367.12" ; ccdsid "CCDS32696.1" ; exon_id "ENSE00003895422.1" ; exon_number 1 ; gene_id "CLTC--VMP1^CLTC^ENSG00000141367.12" ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5" ; havana_transcript "OTTHUMT00000258859.2" ; hgnc_id "HGNC:2092" ; level 2 ; orig_coord_info "chr17,59620132,59620173,+" ; protein_id "ENSP00000269122.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000269122.8" ; transcript_name "CLTC-201" ; transcript_support_level 1 ; transcript_type protein_coding CLTC--VMP1 HAVANA mRNA 1207 35742 . + . FI_gene_label "CLTC^ENSG00000141367.12" ; ID "CLTC--VMP1^ENST00000269122.8" ; Parent "CLTC--VMP1^CLTC^ENSG00000141367.12" ; ccdsid "CCDS32696.1" ; exon_id "ENSE00003895422.1" ; exon_number 1 ; gene_id "CLTC--VMP1^CLTC^ENSG00000141367.12" ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5" ; havana_transcript "OTTHUMT00000258859.2" ; hgnc_id "HGNC:2092" ; level 2 ; orig_coord_info "chr17,59620132,59620173,+" ; protein_id "ENSP00000269122.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CLTC--VMP1^ENST00000269122.8" ; transcript_name "CLTC-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CPSF6--FRA10AC1 HAVANA gene 1048 12978 . + . FI_gene_label "CPSF6^ENSG00000111605.18" ; ID "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18" ; ccdsid "CCDS73494.1" ; exon_id "ENSE00002424959.1" ; exon_number 1 ; gene_id "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18" ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4" ; havana_transcript "OTTHUMT00000403613.1" ; hgnc_id "HGNC:13871" ; level 2 ; orig_coord_info "chr12,69239647,69239706,+" ; protein_id "ENSP00000266679.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000266679.8" ; transcript_name "CPSF6-201" ; transcript_support_level 1 ; transcript_type protein_coding CPSF6--FRA10AC1 HAVANA mRNA 1048 12978 . + . FI_gene_label "CPSF6^ENSG00000111605.18" ; ID "CPSF6--FRA10AC1^ENST00000266679.8" ; Parent "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18" ; ccdsid "CCDS73494.1" ; exon_id "ENSE00002424959.1" ; exon_number 1 ; gene_id "CPSF6--FRA10AC1^CPSF6^ENSG00000111605.18" ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4" ; havana_transcript "OTTHUMT00000403613.1" ; hgnc_id "HGNC:13871" ; level 2 ; orig_coord_info "chr12,69239647,69239706,+" ; protein_id "ENSP00000266679.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000266679.8" ; transcript_name "CPSF6-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CPSF6--FRA10AC1 HAVANA gene 20398 40131 . + . FI_gene_label "FRA10AC1^ENSG00000148690.12" ; ID "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12" ; ccdsid "CCDS7430.1" ; exon_id "ENSE00003459004.1" ; exon_number 2 ; gene_id "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12" ; gene_name FRA10AC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018776.2" ; havana_transcript "OTTHUMT00000049439.2" ; hgnc_id "HGNC:1162" ; level 2 ; orig_coord_info "chr10,93700030,93700106,-" ; protein_id "ENSP00000360488.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000359204.5" ; transcript_name "FRA10AC1-201" ; transcript_support_level 1 ; transcript_type protein_coding CPSF6--FRA10AC1 HAVANA mRNA 20398 40131 . + . FI_gene_label "FRA10AC1^ENSG00000148690.12" ; ID "CPSF6--FRA10AC1^ENST00000359204.5" ; Parent "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12" ; ccdsid "CCDS7430.1" ; exon_id "ENSE00003459004.1" ; exon_number 2 ; gene_id "CPSF6--FRA10AC1^FRA10AC1^ENSG00000148690.12" ; gene_name FRA10AC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018776.2" ; havana_transcript "OTTHUMT00000049439.2" ; hgnc_id "HGNC:1162" ; level 2 ; orig_coord_info "chr10,93700030,93700106,-" ; protein_id "ENSP00000360488.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CPSF6--FRA10AC1^ENST00000359204.5" ; transcript_name "FRA10AC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: E2F1--ZNF341 HAVANA gene 9922 28921 . + . FI_gene_label "ZNF341^ENSG00000131061.14" ; ID "E2F1--ZNF341^ZNF341^ENSG00000131061.14" ; ccdsid "CCDS13227.1" ; exon_id "ENSE00001660419.1" ; exon_number 1 ; gene_id "E2F1--ZNF341^ZNF341^ENSG00000131061.14" ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5" ; havana_transcript "OTTHUMT00000078741.2" ; hgnc_id "HGNC:15992" ; level 2 ; orig_coord_info "chr20,33732022,33732052,+" ; protein_id "ENSP00000344308.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "E2F1--ZNF341^ENST00000342427.6" ; transcript_name "ZNF341-201" ; transcript_support_level 1 ; transcript_type protein_coding E2F1--ZNF341 HAVANA mRNA 9922 28921 . + . FI_gene_label "ZNF341^ENSG00000131061.14" ; ID "E2F1--ZNF341^ENST00000342427.6" ; Parent "E2F1--ZNF341^ZNF341^ENSG00000131061.14" ; ccdsid "CCDS13227.1" ; exon_id "ENSE00001660419.1" ; exon_number 1 ; gene_id "E2F1--ZNF341^ZNF341^ENSG00000131061.14" ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5" ; havana_transcript "OTTHUMT00000078741.2" ; hgnc_id "HGNC:15992" ; level 2 ; orig_coord_info "chr20,33732022,33732052,+" ; protein_id "ENSP00000344308.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "E2F1--ZNF341^ENST00000342427.6" ; transcript_name "ZNF341-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: E2F1--ZNF341 HAVANA gene 1001 6921 . + . FI_gene_label "E2F1^ENSG00000101412.13" ; ID "E2F1--ZNF341^E2F1^ENSG00000101412.13" ; ccdsid "CCDS13224.1" ; exon_id "ENSE00001667355.2" ; exon_number 1 ; gene_id "E2F1--ZNF341^E2F1^ENSG00000101412.13" ; gene_name E2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032265.3" ; havana_transcript "OTTHUMT00000078731.3" ; hgnc_id "HGNC:3113" ; level 2 ; orig_coord_info "chr20,33686004,33686264,-" ; protein_id "ENSP00000345571.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F1--ZNF341^ENST00000343380.6" ; transcript_name "E2F1-201" ; transcript_support_level 1 ; transcript_type protein_coding E2F1--ZNF341 HAVANA mRNA 1001 6921 . + . FI_gene_label "E2F1^ENSG00000101412.13" ; ID "E2F1--ZNF341^ENST00000343380.6" ; Parent "E2F1--ZNF341^E2F1^ENSG00000101412.13" ; ccdsid "CCDS13224.1" ; exon_id "ENSE00001667355.2" ; exon_number 1 ; gene_id "E2F1--ZNF341^E2F1^ENSG00000101412.13" ; gene_name E2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032265.3" ; havana_transcript "OTTHUMT00000078731.3" ; hgnc_id "HGNC:3113" ; level 2 ; orig_coord_info "chr20,33686004,33686264,-" ; protein_id "ENSP00000345571.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F1--ZNF341^ENST00000343380.6" ; transcript_name "E2F1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: F8--IKBKG HAVANA gene 29435 39341 . + . FI_gene_label "F8^ENSG00000185010.15" ; ID "F8--IKBKG^F8^ENSG00000185010.15" ; ccdsid "CCDS44026.1" ; exon_id "ENSE00001515616.3" ; exon_number 1 ; gene_id "F8--IKBKG^F8^ENSG00000185010.15" ; gene_name F8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022688.16" ; havana_transcript "OTTHUMT00000083107.7" ; hgnc_id "HGNC:3546" ; level 1 ; orig_coord_info "chrX,154886134,154886157,-" ; protein_id "ENSP00000327895.6" ; tag basic exp_conf CCDS ; transcript_id "F8--IKBKG^ENST00000330287.10" ; transcript_name "F8-201" ; transcript_support_level 1 ; transcript_type protein_coding F8--IKBKG HAVANA mRNA 29435 39341 . + . FI_gene_label "F8^ENSG00000185010.15" ; ID "F8--IKBKG^ENST00000330287.10" ; Parent "F8--IKBKG^F8^ENSG00000185010.15" ; ccdsid "CCDS44026.1" ; exon_id "ENSE00001515616.3" ; exon_number 1 ; gene_id "F8--IKBKG^F8^ENSG00000185010.15" ; gene_name F8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022688.16" ; havana_transcript "OTTHUMT00000083107.7" ; hgnc_id "HGNC:3546" ; level 1 ; orig_coord_info "chrX,154886134,154886157,-" ; protein_id "ENSP00000327895.6" ; tag basic exp_conf CCDS ; transcript_id "F8--IKBKG^ENST00000330287.10" ; transcript_name "F8-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: F8--IKBKG HAVANA gene 45860 51712 . + . FI_gene_label "IKBKG^ENSG00000269335.6" ; ID "F8--IKBKG^IKBKG^ENSG00000269335.6" ; exon_id "ENSE00001651956.1" ; exon_number 2 ; gene_id "F8--IKBKG^IKBKG^ENSG00000269335.6" ; gene_name IKBKG ; gene_type protein_coding ; havana_gene "OTTHUMG00000024234.17" ; havana_transcript "OTTHUMT00000061161.2" ; hgnc_id "HGNC:5961" ; level 2 ; orig_coord_info "chrX,154552039,154552189,+" ; protein_id "ENSP00000398579.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "F8--IKBKG^ENST00000413620.5" ; transcript_name "IKBKG-201" ; transcript_support_level 5 ; transcript_type protein_coding F8--IKBKG HAVANA mRNA 45860 51712 . + . FI_gene_label "IKBKG^ENSG00000269335.6" ; ID "F8--IKBKG^ENST00000413620.5" ; Parent "F8--IKBKG^IKBKG^ENSG00000269335.6" ; exon_id "ENSE00001651956.1" ; exon_number 2 ; gene_id "F8--IKBKG^IKBKG^ENSG00000269335.6" ; gene_name IKBKG ; gene_type protein_coding ; havana_gene "OTTHUMG00000024234.17" ; havana_transcript "OTTHUMT00000061161.2" ; hgnc_id "HGNC:5961" ; level 2 ; orig_coord_info "chrX,154552039,154552189,+" ; protein_id "ENSP00000398579.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "F8--IKBKG^ENST00000413620.5" ; transcript_name "IKBKG-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: FANCI--ABHD2 HAVANA gene 1005 41482 . + . FI_gene_label "FANCI^ENSG00000140525.19" ; ID "FANCI--ABHD2^FANCI^ENSG00000140525.19" ; ccdsid "CCDS10349.2" ; exon_id "ENSE00003645183.1" ; exon_number 2 ; gene_id "FANCI--ABHD2^FANCI^ENSG00000140525.19" ; gene_name FANCI ; gene_type protein_coding ; havana_gene "OTTHUMG00000132993.7" ; havana_transcript "OTTHUMT00000256568.2" ; hgnc_id "HGNC:25568" ; level 2 ; orig_coord_info "chr15,89247648,89247731,+" ; protein_id "ENSP00000300027.8" ; tag basic CCDS ; transcript_id "FANCI--ABHD2^ENST00000300027.12" ; transcript_name "FANCI-201" ; transcript_support_level 5 ; transcript_type protein_coding FANCI--ABHD2 HAVANA mRNA 1005 41482 . + . FI_gene_label "FANCI^ENSG00000140525.19" ; ID "FANCI--ABHD2^ENST00000300027.12" ; Parent "FANCI--ABHD2^FANCI^ENSG00000140525.19" ; ccdsid "CCDS10349.2" ; exon_id "ENSE00003645183.1" ; exon_number 2 ; gene_id "FANCI--ABHD2^FANCI^ENSG00000140525.19" ; gene_name FANCI ; gene_type protein_coding ; havana_gene "OTTHUMG00000132993.7" ; havana_transcript "OTTHUMT00000256568.2" ; hgnc_id "HGNC:25568" ; level 2 ; orig_coord_info "chr15,89247648,89247731,+" ; protein_id "ENSP00000300027.8" ; tag basic CCDS ; transcript_id "FANCI--ABHD2^ENST00000300027.12" ; transcript_name "FANCI-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: FANCI--ABHD2 HAVANA gene 45480 71592 . + . FI_gene_label "ABHD2^ENSG00000140526.18" ; ID "FANCI--ABHD2^ABHD2^ENSG00000140526.18" ; ccdsid "CCDS10348.1" ; exon_id "ENSE00000943593.2" ; exon_number 3 ; gene_id "FANCI--ABHD2^ABHD2^ENSG00000140526.18" ; gene_name ABHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148684.6" ; havana_transcript "OTTHUMT00000309074.3" ; hgnc_id "HGNC:18717" ; level 2 ; orig_coord_info "chr15,89116328,89116521,+" ; protein_id "ENSP00000268129.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FANCI--ABHD2^ENST00000352732.10" ; transcript_name "ABHD2-201" ; transcript_support_level 1 ; transcript_type protein_coding FANCI--ABHD2 HAVANA mRNA 45480 71592 . + . FI_gene_label "ABHD2^ENSG00000140526.18" ; ID "FANCI--ABHD2^ENST00000352732.10" ; Parent "FANCI--ABHD2^ABHD2^ENSG00000140526.18" ; ccdsid "CCDS10348.1" ; exon_id "ENSE00000943593.2" ; exon_number 3 ; gene_id "FANCI--ABHD2^ABHD2^ENSG00000140526.18" ; gene_name ABHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148684.6" ; havana_transcript "OTTHUMT00000309074.3" ; hgnc_id "HGNC:18717" ; level 2 ; orig_coord_info "chr15,89116328,89116521,+" ; protein_id "ENSP00000268129.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FANCI--ABHD2^ENST00000352732.10" ; transcript_name "ABHD2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KANSL1--ARL17B HAVANA gene 7306 43177 . + . FI_gene_label "KANSL1^ENSG00000120071.15" ; ID "KANSL1--ARL17B^KANSL1^ENSG00000120071.15" ; ccdsid "CCDS11503.2" ; exon_id "ENSE00003614505.1" ; exon_number 2 ; gene_id "KANSL1--ARL17B^KANSL1^ENSG00000120071.15" ; gene_name KANSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178026.11" ; havana_transcript "OTTHUMT00000440274.2" ; hgnc_id "HGNC:24565" ; level 2 ; orig_coord_info "chr17,46170855,46172143,-" ; protein_id "ENSP00000262419.6" ; tag alternative_5_UTR NAGNAG_splice_site basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000262419.10" ; transcript_name "KANSL1-201" ; transcript_support_level 1 ; transcript_type protein_coding KANSL1--ARL17B HAVANA mRNA 7306 43177 . + . FI_gene_label "KANSL1^ENSG00000120071.15" ; ID "KANSL1--ARL17B^ENST00000262419.10" ; Parent "KANSL1--ARL17B^KANSL1^ENSG00000120071.15" ; ccdsid "CCDS11503.2" ; exon_id "ENSE00003614505.1" ; exon_number 2 ; gene_id "KANSL1--ARL17B^KANSL1^ENSG00000120071.15" ; gene_name KANSL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178026.11" ; havana_transcript "OTTHUMT00000440274.2" ; hgnc_id "HGNC:24565" ; level 2 ; orig_coord_info "chr17,46170855,46172143,-" ; protein_id "ENSP00000262419.6" ; tag alternative_5_UTR NAGNAG_splice_site basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000262419.10" ; transcript_name "KANSL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KANSL1--ARL17B HAVANA gene 46270 61341 . + . FI_gene_label "ARL17B^ENSG00000228696.10" ; ID "KANSL1--ARL17B^ARL17B^ENSG00000228696.10" ; ccdsid "CCDS54137.1" ; exon_id "ENSE00002352294.1" ; exon_number 2 ; gene_id "KANSL1--ARL17B^ARL17B^ENSG00000228696.10" ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2" ; havana_transcript "OTTHUMT00000440292.1" ; hgnc_id "HGNC:32387" ; level 2 ; orig_coord_info "chr17,46358250,46358397,-" ; protein_id "ENSP00000391751.2" ; tag basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000434041.6" ; transcript_name "ARL17B-201" ; transcript_support_level 1 ; transcript_type protein_coding KANSL1--ARL17B HAVANA mRNA 46270 61341 . + . FI_gene_label "ARL17B^ENSG00000228696.10" ; ID "KANSL1--ARL17B^ENST00000434041.6" ; Parent "KANSL1--ARL17B^ARL17B^ENSG00000228696.10" ; ccdsid "CCDS54137.1" ; exon_id "ENSE00002352294.1" ; exon_number 2 ; gene_id "KANSL1--ARL17B^ARL17B^ENSG00000228696.10" ; gene_name ARL17B ; gene_type protein_coding ; havana_gene "OTTHUMG00000178031.2" ; havana_transcript "OTTHUMT00000440292.1" ; hgnc_id "HGNC:32387" ; level 2 ; orig_coord_info "chr17,46358250,46358397,-" ; protein_id "ENSP00000391751.2" ; tag basic CCDS ; transcript_id "KANSL1--ARL17B^ENST00000434041.6" ; transcript_name "ARL17B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MTAP--H3P30 HAVANA gene 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--H3P30^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--H3P30^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--H3P30^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay MTAP--H3P30 HAVANA mRNA 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--H3P30^ENST00000419385.5" ; Parent "MTAP--H3P30^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--H3P30^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--H3P30^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay L1 and L2 created: MTAP--KHSRPP1 HAVANA gene 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--KHSRPP1^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--KHSRPP1^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--KHSRPP1^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay MTAP--KHSRPP1 HAVANA mRNA 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--KHSRPP1^ENST00000419385.5" ; Parent "MTAP--KHSRPP1^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--KHSRPP1^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--KHSRPP1^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay L1 and L2 created: PHF12--JMJD1C HAVANA gene 1282 15732 . + . FI_gene_label "PHF12^ENSG00000109118.14" ; ID "PHF12--JMJD1C^PHF12^ENSG00000109118.14" ; ccdsid "CCDS11247.1" ; exon_id "ENSE00001124814.3" ; exon_number 1 ; gene_id "PHF12--JMJD1C^PHF12^ENSG00000109118.14" ; gene_name PHF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132676.7" ; havana_transcript "OTTHUMT00000255942.2" ; hgnc_id "HGNC:20816" ; level 2 ; orig_coord_info "chr17,28950895,28950960,-" ; protein_id "ENSP00000268756.3" ; tag basic CCDS ; transcript_id "PHF12--JMJD1C^ENST00000268756.7" ; transcript_name "PHF12-201" ; transcript_support_level 1 ; transcript_type protein_coding PHF12--JMJD1C HAVANA mRNA 1282 15732 . + . FI_gene_label "PHF12^ENSG00000109118.14" ; ID "PHF12--JMJD1C^ENST00000268756.7" ; Parent "PHF12--JMJD1C^PHF12^ENSG00000109118.14" ; ccdsid "CCDS11247.1" ; exon_id "ENSE00001124814.3" ; exon_number 1 ; gene_id "PHF12--JMJD1C^PHF12^ENSG00000109118.14" ; gene_name PHF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132676.7" ; havana_transcript "OTTHUMT00000255942.2" ; hgnc_id "HGNC:20816" ; level 2 ; orig_coord_info "chr17,28950895,28950960,-" ; protein_id "ENSP00000268756.3" ; tag basic CCDS ; transcript_id "PHF12--JMJD1C^ENST00000268756.7" ; transcript_name "PHF12-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PHF12--JMJD1C HAVANA gene 39439 55295 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PHF12--JMJD1C^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding PHF12--JMJD1C HAVANA mRNA 39439 55295 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "PHF12--JMJD1C^ENST00000327520.7" ; Parent "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "PHF12--JMJD1C^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "PHF12--JMJD1C^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: PXMP4--ZNF341 HAVANA gene 1010 4988 . + . FI_gene_label "PXMP4^ENSG00000101417.12" ; ID "PXMP4--ZNF341^PXMP4^ENSG00000101417.12" ; exon_id "ENSE00001925420.1" ; exon_number 1 ; gene_id "PXMP4--ZNF341^PXMP4^ENSG00000101417.12" ; gene_name PXMP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032273.5" ; havana_transcript "OTTHUMT00000334677.1" ; hgnc_id "HGNC:15920" ; level 2 ; orig_coord_info "chr20,33720095,33720207,-" ; protein_id "ENSP00000217398.3" ; tag basic ; transcript_id "PXMP4--ZNF341^ENST00000217398.3" ; transcript_name "PXMP4-201" ; transcript_support_level 2 ; transcript_type protein_coding PXMP4--ZNF341 HAVANA mRNA 1010 4988 . + . FI_gene_label "PXMP4^ENSG00000101417.12" ; ID "PXMP4--ZNF341^ENST00000217398.3" ; Parent "PXMP4--ZNF341^PXMP4^ENSG00000101417.12" ; exon_id "ENSE00001925420.1" ; exon_number 1 ; gene_id "PXMP4--ZNF341^PXMP4^ENSG00000101417.12" ; gene_name PXMP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032273.5" ; havana_transcript "OTTHUMT00000334677.1" ; hgnc_id "HGNC:15920" ; level 2 ; orig_coord_info "chr20,33720095,33720207,-" ; protein_id "ENSP00000217398.3" ; tag basic ; transcript_id "PXMP4--ZNF341^ENST00000217398.3" ; transcript_name "PXMP4-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: PXMP4--ZNF341 HAVANA gene 12720 31719 . + . FI_gene_label "ZNF341^ENSG00000131061.14" ; ID "PXMP4--ZNF341^ZNF341^ENSG00000131061.14" ; ccdsid "CCDS13227.1" ; exon_id "ENSE00001660419.1" ; exon_number 1 ; gene_id "PXMP4--ZNF341^ZNF341^ENSG00000131061.14" ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5" ; havana_transcript "OTTHUMT00000078741.2" ; hgnc_id "HGNC:15992" ; level 2 ; orig_coord_info "chr20,33732022,33732052,+" ; protein_id "ENSP00000344308.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "PXMP4--ZNF341^ENST00000342427.6" ; transcript_name "ZNF341-201" ; transcript_support_level 1 ; transcript_type protein_coding PXMP4--ZNF341 HAVANA mRNA 12720 31719 . + . FI_gene_label "ZNF341^ENSG00000131061.14" ; ID "PXMP4--ZNF341^ENST00000342427.6" ; Parent "PXMP4--ZNF341^ZNF341^ENSG00000131061.14" ; ccdsid "CCDS13227.1" ; exon_id "ENSE00001660419.1" ; exon_number 1 ; gene_id "PXMP4--ZNF341^ZNF341^ENSG00000131061.14" ; gene_name ZNF341 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032275.5" ; havana_transcript "OTTHUMT00000078741.2" ; hgnc_id "HGNC:15992" ; level 2 ; orig_coord_info "chr20,33732022,33732052,+" ; protein_id "ENSP00000344308.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "PXMP4--ZNF341^ENST00000342427.6" ; transcript_name "ZNF341-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RABGAP1L--CACYBP HAVANA gene 1108 42636 . + . FI_gene_label "RABGAP1L^ENSG00000152061.23" ; ID "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23" ; ccdsid "CCDS1314.1" ; exon_id "ENSE00001445393.1" ; exon_number 2 ; gene_id "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23" ; gene_name RABGAP1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000034899.9" ; havana_transcript "OTTHUMT00000084497.1" ; hgnc_id "HGNC:24663" ; level 2 ; orig_coord_info "chr1,174219158,174219295,+" ; protein_id "ENSP00000251507.4" ; tag basic appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000251507.8" ; transcript_name "RABGAP1L-201" ; transcript_support_level 2 ; transcript_type protein_coding RABGAP1L--CACYBP HAVANA mRNA 1108 42636 . + . FI_gene_label "RABGAP1L^ENSG00000152061.23" ; ID "RABGAP1L--CACYBP^ENST00000251507.8" ; Parent "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23" ; ccdsid "CCDS1314.1" ; exon_id "ENSE00001445393.1" ; exon_number 2 ; gene_id "RABGAP1L--CACYBP^RABGAP1L^ENSG00000152061.23" ; gene_name RABGAP1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000034899.9" ; havana_transcript "OTTHUMT00000084497.1" ; hgnc_id "HGNC:24663" ; level 2 ; orig_coord_info "chr1,174219158,174219295,+" ; protein_id "ENSP00000251507.4" ; tag basic appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000251507.8" ; transcript_name "RABGAP1L-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: RABGAP1L--CACYBP HAVANA gene 59723 67821 . + . FI_gene_label "CACYBP^ENSG00000116161.18" ; ID "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18" ; ccdsid "CCDS1315.1" ; exon_id "ENSE00001273868.9" ; exon_number 1 ; gene_id "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18" ; gene_name CACYBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000034941.8" ; havana_transcript "OTTHUMT00000084583.4" ; hgnc_id "HGNC:30423" ; level 2 ; orig_coord_info "chr1,175000181,175000195,+" ; protein_id "ENSP00000356652.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000367679.7" ; transcript_name "CACYBP-201" ; transcript_support_level 1 ; transcript_type protein_coding RABGAP1L--CACYBP HAVANA mRNA 59723 67821 . + . FI_gene_label "CACYBP^ENSG00000116161.18" ; ID "RABGAP1L--CACYBP^ENST00000367679.7" ; Parent "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18" ; ccdsid "CCDS1315.1" ; exon_id "ENSE00001273868.9" ; exon_number 1 ; gene_id "RABGAP1L--CACYBP^CACYBP^ENSG00000116161.18" ; gene_name CACYBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000034941.8" ; havana_transcript "OTTHUMT00000084583.4" ; hgnc_id "HGNC:30423" ; level 2 ; orig_coord_info "chr1,175000181,175000195,+" ; protein_id "ENSP00000356652.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RABGAP1L--CACYBP^ENST00000367679.7" ; transcript_name "CACYBP-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RNASE10--CD38 HAVANA gene 6254 19390 . + . FI_gene_label "CD38^ENSG00000004468.13" ; ID "RNASE10--CD38^CD38^ENSG00000004468.13" ; ccdsid "CCDS3417.1" ; exon_id "ENSE00001131145.4" ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13" ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6" ; havana_transcript "OTTHUMT00000250322.3" ; hgnc_id "HGNC:1667" ; level 2 ; orig_coord_info "chr4,15778415,15778647,+" ; protein_id "ENSP00000226279.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8" ; transcript_name "CD38-201" ; transcript_support_level 1 ; transcript_type protein_coding RNASE10--CD38 HAVANA mRNA 6254 19390 . + . FI_gene_label "CD38^ENSG00000004468.13" ; ID "RNASE10--CD38^ENST00000226279.8" ; Parent "RNASE10--CD38^CD38^ENSG00000004468.13" ; ccdsid "CCDS3417.1" ; exon_id "ENSE00001131145.4" ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13" ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6" ; havana_transcript "OTTHUMT00000250322.3" ; hgnc_id "HGNC:1667" ; level 2 ; orig_coord_info "chr4,15778415,15778647,+" ; protein_id "ENSP00000226279.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8" ; transcript_name "CD38-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RNASE10--CD38 HAVANA gene 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding RNASE10--CD38 HAVANA mRNA 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--CD38^ENST00000328444.5" ; Parent "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: RPSAP52--HMGA2 HAVANA gene 7036 17922 . + . FI_gene_label "HMGA2^ENSG00000149948.14" ; ID "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14" ; ccdsid "CCDS31854.1" ; exon_id "ENSE00001242304.6" ; exon_number 1 ; gene_id "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14" ; gene_name HMGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168936.2" ; havana_transcript "OTTHUMT00000401660.1" ; hgnc_id "HGNC:5009" ; level 2 ; orig_coord_info "chr12,65825271,65825381,+" ; protein_id "ENSP00000346658.3" ; tag basic CCDS ; transcript_id "RPSAP52--HMGA2^ENST00000354636.7" ; transcript_name "HMGA2-201" ; transcript_support_level 1 ; transcript_type protein_coding RPSAP52--HMGA2 HAVANA mRNA 7036 17922 . + . FI_gene_label "HMGA2^ENSG00000149948.14" ; ID "RPSAP52--HMGA2^ENST00000354636.7" ; Parent "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14" ; ccdsid "CCDS31854.1" ; exon_id "ENSE00001242304.6" ; exon_number 1 ; gene_id "RPSAP52--HMGA2^HMGA2^ENSG00000149948.14" ; gene_name HMGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168936.2" ; havana_transcript "OTTHUMT00000401660.1" ; hgnc_id "HGNC:5009" ; level 2 ; orig_coord_info "chr12,65825271,65825381,+" ; protein_id "ENSP00000346658.3" ; tag basic CCDS ; transcript_id "RPSAP52--HMGA2^ENST00000354636.7" ; transcript_name "HMGA2-201" ; 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: AC015712.1--KLK9 HAVANA gene 1001 5743 . + . FI_gene_label "AC015712.1^ENSG00000232386.9" ; ID "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9" ; exon_id "ENSE00002547857.1" ; exon_number 1 ; gene_id "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9" ; gene_name "AC015712.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186438.3" ; havana_transcript "OTTHUMT00000416693.1" ; level 2 ; orig_coord_info "chr15,100849561,100849910,+" ; transcript_id "AC015712.1--KLK9^ENST00000557962.1" ; transcript_name "AC015712.1-201" ; transcript_support_level 4 ; transcript_type lncRNA AC015712.1--KLK9 HAVANA RNA 1001 5743 . + . FI_gene_label "AC015712.1^ENSG00000232386.9" ; ID "AC015712.1--KLK9^ENST00000557962.1" ; Parent "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9" ; exon_id "ENSE00002547857.1" ; exon_number 1 ; gene_id "AC015712.1--KLK9^AC015712.1^ENSG00000232386.9" ; gene_name "AC015712.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186438.3" ; havana_transcript "OTTHUMT00000416693.1" ; level 2 ; orig_coord_info "chr15,100849561,100849910,+" ; transcript_id "AC015712.1--KLK9^ENST00000557962.1" ; transcript_name "AC015712.1-201" ; transcript_support_level 4 ; transcript_type lncRNA 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: MTAP--H3P30 HAVANA gene 29696 30087 . + . FI_gene_label "H3P30^ENSG00000227443.2" ; ID "MTAP--H3P30^H3P30^ENSG00000227443.2" ; exon_id "ENSE00001628925.2" ; exon_number 1 ; gene_id "MTAP--H3P30^H3P30^ENSG00000227443.2" ; gene_name H3P30 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019682.2" ; havana_transcript "OTTHUMT00000051911.2" ; hgnc_id "HGNC:54463" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,21638285,21638676,+" ; tag pseudo_consens basic ; transcript_id "MTAP--H3P30^ENST00000424386.2" ; transcript_name "H3P30-201" ; transcript_support_level NA ; transcript_type processed_pseudogene MTAP--H3P30 HAVANA RNA 29696 30087 . + . FI_gene_label "H3P30^ENSG00000227443.2" ; ID "MTAP--H3P30^ENST00000424386.2" ; Parent "MTAP--H3P30^H3P30^ENSG00000227443.2" ; exon_id "ENSE00001628925.2" ; exon_number 1 ; gene_id "MTAP--H3P30^H3P30^ENSG00000227443.2" ; gene_name H3P30 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019682.2" ; havana_transcript "OTTHUMT00000051911.2" ; hgnc_id "HGNC:54463" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,21638285,21638676,+" ; tag pseudo_consens basic ; transcript_id "MTAP--H3P30^ENST00000424386.2" ; transcript_name "H3P30-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: MTAP--KHSRPP1 HAVANA gene 29696 31463 . + . FI_gene_label "KHSRPP1^ENSG00000229835.2" ; ID "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2" ; exon_id "ENSE00001689429.2" ; exon_number 1 ; gene_id "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2" ; gene_name KHSRPP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019683.2" ; havana_transcript "OTTHUMT00000051912.2" ; hgnc_id "HGNC:39198" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,21695176,21696943,+" ; tag pseudo_consens basic ; transcript_id "MTAP--KHSRPP1^ENST00000427983.2" ; transcript_name "KHSRPP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene MTAP--KHSRPP1 HAVANA RNA 29696 31463 . + . FI_gene_label "KHSRPP1^ENSG00000229835.2" ; ID "MTAP--KHSRPP1^ENST00000427983.2" ; Parent "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2" ; exon_id "ENSE00001689429.2" ; exon_number 1 ; gene_id "MTAP--KHSRPP1^KHSRPP1^ENSG00000229835.2" ; gene_name KHSRPP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019683.2" ; havana_transcript "OTTHUMT00000051912.2" ; hgnc_id "HGNC:39198" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,21695176,21696943,+" ; tag pseudo_consens basic ; transcript_id "MTAP--KHSRPP1^ENST00000427983.2" ; transcript_name "KHSRPP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: RPSAP52--HMGA2 HAVANA gene 1024 4035 . + . FI_gene_label "RPSAP52^ENSG00000241749.4" ; ID "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4" ; exon_id "ENSE00001887935.1" ; exon_number 1 ; gene_id "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4" ; gene_name RPSAP52 ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000157608.3" ; havana_transcript "OTTHUMT00000349256.2" ; hgnc_id "HGNC:35752" ; level 2 ; orig_coord_info "chr12,65826843,65826974,-" ; tag basic ; transcript_id "RPSAP52--HMGA2^ENST00000489520.2" ; transcript_name "RPSAP52-201" ; transcript_support_level 1 ; transcript_type processed_transcript RPSAP52--HMGA2 HAVANA RNA 1024 4035 . + . FI_gene_label "RPSAP52^ENSG00000241749.4" ; ID "RPSAP52--HMGA2^ENST00000489520.2" ; Parent "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4" ; exon_id "ENSE00001887935.1" ; exon_number 1 ; gene_id "RPSAP52--HMGA2^RPSAP52^ENSG00000241749.4" ; gene_name RPSAP52 ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000157608.3" ; havana_transcript "OTTHUMT00000349256.2" ; hgnc_id "HGNC:35752" ; level 2 ; orig_coord_info "chr12,65826843,65826974,-" ; tag basic ; transcript_id "RPSAP52--HMGA2^ENST00000489520.2" ; transcript_name "RPSAP52-201" ; transcript_support_level 1 ; transcript_type processed_transcript L1 and L2 created: TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript 344 cases fixed where L3 features have parent feature(s) missing ------------------------------ done in 1 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 ------------------------------ 611 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 1 second) ------ GFF3 file parsed