Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/50b62780288ca327d96e45869a9c83/fi_workdir/aih-tih-sc-184b05-R1_A23YTGFLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b1f5fb5d81b2ab46cc668b114de399/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b1f5fb5d81b2ab46cc668b114de399/.command.run ==> STAGING COMPLETE (3 inputs) Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file ------------------------------------------------------------------------------ | Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 | | https://github.com/NBISweden/AGAT | | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | ------------------------------------------------------------------------------ ------ Start parsing ------ -------------------------- parse options and metadata -------------------------- => Accessing the feature_levels YAML file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file => Attribute used to group features when no Parent/ID relationship exists (i.e common tag): * locus_tag * gene_id => merge_loci option deactivated => Machine information: This script is being run by perl v5.32.1 Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/ Operating system being used: linux => Accessing Ontology No ontology accessible from the gff file header! We use the SOFA ontology distributed with AGAT: /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo: 4 root terms, and 2596 total terms, and 1516 leaf terms Filtering ontology: We found 1861 terms that are sequence_feature or is_a child of it. --------------------------------- parsing file --------------------------------- => Number of line in file: 5562 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 5562 => 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:5562 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 2 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: AC026336.1--PIWIL1 HAVANA gene 4352 24217 . + . FI_gene_label "PIWIL1^ENSG00000125207.7" ; ID "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7" ; ccdsid "CCDS9268.1" ; exon_id "ENSE00001002623.3" ; exon_number 2 ; gene_id "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7" ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3" ; havana_transcript "OTTHUMT00000399510.1" ; hgnc_id "HGNC:9007" ; level 2 ; orig_coord_info "chr12,130342592,130342669,+" ; protein_id "ENSP00000245255.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026336.1--PIWIL1^ENST00000245255.7" ; transcript_name "PIWIL1-201" ; transcript_support_level 1 ; transcript_type protein_coding AC026336.1--PIWIL1 HAVANA mRNA 4352 24217 . + . FI_gene_label "PIWIL1^ENSG00000125207.7" ; ID "AC026336.1--PIWIL1^ENST00000245255.7" ; Parent "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7" ; ccdsid "CCDS9268.1" ; exon_id "ENSE00001002623.3" ; exon_number 2 ; gene_id "AC026336.1--PIWIL1^PIWIL1^ENSG00000125207.7" ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3" ; havana_transcript "OTTHUMT00000399510.1" ; hgnc_id "HGNC:9007" ; level 2 ; orig_coord_info "chr12,130342592,130342669,+" ; protein_id "ENSP00000245255.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC026336.1--PIWIL1^ENST00000245255.7" ; transcript_name "PIWIL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ACTBP6--ACTB HAVANA gene 6203 10583 . + . FI_gene_label "ACTB^ENSG00000075624.17" ; ID "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; exon_id "ENSE00003542066.1" ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12" ; havana_transcript "OTTHUMT00000324028.2" ; hgnc_id "HGNC:132" ; level 2 ; orig_coord_info "chr7,5529535,5529657,-" ; protein_id "ENSP00000401032.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1" ; transcript_name "ACTB-201" ; transcript_support_level 4 ; transcript_type protein_coding ACTBP6--ACTB HAVANA mRNA 6203 10583 . + . FI_gene_label "ACTB^ENSG00000075624.17" ; ID "ACTBP6--ACTB^ENST00000414620.1" ; Parent "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; exon_id "ENSE00003542066.1" ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17" ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12" ; havana_transcript "OTTHUMT00000324028.2" ; hgnc_id "HGNC:132" ; level 2 ; orig_coord_info "chr7,5529535,5529657,-" ; protein_id "ENSP00000401032.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1" ; transcript_name "ACTB-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: AGAP12P--FRMPD2 HAVANA gene 13554 48555 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding AGAP12P--FRMPD2 HAVANA mRNA 13554 48555 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP12P--FRMPD2^ENST00000305531.3" ; Parent "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: BICD1--ITPR2 HAVANA gene 26282 32017 . + . FI_gene_label "ITPR2^ENSG00000123104.12" ; ID "BICD1--ITPR2^ITPR2^ENSG00000123104.12" ; exon_id "ENSE00002282656.1" ; exon_number 1 ; gene_id "BICD1--ITPR2^ITPR2^ENSG00000123104.12" ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5" ; havana_transcript "OTTHUMT00000402735.1" ; hgnc_id "HGNC:6181" ; level 2 ; orig_coord_info "chr12,26832690,26832781,-" ; protein_id "ENSP00000242737.5" ; tag basic ; transcript_id "BICD1--ITPR2^ENST00000242737.5" ; transcript_name "ITPR2-201" ; transcript_support_level 1 ; transcript_type protein_coding BICD1--ITPR2 HAVANA mRNA 26282 32017 . + . FI_gene_label "ITPR2^ENSG00000123104.12" ; ID "BICD1--ITPR2^ENST00000242737.5" ; Parent "BICD1--ITPR2^ITPR2^ENSG00000123104.12" ; exon_id "ENSE00002282656.1" ; exon_number 1 ; gene_id "BICD1--ITPR2^ITPR2^ENSG00000123104.12" ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5" ; havana_transcript "OTTHUMT00000402735.1" ; hgnc_id "HGNC:6181" ; level 2 ; orig_coord_info "chr12,26832690,26832781,-" ; protein_id "ENSP00000242737.5" ; tag basic ; transcript_id "BICD1--ITPR2^ENST00000242737.5" ; transcript_name "ITPR2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BICD1--ITPR2 HAVANA gene 1418 17158 . + . FI_gene_label "BICD1^ENSG00000151746.15" ; ID "BICD1--ITPR2^BICD1^ENSG00000151746.15" ; ccdsid "CCDS86290.1" ; exon_id "ENSE00001269108.5" ; exon_number 1 ; gene_id "BICD1--ITPR2^BICD1^ENSG00000151746.15" ; gene_name BICD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169307.6" ; havana_transcript "OTTHUMT00000403381.1" ; hgnc_id "HGNC:1049" ; level 2 ; orig_coord_info "chr12,32107332,32107544,+" ; protein_id "ENSP00000379107.3" ; tag CCDS ; transcript_id "BICD1--ITPR2^ENST00000395758.3" ; transcript_name "BICD1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay BICD1--ITPR2 HAVANA mRNA 1418 17158 . + . FI_gene_label "BICD1^ENSG00000151746.15" ; ID "BICD1--ITPR2^ENST00000395758.3" ; Parent "BICD1--ITPR2^BICD1^ENSG00000151746.15" ; ccdsid "CCDS86290.1" ; exon_id "ENSE00001269108.5" ; exon_number 1 ; gene_id "BICD1--ITPR2^BICD1^ENSG00000151746.15" ; gene_name BICD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169307.6" ; havana_transcript "OTTHUMT00000403381.1" ; hgnc_id "HGNC:1049" ; level 2 ; orig_coord_info "chr12,32107332,32107544,+" ; protein_id "ENSP00000379107.3" ; tag CCDS ; transcript_id "BICD1--ITPR2^ENST00000395758.3" ; transcript_name "BICD1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay L1 and L2 created: FGD4--PIK3C2G HAVANA gene 3702 28028 . + . FI_gene_label "FGD4^ENSG00000139132.15" ; ID "FGD4--PIK3C2G^FGD4^ENSG00000139132.15" ; exon_id "ENSE00003586205.1" ; exon_number 3 ; gene_id "FGD4--PIK3C2G^FGD4^ENSG00000139132.15" ; gene_name FGD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137374.7" ; havana_transcript "OTTHUMT00000268019.2" ; hgnc_id "HGNC:19125" ; level 2 ; orig_coord_info "chr12,32576358,32576449,+" ; protein_id "ENSP00000379089.1" ; transcript_id "FGD4--PIK3C2G^ENST00000395740.5" ; transcript_name "FGD4-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay FGD4--PIK3C2G HAVANA mRNA 3702 28028 . + . FI_gene_label "FGD4^ENSG00000139132.15" ; ID "FGD4--PIK3C2G^ENST00000395740.5" ; Parent "FGD4--PIK3C2G^FGD4^ENSG00000139132.15" ; exon_id "ENSE00003586205.1" ; exon_number 3 ; gene_id "FGD4--PIK3C2G^FGD4^ENSG00000139132.15" ; gene_name FGD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137374.7" ; havana_transcript "OTTHUMT00000268019.2" ; hgnc_id "HGNC:19125" ; level 2 ; orig_coord_info "chr12,32576358,32576449,+" ; protein_id "ENSP00000379089.1" ; transcript_id "FGD4--PIK3C2G^ENST00000395740.5" ; transcript_name "FGD4-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay L1 and L2 created: FGD4--PIK3C2G HAVANA gene 40383 79838 . + . FI_gene_label "PIK3C2G^ENSG00000139144.11" ; ID "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11" ; ccdsid "CCDS44839.1" ; exon_id "ENSE00001121910.3" ; exon_number 2 ; gene_id "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11" ; gene_name PIK3C2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000168841.7" ; havana_transcript "OTTHUMT00000401316.4" ; hgnc_id "HGNC:8973" ; level 2 ; orig_coord_info "chr12,18282082,18282759,+" ; protein_id "ENSP00000404845.1" ; tag basic CCDS ; transcript_id "FGD4--PIK3C2G^ENST00000433979.6" ; transcript_name "PIK3C2G-201" ; transcript_support_level 5 ; transcript_type protein_coding FGD4--PIK3C2G HAVANA mRNA 40383 79838 . + . FI_gene_label "PIK3C2G^ENSG00000139144.11" ; ID "FGD4--PIK3C2G^ENST00000433979.6" ; Parent "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11" ; ccdsid "CCDS44839.1" ; exon_id "ENSE00001121910.3" ; exon_number 2 ; gene_id "FGD4--PIK3C2G^PIK3C2G^ENSG00000139144.11" ; gene_name PIK3C2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000168841.7" ; havana_transcript "OTTHUMT00000401316.4" ; hgnc_id "HGNC:8973" ; level 2 ; orig_coord_info "chr12,18282082,18282759,+" ; protein_id "ENSP00000404845.1" ; tag basic CCDS ; transcript_id "FGD4--PIK3C2G^ENST00000433979.6" ; transcript_name "PIK3C2G-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: FZD10--PIWIL1 ENSEMBL gene 1001 4281 . + . FI_gene_label "FZD10^ENSG00000111432.4" ; ID "FZD10--PIWIL1^FZD10^ENSG00000111432.4" ; ccdsid "CCDS9267.1" ; exon_id "ENSE00002290283.1" ; exon_number 1 ; gene_id "FZD10--PIWIL1^FZD10^ENSG00000111432.4" ; gene_name FZD10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168380.3" ; hgnc_id "HGNC:4039" ; level 3 ; orig_coord_info "chr12,130162943,130164685,+" ; protein_id "ENSP00000229030.4" ; tag basic appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000229030.4" ; transcript_name "FZD10-201" ; transcript_support_level NA ; transcript_type protein_coding FZD10--PIWIL1 ENSEMBL mRNA 1001 4281 . + . FI_gene_label "FZD10^ENSG00000111432.4" ; ID "FZD10--PIWIL1^ENST00000229030.4" ; Parent "FZD10--PIWIL1^FZD10^ENSG00000111432.4" ; ccdsid "CCDS9267.1" ; exon_id "ENSE00002290283.1" ; exon_number 1 ; gene_id "FZD10--PIWIL1^FZD10^ENSG00000111432.4" ; gene_name FZD10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168380.3" ; hgnc_id "HGNC:4039" ; level 3 ; orig_coord_info "chr12,130162943,130164685,+" ; protein_id "ENSP00000229030.4" ; tag basic appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000229030.4" ; transcript_name "FZD10-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: FZD10--PIWIL1 HAVANA gene 7283 27148 . + . FI_gene_label "PIWIL1^ENSG00000125207.7" ; ID "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7" ; ccdsid "CCDS9268.1" ; exon_id "ENSE00001002623.3" ; exon_number 2 ; gene_id "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7" ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3" ; havana_transcript "OTTHUMT00000399510.1" ; hgnc_id "HGNC:9007" ; level 2 ; orig_coord_info "chr12,130342592,130342669,+" ; protein_id "ENSP00000245255.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000245255.7" ; transcript_name "PIWIL1-201" ; transcript_support_level 1 ; transcript_type protein_coding FZD10--PIWIL1 HAVANA mRNA 7283 27148 . + . FI_gene_label "PIWIL1^ENSG00000125207.7" ; ID "FZD10--PIWIL1^ENST00000245255.7" ; Parent "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7" ; ccdsid "CCDS9268.1" ; exon_id "ENSE00001002623.3" ; exon_number 2 ; gene_id "FZD10--PIWIL1^PIWIL1^ENSG00000125207.7" ; gene_name PIWIL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168382.3" ; havana_transcript "OTTHUMT00000399510.1" ; hgnc_id "HGNC:9007" ; level 2 ; orig_coord_info "chr12,130342592,130342669,+" ; protein_id "ENSP00000245255.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FZD10--PIWIL1^ENST00000245255.7" ; transcript_name "PIWIL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GTF2F2--CBY2 HAVANA gene 16609 20258 . + . FI_gene_label "CBY2^ENSG00000174015.10" ; ID "GTF2F2--CBY2^CBY2^ENSG00000174015.10" ; ccdsid "CCDS9399.1" ; exon_id "ENSE00002150255.1" ; exon_number 1 ; gene_id "GTF2F2--CBY2^CBY2^ENSG00000174015.10" ; gene_name CBY2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016861.5" ; havana_transcript "OTTHUMT00000044786.3" ; hgnc_id "HGNC:30720" ; level 2 ; orig_coord_info "chr13,45702391,45702465,+" ; protein_id "ENSP00000309189.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000310521.6" ; transcript_name "CBY2-201" ; transcript_support_level 1 ; transcript_type protein_coding GTF2F2--CBY2 HAVANA mRNA 16609 20258 . + . FI_gene_label "CBY2^ENSG00000174015.10" ; ID "GTF2F2--CBY2^ENST00000310521.6" ; Parent "GTF2F2--CBY2^CBY2^ENSG00000174015.10" ; ccdsid "CCDS9399.1" ; exon_id "ENSE00002150255.1" ; exon_number 1 ; gene_id "GTF2F2--CBY2^CBY2^ENSG00000174015.10" ; gene_name CBY2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016861.5" ; havana_transcript "OTTHUMT00000044786.3" ; hgnc_id "HGNC:30720" ; level 2 ; orig_coord_info "chr13,45702391,45702465,+" ; protein_id "ENSP00000309189.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000310521.6" ; transcript_name "CBY2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GTF2F2--CBY2 HAVANA gene 1001 13608 . + . FI_gene_label "GTF2F2^ENSG00000188342.12" ; ID "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12" ; ccdsid "CCDS9395.1" ; exon_id "ENSE00001479865.5" ; exon_number 1 ; gene_id "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12" ; gene_name GTF2F2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016849.5" ; havana_transcript "OTTHUMT00000044767.5" ; hgnc_id "HGNC:4653" ; level 2 ; orig_coord_info "chr13,45120656,45120721,+" ; protein_id "ENSP00000340823.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000340473.8" ; transcript_name "GTF2F2-201" ; transcript_support_level 1 ; transcript_type protein_coding GTF2F2--CBY2 HAVANA mRNA 1001 13608 . + . FI_gene_label "GTF2F2^ENSG00000188342.12" ; ID "GTF2F2--CBY2^ENST00000340473.8" ; Parent "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12" ; ccdsid "CCDS9395.1" ; exon_id "ENSE00001479865.5" ; exon_number 1 ; gene_id "GTF2F2--CBY2^GTF2F2^ENSG00000188342.12" ; gene_name GTF2F2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016849.5" ; havana_transcript "OTTHUMT00000044767.5" ; hgnc_id "HGNC:4653" ; level 2 ; orig_coord_info "chr13,45120656,45120721,+" ; protein_id "ENSP00000340823.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F2--CBY2^ENST00000340473.8" ; transcript_name "GTF2F2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ITPR2--AC048344.1 HAVANA gene 1414 7149 . + . FI_gene_label "ITPR2^ENSG00000123104.12" ; ID "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12" ; exon_id "ENSE00002282656.1" ; exon_number 1 ; gene_id "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12" ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5" ; havana_transcript "OTTHUMT00000402735.1" ; hgnc_id "HGNC:6181" ; level 2 ; orig_coord_info "chr12,26832690,26832781,-" ; protein_id "ENSP00000242737.5" ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000242737.5" ; transcript_name "ITPR2-201" ; transcript_support_level 1 ; transcript_type protein_coding ITPR2--AC048344.1 HAVANA mRNA 1414 7149 . + . FI_gene_label "ITPR2^ENSG00000123104.12" ; ID "ITPR2--AC048344.1^ENST00000242737.5" ; Parent "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12" ; exon_id "ENSE00002282656.1" ; exon_number 1 ; gene_id "ITPR2--AC048344.1^ITPR2^ENSG00000123104.12" ; gene_name ITPR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169181.5" ; havana_transcript "OTTHUMT00000402735.1" ; hgnc_id "HGNC:6181" ; level 2 ; orig_coord_info "chr12,26832690,26832781,-" ; protein_id "ENSP00000242737.5" ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000242737.5" ; transcript_name "ITPR2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NPM1--VPS72 HAVANA gene 1734 14723 . + . FI_gene_label "NPM1^ENSG00000181163.14" ; ID "NPM1--VPS72^NPM1^ENSG00000181163.14" ; ccdsid "CCDS4376.1" ; exon_id "ENSE00003906984.1" ; exon_number 1 ; gene_id "NPM1--VPS72^NPM1^ENSG00000181163.14" ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4" ; havana_transcript "OTTHUMT00000252858.2" ; hgnc_id "HGNC:7910" ; level 2 ; orig_coord_info "chr5,171387949,171388006,+" ; protein_id "ENSP00000296930.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--VPS72^ENST00000296930.10" ; transcript_name "NPM1-201" ; transcript_support_level 1 ; transcript_type protein_coding NPM1--VPS72 HAVANA mRNA 1734 14723 . + . FI_gene_label "NPM1^ENSG00000181163.14" ; ID "NPM1--VPS72^ENST00000296930.10" ; Parent "NPM1--VPS72^NPM1^ENSG00000181163.14" ; ccdsid "CCDS4376.1" ; exon_id "ENSE00003906984.1" ; exon_number 1 ; gene_id "NPM1--VPS72^NPM1^ENSG00000181163.14" ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4" ; havana_transcript "OTTHUMT00000252858.2" ; hgnc_id "HGNC:7910" ; level 2 ; orig_coord_info "chr5,171387949,171388006,+" ; protein_id "ENSP00000296930.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--VPS72^ENST00000296930.10" ; transcript_name "NPM1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NPM1--VPS72 HAVANA gene 19732 25191 . + . FI_gene_label "VPS72^ENSG00000163159.14" ; ID "NPM1--VPS72^VPS72^ENSG00000163159.14" ; ccdsid "CCDS59201.1" ; exon_id "ENSE00001932993.1" ; exon_number 1 ; gene_id "NPM1--VPS72^VPS72^ENSG00000163159.14" ; gene_name VPS72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012345.10" ; havana_transcript "OTTHUMT00000034394.3" ; hgnc_id "HGNC:11644" ; level 1 ; orig_coord_info "chr1,151190005,151190121,-" ; protein_id "ENSP00000346464.4" ; tag mRNA_start_NF exp_conf CCDS ; transcript_id "NPM1--VPS72^ENST00000354473.4" ; transcript_name "VPS72-201" ; transcript_support_level 3 ; transcript_type protein_coding NPM1--VPS72 HAVANA mRNA 19732 25191 . + . FI_gene_label "VPS72^ENSG00000163159.14" ; ID "NPM1--VPS72^ENST00000354473.4" ; Parent "NPM1--VPS72^VPS72^ENSG00000163159.14" ; ccdsid "CCDS59201.1" ; exon_id "ENSE00001932993.1" ; exon_number 1 ; gene_id "NPM1--VPS72^VPS72^ENSG00000163159.14" ; gene_name VPS72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012345.10" ; havana_transcript "OTTHUMT00000034394.3" ; hgnc_id "HGNC:11644" ; level 1 ; orig_coord_info "chr1,151190005,151190121,-" ; protein_id "ENSP00000346464.4" ; tag mRNA_start_NF exp_conf CCDS ; transcript_id "NPM1--VPS72^ENST00000354473.4" ; transcript_name "VPS72-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: PCDHB14--PCDHB15 HAVANA gene 8418 12388 . + . FI_gene_label "PCDHB15^ENSG00000113248.6" ; ID "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6" ; ccdsid "CCDS4257.1" ; exon_id "ENSE00000766437.10" ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6" ; gene_name PCDHB15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129609.6" ; havana_transcript "OTTHUMT00000251804.5" ; hgnc_id "HGNC:8686" ; level 2 ; orig_coord_info "chr5,141245579,141247939,+" ; protein_id "ENSP00000231173.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000231173.6" ; transcript_name "PCDHB15-201" ; transcript_support_level NA ; transcript_type protein_coding PCDHB14--PCDHB15 HAVANA mRNA 8418 12388 . + . FI_gene_label "PCDHB15^ENSG00000113248.6" ; ID "PCDHB14--PCDHB15^ENST00000231173.6" ; Parent "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6" ; ccdsid "CCDS4257.1" ; exon_id "ENSE00000766437.10" ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB15^ENSG00000113248.6" ; gene_name PCDHB15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129609.6" ; havana_transcript "OTTHUMT00000251804.5" ; hgnc_id "HGNC:8686" ; level 2 ; orig_coord_info "chr5,141245579,141247939,+" ; protein_id "ENSP00000231173.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000231173.6" ; transcript_name "PCDHB15-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PCDHB14--PCDHB15 HAVANA gene 1001 5417 . + . FI_gene_label "PCDHB14^ENSG00000120327.7" ; ID "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7" ; ccdsid "CCDS4256.1" ; exon_id "ENSE00001430609.6" ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7" ; gene_name PCDHB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129619.4" ; havana_transcript "OTTHUMT00000251814.3" ; hgnc_id "HGNC:8685" ; level 2 ; orig_coord_info "chr5,141223506,141225899,+" ; protein_id "ENSP00000239449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000239449.7" ; transcript_name "PCDHB14-201" ; transcript_support_level NA ; transcript_type protein_coding PCDHB14--PCDHB15 HAVANA mRNA 1001 5417 . + . FI_gene_label "PCDHB14^ENSG00000120327.7" ; ID "PCDHB14--PCDHB15^ENST00000239449.7" ; Parent "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7" ; ccdsid "CCDS4256.1" ; exon_id "ENSE00001430609.6" ; exon_number 1 ; gene_id "PCDHB14--PCDHB15^PCDHB14^ENSG00000120327.7" ; gene_name PCDHB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129619.4" ; havana_transcript "OTTHUMT00000251814.3" ; hgnc_id "HGNC:8685" ; level 2 ; orig_coord_info "chr5,141223506,141225899,+" ; protein_id "ENSP00000239449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHB14--PCDHB15^ENST00000239449.7" ; transcript_name "PCDHB14-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: PDXDC2P--NPIPB3 HAVANA gene 27345 37259 . + . FI_gene_label "NPIPB3^ENSG00000169246.16" ; ID "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; exon_id "ENSE00003561690.1" ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5" ; havana_transcript "OTTHUMT00000400432.2" ; hgnc_id "HGNC:28989" ; level 2 ; orig_coord_info "chr16,21424979,21425003,-" ; protein_id "ENSP00000413141.2" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6" ; transcript_name "NPIPB3-201" ; transcript_support_level 3 ; transcript_type protein_coding PDXDC2P--NPIPB3 HAVANA mRNA 27345 37259 . + . FI_gene_label "NPIPB3^ENSG00000169246.16" ; ID "PDXDC2P--NPIPB3^ENST00000419180.6" ; Parent "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; exon_id "ENSE00003561690.1" ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5" ; havana_transcript "OTTHUMT00000400432.2" ; hgnc_id "HGNC:28989" ; level 2 ; orig_coord_info "chr16,21424979,21425003,-" ; protein_id "ENSP00000413141.2" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6" ; transcript_name "NPIPB3-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: PRPF40B--DERA HAVANA gene 10252 22842 . + . FI_gene_label "PRPF40B^ENSG00000110844.14" ; ID "PRPF40B--DERA^PRPF40B^ENSG00000110844.14" ; exon_id "ENSE00003759647.1" ; exon_number 2 ; gene_id "PRPF40B--DERA^PRPF40B^ENSG00000110844.14" ; gene_name PRPF40B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169568.7" ; havana_transcript "OTTHUMT00000404847.1" ; hgnc_id "HGNC:25031" ; level 2 ; orig_coord_info "chr12,49631401,49631544,+" ; protein_id "ENSP00000261897.1" ; tag basic appris_alternative_2 ; transcript_id "PRPF40B--DERA^ENST00000261897.5" ; transcript_name "PRPF40B-201" ; transcript_support_level 1 ; transcript_type protein_coding PRPF40B--DERA HAVANA mRNA 10252 22842 . + . FI_gene_label "PRPF40B^ENSG00000110844.14" ; ID "PRPF40B--DERA^ENST00000261897.5" ; Parent "PRPF40B--DERA^PRPF40B^ENSG00000110844.14" ; exon_id "ENSE00003759647.1" ; exon_number 2 ; gene_id "PRPF40B--DERA^PRPF40B^ENSG00000110844.14" ; gene_name PRPF40B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169568.7" ; havana_transcript "OTTHUMT00000404847.1" ; hgnc_id "HGNC:25031" ; level 2 ; orig_coord_info "chr12,49631401,49631544,+" ; protein_id "ENSP00000261897.1" ; tag basic appris_alternative_2 ; transcript_id "PRPF40B--DERA^ENST00000261897.5" ; transcript_name "PRPF40B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PRPF40B--DERA HAVANA gene 25873 39428 . + . FI_gene_label "DERA^ENSG00000023697.13" ; ID "PRPF40B--DERA^DERA^ENSG00000023697.13" ; ccdsid "CCDS44838.1" ; exon_id "ENSE00002203313.2" ; exon_number 1 ; gene_id "PRPF40B--DERA^DERA^ENSG00000023697.13" ; gene_name DERA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165537.4" ; havana_transcript "OTTHUMT00000384731.3" ; hgnc_id "HGNC:24269" ; level 2 ; orig_coord_info "chr12,15911384,15911414,+" ; protein_id "ENSP00000416583.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF40B--DERA^ENST00000428559.7" ; transcript_name "DERA-201" ; transcript_support_level 1 ; transcript_type protein_coding PRPF40B--DERA HAVANA mRNA 25873 39428 . + . FI_gene_label "DERA^ENSG00000023697.13" ; ID "PRPF40B--DERA^ENST00000428559.7" ; Parent "PRPF40B--DERA^DERA^ENSG00000023697.13" ; ccdsid "CCDS44838.1" ; exon_id "ENSE00002203313.2" ; exon_number 1 ; gene_id "PRPF40B--DERA^DERA^ENSG00000023697.13" ; gene_name DERA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165537.4" ; havana_transcript "OTTHUMT00000384731.3" ; hgnc_id "HGNC:24269" ; level 2 ; orig_coord_info "chr12,15911384,15911414,+" ; protein_id "ENSP00000416583.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRPF40B--DERA^ENST00000428559.7" ; transcript_name "DERA-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RMND5B--AC026403.1 HAVANA gene 1019 15232 . + . FI_gene_label "RMND5B^ENSG00000145916.19" ; ID "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19" ; ccdsid "CCDS4431.1" ; exon_id "ENSE00003577478.1" ; exon_number 3 ; gene_id "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19" ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4" ; havana_transcript "OTTHUMT00000253483.2" ; hgnc_id "HGNC:26181" ; level 2 ; orig_coord_info "chr5,178138120,178138258,+" ; protein_id "ENSP00000320623.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC026403.1^ENST00000313386.9" ; transcript_name "RMND5B-201" ; transcript_support_level 1 ; transcript_type protein_coding RMND5B--AC026403.1 HAVANA mRNA 1019 15232 . + . FI_gene_label "RMND5B^ENSG00000145916.19" ; ID "RMND5B--AC026403.1^ENST00000313386.9" ; Parent "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19" ; ccdsid "CCDS4431.1" ; exon_id "ENSE00003577478.1" ; exon_number 3 ; gene_id "RMND5B--AC026403.1^RMND5B^ENSG00000145916.19" ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4" ; havana_transcript "OTTHUMT00000253483.2" ; hgnc_id "HGNC:26181" ; level 2 ; orig_coord_info "chr5,178138120,178138258,+" ; protein_id "ENSP00000320623.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC026403.1^ENST00000313386.9" ; transcript_name "RMND5B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RMND5B--AC114321.1 HAVANA gene 1019 15232 . + . FI_gene_label "RMND5B^ENSG00000145916.19" ; ID "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19" ; ccdsid "CCDS4431.1" ; exon_id "ENSE00003577478.1" ; exon_number 3 ; gene_id "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19" ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4" ; havana_transcript "OTTHUMT00000253483.2" ; hgnc_id "HGNC:26181" ; level 2 ; orig_coord_info "chr5,178138120,178138258,+" ; protein_id "ENSP00000320623.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC114321.1^ENST00000313386.9" ; transcript_name "RMND5B-201" ; transcript_support_level 1 ; transcript_type protein_coding RMND5B--AC114321.1 HAVANA mRNA 1019 15232 . + . FI_gene_label "RMND5B^ENSG00000145916.19" ; ID "RMND5B--AC114321.1^ENST00000313386.9" ; Parent "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19" ; ccdsid "CCDS4431.1" ; exon_id "ENSE00003577478.1" ; exon_number 3 ; gene_id "RMND5B--AC114321.1^RMND5B^ENSG00000145916.19" ; gene_name RMND5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130897.4" ; havana_transcript "OTTHUMT00000253483.2" ; hgnc_id "HGNC:26181" ; level 2 ; orig_coord_info "chr5,178138120,178138258,+" ; protein_id "ENSP00000320623.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RMND5B--AC114321.1^ENST00000313386.9" ; transcript_name "RMND5B-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SELENBP1--FABP6-AS1 HAVANA gene 1003 8052 . + . FI_gene_label "SELENBP1^ENSG00000143416.21" ; ID "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21" ; ccdsid "CCDS995.1" ; exon_id "ENSE00003513345.1" ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21" ; gene_name SELENBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012498.26" ; havana_transcript "OTTHUMT00000034904.5" ; hgnc_id "HGNC:10719" ; level 2 ; orig_coord_info "chr1,151372638,151372641,-" ; protein_id "ENSP00000357861.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENBP1--FABP6-AS1^ENST00000368868.10" ; transcript_name "SELENBP1-201" ; transcript_support_level 1 ; transcript_type protein_coding SELENBP1--FABP6-AS1 HAVANA mRNA 1003 8052 . + . FI_gene_label "SELENBP1^ENSG00000143416.21" ; ID "SELENBP1--FABP6-AS1^ENST00000368868.10" ; Parent "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21" ; ccdsid "CCDS995.1" ; exon_id "ENSE00003513345.1" ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^SELENBP1^ENSG00000143416.21" ; gene_name SELENBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012498.26" ; havana_transcript "OTTHUMT00000034904.5" ; hgnc_id "HGNC:10719" ; level 2 ; orig_coord_info "chr1,151372638,151372641,-" ; protein_id "ENSP00000357861.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SELENBP1--FABP6-AS1^ENST00000368868.10" ; transcript_name "SELENBP1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: STAG1--COPB2 HAVANA gene 1026 42018 . + . FI_gene_label "STAG1^ENSG00000118007.13" ; ID "STAG1--COPB2^STAG1^ENSG00000118007.13" ; exon_id "ENSE00003662307.1" ; exon_number 2 ; gene_id "STAG1--COPB2^STAG1^ENSG00000118007.13" ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5" ; havana_transcript "OTTHUMT00000357403.1" ; hgnc_id "HGNC:11354" ; level 1 ; orig_coord_info "chr3,136630870,136630898,-" ; protein_id "ENSP00000236698.5" ; tag basic exp_conf ; transcript_id "STAG1--COPB2^ENST00000236698.9" ; transcript_name "STAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding STAG1--COPB2 HAVANA mRNA 1026 42018 . + . FI_gene_label "STAG1^ENSG00000118007.13" ; ID "STAG1--COPB2^ENST00000236698.9" ; Parent "STAG1--COPB2^STAG1^ENSG00000118007.13" ; exon_id "ENSE00003662307.1" ; exon_number 2 ; gene_id "STAG1--COPB2^STAG1^ENSG00000118007.13" ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5" ; havana_transcript "OTTHUMT00000357403.1" ; hgnc_id "HGNC:11354" ; level 1 ; orig_coord_info "chr3,136630870,136630898,-" ; protein_id "ENSP00000236698.5" ; tag basic exp_conf ; transcript_id "STAG1--COPB2^ENST00000236698.9" ; transcript_name "STAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: STAG1--COPB2 HAVANA gene 45108 70759 . + . FI_gene_label "COPB2^ENSG00000184432.11" ; ID "STAG1--COPB2^COPB2^ENSG00000184432.11" ; ccdsid "CCDS3108.1" ; exon_id "ENSE00002035761.2" ; exon_number 1 ; gene_id "STAG1--COPB2^COPB2^ENSG00000184432.11" ; gene_name COPB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159959.5" ; havana_transcript "OTTHUMT00000358495.3" ; hgnc_id "HGNC:2232" ; level 2 ; orig_coord_info "chr3,139389548,139389550,-" ; protein_id "ENSP00000329419.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STAG1--COPB2^ENST00000333188.10" ; transcript_name "COPB2-201" ; transcript_support_level 1 ; transcript_type protein_coding STAG1--COPB2 HAVANA mRNA 45108 70759 . + . FI_gene_label "COPB2^ENSG00000184432.11" ; ID "STAG1--COPB2^ENST00000333188.10" ; Parent "STAG1--COPB2^COPB2^ENSG00000184432.11" ; ccdsid "CCDS3108.1" ; exon_id "ENSE00002035761.2" ; exon_number 1 ; gene_id "STAG1--COPB2^COPB2^ENSG00000184432.11" ; gene_name COPB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159959.5" ; havana_transcript "OTTHUMT00000358495.3" ; hgnc_id "HGNC:2232" ; level 2 ; orig_coord_info "chr3,139389548,139389550,-" ; protein_id "ENSP00000329419.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STAG1--COPB2^ENST00000333188.10" ; transcript_name "COPB2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--BET1L HAVANA gene 40092 44550 . + . FI_gene_label "BET1L^ENSG00000177951.17" ; ID "TLK2--BET1L^BET1L^ENSG00000177951.17" ; ccdsid "CCDS7689.1" ; exon_id "ENSE00001955579.1" ; exon_number 1 ; gene_id "TLK2--BET1L^BET1L^ENSG00000177951.17" ; gene_name BET1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000119071.4" ; havana_transcript "OTTHUMT00000239284.1" ; hgnc_id "HGNC:19348" ; level 2 ; orig_coord_info "chr11,207303,207321,-" ; protein_id "ENSP00000339093.7" ; tag basic CCDS ; transcript_id "TLK2--BET1L^ENST00000325147.13" ; transcript_name "BET1L-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--BET1L HAVANA mRNA 40092 44550 . + . FI_gene_label "BET1L^ENSG00000177951.17" ; ID "TLK2--BET1L^ENST00000325147.13" ; Parent "TLK2--BET1L^BET1L^ENSG00000177951.17" ; ccdsid "CCDS7689.1" ; exon_id "ENSE00001955579.1" ; exon_number 1 ; gene_id "TLK2--BET1L^BET1L^ENSG00000177951.17" ; gene_name BET1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000119071.4" ; havana_transcript "OTTHUMT00000239284.1" ; hgnc_id "HGNC:19348" ; level 2 ; orig_coord_info "chr11,207303,207321,-" ; protein_id "ENSP00000339093.7" ; tag basic CCDS ; transcript_id "TLK2--BET1L^ENST00000325147.13" ; transcript_name "BET1L-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--BET1L HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--BET1L^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--BET1L^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--BET1L^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--BET1L HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--BET1L^ENST00000326270.13" ; Parent "TLK2--BET1L^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--BET1L^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--BET1L^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TRPV5--AC245427.1 HAVANA gene 1001 12415 . + . FI_gene_label "TRPV5^ENSG00000127412.7" ; ID "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7" ; ccdsid "CCDS5875.1" ; exon_id "ENSE00001047561.2" ; exon_number 1 ; gene_id "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7" ; gene_name TRPV5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157157.5" ; havana_transcript "OTTHUMT00000347660.3" ; hgnc_id "HGNC:3145" ; level 2 ; orig_coord_info "chr7,142933332,142933459,-" ; protein_id "ENSP00000265310.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPV5--AC245427.1^ENST00000265310.6" ; transcript_name "TRPV5-201" ; transcript_support_level 1 ; transcript_type protein_coding TRPV5--AC245427.1 HAVANA mRNA 1001 12415 . + . FI_gene_label "TRPV5^ENSG00000127412.7" ; ID "TRPV5--AC245427.1^ENST00000265310.6" ; Parent "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7" ; ccdsid "CCDS5875.1" ; exon_id "ENSE00001047561.2" ; exon_number 1 ; gene_id "TRPV5--AC245427.1^TRPV5^ENSG00000127412.7" ; gene_name TRPV5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157157.5" ; havana_transcript "OTTHUMT00000347660.3" ; hgnc_id "HGNC:3145" ; level 2 ; orig_coord_info "chr7,142933332,142933459,-" ; protein_id "ENSP00000265310.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPV5--AC245427.1^ENST00000265310.6" ; transcript_name "TRPV5-201" ; 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: ZFAT--AC084116.2 HAVANA gene 1019 29713 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC084116.2^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding ZFAT--AC084116.2 HAVANA mRNA 1019 29713 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "ZFAT--AC084116.2^ENST00000377838.8" ; Parent "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "ZFAT--AC084116.2^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC084116.2^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ZFAT--AC087667.1 HAVANA gene 1019 29713 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC087667.1^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding ZFAT--AC087667.1 HAVANA mRNA 1019 29713 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "ZFAT--AC087667.1^ENST00000377838.8" ; Parent "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "ZFAT--AC087667.1^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZFAT--AC087667.1^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC004923.1--AC127526.2 HAVANA gene 7777 10354 . + . FI_gene_label "AC127526.2^ENSG00000255367.3" ; ID "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3" ; exon_id "ENSE00002167014.1" ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3" ; gene_name "AC127526.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166987.2" ; havana_transcript "OTTHUMT00000392274.1" ; level 1 ; orig_coord_info "chr11,3571935,3571987,-" ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000526533.1" ; transcript_name "AC127526.2-202" ; transcript_support_level 4 ; transcript_type lncRNA AC004923.1--AC127526.2 HAVANA RNA 7777 10354 . + . FI_gene_label "AC127526.2^ENSG00000255367.3" ; ID "AC004923.1--AC127526.2^ENST00000526533.1" ; Parent "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3" ; exon_id "ENSE00002167014.1" ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC127526.2^ENSG00000255367.3" ; gene_name "AC127526.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166987.2" ; havana_transcript "OTTHUMT00000392274.1" ; level 1 ; orig_coord_info "chr11,3571935,3571987,-" ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000526533.1" ; transcript_name "AC127526.2-202" ; transcript_support_level 4 ; transcript_type lncRNA L1 and L2 created: AC004923.1--AC127526.2 HAVANA gene 1001 4776 . + . FI_gene_label "AC004923.1^ENSG00000254610.3" ; ID "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3" ; exon_id "ENSE00003779619.1" ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3" ; gene_name "AC004923.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167303.4" ; havana_transcript "OTTHUMT00000394105.2" ; level 1 ; orig_coord_info "chr11,67955482,67955802,-" ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000527543.2" ; transcript_name "AC004923.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript AC004923.1--AC127526.2 HAVANA RNA 1001 4776 . + . FI_gene_label "AC004923.1^ENSG00000254610.3" ; ID "AC004923.1--AC127526.2^ENST00000527543.2" ; Parent "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3" ; exon_id "ENSE00003779619.1" ; exon_number 1 ; gene_id "AC004923.1--AC127526.2^AC004923.1^ENSG00000254610.3" ; gene_name "AC004923.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167303.4" ; havana_transcript "OTTHUMT00000394105.2" ; level 1 ; orig_coord_info "chr11,67955482,67955802,-" ; tag basic exp_conf ; transcript_id "AC004923.1--AC127526.2^ENST00000527543.2" ; transcript_name "AC004923.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: AC026336.1--PIWIL1 HAVANA gene 1001 1351 . + . FI_gene_label "AC026336.1^ENSG00000242963.1" ; ID "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1" ; exon_id "ENSE00001847789.1" ; exon_number 1 ; gene_id "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1" ; gene_name "AC026336.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157836.1" ; havana_transcript "OTTHUMT00000349760.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,130216807,130217157,-" ; tag pseudo_consens basic ; transcript_id "AC026336.1--PIWIL1^ENST00000466577.1" ; transcript_name "AC026336.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene AC026336.1--PIWIL1 HAVANA RNA 1001 1351 . + . FI_gene_label "AC026336.1^ENSG00000242963.1" ; ID "AC026336.1--PIWIL1^ENST00000466577.1" ; Parent "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1" ; exon_id "ENSE00001847789.1" ; exon_number 1 ; gene_id "AC026336.1--PIWIL1^AC026336.1^ENSG00000242963.1" ; gene_name "AC026336.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157836.1" ; havana_transcript "OTTHUMT00000349760.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,130216807,130217157,-" ; tag pseudo_consens basic ; transcript_id "AC026336.1--PIWIL1^ENST00000466577.1" ; transcript_name "AC026336.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: ACTBP6--ACTB HAVANA gene 1001 2090 . + . FI_gene_label "ACTBP6^ENSG00000203413.3" ; ID "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; exon_id "ENSE00002116857.1" ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2" ; havana_transcript "OTTHUMT00000379462.2" ; hgnc_id "HGNC:139" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,84948585,84949674,+" ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1" ; transcript_name "ACTBP6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene ACTBP6--ACTB HAVANA RNA 1001 2090 . + . FI_gene_label "ACTBP6^ENSG00000203413.3" ; ID "ACTBP6--ACTB^ENST00000520036.1" ; Parent "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; exon_id "ENSE00002116857.1" ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3" ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2" ; havana_transcript "OTTHUMT00000379462.2" ; hgnc_id "HGNC:139" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,84948585,84949674,+" ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1" ; transcript_name "ACTBP6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: AGAP12P--FRMPD2 HAVANA gene 1042 9399 . + . FI_gene_label "AGAP12P^ENSG00000265018.6" ; ID "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; exon_id "ENSE00002718806.2" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4" ; havana_transcript "OTTHUMT00000047912.4" ; hgnc_id "HGNC:23661" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48031376,48031599,-" ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6" ; transcript_name "AGAP12P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene AGAP12P--FRMPD2 HAVANA RNA 1042 9399 . + . FI_gene_label "AGAP12P^ENSG00000265018.6" ; ID "AGAP12P--FRMPD2^ENST00000585227.6" ; Parent "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; exon_id "ENSE00002718806.2" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4" ; havana_transcript "OTTHUMT00000047912.4" ; hgnc_id "HGNC:23661" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48031376,48031599,-" ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6" ; transcript_name "AGAP12P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: AP006294.2--ENPP7P3 HAVANA gene 4210 4450 . + . FI_gene_label "ENPP7P3^ENSG00000248618.1" ; ID "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1" ; exon_id "ENSE00002066185.1" ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1" ; gene_name ENPP7P3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000159714.4" ; havana_transcript "OTTHUMT00000357026.3" ; hgnc_id "HGNC:48686" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr3,130167790,130168030,-" ; tag basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000509123.1" ; transcript_name "ENPP7P3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene AP006294.2--ENPP7P3 HAVANA RNA 4210 4450 . + . FI_gene_label "ENPP7P3^ENSG00000248618.1" ; ID "AP006294.2--ENPP7P3^ENST00000509123.1" ; Parent "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1" ; exon_id "ENSE00002066185.1" ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^ENPP7P3^ENSG00000248618.1" ; gene_name ENPP7P3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000159714.4" ; havana_transcript "OTTHUMT00000357026.3" ; hgnc_id "HGNC:48686" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr3,130167790,130168030,-" ; tag basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000509123.1" ; transcript_name "ENPP7P3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: AP006294.2--ENPP7P3 HAVANA gene 1001 1209 . + . FI_gene_label "AP006294.2^ENSG00000284639.1" ; ID "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1" ; exon_id "ENSE00003812576.1" ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1" ; gene_name "AP006294.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1" ; havana_transcript "OTTHUMT00000492980.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3580927,3581135,-" ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000641667.1" ; transcript_name "AP006294.2-201" ; transcript_type transcribed_unprocessed_pseudogene AP006294.2--ENPP7P3 HAVANA RNA 1001 1209 . + . FI_gene_label "AP006294.2^ENSG00000284639.1" ; ID "AP006294.2--ENPP7P3^ENST00000641667.1" ; Parent "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1" ; exon_id "ENSE00003812576.1" ; exon_number 1 ; gene_id "AP006294.2--ENPP7P3^AP006294.2^ENSG00000284639.1" ; gene_name "AP006294.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1" ; havana_transcript "OTTHUMT00000492980.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3580927,3581135,-" ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--ENPP7P3^ENST00000641667.1" ; transcript_name "AP006294.2-201" ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: AP006294.2--LINC00665 HAVANA gene 4246 18758 . + . FI_gene_label "LINC00665^ENSG00000232677.9" ; ID "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9" ; exon_id "ENSE00003882974.1" ; exon_number 1 ; gene_id "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9" ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6" ; havana_transcript "OTTHUMT00000109548.1" ; hgnc_id "HGNC:44323" ; level 1 ; orig_coord_info "chr19,36331447,36331734,-" ; tag exp_conf ; transcript_id "AP006294.2--LINC00665^ENST00000412740.7" ; transcript_name "LINC00665-201" ; transcript_support_level 3 ; transcript_type lncRNA AP006294.2--LINC00665 HAVANA RNA 4246 18758 . + . FI_gene_label "LINC00665^ENSG00000232677.9" ; ID "AP006294.2--LINC00665^ENST00000412740.7" ; Parent "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9" ; exon_id "ENSE00003882974.1" ; exon_number 1 ; gene_id "AP006294.2--LINC00665^LINC00665^ENSG00000232677.9" ; gene_name LINC00665 ; gene_type lncRNA ; havana_gene "OTTHUMG00000048145.6" ; havana_transcript "OTTHUMT00000109548.1" ; hgnc_id "HGNC:44323" ; level 1 ; orig_coord_info "chr19,36331447,36331734,-" ; tag exp_conf ; transcript_id "AP006294.2--LINC00665^ENST00000412740.7" ; transcript_name "LINC00665-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: AP006294.2--LINC00665 HAVANA gene 1001 1209 . + . FI_gene_label "AP006294.2^ENSG00000284639.1" ; ID "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1" ; exon_id "ENSE00003812576.1" ; exon_number 1 ; gene_id "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1" ; gene_name "AP006294.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1" ; havana_transcript "OTTHUMT00000492980.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3580927,3581135,-" ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--LINC00665^ENST00000641667.1" ; transcript_name "AP006294.2-201" ; transcript_type transcribed_unprocessed_pseudogene AP006294.2--LINC00665 HAVANA RNA 1001 1209 . + . FI_gene_label "AP006294.2^ENSG00000284639.1" ; ID "AP006294.2--LINC00665^ENST00000641667.1" ; Parent "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1" ; exon_id "ENSE00003812576.1" ; exon_number 1 ; gene_id "AP006294.2--LINC00665^AP006294.2^ENSG00000284639.1" ; gene_name "AP006294.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192241.1" ; havana_transcript "OTTHUMT00000492980.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3580927,3581135,-" ; tag non_submitted_evidence basic ; transcript_id "AP006294.2--LINC00665^ENST00000641667.1" ; transcript_name "AP006294.2-201" ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: ITPR2--AC048344.1 HAVANA gene 70020 71811 . + . FI_gene_label "AC048344.1^ENSG00000257530.1" ; ID "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1" ; exon_id "ENSE00002386363.1" ; exon_number 1 ; gene_id "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1" ; gene_name "AC048344.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169306.1" ; havana_transcript "OTTHUMT00000403378.1" ; level 2 ; orig_coord_info "chr12,32107394,32107528,-" ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000551974.1" ; transcript_name "AC048344.1-201" ; transcript_support_level 4 ; transcript_type lncRNA ITPR2--AC048344.1 HAVANA RNA 70020 71811 . + . FI_gene_label "AC048344.1^ENSG00000257530.1" ; ID "ITPR2--AC048344.1^ENST00000551974.1" ; Parent "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1" ; exon_id "ENSE00002386363.1" ; exon_number 1 ; gene_id "ITPR2--AC048344.1^AC048344.1^ENSG00000257530.1" ; gene_name "AC048344.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000169306.1" ; havana_transcript "OTTHUMT00000403378.1" ; level 2 ; orig_coord_info "chr12,32107394,32107528,-" ; tag basic ; transcript_id "ITPR2--AC048344.1^ENST00000551974.1" ; transcript_name "AC048344.1-201" ; transcript_support_level 4 ; transcript_type lncRNA L1 and L2 created: PDXDC2P--NPIPB3 HAVANA gene 1161 3891 . + . FI_gene_label "PDXDC2P^ENSG00000255185.6" ; ID "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; exon_id "ENSE00002159321.1" ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2" ; havana_transcript "OTTHUMT00000395272.1" ; hgnc_id "HGNC:27559" ; level 2 ; orig_coord_info "chr16,70065756,70065785,-" ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1" ; transcript_name "PDXDC2P-201" ; transcript_support_level 5 ; transcript_type processed_transcript PDXDC2P--NPIPB3 HAVANA RNA 1161 3891 . + . FI_gene_label "PDXDC2P^ENSG00000255185.6" ; ID "PDXDC2P--NPIPB3^ENST00000525173.1" ; Parent "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; exon_id "ENSE00002159321.1" ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2" ; havana_transcript "OTTHUMT00000395272.1" ; hgnc_id "HGNC:27559" ; level 2 ; orig_coord_info "chr16,70065756,70065785,-" ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1" ; transcript_name "PDXDC2P-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: RMND5B--AC026403.1 HAVANA gene 18233 18527 . + . FI_gene_label "AC026403.1^ENSG00000229119.3" ; ID "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3" ; exon_id "ENSE00002132375.1" ; exon_number 1 ; gene_id "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3" ; gene_name "AC026403.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162895.1" ; havana_transcript "OTTHUMT00000370958.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr5,166382305,166382599,+" ; tag pseudo_consens basic ; transcript_id "RMND5B--AC026403.1^ENST00000518938.1" ; transcript_name "AC026403.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene RMND5B--AC026403.1 HAVANA RNA 18233 18527 . + . FI_gene_label "AC026403.1^ENSG00000229119.3" ; ID "RMND5B--AC026403.1^ENST00000518938.1" ; Parent "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3" ; exon_id "ENSE00002132375.1" ; exon_number 1 ; gene_id "RMND5B--AC026403.1^AC026403.1^ENSG00000229119.3" ; gene_name "AC026403.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162895.1" ; havana_transcript "OTTHUMT00000370958.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr5,166382305,166382599,+" ; tag pseudo_consens basic ; transcript_id "RMND5B--AC026403.1^ENST00000518938.1" ; transcript_name "AC026403.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: RMND5B--AC114321.1 HAVANA gene 18233 20765 . + . FI_gene_label "AC114321.1^ENSG00000254171.1" ; ID "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1" ; exon_id "ENSE00002130197.1" ; exon_number 1 ; gene_id "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1" ; gene_name "AC114321.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163917.1" ; havana_transcript "OTTHUMT00000376394.1" ; level 1 ; orig_coord_info "chr5,166128498,166128650,+" ; tag basic exp_conf ; transcript_id "RMND5B--AC114321.1^ENST00000520075.1" ; transcript_name "AC114321.1-201" ; transcript_support_level 3 ; transcript_type lncRNA RMND5B--AC114321.1 HAVANA RNA 18233 20765 . + . FI_gene_label "AC114321.1^ENSG00000254171.1" ; ID "RMND5B--AC114321.1^ENST00000520075.1" ; Parent "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1" ; exon_id "ENSE00002130197.1" ; exon_number 1 ; gene_id "RMND5B--AC114321.1^AC114321.1^ENSG00000254171.1" ; gene_name "AC114321.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163917.1" ; havana_transcript "OTTHUMT00000376394.1" ; level 1 ; orig_coord_info "chr5,166128498,166128650,+" ; tag basic exp_conf ; transcript_id "RMND5B--AC114321.1^ENST00000520075.1" ; transcript_name "AC114321.1-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: SELENBP1--FABP6-AS1 HAVANA gene 11053 14738 . + . FI_gene_label "FABP6-AS1^ENSG00000247699.2" ; ID "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2" ; exon_id "ENSE00001637490.2" ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2" ; gene_name "FABP6-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163565.1" ; havana_transcript "OTTHUMT00000374243.1" ; hgnc_id "HGNC:40226" ; level 2 ; orig_coord_info "chr5,160204722,160204826,-" ; tag basic ; transcript_id "SELENBP1--FABP6-AS1^ENST00000501818.1" ; transcript_name "FABP6-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA SELENBP1--FABP6-AS1 HAVANA RNA 11053 14738 . + . FI_gene_label "FABP6-AS1^ENSG00000247699.2" ; ID "SELENBP1--FABP6-AS1^ENST00000501818.1" ; Parent "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2" ; exon_id "ENSE00001637490.2" ; exon_number 1 ; gene_id "SELENBP1--FABP6-AS1^FABP6-AS1^ENSG00000247699.2" ; gene_name "FABP6-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163565.1" ; havana_transcript "OTTHUMT00000374243.1" ; hgnc_id "HGNC:40226" ; level 2 ; orig_coord_info "chr5,160204722,160204826,-" ; tag basic ; transcript_id "SELENBP1--FABP6-AS1^ENST00000501818.1" ; transcript_name "FABP6-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: TRPV5--AC245427.1 HAVANA gene 15416 16678 . + . FI_gene_label "AC245427.1^ENSG00000224970.2" ; ID "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2" ; exon_id "ENSE00001646161.1" ; exon_number 1 ; gene_id "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2" ; gene_name "AC245427.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000157156.2" ; havana_transcript "OTTHUMT00000347659.2" ; level 1 ; orig_coord_info "chr7,142875836,142875934,+" ; tag mRNA_start_NF nested_454_RNA_Seq_supported 3_nested_supported_extension basic exp_conf ; transcript_id "TRPV5--AC245427.1^ENST00000438839.2" ; transcript_name "AC245427.1-201" ; transcript_support_level 3 ; transcript_type lncRNA TRPV5--AC245427.1 HAVANA RNA 15416 16678 . + . FI_gene_label "AC245427.1^ENSG00000224970.2" ; ID "TRPV5--AC245427.1^ENST00000438839.2" ; Parent "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2" ; exon_id "ENSE00001646161.1" ; exon_number 1 ; gene_id "TRPV5--AC245427.1^AC245427.1^ENSG00000224970.2" ; gene_name "AC245427.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000157156.2" ; havana_transcript "OTTHUMT00000347659.2" ; level 1 ; orig_coord_info "chr7,142875836,142875934,+" ; tag mRNA_start_NF nested_454_RNA_Seq_supported 3_nested_supported_extension basic exp_conf ; transcript_id "TRPV5--AC245427.1^ENST00000438839.2" ; transcript_name "AC245427.1-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: ZFAT--AC084116.2 HAVANA gene 32714 35128 . + . FI_gene_label "AC084116.2^ENSG00000253427.1" ; ID "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1" ; exon_id "ENSE00002122040.1" ; exon_number 1 ; gene_id "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1" ; gene_name "AC084116.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165031.1" ; havana_transcript "OTTHUMT00000381484.1" ; level 2 ; orig_coord_info "chr8,126474189,126474287,+" ; tag basic ; transcript_id "ZFAT--AC084116.2^ENST00000520171.1" ; transcript_name "AC084116.2-201" ; transcript_support_level 4 ; transcript_type lncRNA ZFAT--AC084116.2 HAVANA RNA 32714 35128 . + . FI_gene_label "AC084116.2^ENSG00000253427.1" ; ID "ZFAT--AC084116.2^ENST00000520171.1" ; Parent "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1" ; exon_id "ENSE00002122040.1" ; exon_number 1 ; gene_id "ZFAT--AC084116.2^AC084116.2^ENSG00000253427.1" ; gene_name "AC084116.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165031.1" ; havana_transcript "OTTHUMT00000381484.1" ; level 2 ; orig_coord_info "chr8,126474189,126474287,+" ; tag basic ; transcript_id "ZFAT--AC084116.2^ENST00000520171.1" ; transcript_name "AC084116.2-201" ; transcript_support_level 4 ; transcript_type lncRNA L1 and L2 created: ZFAT--AC087667.1 HAVANA gene 32714 36100 . + . FI_gene_label "AC087667.1^ENSG00000244791.3" ; ID "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3" ; exon_id "ENSE00003879284.1" ; exon_number 1 ; gene_id "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3" ; gene_name "AC087667.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165030.4" ; havana_transcript "OTTHUMT00000381483.2" ; level 2 ; orig_coord_info "chr8,126325454,126325557,+" ; tag basic TAGENE ; transcript_id "ZFAT--AC087667.1^ENST00000500180.3" ; transcript_name "AC087667.1-201" ; transcript_support_level 1 ; transcript_type lncRNA ZFAT--AC087667.1 HAVANA RNA 32714 36100 . + . FI_gene_label "AC087667.1^ENSG00000244791.3" ; ID "ZFAT--AC087667.1^ENST00000500180.3" ; Parent "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3" ; exon_id "ENSE00003879284.1" ; exon_number 1 ; gene_id "ZFAT--AC087667.1^AC087667.1^ENSG00000244791.3" ; gene_name "AC087667.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165030.4" ; havana_transcript "OTTHUMT00000381483.2" ; level 2 ; orig_coord_info "chr8,126325454,126325557,+" ; tag basic TAGENE ; transcript_id "ZFAT--AC087667.1^ENST00000500180.3" ; transcript_name "AC087667.1-201" ; transcript_support_level 1 ; transcript_type lncRNA 434 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 ------------------------------ 1001 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