Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/954c617daabf7b8918525269f7b97f/fi_workdir/659_ezg-T1-TRNA-1_B23MHV2LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/569162e078928faf18627b03c086ac/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/569162e078928faf18627b03c086ac/.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: 6426 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 6426 => 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:6426 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 2 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: 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: AGAP3--BRAF HAVANA gene 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding AGAP3--BRAF HAVANA mRNA 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^ENST00000288602.11" ; Parent "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AGAP3--BRAF HAVANA gene 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding AGAP3--BRAF HAVANA mRNA 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^ENST00000335367.7" ; Parent "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ARHGAP39--ZNF16 HAVANA gene 18506 26943 . + . FI_gene_label "ZNF16^ENSG00000170631.15" ; ID "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15" ; ccdsid "CCDS6437.1" ; exon_id "ENSE00003564928.1" ; exon_number 3 ; gene_id "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15" ; gene_name ZNF16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165253.3" ; havana_transcript "OTTHUMT00000382978.1" ; hgnc_id "HGNC:12947" ; level 1 ; orig_coord_info "chr8,144946011,144946206,-" ; protein_id "ENSP00000276816.4" ; tag alternative_5_UTR basic appris_principal_1 exp_conf CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276816.8" ; transcript_name "ZNF16-201" ; transcript_support_level 1 ; transcript_type protein_coding ARHGAP39--ZNF16 HAVANA mRNA 18506 26943 . + . FI_gene_label "ZNF16^ENSG00000170631.15" ; ID "ARHGAP39--ZNF16^ENST00000276816.8" ; Parent "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15" ; ccdsid "CCDS6437.1" ; exon_id "ENSE00003564928.1" ; exon_number 3 ; gene_id "ARHGAP39--ZNF16^ZNF16^ENSG00000170631.15" ; gene_name ZNF16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165253.3" ; havana_transcript "OTTHUMT00000382978.1" ; hgnc_id "HGNC:12947" ; level 1 ; orig_coord_info "chr8,144946011,144946206,-" ; protein_id "ENSP00000276816.4" ; tag alternative_5_UTR basic appris_principal_1 exp_conf CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276816.8" ; transcript_name "ZNF16-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ARHGAP39--ZNF16 HAVANA gene 1001 15505 . + . FI_gene_label "ARHGAP39^ENSG00000147799.11" ; ID "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11" ; ccdsid "CCDS78374.1" ; exon_id "ENSE00002184188.1" ; exon_number 1 ; gene_id "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11" ; gene_name ARHGAP39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165182.1" ; havana_transcript "OTTHUMT00000382509.1" ; hgnc_id "HGNC:29351" ; level 2 ; orig_coord_info "chr8,144605535,144605614,-" ; protein_id "ENSP00000276826.5" ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276826.5" ; transcript_name "ARHGAP39-201" ; transcript_support_level 2 ; transcript_type protein_coding ARHGAP39--ZNF16 HAVANA mRNA 1001 15505 . + . FI_gene_label "ARHGAP39^ENSG00000147799.11" ; ID "ARHGAP39--ZNF16^ENST00000276826.5" ; Parent "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11" ; ccdsid "CCDS78374.1" ; exon_id "ENSE00002184188.1" ; exon_number 1 ; gene_id "ARHGAP39--ZNF16^ARHGAP39^ENSG00000147799.11" ; gene_name ARHGAP39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165182.1" ; havana_transcript "OTTHUMT00000382509.1" ; hgnc_id "HGNC:29351" ; level 2 ; orig_coord_info "chr8,144605535,144605614,-" ; protein_id "ENSP00000276826.5" ; tag basic appris_principal_1 CCDS ; transcript_id "ARHGAP39--ZNF16^ENST00000276826.5" ; transcript_name "ARHGAP39-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: ATP11C--MCF2 HAVANA gene 4133 38542 . + . FI_gene_label "ATP11C^ENSG00000101974.14" ; ID "ATP11C--MCF2^ATP11C^ENSG00000101974.14" ; ccdsid "CCDS14668.1" ; exon_id "ENSE00001415779.1" ; exon_number 1 ; gene_id "ATP11C--MCF2^ATP11C^ENSG00000101974.14" ; gene_name ATP11C ; gene_type protein_coding ; havana_gene "OTTHUMG00000022538.7" ; havana_transcript "OTTHUMT00000354945.1" ; hgnc_id "HGNC:13554" ; level 2 ; orig_coord_info "chrX,139832154,139832189,-" ; protein_id "ENSP00000332756.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000327569.7" ; transcript_name "ATP11C-201" ; transcript_support_level 1 ; transcript_type protein_coding ATP11C--MCF2 HAVANA mRNA 4133 38542 . + . FI_gene_label "ATP11C^ENSG00000101974.14" ; ID "ATP11C--MCF2^ENST00000327569.7" ; Parent "ATP11C--MCF2^ATP11C^ENSG00000101974.14" ; ccdsid "CCDS14668.1" ; exon_id "ENSE00001415779.1" ; exon_number 1 ; gene_id "ATP11C--MCF2^ATP11C^ENSG00000101974.14" ; gene_name ATP11C ; gene_type protein_coding ; havana_gene "OTTHUMG00000022538.7" ; havana_transcript "OTTHUMT00000354945.1" ; hgnc_id "HGNC:13554" ; level 2 ; orig_coord_info "chrX,139832154,139832189,-" ; protein_id "ENSP00000332756.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000327569.7" ; transcript_name "ATP11C-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: ATP11C--MCF2 HAVANA gene 47570 72966 . + . FI_gene_label "MCF2^ENSG00000101977.21" ; ID "ATP11C--MCF2^MCF2^ENSG00000101977.21" ; ccdsid "CCDS55516.1" ; exon_id "ENSE00001598942.1" ; exon_number 1 ; gene_id "ATP11C--MCF2^MCF2^ENSG00000101977.21" ; gene_name MCF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022537.6" ; havana_transcript "OTTHUMT00000058562.2" ; hgnc_id "HGNC:6940" ; level 2 ; orig_coord_info "chrX,139642468,139642518,-" ; protein_id "ENSP00000342204.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000338585.6" ; transcript_name "MCF2-201" ; transcript_support_level 1 ; transcript_type protein_coding ATP11C--MCF2 HAVANA mRNA 47570 72966 . + . FI_gene_label "MCF2^ENSG00000101977.21" ; ID "ATP11C--MCF2^ENST00000338585.6" ; Parent "ATP11C--MCF2^MCF2^ENSG00000101977.21" ; ccdsid "CCDS55516.1" ; exon_id "ENSE00001598942.1" ; exon_number 1 ; gene_id "ATP11C--MCF2^MCF2^ENSG00000101977.21" ; gene_name MCF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022537.6" ; havana_transcript "OTTHUMT00000058562.2" ; hgnc_id "HGNC:6940" ; level 2 ; orig_coord_info "chrX,139642468,139642518,-" ; protein_id "ENSP00000342204.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATP11C--MCF2^ENST00000338585.6" ; transcript_name "MCF2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BRAF--AGAP3 HAVANA gene 1198 35070 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "BRAF--AGAP3^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "BRAF--AGAP3^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "BRAF--AGAP3^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding BRAF--AGAP3 HAVANA mRNA 1198 35070 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "BRAF--AGAP3^ENST00000288602.11" ; Parent "BRAF--AGAP3^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "BRAF--AGAP3^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "BRAF--AGAP3^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BRAF--AGAP3 HAVANA gene 55353 63622 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "BRAF--AGAP3^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "BRAF--AGAP3^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "BRAF--AGAP3^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding BRAF--AGAP3 HAVANA mRNA 55353 63622 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "BRAF--AGAP3^ENST00000335367.7" ; Parent "BRAF--AGAP3^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "BRAF--AGAP3^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "BRAF--AGAP3^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CHCHD6--EPB41L1 HAVANA gene 18841 55808 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding CHCHD6--EPB41L1 HAVANA mRNA 18841 55808 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "CHCHD6--EPB41L1^ENST00000202028.9" ; Parent "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "CHCHD6--EPB41L1^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CHCHD6--EPB41L1 HAVANA gene 1001 15840 . + . FI_gene_label "CHCHD6^ENSG00000159685.11" ; ID "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11" ; ccdsid "CCDS3041.1" ; exon_id "ENSE00002077922.1" ; exon_number 1 ; gene_id "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11" ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3" ; havana_transcript "OTTHUMT00000356432.2" ; hgnc_id "HGNC:28184" ; level 2 ; orig_coord_info "chr3,126704313,126704399,+" ; protein_id "ENSP00000290913.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000290913.8" ; transcript_name "CHCHD6-201" ; transcript_support_level 1 ; transcript_type protein_coding CHCHD6--EPB41L1 HAVANA mRNA 1001 15840 . + . FI_gene_label "CHCHD6^ENSG00000159685.11" ; ID "CHCHD6--EPB41L1^ENST00000290913.8" ; Parent "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11" ; ccdsid "CCDS3041.1" ; exon_id "ENSE00002077922.1" ; exon_number 1 ; gene_id "CHCHD6--EPB41L1^CHCHD6^ENSG00000159685.11" ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3" ; havana_transcript "OTTHUMT00000356432.2" ; hgnc_id "HGNC:28184" ; level 2 ; orig_coord_info "chr3,126704313,126704399,+" ; protein_id "ENSP00000290913.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CHCHD6--EPB41L1^ENST00000290913.8" ; transcript_name "CHCHD6-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: DIS3L--MAP2K1 HAVANA gene 22724 35798 . + . FI_gene_label "MAP2K1^ENSG00000169032.10" ; ID "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10" ; ccdsid "CCDS10216.1" ; exon_id "ENSE00001257104.5" ; exon_number 1 ; gene_id "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10" ; gene_name MAP2K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133196.5" ; havana_transcript "OTTHUMT00000256906.4" ; hgnc_id "HGNC:6840" ; level 2 ; orig_coord_info "chr15,66387348,66387427,+" ; protein_id "ENSP00000302486.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000307102.10" ; transcript_name "MAP2K1-201" ; transcript_support_level 1 ; transcript_type protein_coding DIS3L--MAP2K1 HAVANA mRNA 22724 35798 . + . FI_gene_label "MAP2K1^ENSG00000169032.10" ; ID "DIS3L--MAP2K1^ENST00000307102.10" ; Parent "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10" ; ccdsid "CCDS10216.1" ; exon_id "ENSE00001257104.5" ; exon_number 1 ; gene_id "DIS3L--MAP2K1^MAP2K1^ENSG00000169032.10" ; gene_name MAP2K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133196.5" ; havana_transcript "OTTHUMT00000256906.4" ; hgnc_id "HGNC:6840" ; level 2 ; orig_coord_info "chr15,66387348,66387427,+" ; protein_id "ENSP00000302486.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000307102.10" ; transcript_name "MAP2K1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: DIS3L--MAP2K1 HAVANA gene 1001 19648 . + . FI_gene_label "DIS3L^ENSG00000166938.13" ; ID "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13" ; ccdsid "CCDS10214.1" ; exon_id "ENSE00003612725.1" ; exon_number 2 ; gene_id "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13" ; gene_name DIS3L ; gene_type protein_coding ; havana_gene "OTTHUMG00000133181.10" ; havana_transcript "OTTHUMT00000256889.3" ; hgnc_id "HGNC:28698" ; level 2 ; orig_coord_info "chr15,66295098,66295141,+" ; protein_id "ENSP00000321583.5" ; tag basic CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000319194.9" ; transcript_name "DIS3L-201" ; transcript_support_level 1 ; transcript_type protein_coding DIS3L--MAP2K1 HAVANA mRNA 1001 19648 . + . FI_gene_label "DIS3L^ENSG00000166938.13" ; ID "DIS3L--MAP2K1^ENST00000319194.9" ; Parent "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13" ; ccdsid "CCDS10214.1" ; exon_id "ENSE00003612725.1" ; exon_number 2 ; gene_id "DIS3L--MAP2K1^DIS3L^ENSG00000166938.13" ; gene_name DIS3L ; gene_type protein_coding ; havana_gene "OTTHUMG00000133181.10" ; havana_transcript "OTTHUMT00000256889.3" ; hgnc_id "HGNC:28698" ; level 2 ; orig_coord_info "chr15,66295098,66295141,+" ; protein_id "ENSP00000321583.5" ; tag basic CCDS ; transcript_id "DIS3L--MAP2K1^ENST00000319194.9" ; transcript_name "DIS3L-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EPB41L1--CHCHD6 HAVANA gene 1001 37968 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding EPB41L1--CHCHD6 HAVANA mRNA 1001 37968 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "EPB41L1--CHCHD6^ENST00000202028.9" ; Parent "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "EPB41L1--CHCHD6^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EPB41L1--CHCHD6 HAVANA gene 43427 58266 . + . FI_gene_label "CHCHD6^ENSG00000159685.11" ; ID "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11" ; ccdsid "CCDS3041.1" ; exon_id "ENSE00002077922.1" ; exon_number 1 ; gene_id "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11" ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3" ; havana_transcript "OTTHUMT00000356432.2" ; hgnc_id "HGNC:28184" ; level 2 ; orig_coord_info "chr3,126704313,126704399,+" ; protein_id "ENSP00000290913.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000290913.8" ; transcript_name "CHCHD6-201" ; transcript_support_level 1 ; transcript_type protein_coding EPB41L1--CHCHD6 HAVANA mRNA 43427 58266 . + . FI_gene_label "CHCHD6^ENSG00000159685.11" ; ID "EPB41L1--CHCHD6^ENST00000290913.8" ; Parent "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11" ; ccdsid "CCDS3041.1" ; exon_id "ENSE00002077922.1" ; exon_number 1 ; gene_id "EPB41L1--CHCHD6^CHCHD6^ENSG00000159685.11" ; gene_name CHCHD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159601.3" ; havana_transcript "OTTHUMT00000356432.2" ; hgnc_id "HGNC:28184" ; level 2 ; orig_coord_info "chr3,126704313,126704399,+" ; protein_id "ENSP00000290913.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPB41L1--CHCHD6^ENST00000290913.8" ; transcript_name "CHCHD6-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GPBP1L1--PRDX1 HAVANA gene 25570 30696 . + . FI_gene_label "PRDX1^ENSG00000117450.15" ; ID "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15" ; ccdsid "CCDS522.1" ; exon_id "ENSE00003648037.1" ; exon_number 2 ; gene_id "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15" ; gene_name PRDX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007738.7" ; hgnc_id "HGNC:9352" ; level 2 ; orig_coord_info "chr1,45518938,45519043,-" ; protein_id "ENSP00000262746.1" ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000262746.5" ; transcript_name "PRDX1-201" ; transcript_support_level 5 ; transcript_type protein_coding GPBP1L1--PRDX1 HAVANA mRNA 25570 30696 . + . FI_gene_label "PRDX1^ENSG00000117450.15" ; ID "GPBP1L1--PRDX1^ENST00000262746.5" ; Parent "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15" ; ccdsid "CCDS522.1" ; exon_id "ENSE00003648037.1" ; exon_number 2 ; gene_id "GPBP1L1--PRDX1^PRDX1^ENSG00000117450.15" ; gene_name PRDX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007738.7" ; hgnc_id "HGNC:9352" ; level 2 ; orig_coord_info "chr1,45518938,45519043,-" ; protein_id "ENSP00000262746.1" ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000262746.5" ; transcript_name "PRDX1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: GPBP1L1--PRDX1 HAVANA gene 2578 20404 . + . FI_gene_label "GPBP1L1^ENSG00000159592.11" ; ID "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11" ; ccdsid "CCDS528.1" ; exon_id "ENSE00003888808.1" ; exon_number 3 ; gene_id "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11" ; gene_name GPBP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040990.3" ; havana_transcript "OTTHUMT00000098375.1" ; hgnc_id "HGNC:28843" ; level 2 ; orig_coord_info "chr1,45659028,45659087,-" ; protein_id "ENSP00000290795.3" ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000290795.7" ; transcript_name "GPBP1L1-201" ; transcript_support_level 5 ; transcript_type protein_coding GPBP1L1--PRDX1 HAVANA mRNA 2578 20404 . + . FI_gene_label "GPBP1L1^ENSG00000159592.11" ; ID "GPBP1L1--PRDX1^ENST00000290795.7" ; Parent "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11" ; ccdsid "CCDS528.1" ; exon_id "ENSE00003888808.1" ; exon_number 3 ; gene_id "GPBP1L1--PRDX1^GPBP1L1^ENSG00000159592.11" ; gene_name GPBP1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040990.3" ; havana_transcript "OTTHUMT00000098375.1" ; hgnc_id "HGNC:28843" ; level 2 ; orig_coord_info "chr1,45659028,45659087,-" ; protein_id "ENSP00000290795.3" ; tag basic appris_principal_1 CCDS ; transcript_id "GPBP1L1--PRDX1^ENST00000290795.7" ; transcript_name "GPBP1L1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: MED15--ATXN3 HAVANA gene 3290 26140 . + . FI_gene_label "MED15^ENSG00000099917.17" ; ID "MED15--ATXN3^MED15^ENSG00000099917.17" ; ccdsid "CCDS33602.1" ; exon_id "ENSE00001871169.1" ; exon_number 1 ; gene_id "MED15--ATXN3^MED15^ENSG00000099917.17" ; gene_name MED15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150810.9" ; havana_transcript "OTTHUMT00000320177.2" ; hgnc_id "HGNC:14248" ; level 2 ; orig_coord_info "chr22,20507679,20507746,+" ; protein_id "ENSP00000263205.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MED15--ATXN3^ENST00000263205.11" ; transcript_name "MED15-201" ; transcript_support_level 1 ; transcript_type protein_coding MED15--ATXN3 HAVANA mRNA 3290 26140 . + . FI_gene_label "MED15^ENSG00000099917.17" ; ID "MED15--ATXN3^ENST00000263205.11" ; Parent "MED15--ATXN3^MED15^ENSG00000099917.17" ; ccdsid "CCDS33602.1" ; exon_id "ENSE00001871169.1" ; exon_number 1 ; gene_id "MED15--ATXN3^MED15^ENSG00000099917.17" ; gene_name MED15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150810.9" ; havana_transcript "OTTHUMT00000320177.2" ; hgnc_id "HGNC:14248" ; level 2 ; orig_coord_info "chr22,20507679,20507746,+" ; protein_id "ENSP00000263205.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MED15--ATXN3^ENST00000263205.11" ; transcript_name "MED15-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MED15--ATXN3 HAVANA gene 29165 44314 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "MED15--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "MED15--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "MED15--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding MED15--ATXN3 HAVANA mRNA 29165 44314 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "MED15--ATXN3^ENST00000340660.10" ; Parent "MED15--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "MED15--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "MED15--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PCCA--NALCN-AS1 ENSEMBL gene 1001 37641 . + . FI_gene_label "PCCA^ENSG00000175198.17" ; ID "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17" ; ccdsid "CCDS53878.1" ; exon_id "ENSE00002300882.1" ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17" ; gene_name PCCA ; gene_type protein_coding ; havana_gene "OTTHUMG00000017284.13" ; hgnc_id "HGNC:8653" ; level 3 ; orig_coord_info "chr13,100089121,100089225,+" ; protein_id "ENSP00000365456.3" ; tag basic CCDS ; transcript_id "PCCA--NALCN-AS1^ENST00000376279.7" ; transcript_name "PCCA-201" ; transcript_support_level 2 ; transcript_type protein_coding PCCA--NALCN-AS1 ENSEMBL mRNA 1001 37641 . + . FI_gene_label "PCCA^ENSG00000175198.17" ; ID "PCCA--NALCN-AS1^ENST00000376279.7" ; Parent "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17" ; ccdsid "CCDS53878.1" ; exon_id "ENSE00002300882.1" ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^PCCA^ENSG00000175198.17" ; gene_name PCCA ; gene_type protein_coding ; havana_gene "OTTHUMG00000017284.13" ; hgnc_id "HGNC:8653" ; level 3 ; orig_coord_info "chr13,100089121,100089225,+" ; protein_id "ENSP00000365456.3" ; tag basic CCDS ; transcript_id "PCCA--NALCN-AS1^ENST00000376279.7" ; transcript_name "PCCA-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: PDIA3--STRC HAVANA gene 1029 16180 . + . FI_gene_label "PDIA3^ENSG00000167004.13" ; ID "PDIA3--STRC^PDIA3^ENSG00000167004.13" ; ccdsid "CCDS10101.1" ; exon_id "ENSE00001489318.2" ; exon_number 1 ; gene_id "PDIA3--STRC^PDIA3^ENSG00000167004.13" ; gene_name PDIA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044444.9" ; havana_transcript "OTTHUMT00000103532.4" ; hgnc_id "HGNC:4606" ; level 2 ; orig_coord_info "chr15,43746540,43746706,+" ; protein_id "ENSP00000300289.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDIA3--STRC^ENST00000300289.10" ; transcript_name "PDIA3-201" ; transcript_support_level 1 ; transcript_type protein_coding PDIA3--STRC HAVANA mRNA 1029 16180 . + . FI_gene_label "PDIA3^ENSG00000167004.13" ; ID "PDIA3--STRC^ENST00000300289.10" ; Parent "PDIA3--STRC^PDIA3^ENSG00000167004.13" ; ccdsid "CCDS10101.1" ; exon_id "ENSE00001489318.2" ; exon_number 1 ; gene_id "PDIA3--STRC^PDIA3^ENSG00000167004.13" ; gene_name PDIA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044444.9" ; havana_transcript "OTTHUMT00000103532.4" ; hgnc_id "HGNC:4606" ; level 2 ; orig_coord_info "chr15,43746540,43746706,+" ; protein_id "ENSP00000300289.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDIA3--STRC^ENST00000300289.10" ; transcript_name "PDIA3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PDIA3--STRC HAVANA gene 19183 36247 . + . FI_gene_label "STRC^ENSG00000242866.10" ; ID "PDIA3--STRC^STRC^ENSG00000242866.10" ; exon_id "ENSE00001642185.1" ; exon_number 1 ; gene_id "PDIA3--STRC^STRC^ENSG00000242866.10" ; gene_name STRC ; gene_type protein_coding ; havana_gene "OTTHUMG00000059899.6" ; havana_transcript "OTTHUMT00000317302.2" ; hgnc_id "HGNC:16035" ; level 2 ; orig_coord_info "chr15,43618659,43618722,-" ; protein_id "ENSP00000415991.1" ; transcript_id "PDIA3--STRC^ENST00000428650.5" ; transcript_name "STRC-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay PDIA3--STRC HAVANA mRNA 19183 36247 . + . FI_gene_label "STRC^ENSG00000242866.10" ; ID "PDIA3--STRC^ENST00000428650.5" ; Parent "PDIA3--STRC^STRC^ENSG00000242866.10" ; exon_id "ENSE00001642185.1" ; exon_number 1 ; gene_id "PDIA3--STRC^STRC^ENSG00000242866.10" ; gene_name STRC ; gene_type protein_coding ; havana_gene "OTTHUMG00000059899.6" ; havana_transcript "OTTHUMT00000317302.2" ; hgnc_id "HGNC:16035" ; level 2 ; orig_coord_info "chr15,43618659,43618722,-" ; protein_id "ENSP00000415991.1" ; transcript_id "PDIA3--STRC^ENST00000428650.5" ; transcript_name "STRC-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay L1 and L2 created: RFNG--IGH@-ext HAVANA gene 1021 4930 . + . FI_gene_label "RFNG^ENSG00000169733.12" ; ID "RFNG--IGH@-ext^RFNG^ENSG00000169733.12" ; ccdsid "CCDS32773.1" ; exon_id "ENSE00002222540.2" ; exon_number 1 ; gene_id "RFNG--IGH@-ext^RFNG^ENSG00000169733.12" ; gene_name RFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000178512.3" ; havana_transcript "OTTHUMT00000442263.2" ; hgnc_id "HGNC:9974" ; level 2 ; orig_coord_info "chr17,82051500,82051766,-" ; protein_id "ENSP00000307971.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RFNG--IGH@-ext^ENST00000310496.9" ; transcript_name "RFNG-201" ; transcript_support_level 2 ; transcript_type protein_coding RFNG--IGH@-ext HAVANA mRNA 1021 4930 . + . FI_gene_label "RFNG^ENSG00000169733.12" ; ID "RFNG--IGH@-ext^ENST00000310496.9" ; Parent "RFNG--IGH@-ext^RFNG^ENSG00000169733.12" ; ccdsid "CCDS32773.1" ; exon_id "ENSE00002222540.2" ; exon_number 1 ; gene_id "RFNG--IGH@-ext^RFNG^ENSG00000169733.12" ; gene_name RFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000178512.3" ; havana_transcript "OTTHUMT00000442263.2" ; hgnc_id "HGNC:9974" ; level 2 ; orig_coord_info "chr17,82051500,82051766,-" ; protein_id "ENSP00000307971.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RFNG--IGH@-ext^ENST00000310496.9" ; transcript_name "RFNG-201" ; transcript_support_level 2 ; 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--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA L1 and L2 created: 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: HERC2P2--AC009563.1 HAVANA gene 34902 37659 . + . FI_gene_label "AC009563.1^ENSG00000253961.1" ; ID "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1" ; exon_id "ENSE00002123895.1" ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1" ; gene_name "AC009563.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163915.1" ; havana_transcript "OTTHUMT00000376382.1" ; level 1 ; orig_coord_info "chr8,31176692,31176872,-" ; tag exp_conf ; transcript_id "HERC2P2--AC009563.1^ENST00000521252.1" ; transcript_name "AC009563.1-201" ; transcript_support_level 5 ; transcript_type lncRNA HERC2P2--AC009563.1 HAVANA RNA 34902 37659 . + . FI_gene_label "AC009563.1^ENSG00000253961.1" ; ID "HERC2P2--AC009563.1^ENST00000521252.1" ; Parent "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1" ; exon_id "ENSE00002123895.1" ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^AC009563.1^ENSG00000253961.1" ; gene_name "AC009563.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163915.1" ; havana_transcript "OTTHUMT00000376382.1" ; level 1 ; orig_coord_info "chr8,31176692,31176872,-" ; tag exp_conf ; transcript_id "HERC2P2--AC009563.1^ENST00000521252.1" ; transcript_name "AC009563.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: HERC2P2--AC009563.1 HAVANA gene 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--AC009563.1^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene HERC2P2--AC009563.1 HAVANA RNA 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--AC009563.1^ENST00000613386.4" ; Parent "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--AC009563.1^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--AC009563.1^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: HERC2P2--AC068672.2 HAVANA gene 34661 37080 . + . FI_gene_label "AC068672.2^ENSG00000253377.2" ; ID "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2" ; exon_id "ENSE00002091619.1" ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2" ; gene_name "AC068672.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163916.3" ; havana_transcript "OTTHUMT00000376384.1" ; level 2 ; orig_coord_info "chr8,31275596,31275808,+" ; transcript_id "HERC2P2--AC068672.2^ENST00000524022.1" ; transcript_name "AC068672.2-201" ; transcript_support_level 3 ; transcript_type lncRNA HERC2P2--AC068672.2 HAVANA RNA 34661 37080 . + . FI_gene_label "AC068672.2^ENSG00000253377.2" ; ID "HERC2P2--AC068672.2^ENST00000524022.1" ; Parent "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2" ; exon_id "ENSE00002091619.1" ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^AC068672.2^ENSG00000253377.2" ; gene_name "AC068672.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163916.3" ; havana_transcript "OTTHUMT00000376384.1" ; level 2 ; orig_coord_info "chr8,31275596,31275808,+" ; transcript_id "HERC2P2--AC068672.2^ENST00000524022.1" ; transcript_name "AC068672.2-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: HERC2P2--AC068672.2 HAVANA gene 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--AC068672.2^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene HERC2P2--AC068672.2 HAVANA RNA 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--AC068672.2^ENST00000613386.4" ; Parent "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--AC068672.2^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--AC068672.2^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: HERC2P2--KCTD9P6 HAVANA gene 34607 35697 . + . FI_gene_label "KCTD9P6^ENSG00000229211.3" ; ID "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3" ; exon_id "ENSE00002113312.1" ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3" ; gene_name KCTD9P6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163896.1" ; havana_transcript "OTTHUMT00000376252.1" ; hgnc_id "HGNC:49915" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,31220519,31220984,-" ; tag pseudo_consens basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000522306.1" ; transcript_name "KCTD9P6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene HERC2P2--KCTD9P6 HAVANA RNA 34607 35697 . + . FI_gene_label "KCTD9P6^ENSG00000229211.3" ; ID "HERC2P2--KCTD9P6^ENST00000522306.1" ; Parent "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3" ; exon_id "ENSE00002113312.1" ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^KCTD9P6^ENSG00000229211.3" ; gene_name KCTD9P6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000163896.1" ; havana_transcript "OTTHUMT00000376252.1" ; hgnc_id "HGNC:49915" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,31220519,31220984,-" ; tag pseudo_consens basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000522306.1" ; transcript_name "KCTD9P6-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: HERC2P2--KCTD9P6 HAVANA gene 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene HERC2P2--KCTD9P6 HAVANA RNA 1001 28200 . + . FI_gene_label "HERC2P2^ENSG00000276550.4" ; ID "HERC2P2--KCTD9P6^ENST00000613386.4" ; Parent "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4" ; exon_id "ENSE00003716657.1" ; exon_number 1 ; gene_id "HERC2P2--KCTD9P6^HERC2P2^ENSG00000276550.4" ; gene_name HERC2P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000188262.2" ; havana_transcript "OTTHUMT00000476788.1" ; hgnc_id "HGNC:4870" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr15,22495570,22495672,+" ; tag basic ; transcript_id "HERC2P2--KCTD9P6^ENST00000613386.4" ; transcript_name "HERC2P2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene L1 and L2 created: PCCA--NALCN-AS1 HAVANA gene 40647 49753 . + . FI_gene_label "NALCN-AS1^ENSG00000233009.1" ; ID "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1" ; exon_id "ENSE00001597756.1" ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1" ; gene_name "NALCN-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017294.1" ; havana_transcript "OTTHUMT00000045662.1" ; hgnc_id "HGNC:42743" ; level 2 ; orig_coord_info "chr13,100708325,100708393,+" ; tag basic ; transcript_id "PCCA--NALCN-AS1^ENST00000457843.1" ; transcript_name "NALCN-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA PCCA--NALCN-AS1 HAVANA RNA 40647 49753 . + . FI_gene_label "NALCN-AS1^ENSG00000233009.1" ; ID "PCCA--NALCN-AS1^ENST00000457843.1" ; Parent "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1" ; exon_id "ENSE00001597756.1" ; exon_number 1 ; gene_id "PCCA--NALCN-AS1^NALCN-AS1^ENSG00000233009.1" ; gene_name "NALCN-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017294.1" ; havana_transcript "OTTHUMT00000045662.1" ; hgnc_id "HGNC:42743" ; level 2 ; orig_coord_info "chr13,100708325,100708393,+" ; tag basic ; transcript_id "PCCA--NALCN-AS1^ENST00000457843.1" ; transcript_name "NALCN-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA L1 and L2 created: RFNG--IGH@-ext SuperLocus-ext gene 7931 1299271 . + . FI_gene_label "IGH@-ext^IGH.g@-ext" ; ID "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_id "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_name "IGH@-ext" ; orig_coord_info "chr14,105583731,106875071,-" ; transcript_id "RFNG--IGH@-ext^IGH.t@-ext" RFNG--IGH@-ext SuperLocus-ext RNA 7931 1299271 . + . FI_gene_label "IGH@-ext^IGH.g@-ext" ; ID "RFNG--IGH@-ext^IGH.t@-ext" ; Parent "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_id "RFNG--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_name "IGH@-ext" ; orig_coord_info "chr14,105583731,106875071,-" ; transcript_id "RFNG--IGH@-ext^IGH.t@-ext" 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 470 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 ------------------------------ 923 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