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: 3229 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3229 => 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:3229 => 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: AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ACSF2--AC018521.3 HAVANA gene 1061 14951 . + . FI_gene_label "ACSF2^ENSG00000167107.13" ; ID "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13" ; ccdsid "CCDS11567.1" ; exon_id "ENSE00003678158.1" ; exon_number 1 ; gene_id "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13" ; gene_name ACSF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162128.5" ; havana_transcript "OTTHUMT00000367423.3" ; hgnc_id "HGNC:26101" ; level 2 ; orig_coord_info "chr17,50426262,50426389,+" ; protein_id "ENSP00000300441.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACSF2--AC018521.3^ENST00000300441.9" ; transcript_name "ACSF2-201" ; transcript_support_level 1 ; transcript_type protein_coding ACSF2--AC018521.3 HAVANA mRNA 1061 14951 . + . FI_gene_label "ACSF2^ENSG00000167107.13" ; ID "ACSF2--AC018521.3^ENST00000300441.9" ; Parent "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13" ; ccdsid "CCDS11567.1" ; exon_id "ENSE00003678158.1" ; exon_number 1 ; gene_id "ACSF2--AC018521.3^ACSF2^ENSG00000167107.13" ; gene_name ACSF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162128.5" ; havana_transcript "OTTHUMT00000367423.3" ; hgnc_id "HGNC:26101" ; level 2 ; orig_coord_info "chr17,50426262,50426389,+" ; protein_id "ENSP00000300441.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ACSF2--AC018521.3^ENST00000300441.9" ; transcript_name "ACSF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ASCC2--ANKFN1 HAVANA gene 1031 28012 . + . FI_gene_label "ASCC2^ENSG00000100325.15" ; ID "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15" ; ccdsid "CCDS13869.1" ; exon_id "ENSE00003557333.1" ; exon_number 2 ; gene_id "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15" ; gene_name ASCC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067658.7" ; havana_transcript "OTTHUMT00000145221.4" ; hgnc_id "HGNC:24103" ; level 2 ; orig_coord_info "chr22,29832245,29832325,-" ; protein_id "ENSP00000305502.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000307790.8" ; transcript_name "ASCC2-201" ; transcript_support_level 1 ; transcript_type protein_coding ASCC2--ANKFN1 HAVANA mRNA 1031 28012 . + . FI_gene_label "ASCC2^ENSG00000100325.15" ; ID "ASCC2--ANKFN1^ENST00000307790.8" ; Parent "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15" ; ccdsid "CCDS13869.1" ; exon_id "ENSE00003557333.1" ; exon_number 2 ; gene_id "ASCC2--ANKFN1^ASCC2^ENSG00000100325.15" ; gene_name ASCC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067658.7" ; havana_transcript "OTTHUMT00000145221.4" ; hgnc_id "HGNC:24103" ; level 2 ; orig_coord_info "chr22,29832245,29832325,-" ; protein_id "ENSP00000305502.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000307790.8" ; transcript_name "ASCC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ASCC2--ANKFN1 HAVANA gene 37793 72255 . + . FI_gene_label "ANKFN1^ENSG00000153930.12" ; ID "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12" ; ccdsid "CCDS32686.1" ; exon_id "ENSE00001239155.3" ; exon_number 1 ; gene_id "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12" ; gene_name ANKFN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155010.6" ; havana_transcript "OTTHUMT00000338043.1" ; hgnc_id "HGNC:26766" ; level 2 ; orig_coord_info "chr17,56153510,56153530,+" ; protein_id "ENSP00000321627.2" ; tag basic appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000318698.6" ; transcript_name "ANKFN1-201" ; transcript_support_level 2 ; transcript_type protein_coding ASCC2--ANKFN1 HAVANA mRNA 37793 72255 . + . FI_gene_label "ANKFN1^ENSG00000153930.12" ; ID "ASCC2--ANKFN1^ENST00000318698.6" ; Parent "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12" ; ccdsid "CCDS32686.1" ; exon_id "ENSE00001239155.3" ; exon_number 1 ; gene_id "ASCC2--ANKFN1^ANKFN1^ENSG00000153930.12" ; gene_name ANKFN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155010.6" ; havana_transcript "OTTHUMT00000338043.1" ; hgnc_id "HGNC:26766" ; level 2 ; orig_coord_info "chr17,56153510,56153530,+" ; protein_id "ENSP00000321627.2" ; tag basic appris_principal_2 CCDS ; transcript_id "ASCC2--ANKFN1^ENST00000318698.6" ; transcript_name "ANKFN1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: BCR--CABIN1 HAVANA gene 41099 88248 . + . FI_gene_label "CABIN1^ENSG00000099991.18" ; ID "BCR--CABIN1^CABIN1^ENSG00000099991.18" ; ccdsid "CCDS13823.1" ; exon_id "ENSE00001361081.2" ; exon_number 2 ; gene_id "BCR--CABIN1^CABIN1^ENSG00000099991.18" ; gene_name CABIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150797.6" ; havana_transcript "OTTHUMT00000340949.3" ; hgnc_id "HGNC:24187" ; level 2 ; orig_coord_info "chr22,24035518,24035520,+" ; protein_id "ENSP00000263119.5" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "BCR--CABIN1^ENST00000263119.10" ; transcript_name "CABIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding BCR--CABIN1 HAVANA mRNA 41099 88248 . + . FI_gene_label "CABIN1^ENSG00000099991.18" ; ID "BCR--CABIN1^ENST00000263119.10" ; Parent "BCR--CABIN1^CABIN1^ENSG00000099991.18" ; ccdsid "CCDS13823.1" ; exon_id "ENSE00001361081.2" ; exon_number 2 ; gene_id "BCR--CABIN1^CABIN1^ENSG00000099991.18" ; gene_name CABIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150797.6" ; havana_transcript "OTTHUMT00000340949.3" ; hgnc_id "HGNC:24187" ; level 2 ; orig_coord_info "chr22,24035518,24035520,+" ; protein_id "ENSP00000263119.5" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "BCR--CABIN1^ENST00000263119.10" ; transcript_name "CABIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BCR--CABIN1 HAVANA gene 1806 37986 . + . FI_gene_label "BCR^ENSG00000186716.21" ; ID "BCR--CABIN1^BCR^ENSG00000186716.21" ; ccdsid "CCDS13806.1" ; exon_id "ENSE00001897802.2" ; exon_number 1 ; gene_id "BCR--CABIN1^BCR^ENSG00000186716.21" ; gene_name BCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000150655.5" ; havana_transcript "OTTHUMT00000075819.2" ; hgnc_id "HGNC:1014" ; level 2 ; orig_coord_info "chr22,23180961,23182239,+" ; protein_id "ENSP00000303507.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCR--CABIN1^ENST00000305877.13" ; transcript_name "BCR-201" ; transcript_support_level 1 ; transcript_type protein_coding BCR--CABIN1 HAVANA mRNA 1806 37986 . + . FI_gene_label "BCR^ENSG00000186716.21" ; ID "BCR--CABIN1^ENST00000305877.13" ; Parent "BCR--CABIN1^BCR^ENSG00000186716.21" ; ccdsid "CCDS13806.1" ; exon_id "ENSE00001897802.2" ; exon_number 1 ; gene_id "BCR--CABIN1^BCR^ENSG00000186716.21" ; gene_name BCR ; gene_type protein_coding ; havana_gene "OTTHUMG00000150655.5" ; havana_transcript "OTTHUMT00000075819.2" ; hgnc_id "HGNC:1014" ; level 2 ; orig_coord_info "chr22,23180961,23182239,+" ; protein_id "ENSP00000303507.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCR--CABIN1^ENST00000305877.13" ; transcript_name "BCR-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: C17orf80--LINC00469 HAVANA gene 1001 7545 . + . FI_gene_label "C17orf80^ENSG00000141219.15" ; ID "C17orf80--LINC00469^C17orf80^ENSG00000141219.15" ; ccdsid "CCDS74145.1" ; exon_id "ENSE00001340095.1" ; exon_number 3 ; gene_id "C17orf80--LINC00469^C17orf80^ENSG00000141219.15" ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2" ; havana_transcript "OTTHUMT00000441887.1" ; hgnc_id "HGNC:29601" ; level 2 ; orig_coord_info "chr17,73235483,73236995,+" ; protein_id "ENSP00000255557.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "C17orf80--LINC00469^ENST00000255557.8" ; transcript_name "C17orf80-201" ; transcript_support_level 2 ; transcript_type protein_coding C17orf80--LINC00469 HAVANA mRNA 1001 7545 . + . FI_gene_label "C17orf80^ENSG00000141219.15" ; ID "C17orf80--LINC00469^ENST00000255557.8" ; Parent "C17orf80--LINC00469^C17orf80^ENSG00000141219.15" ; ccdsid "CCDS74145.1" ; exon_id "ENSE00001340095.1" ; exon_number 3 ; gene_id "C17orf80--LINC00469^C17orf80^ENSG00000141219.15" ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2" ; havana_transcript "OTTHUMT00000441887.1" ; hgnc_id "HGNC:29601" ; level 2 ; orig_coord_info "chr17,73235483,73236995,+" ; protein_id "ENSP00000255557.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "C17orf80--LINC00469^ENST00000255557.8" ; transcript_name "C17orf80-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CEP112--AC134698.1 HAVANA gene 29887 41644 . + . FI_gene_label "CEP112^ENSG00000154240.17" ; ID "CEP112--AC134698.1^CEP112^ENSG00000154240.17" ; ccdsid "CCDS32711.1" ; exon_id "ENSE00001276658.7" ; exon_number 1 ; gene_id "CEP112--AC134698.1^CEP112^ENSG00000154240.17" ; gene_name CEP112 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179474.6" ; havana_transcript "OTTHUMT00000446583.1" ; hgnc_id "HGNC:28514" ; level 2 ; orig_coord_info "chr17,65826138,65826299,-" ; protein_id "ENSP00000320592.5" ; tag basic CCDS ; transcript_id "CEP112--AC134698.1^ENST00000317442.12" ; transcript_name "CEP112-201" ; transcript_support_level 1 ; transcript_type protein_coding CEP112--AC134698.1 HAVANA mRNA 29887 41644 . + . FI_gene_label "CEP112^ENSG00000154240.17" ; ID "CEP112--AC134698.1^ENST00000317442.12" ; Parent "CEP112--AC134698.1^CEP112^ENSG00000154240.17" ; ccdsid "CCDS32711.1" ; exon_id "ENSE00001276658.7" ; exon_number 1 ; gene_id "CEP112--AC134698.1^CEP112^ENSG00000154240.17" ; gene_name CEP112 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179474.6" ; havana_transcript "OTTHUMT00000446583.1" ; hgnc_id "HGNC:28514" ; level 2 ; orig_coord_info "chr17,65826138,65826299,-" ; protein_id "ENSP00000320592.5" ; tag basic CCDS ; transcript_id "CEP112--AC134698.1^ENST00000317442.12" ; transcript_name "CEP112-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: COX6CP1--COX6C HAVANA gene 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding COX6CP1--COX6C HAVANA mRNA 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^ENST00000297564.6" ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CSNK1D--C17orf80 HAVANA gene 24148 30692 . + . FI_gene_label "C17orf80^ENSG00000141219.15" ; ID "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15" ; ccdsid "CCDS74145.1" ; exon_id "ENSE00001340095.1" ; exon_number 3 ; gene_id "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15" ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2" ; havana_transcript "OTTHUMT00000441887.1" ; hgnc_id "HGNC:29601" ; level 2 ; orig_coord_info "chr17,73235483,73236995,+" ; protein_id "ENSP00000255557.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "CSNK1D--C17orf80^ENST00000255557.8" ; transcript_name "C17orf80-201" ; transcript_support_level 2 ; transcript_type protein_coding CSNK1D--C17orf80 HAVANA mRNA 24148 30692 . + . FI_gene_label "C17orf80^ENSG00000141219.15" ; ID "CSNK1D--C17orf80^ENST00000255557.8" ; Parent "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15" ; ccdsid "CCDS74145.1" ; exon_id "ENSE00001340095.1" ; exon_number 3 ; gene_id "CSNK1D--C17orf80^C17orf80^ENSG00000141219.15" ; gene_name C17orf80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178417.2" ; havana_transcript "OTTHUMT00000441887.1" ; hgnc_id "HGNC:29601" ; level 2 ; orig_coord_info "chr17,73235483,73236995,+" ; protein_id "ENSP00000255557.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "CSNK1D--C17orf80^ENST00000255557.8" ; transcript_name "C17orf80-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: CSNK1D--C17orf80 HAVANA gene 6457 17094 . + . FI_gene_label "CSNK1D^ENSG00000141551.14" ; ID "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14" ; exon_id "ENSE00002716627.1" ; exon_number 1 ; gene_id "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14" ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2" ; havana_transcript "OTTHUMT00000442642.1" ; hgnc_id "HGNC:2452" ; level 2 ; orig_coord_info "chr17,82255429,82255516,-" ; protein_id "ENSP00000269361.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CSNK1D--C17orf80^ENST00000269361.11" ; transcript_name "CSNK1D-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay CSNK1D--C17orf80 HAVANA mRNA 6457 17094 . + . FI_gene_label "CSNK1D^ENSG00000141551.14" ; ID "CSNK1D--C17orf80^ENST00000269361.11" ; Parent "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14" ; exon_id "ENSE00002716627.1" ; exon_number 1 ; gene_id "CSNK1D--C17orf80^CSNK1D^ENSG00000141551.14" ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2" ; havana_transcript "OTTHUMT00000442642.1" ; hgnc_id "HGNC:2452" ; level 2 ; orig_coord_info "chr17,82255429,82255516,-" ; protein_id "ENSP00000269361.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CSNK1D--C17orf80^ENST00000269361.11" ; transcript_name "CSNK1D-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay L1 and L2 created: EIF4E--AP002026.1 HAVANA gene 1042 13518 . + . FI_gene_label "EIF4E^ENSG00000151247.13" ; ID "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13" ; ccdsid "CCDS47109.1" ; exon_id "ENSE00001609349.1" ; exon_number 1 ; gene_id "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13" ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2" ; havana_transcript "OTTHUMT00000363740.1" ; hgnc_id "HGNC:3287" ; level 2 ; orig_coord_info "chr4,98928895,98928972,-" ; protein_id "ENSP00000280892.6" ; tag basic CCDS ; transcript_id "EIF4E--AP002026.1^ENST00000280892.10" ; transcript_name "EIF4E-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF4E--AP002026.1 HAVANA mRNA 1042 13518 . + . FI_gene_label "EIF4E^ENSG00000151247.13" ; ID "EIF4E--AP002026.1^ENST00000280892.10" ; Parent "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13" ; ccdsid "CCDS47109.1" ; exon_id "ENSE00001609349.1" ; exon_number 1 ; gene_id "EIF4E--AP002026.1^EIF4E^ENSG00000151247.13" ; gene_name EIF4E ; gene_type protein_coding ; havana_gene "OTTHUMG00000161090.2" ; havana_transcript "OTTHUMT00000363740.1" ; hgnc_id "HGNC:3287" ; level 2 ; orig_coord_info "chr4,98928895,98928972,-" ; protein_id "ENSP00000280892.6" ; tag basic CCDS ; transcript_id "EIF4E--AP002026.1^ENST00000280892.10" ; transcript_name "EIF4E-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; 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: PCDHA11--PCDHA13 HAVANA gene 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA11--PCDHA13 HAVANA mRNA 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^ENST00000289272.3" ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA11--PCDHA13 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA11--PCDHA13 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^ENST00000616325.1" ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA11--PCDHAC1 HAVANA gene 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA11--PCDHAC1 HAVANA mRNA 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA11--PCDHAC1 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA11--PCDHAC1 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA11--PCDHAC2 HAVANA gene 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA11--PCDHAC2 HAVANA mRNA 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA11--PCDHAC2 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding PCDHA11--PCDHAC2 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: PLXNA3--AC245140.3 HAVANA gene 1001 19691 . + . FI_gene_label "PLXNA3^ENSG00000130827.6" ; ID "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6" ; ccdsid "CCDS14752.1" ; exon_id "ENSE00001450662.1" ; exon_number 2 ; gene_id "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6" ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6" ; havana_transcript "OTTHUMT00000081634.3" ; hgnc_id "HGNC:9101" ; level 2 ; orig_coord_info "chrX,154460184,154460777,+" ; protein_id "ENSP00000358696.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--AC245140.3^ENST00000369682.4" ; transcript_name "PLXNA3-201" ; transcript_support_level 1 ; transcript_type protein_coding PLXNA3--AC245140.3 HAVANA mRNA 1001 19691 . + . FI_gene_label "PLXNA3^ENSG00000130827.6" ; ID "PLXNA3--AC245140.3^ENST00000369682.4" ; Parent "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6" ; ccdsid "CCDS14752.1" ; exon_id "ENSE00001450662.1" ; exon_number 2 ; gene_id "PLXNA3--AC245140.3^PLXNA3^ENSG00000130827.6" ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6" ; havana_transcript "OTTHUMT00000081634.3" ; hgnc_id "HGNC:9101" ; level 2 ; orig_coord_info "chrX,154460184,154460777,+" ; protein_id "ENSP00000358696.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--AC245140.3^ENST00000369682.4" ; transcript_name "PLXNA3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PLXNA3--EMD HAVANA gene 1001 19691 . + . FI_gene_label "PLXNA3^ENSG00000130827.6" ; ID "PLXNA3--EMD^PLXNA3^ENSG00000130827.6" ; ccdsid "CCDS14752.1" ; exon_id "ENSE00001450662.1" ; exon_number 2 ; gene_id "PLXNA3--EMD^PLXNA3^ENSG00000130827.6" ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6" ; havana_transcript "OTTHUMT00000081634.3" ; hgnc_id "HGNC:9101" ; level 2 ; orig_coord_info "chrX,154460184,154460777,+" ; protein_id "ENSP00000358696.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--EMD^ENST00000369682.4" ; transcript_name "PLXNA3-201" ; transcript_support_level 1 ; transcript_type protein_coding PLXNA3--EMD HAVANA mRNA 1001 19691 . + . FI_gene_label "PLXNA3^ENSG00000130827.6" ; ID "PLXNA3--EMD^ENST00000369682.4" ; Parent "PLXNA3--EMD^PLXNA3^ENSG00000130827.6" ; ccdsid "CCDS14752.1" ; exon_id "ENSE00001450662.1" ; exon_number 2 ; gene_id "PLXNA3--EMD^PLXNA3^ENSG00000130827.6" ; gene_name PLXNA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033290.6" ; havana_transcript "OTTHUMT00000081634.3" ; hgnc_id "HGNC:9101" ; level 2 ; orig_coord_info "chrX,154460184,154460777,+" ; protein_id "ENSP00000358696.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLXNA3--EMD^ENST00000369682.4" ; transcript_name "PLXNA3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PLXNA3--EMD HAVANA gene 22692 24710 . + . FI_gene_label "EMD^ENSG00000102119.11" ; ID "PLXNA3--EMD^EMD^ENSG00000102119.11" ; exon_id "ENSE00001909734.1" ; exon_number 1 ; gene_id "PLXNA3--EMD^EMD^ENSG00000102119.11" ; gene_name EMD ; gene_type protein_coding ; havana_gene "OTTHUMG00000033186.6" ; havana_transcript "OTTHUMT00000130306.1" ; hgnc_id "HGNC:3331" ; level 2 ; orig_coord_info "chrX,154379485,154379566,+" ; protein_id "ENSP00000358850.3" ; tag basic ; transcript_id "PLXNA3--EMD^ENST00000369835.3" ; transcript_name "EMD-201" ; transcript_support_level 3 ; transcript_type protein_coding PLXNA3--EMD HAVANA mRNA 22692 24710 . + . FI_gene_label "EMD^ENSG00000102119.11" ; ID "PLXNA3--EMD^ENST00000369835.3" ; Parent "PLXNA3--EMD^EMD^ENSG00000102119.11" ; exon_id "ENSE00001909734.1" ; exon_number 1 ; gene_id "PLXNA3--EMD^EMD^ENSG00000102119.11" ; gene_name EMD ; gene_type protein_coding ; havana_gene "OTTHUMG00000033186.6" ; havana_transcript "OTTHUMT00000130306.1" ; hgnc_id "HGNC:3331" ; level 2 ; orig_coord_info "chrX,154379485,154379566,+" ; protein_id "ENSP00000358850.3" ; tag basic ; transcript_id "PLXNA3--EMD^ENST00000369835.3" ; transcript_name "EMD-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: SLC16A5--CSNK1D HAVANA gene 19340 29977 . + . FI_gene_label "CSNK1D^ENSG00000141551.14" ; ID "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14" ; exon_id "ENSE00002716627.1" ; exon_number 1 ; gene_id "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14" ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2" ; havana_transcript "OTTHUMT00000442642.1" ; hgnc_id "HGNC:2452" ; level 2 ; orig_coord_info "chr17,82255429,82255516,-" ; protein_id "ENSP00000269361.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SLC16A5--CSNK1D^ENST00000269361.11" ; transcript_name "CSNK1D-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay SLC16A5--CSNK1D HAVANA mRNA 19340 29977 . + . FI_gene_label "CSNK1D^ENSG00000141551.14" ; ID "SLC16A5--CSNK1D^ENST00000269361.11" ; Parent "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14" ; exon_id "ENSE00002716627.1" ; exon_number 1 ; gene_id "SLC16A5--CSNK1D^CSNK1D^ENSG00000141551.14" ; gene_name CSNK1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000178601.2" ; havana_transcript "OTTHUMT00000442642.1" ; hgnc_id "HGNC:2452" ; level 2 ; orig_coord_info "chr17,82255429,82255516,-" ; protein_id "ENSP00000269361.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SLC16A5--CSNK1D^ENST00000269361.11" ; transcript_name "CSNK1D-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay L1 and L2 created: SLC16A5--CSNK1D HAVANA gene 1228 10883 . + . FI_gene_label "SLC16A5^ENSG00000170190.16" ; ID "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16" ; ccdsid "CCDS11713.1" ; exon_id "ENSE00003508349.1" ; exon_number 3 ; gene_id "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16" ; gene_name SLC16A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179277.5" ; havana_transcript "OTTHUMT00000445545.2" ; hgnc_id "HGNC:10926" ; level 2 ; orig_coord_info "chr17,75093637,75093835,+" ; protein_id "ENSP00000330141.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SLC16A5--CSNK1D^ENST00000329783.9" ; transcript_name "SLC16A5-201" ; transcript_support_level 1 ; transcript_type protein_coding SLC16A5--CSNK1D HAVANA mRNA 1228 10883 . + . FI_gene_label "SLC16A5^ENSG00000170190.16" ; ID "SLC16A5--CSNK1D^ENST00000329783.9" ; Parent "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16" ; ccdsid "CCDS11713.1" ; exon_id "ENSE00003508349.1" ; exon_number 3 ; gene_id "SLC16A5--CSNK1D^SLC16A5^ENSG00000170190.16" ; gene_name SLC16A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179277.5" ; havana_transcript "OTTHUMT00000445545.2" ; hgnc_id "HGNC:10926" ; level 2 ; orig_coord_info "chr17,75093637,75093835,+" ; protein_id "ENSP00000330141.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SLC16A5--CSNK1D^ENST00000329783.9" ; transcript_name "SLC16A5-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SLX4IP--FRG1DP HAVANA gene 1001 14056 . + . FI_gene_label "SLX4IP^ENSG00000149346.15" ; ID "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15" ; ccdsid "CCDS33439.1" ; exon_id "ENSE00001175305.1" ; exon_number 2 ; gene_id "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15" ; gene_name SLX4IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000031873.6" ; havana_transcript "OTTHUMT00000078000.5" ; hgnc_id "HGNC:16225" ; level 2 ; orig_coord_info "chr20,10458205,10458231,+" ; protein_id "ENSP00000335557.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLX4IP--FRG1DP^ENST00000334534.10" ; transcript_name "SLX4IP-201" ; transcript_support_level 1 ; transcript_type protein_coding SLX4IP--FRG1DP HAVANA mRNA 1001 14056 . + . FI_gene_label "SLX4IP^ENSG00000149346.15" ; ID "SLX4IP--FRG1DP^ENST00000334534.10" ; Parent "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15" ; ccdsid "CCDS33439.1" ; exon_id "ENSE00001175305.1" ; exon_number 2 ; gene_id "SLX4IP--FRG1DP^SLX4IP^ENSG00000149346.15" ; gene_name SLX4IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000031873.6" ; havana_transcript "OTTHUMT00000078000.5" ; hgnc_id "HGNC:16225" ; level 2 ; orig_coord_info "chr20,10458205,10458231,+" ; protein_id "ENSP00000335557.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLX4IP--FRG1DP^ENST00000334534.10" ; transcript_name "SLX4IP-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: AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA L1 and L2 created: ACSF2--AC018521.3 HAVANA gene 17960 19775 . + . FI_gene_label "AC018521.3^ENSG00000264243.1" ; ID "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1" ; exon_id "ENSE00002694001.1" ; exon_number 1 ; gene_id "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1" ; gene_name "AC018521.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000178291.1" ; havana_transcript "OTTHUMT00000441396.1" ; level 2 ; orig_coord_info "chr17,47863342,47863419,+" ; tag basic ; transcript_id "ACSF2--AC018521.3^ENST00000581213.1" ; transcript_name "AC018521.3-201" ; transcript_support_level 1 ; transcript_type lncRNA ACSF2--AC018521.3 HAVANA RNA 17960 19775 . + . FI_gene_label "AC018521.3^ENSG00000264243.1" ; ID "ACSF2--AC018521.3^ENST00000581213.1" ; Parent "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1" ; exon_id "ENSE00002694001.1" ; exon_number 1 ; gene_id "ACSF2--AC018521.3^AC018521.3^ENSG00000264243.1" ; gene_name "AC018521.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000178291.1" ; havana_transcript "OTTHUMT00000441396.1" ; level 2 ; orig_coord_info "chr17,47863342,47863419,+" ; tag basic ; transcript_id "ACSF2--AC018521.3^ENST00000581213.1" ; transcript_name "AC018521.3-201" ; transcript_support_level 1 ; transcript_type lncRNA L1 and L2 created: C17orf80--LINC00469 HAVANA gene 13258 18525 . + . FI_gene_label "LINC00469^ENSG00000177338.14" ; ID "C17orf80--LINC00469^LINC00469^ENSG00000177338.14" ; exon_id "ENSE00001556257.1" ; exon_number 1 ; gene_id "C17orf80--LINC00469^LINC00469^ENSG00000177338.14" ; gene_name LINC00469 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167833.4" ; havana_transcript "OTTHUMT00000396490.1" ; hgnc_id "HGNC:26863" ; level 2 ; orig_coord_info "chr17,73828448,73828520,-" ; tag basic ; transcript_id "C17orf80--LINC00469^ENST00000321800.11" ; transcript_name "LINC00469-201" ; transcript_support_level 1 ; transcript_type lncRNA C17orf80--LINC00469 HAVANA RNA 13258 18525 . + . FI_gene_label "LINC00469^ENSG00000177338.14" ; ID "C17orf80--LINC00469^ENST00000321800.11" ; Parent "C17orf80--LINC00469^LINC00469^ENSG00000177338.14" ; exon_id "ENSE00001556257.1" ; exon_number 1 ; gene_id "C17orf80--LINC00469^LINC00469^ENSG00000177338.14" ; gene_name LINC00469 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167833.4" ; havana_transcript "OTTHUMT00000396490.1" ; hgnc_id "HGNC:26863" ; level 2 ; orig_coord_info "chr17,73828448,73828520,-" ; tag basic ; transcript_id "C17orf80--LINC00469^ENST00000321800.11" ; transcript_name "LINC00469-201" ; transcript_support_level 1 ; transcript_type lncRNA L1 and L2 created: CEP112--AC134698.1 HAVANA gene 44924 49566 . + . FI_gene_label "AC134698.1^ENSG00000250637.2" ; ID "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2" ; exon_id "ENSE00002076945.1" ; exon_number 1 ; gene_id "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2" ; gene_name "AC134698.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160408.2" ; havana_transcript "OTTHUMT00000360482.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,43442902,43443081,+" ; tag basic ; transcript_id "CEP112--AC134698.1^ENST00000511619.2" ; transcript_name "AC134698.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene CEP112--AC134698.1 HAVANA RNA 44924 49566 . + . FI_gene_label "AC134698.1^ENSG00000250637.2" ; ID "CEP112--AC134698.1^ENST00000511619.2" ; Parent "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2" ; exon_id "ENSE00002076945.1" ; exon_number 1 ; gene_id "CEP112--AC134698.1^AC134698.1^ENSG00000250637.2" ; gene_name "AC134698.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160408.2" ; havana_transcript "OTTHUMT00000360482.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,43442902,43443081,+" ; tag basic ; transcript_id "CEP112--AC134698.1^ENST00000511619.2" ; transcript_name "AC134698.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene L1 and L2 created: COX6CP1--COX6C HAVANA gene 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene COX6CP1--COX6C HAVANA RNA 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^ENST00000564972.1" ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: EIF4E--AP002026.1 HAVANA gene 18154 19918 . + . FI_gene_label "AP002026.1^ENSG00000246090.7" ; ID "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7" ; exon_id "ENSE00001962097.2" ; exon_number 1 ; gene_id "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7" ; gene_name "AP002026.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000161232.6" ; havana_transcript "OTTHUMT00000364249.1" ; level 2 ; orig_coord_info "chr4,99088951,99089284,+" ; transcript_id "EIF4E--AP002026.1^ENST00000499178.2" ; transcript_name "AP002026.1-202" ; transcript_support_level 3 ; transcript_type lncRNA EIF4E--AP002026.1 HAVANA RNA 18154 19918 . + . FI_gene_label "AP002026.1^ENSG00000246090.7" ; ID "EIF4E--AP002026.1^ENST00000499178.2" ; Parent "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7" ; exon_id "ENSE00001962097.2" ; exon_number 1 ; gene_id "EIF4E--AP002026.1^AP002026.1^ENSG00000246090.7" ; gene_name "AP002026.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000161232.6" ; havana_transcript "OTTHUMT00000364249.1" ; level 2 ; orig_coord_info "chr4,99088951,99089284,+" ; transcript_id "EIF4E--AP002026.1^ENST00000499178.2" ; transcript_name "AP002026.1-202" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: PLXNA3--AC245140.3 HAVANA gene 22692 24371 . + . FI_gene_label "AC245140.3^ENSG00000285018.1" ; ID "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1" ; exon_id "ENSE00003819558.1" ; exon_number 1 ; gene_id "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1" ; gene_name "AC245140.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192605.1" ; havana_transcript "OTTHUMT00000497131.1" ; level 2 ; orig_coord_info "chrX,154374595,154374727,+" ; tag basic ; transcript_id "PLXNA3--AC245140.3^ENST00000644854.1" ; transcript_name "AC245140.3-201" ; transcript_type lncRNA PLXNA3--AC245140.3 HAVANA RNA 22692 24371 . + . FI_gene_label "AC245140.3^ENSG00000285018.1" ; ID "PLXNA3--AC245140.3^ENST00000644854.1" ; Parent "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1" ; exon_id "ENSE00003819558.1" ; exon_number 1 ; gene_id "PLXNA3--AC245140.3^AC245140.3^ENSG00000285018.1" ; gene_name "AC245140.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192605.1" ; havana_transcript "OTTHUMT00000497131.1" ; level 2 ; orig_coord_info "chrX,154374595,154374727,+" ; tag basic ; transcript_id "PLXNA3--AC245140.3^ENST00000644854.1" ; transcript_name "AC245140.3-201" ; transcript_type lncRNA L1 and L2 created: SLX4IP--FRG1DP HAVANA gene 18591 27121 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "SLX4IP--FRG1DP^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene SLX4IP--FRG1DP HAVANA RNA 18591 27121 . + . FI_gene_label "FRG1DP^ENSG00000282870.1" ; ID "SLX4IP--FRG1DP^ENST00000635586.1" ; Parent "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1" ; exon_id "ENSE00003790844.1" ; exon_number 1 ; gene_id "SLX4IP--FRG1DP^FRG1DP^ENSG00000282870.1" ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1" ; havana_transcript "OTTHUMT00000488295.1" ; hgnc_id "HGNC:51763" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr20,29080390,29080455,+" ; tag basic ; transcript_id "SLX4IP--FRG1DP^ENST00000635586.1" ; transcript_name "FRG1DP-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene 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 353 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 ------------------------------ 506 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 30 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