Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/734b135d74cea1167c894a855fbd83/fi_workdir/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/569582cb532469a83da223add097b0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/569582cb532469a83da223add097b0/.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: 3659 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 3659 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => exon CDS * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:3659 => 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: CRK--AC004253.2 HAVANA gene 2211 8060 . + . FI_gene_label "CRK^ENSG00000167193.8" ; ID "CRK--AC004253.2^CRK^ENSG00000167193.8" ; ccdsid "CCDS11002.1" ; exon_id "ENSE00001199129.3" ; exon_number 1 ; gene_id "CRK--AC004253.2^CRK^ENSG00000167193.8" ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4" ; havana_transcript "OTTHUMT00000206679.2" ; hgnc_id "HGNC:2362" ; level 2 ; orig_coord_info "chr17,1455877,1456117,-" ; protein_id "ENSP00000300574.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--AC004253.2^ENST00000300574.3" ; transcript_name "CRK-201" ; transcript_support_level 1 ; transcript_type protein_coding CRK--AC004253.2 HAVANA mRNA 2211 8060 . + . FI_gene_label "CRK^ENSG00000167193.8" ; ID "CRK--AC004253.2^ENST00000300574.3" ; Parent "CRK--AC004253.2^CRK^ENSG00000167193.8" ; ccdsid "CCDS11002.1" ; exon_id "ENSE00001199129.3" ; exon_number 1 ; gene_id "CRK--AC004253.2^CRK^ENSG00000167193.8" ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4" ; havana_transcript "OTTHUMT00000206679.2" ; hgnc_id "HGNC:2362" ; level 2 ; orig_coord_info "chr17,1455877,1456117,-" ; protein_id "ENSP00000300574.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--AC004253.2^ENST00000300574.3" ; transcript_name "CRK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CRK--COPRS HAVANA gene 2211 8060 . + . FI_gene_label "CRK^ENSG00000167193.8" ; ID "CRK--COPRS^CRK^ENSG00000167193.8" ; ccdsid "CCDS11002.1" ; exon_id "ENSE00001199129.3" ; exon_number 1 ; gene_id "CRK--COPRS^CRK^ENSG00000167193.8" ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4" ; havana_transcript "OTTHUMT00000206679.2" ; hgnc_id "HGNC:2362" ; level 2 ; orig_coord_info "chr17,1455877,1456117,-" ; protein_id "ENSP00000300574.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--COPRS^ENST00000300574.3" ; transcript_name "CRK-201" ; transcript_support_level 1 ; transcript_type protein_coding CRK--COPRS HAVANA mRNA 2211 8060 . + . FI_gene_label "CRK^ENSG00000167193.8" ; ID "CRK--COPRS^ENST00000300574.3" ; Parent "CRK--COPRS^CRK^ENSG00000167193.8" ; ccdsid "CCDS11002.1" ; exon_id "ENSE00001199129.3" ; exon_number 1 ; gene_id "CRK--COPRS^CRK^ENSG00000167193.8" ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4" ; havana_transcript "OTTHUMT00000206679.2" ; hgnc_id "HGNC:2362" ; level 2 ; orig_coord_info "chr17,1455877,1456117,-" ; protein_id "ENSP00000300574.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--COPRS^ENST00000300574.3" ; transcript_name "CRK-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CRK--COPRS HAVANA gene 11112 15059 . + . FI_gene_label "COPRS^ENSG00000172301.11" ; ID "CRK--COPRS^COPRS^ENSG00000172301.11" ; ccdsid "CCDS11268.1" ; exon_id "ENSE00002720400.2" ; exon_number 1 ; gene_id "CRK--COPRS^COPRS^ENSG00000172301.11" ; gene_name COPRS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132812.4" ; havana_transcript "OTTHUMT00000256257.3" ; hgnc_id "HGNC:28848" ; level 2 ; orig_coord_info "chr17,31859101,31859199,-" ; protein_id "ENSP00000304327.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRK--COPRS^ENST00000302362.11" ; transcript_name "COPRS-201" ; transcript_support_level 1 ; transcript_type protein_coding CRK--COPRS HAVANA mRNA 11112 15059 . + . FI_gene_label "COPRS^ENSG00000172301.11" ; ID "CRK--COPRS^ENST00000302362.11" ; Parent "CRK--COPRS^COPRS^ENSG00000172301.11" ; ccdsid "CCDS11268.1" ; exon_id "ENSE00002720400.2" ; exon_number 1 ; gene_id "CRK--COPRS^COPRS^ENSG00000172301.11" ; gene_name COPRS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132812.4" ; havana_transcript "OTTHUMT00000256257.3" ; hgnc_id "HGNC:28848" ; level 2 ; orig_coord_info "chr17,31859101,31859199,-" ; protein_id "ENSP00000304327.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRK--COPRS^ENST00000302362.11" ; transcript_name "COPRS-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: H4-16--CD163 HAVANA gene 1001 4133 . + . FI_gene_label "H4-16^ENSG00000197837.3" ; ID "H4-16--CD163^H4-16^ENSG00000197837.3" ; ccdsid "CCDS8665.1" ; exon_id "ENSE00001428888.2" ; exon_number 1 ; gene_id "H4-16--CD163^H4-16^ENSG00000197837.3" ; gene_name "H4-16" ; gene_type protein_coding ; havana_gene "OTTHUMG00000168735.1" ; havana_transcript "OTTHUMT00000400839.1" ; hgnc_id "HGNC:20510" ; level 2 ; orig_coord_info "chr12,14770776,14771084,-" ; protein_id "ENSP00000350767.3" ; tag CCDS ; transcript_id "H4-16--CD163^ENST00000358064.3" ; transcript_name "H4-16-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay H4-16--CD163 HAVANA mRNA 1001 4133 . + . FI_gene_label "H4-16^ENSG00000197837.3" ; ID "H4-16--CD163^ENST00000358064.3" ; Parent "H4-16--CD163^H4-16^ENSG00000197837.3" ; ccdsid "CCDS8665.1" ; exon_id "ENSE00001428888.2" ; exon_number 1 ; gene_id "H4-16--CD163^H4-16^ENSG00000197837.3" ; gene_name "H4-16" ; gene_type protein_coding ; havana_gene "OTTHUMG00000168735.1" ; havana_transcript "OTTHUMT00000400839.1" ; hgnc_id "HGNC:20510" ; level 2 ; orig_coord_info "chr12,14770776,14771084,-" ; protein_id "ENSP00000350767.3" ; tag CCDS ; transcript_id "H4-16--CD163^ENST00000358064.3" ; transcript_name "H4-16-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay L1 and L2 created: H4-16--CD163 HAVANA gene 7134 25397 . + . FI_gene_label "CD163^ENSG00000177575.13" ; ID "H4-16--CD163^CD163^ENSG00000177575.13" ; ccdsid "CCDS8578.1" ; exon_id "ENSE00002286128.1" ; exon_number 1 ; gene_id "H4-16--CD163^CD163^ENSG00000177575.13" ; gene_name CD163 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168353.2" ; havana_transcript "OTTHUMT00000399396.2" ; hgnc_id "HGNC:1631" ; level 2 ; orig_coord_info "chr12,7503645,7503690,-" ; protein_id "ENSP00000352071.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "H4-16--CD163^ENST00000359156.8" ; transcript_name "CD163-201" ; transcript_support_level 1 ; transcript_type protein_coding H4-16--CD163 HAVANA mRNA 7134 25397 . + . FI_gene_label "CD163^ENSG00000177575.13" ; ID "H4-16--CD163^ENST00000359156.8" ; Parent "H4-16--CD163^CD163^ENSG00000177575.13" ; ccdsid "CCDS8578.1" ; exon_id "ENSE00002286128.1" ; exon_number 1 ; gene_id "H4-16--CD163^CD163^ENSG00000177575.13" ; gene_name CD163 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168353.2" ; havana_transcript "OTTHUMT00000399396.2" ; hgnc_id "HGNC:1631" ; level 2 ; orig_coord_info "chr12,7503645,7503690,-" ; protein_id "ENSP00000352071.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "H4-16--CD163^ENST00000359156.8" ; transcript_name "CD163-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: HS3ST3B1--LRRC75A HAVANA gene 1001 7369 . + . FI_gene_label "HS3ST3B1^ENSG00000125430.9" ; ID "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9" ; ccdsid "CCDS11167.1" ; exon_id "ENSE00003842317.1" ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9" ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4" ; havana_transcript "OTTHUMT00000129998.2" ; hgnc_id "HGNC:5198" ; level 2 ; orig_coord_info "chr17,14301519,14302072,+" ; protein_id "ENSP00000354213.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000360954.3" ; transcript_name "HS3ST3B1-201" ; transcript_support_level 1 ; transcript_type protein_coding HS3ST3B1--LRRC75A HAVANA mRNA 1001 7369 . + . FI_gene_label "HS3ST3B1^ENSG00000125430.9" ; ID "HS3ST3B1--LRRC75A^ENST00000360954.3" ; Parent "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9" ; ccdsid "CCDS11167.1" ; exon_id "ENSE00003842317.1" ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9" ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4" ; havana_transcript "OTTHUMT00000129998.2" ; hgnc_id "HGNC:5198" ; level 2 ; orig_coord_info "chr17,14301519,14302072,+" ; protein_id "ENSP00000354213.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000360954.3" ; transcript_name "HS3ST3B1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: HS3ST3B1--LRRC75A HAVANA gene 10410 17480 . + . FI_gene_label "LRRC75A^ENSG00000181350.12" ; ID "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12" ; ccdsid "CCDS11178.2" ; exon_id "ENSE00001812457.1" ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12" ; gene_name LRRC75A ; gene_type protein_coding ; havana_gene "OTTHUMG00000058988.4" ; havana_transcript "OTTHUMT00000130461.2" ; hgnc_id "HGNC:32403" ; level 1 ; orig_coord_info "chr17,16491745,16491990,-" ; protein_id "ENSP00000386504.3" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000409083.7" ; transcript_name "LRRC75A-201" ; transcript_support_level 2 ; transcript_type protein_coding HS3ST3B1--LRRC75A HAVANA mRNA 10410 17480 . + . FI_gene_label "LRRC75A^ENSG00000181350.12" ; ID "HS3ST3B1--LRRC75A^ENST00000409083.7" ; Parent "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12" ; ccdsid "CCDS11178.2" ; exon_id "ENSE00001812457.1" ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12" ; gene_name LRRC75A ; gene_type protein_coding ; havana_gene "OTTHUMG00000058988.4" ; havana_transcript "OTTHUMT00000130461.2" ; hgnc_id "HGNC:32403" ; level 1 ; orig_coord_info "chr17,16491745,16491990,-" ; protein_id "ENSP00000386504.3" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000409083.7" ; transcript_name "LRRC75A-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: HS3ST3B1--ZNF287 HAVANA gene 1001 7369 . + . FI_gene_label "HS3ST3B1^ENSG00000125430.9" ; ID "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9" ; ccdsid "CCDS11167.1" ; exon_id "ENSE00003842317.1" ; exon_number 1 ; gene_id "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9" ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4" ; havana_transcript "OTTHUMT00000129998.2" ; hgnc_id "HGNC:5198" ; level 2 ; orig_coord_info "chr17,14301519,14302072,+" ; protein_id "ENSP00000354213.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000360954.3" ; transcript_name "HS3ST3B1-201" ; transcript_support_level 1 ; transcript_type protein_coding HS3ST3B1--ZNF287 HAVANA mRNA 1001 7369 . + . FI_gene_label "HS3ST3B1^ENSG00000125430.9" ; ID "HS3ST3B1--ZNF287^ENST00000360954.3" ; Parent "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9" ; ccdsid "CCDS11167.1" ; exon_id "ENSE00003842317.1" ; exon_number 1 ; gene_id "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9" ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4" ; havana_transcript "OTTHUMT00000129998.2" ; hgnc_id "HGNC:5198" ; level 2 ; orig_coord_info "chr17,14301519,14302072,+" ; protein_id "ENSP00000354213.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000360954.3" ; transcript_name "HS3ST3B1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: HS3ST3B1--ZNF287 HAVANA gene 10405 17769 . + . FI_gene_label "ZNF287^ENSG00000141040.15" ; ID "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15" ; ccdsid "CCDS11179.2" ; exon_id "ENSE00000946324.1" ; exon_number 2 ; gene_id "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15" ; gene_name ZNF287 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058993.6" ; havana_transcript "OTTHUMT00000130504.1" ; hgnc_id "HGNC:13502" ; level 2 ; orig_coord_info "chr17,16567329,16567731,-" ; protein_id "ENSP00000379168.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000395824.5" ; transcript_name "ZNF287-201" ; transcript_support_level 1 ; transcript_type protein_coding HS3ST3B1--ZNF287 HAVANA mRNA 10405 17769 . + . FI_gene_label "ZNF287^ENSG00000141040.15" ; ID "HS3ST3B1--ZNF287^ENST00000395824.5" ; Parent "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15" ; ccdsid "CCDS11179.2" ; exon_id "ENSE00000946324.1" ; exon_number 2 ; gene_id "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15" ; gene_name ZNF287 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058993.6" ; havana_transcript "OTTHUMT00000130504.1" ; hgnc_id "HGNC:13502" ; level 2 ; orig_coord_info "chr17,16567329,16567731,-" ; protein_id "ENSP00000379168.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000395824.5" ; transcript_name "ZNF287-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MAP2--ERBB4 HAVANA gene 1001 28320 . + . FI_gene_label "MAP2^ENSG00000078018.20" ; ID "MAP2--ERBB4^MAP2^ENSG00000078018.20" ; ccdsid "CCDS33369.1" ; exon_id "ENSE00000934702.2" ; exon_number 5 ; gene_id "MAP2--ERBB4^MAP2^ENSG00000078018.20" ; gene_name MAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132962.7" ; havana_transcript "OTTHUMT00000258126.1" ; hgnc_id "HGNC:6839" ; level 2 ; orig_coord_info "chr2,209653171,209653432,+" ; protein_id "ENSP00000199940.6" ; tag basic CCDS ; transcript_id "MAP2--ERBB4^ENST00000199940.10" ; transcript_name "MAP2-201" ; transcript_support_level 1 ; transcript_type protein_coding MAP2--ERBB4 HAVANA mRNA 1001 28320 . + . FI_gene_label "MAP2^ENSG00000078018.20" ; ID "MAP2--ERBB4^ENST00000199940.10" ; Parent "MAP2--ERBB4^MAP2^ENSG00000078018.20" ; ccdsid "CCDS33369.1" ; exon_id "ENSE00000934702.2" ; exon_number 5 ; gene_id "MAP2--ERBB4^MAP2^ENSG00000078018.20" ; gene_name MAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132962.7" ; havana_transcript "OTTHUMT00000258126.1" ; hgnc_id "HGNC:6839" ; level 2 ; orig_coord_info "chr2,209653171,209653432,+" ; protein_id "ENSP00000199940.6" ; tag basic CCDS ; transcript_id "MAP2--ERBB4^ENST00000199940.10" ; transcript_name "MAP2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MAP2--ERBB4 HAVANA gene 35233 58465 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "MAP2--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "MAP2--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "MAP2--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding MAP2--ERBB4 HAVANA mRNA 35233 58465 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "MAP2--ERBB4^ENST00000260943.10" ; Parent "MAP2--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "MAP2--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "MAP2--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: MPRIP--ASIC2 HAVANA gene 54157 67638 . + . FI_gene_label "ASIC2^ENSG00000108684.15" ; ID "MPRIP--ASIC2^ASIC2^ENSG00000108684.15" ; ccdsid "CCDS11276.1" ; exon_id "ENSE00001248823.4" ; exon_number 1 ; gene_id "MPRIP--ASIC2^ASIC2^ENSG00000108684.15" ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4" ; havana_transcript "OTTHUMT00000256378.1" ; hgnc_id "HGNC:99" ; level 2 ; orig_coord_info "chr17,33291408,33292115,-" ; protein_id "ENSP00000225823.2" ; tag basic MANE_Select CCDS ; transcript_id "MPRIP--ASIC2^ENST00000225823.7" ; transcript_name "ASIC2-201" ; transcript_support_level 1 ; transcript_type protein_coding MPRIP--ASIC2 HAVANA mRNA 54157 67638 . + . FI_gene_label "ASIC2^ENSG00000108684.15" ; ID "MPRIP--ASIC2^ENST00000225823.7" ; Parent "MPRIP--ASIC2^ASIC2^ENSG00000108684.15" ; ccdsid "CCDS11276.1" ; exon_id "ENSE00001248823.4" ; exon_number 1 ; gene_id "MPRIP--ASIC2^ASIC2^ENSG00000108684.15" ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4" ; havana_transcript "OTTHUMT00000256378.1" ; hgnc_id "HGNC:99" ; level 2 ; orig_coord_info "chr17,33291408,33292115,-" ; protein_id "ENSP00000225823.2" ; tag basic MANE_Select CCDS ; transcript_id "MPRIP--ASIC2^ENST00000225823.7" ; transcript_name "ASIC2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MPRIP--ASIC2 HAVANA gene 20478 37980 . + . FI_gene_label "MPRIP^ENSG00000133030.22" ; ID "MPRIP--ASIC2^MPRIP^ENSG00000133030.22" ; exon_id "ENSE00001699698.1" ; exon_number 1 ; gene_id "MPRIP--ASIC2^MPRIP^ENSG00000133030.22" ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11" ; havana_transcript "OTTHUMT00000131588.4" ; hgnc_id "HGNC:30321" ; level 2 ; orig_coord_info "chr17,17158497,17159002,+" ; protein_id "ENSP00000317786.6" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--ASIC2^ENST00000313485.10" ; transcript_name "MPRIP-201" ; transcript_support_level 5 ; transcript_type protein_coding MPRIP--ASIC2 HAVANA mRNA 20478 37980 . + . FI_gene_label "MPRIP^ENSG00000133030.22" ; ID "MPRIP--ASIC2^ENST00000313485.10" ; Parent "MPRIP--ASIC2^MPRIP^ENSG00000133030.22" ; exon_id "ENSE00001699698.1" ; exon_number 1 ; gene_id "MPRIP--ASIC2^MPRIP^ENSG00000133030.22" ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11" ; havana_transcript "OTTHUMT00000131588.4" ; hgnc_id "HGNC:30321" ; level 2 ; orig_coord_info "chr17,17158497,17159002,+" ; protein_id "ENSP00000317786.6" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--ASIC2^ENST00000313485.10" ; transcript_name "MPRIP-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: MPRIP--POLDIP2 HAVANA gene 20478 37980 . + . FI_gene_label "MPRIP^ENSG00000133030.22" ; ID "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22" ; exon_id "ENSE00001699698.1" ; exon_number 1 ; gene_id "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22" ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11" ; havana_transcript "OTTHUMT00000131588.4" ; hgnc_id "HGNC:30321" ; level 2 ; orig_coord_info "chr17,17158497,17159002,+" ; protein_id "ENSP00000317786.6" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--POLDIP2^ENST00000313485.10" ; transcript_name "MPRIP-201" ; transcript_support_level 5 ; transcript_type protein_coding MPRIP--POLDIP2 HAVANA mRNA 20478 37980 . + . FI_gene_label "MPRIP^ENSG00000133030.22" ; ID "MPRIP--POLDIP2^ENST00000313485.10" ; Parent "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22" ; exon_id "ENSE00001699698.1" ; exon_number 1 ; gene_id "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22" ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11" ; havana_transcript "OTTHUMT00000131588.4" ; hgnc_id "HGNC:30321" ; level 2 ; orig_coord_info "chr17,17158497,17159002,+" ; protein_id "ENSP00000317786.6" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--POLDIP2^ENST00000313485.10" ; transcript_name "MPRIP-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: MPRIP--POLDIP2 HAVANA gene 50435 60323 . + . FI_gene_label "POLDIP2^ENSG00000004142.12" ; ID "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12" ; ccdsid "CCDS74018.1" ; exon_id "ENSE00002245633.3" ; exon_number 1 ; gene_id "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12" ; gene_name POLDIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132065.9" ; havana_transcript "OTTHUMT00000446163.5" ; hgnc_id "HGNC:23781" ; level 2 ; orig_coord_info "chr17,28357288,28357448,-" ; protein_id "ENSP00000475924.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MPRIP--POLDIP2^ENST00000540200.6" ; transcript_name "POLDIP2-201" ; transcript_support_level 1 ; transcript_type protein_coding MPRIP--POLDIP2 HAVANA mRNA 50435 60323 . + . FI_gene_label "POLDIP2^ENSG00000004142.12" ; ID "MPRIP--POLDIP2^ENST00000540200.6" ; Parent "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12" ; ccdsid "CCDS74018.1" ; exon_id "ENSE00002245633.3" ; exon_number 1 ; gene_id "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12" ; gene_name POLDIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132065.9" ; havana_transcript "OTTHUMT00000446163.5" ; hgnc_id "HGNC:23781" ; level 2 ; orig_coord_info "chr17,28357288,28357448,-" ; protein_id "ENSP00000475924.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MPRIP--POLDIP2^ENST00000540200.6" ; transcript_name "POLDIP2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: POLR3E--BCLAF1P2 HAVANA gene 1035 24635 . + . FI_gene_label "POLR3E^ENSG00000058600.16" ; ID "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16" ; ccdsid "CCDS10605.1" ; exon_id "ENSE00003533384.1" ; exon_number 2 ; gene_id "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16" ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4" ; havana_transcript "OTTHUMT00000211590.2" ; hgnc_id "HGNC:30347" ; level 2 ; orig_coord_info "chr16,22302969,22303004,+" ; protein_id "ENSP00000299853.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--BCLAF1P2^ENST00000299853.10" ; transcript_name "POLR3E-201" ; transcript_support_level 1 ; transcript_type protein_coding POLR3E--BCLAF1P2 HAVANA mRNA 1035 24635 . + . FI_gene_label "POLR3E^ENSG00000058600.16" ; ID "POLR3E--BCLAF1P2^ENST00000299853.10" ; Parent "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16" ; ccdsid "CCDS10605.1" ; exon_id "ENSE00003533384.1" ; exon_number 2 ; gene_id "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16" ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4" ; havana_transcript "OTTHUMT00000211590.2" ; hgnc_id "HGNC:30347" ; level 2 ; orig_coord_info "chr16,22302969,22303004,+" ; protein_id "ENSP00000299853.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--BCLAF1P2^ENST00000299853.10" ; transcript_name "POLR3E-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: POLR3E--RNA5-8SP2 HAVANA gene 1035 24635 . + . FI_gene_label "POLR3E^ENSG00000058600.16" ; ID "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16" ; ccdsid "CCDS10605.1" ; exon_id "ENSE00003533384.1" ; exon_number 2 ; gene_id "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16" ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4" ; havana_transcript "OTTHUMT00000211590.2" ; hgnc_id "HGNC:30347" ; level 2 ; orig_coord_info "chr16,22302969,22303004,+" ; protein_id "ENSP00000299853.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--RNA5-8SP2^ENST00000299853.10" ; transcript_name "POLR3E-201" ; transcript_support_level 1 ; transcript_type protein_coding POLR3E--RNA5-8SP2 HAVANA mRNA 1035 24635 . + . FI_gene_label "POLR3E^ENSG00000058600.16" ; ID "POLR3E--RNA5-8SP2^ENST00000299853.10" ; Parent "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16" ; ccdsid "CCDS10605.1" ; exon_id "ENSE00003533384.1" ; exon_number 2 ; gene_id "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16" ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4" ; havana_transcript "OTTHUMT00000211590.2" ; hgnc_id "HGNC:30347" ; level 2 ; orig_coord_info "chr16,22302969,22303004,+" ; protein_id "ENSP00000299853.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--RNA5-8SP2^ENST00000299853.10" ; transcript_name "POLR3E-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PURB--CDHR3 HAVANA gene 24617 49038 . + . FI_gene_label "CDHR3^ENSG00000128536.16" ; ID "PURB--CDHR3^CDHR3^ENSG00000128536.16" ; ccdsid "CCDS47684.1" ; exon_id "ENSE00001844362.2" ; exon_number 1 ; gene_id "PURB--CDHR3^CDHR3^ENSG00000128536.16" ; gene_name CDHR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157520.3" ; havana_transcript "OTTHUMT00000349025.3" ; hgnc_id "HGNC:26308" ; level 2 ; orig_coord_info "chr7,105963319,105963364,+" ; protein_id "ENSP00000325954.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000317716.14" ; transcript_name "CDHR3-201" ; transcript_support_level 1 ; transcript_type protein_coding PURB--CDHR3 HAVANA mRNA 24617 49038 . + . FI_gene_label "CDHR3^ENSG00000128536.16" ; ID "PURB--CDHR3^ENST00000317716.14" ; Parent "PURB--CDHR3^CDHR3^ENSG00000128536.16" ; ccdsid "CCDS47684.1" ; exon_id "ENSE00001844362.2" ; exon_number 1 ; gene_id "PURB--CDHR3^CDHR3^ENSG00000128536.16" ; gene_name CDHR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157520.3" ; havana_transcript "OTTHUMT00000349025.3" ; hgnc_id "HGNC:26308" ; level 2 ; orig_coord_info "chr7,105963319,105963364,+" ; protein_id "ENSP00000325954.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000317716.14" ; transcript_name "CDHR3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PURB--CDHR3 HAVANA gene 1001 10232 . + . FI_gene_label "PURB^ENSG00000146676.10" ; ID "PURB--CDHR3^PURB^ENSG00000146676.10" ; ccdsid "CCDS5499.1" ; exon_id "ENSE00001522527.5" ; exon_number 1 ; gene_id "PURB--CDHR3^PURB^ENSG00000146676.10" ; gene_name PURB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023578.6" ; havana_transcript "OTTHUMT00000251332.4" ; hgnc_id "HGNC:9702" ; level 2 ; orig_coord_info "chr7,44884413,44885348,-" ; protein_id "ENSP00000379051.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000395699.5" ; transcript_name "PURB-201" ; transcript_support_level NA ; transcript_type protein_coding PURB--CDHR3 HAVANA mRNA 1001 10232 . + . FI_gene_label "PURB^ENSG00000146676.10" ; ID "PURB--CDHR3^ENST00000395699.5" ; Parent "PURB--CDHR3^PURB^ENSG00000146676.10" ; ccdsid "CCDS5499.1" ; exon_id "ENSE00001522527.5" ; exon_number 1 ; gene_id "PURB--CDHR3^PURB^ENSG00000146676.10" ; gene_name PURB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023578.6" ; havana_transcript "OTTHUMT00000251332.4" ; hgnc_id "HGNC:9702" ; level 2 ; orig_coord_info "chr7,44884413,44885348,-" ; protein_id "ENSP00000379051.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000395699.5" ; transcript_name "PURB-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: SMG1P1--GAS7 HAVANA gene 32022 61058 . + . FI_gene_label "GAS7^ENSG00000007237.19" ; ID "SMG1P1--GAS7^GAS7^ENSG00000007237.19" ; exon_id "ENSE00002725781.1" ; exon_number 2 ; gene_id "SMG1P1--GAS7^GAS7^ENSG00000007237.19" ; gene_name GAS7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177945.15" ; havana_transcript "OTTHUMT00000439868.3" ; hgnc_id "HGNC:4169" ; level 2 ; orig_coord_info "chr17,10039742,10039744,-" ; protein_id "ENSP00000322608.5" ; tag CAGE_supported_TSS basic ; transcript_id "SMG1P1--GAS7^ENST00000323816.8" ; transcript_name "GAS7-201" ; transcript_support_level 1 ; transcript_type protein_coding SMG1P1--GAS7 HAVANA mRNA 32022 61058 . + . FI_gene_label "GAS7^ENSG00000007237.19" ; ID "SMG1P1--GAS7^ENST00000323816.8" ; Parent "SMG1P1--GAS7^GAS7^ENSG00000007237.19" ; exon_id "ENSE00002725781.1" ; exon_number 2 ; gene_id "SMG1P1--GAS7^GAS7^ENSG00000007237.19" ; gene_name GAS7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177945.15" ; havana_transcript "OTTHUMT00000439868.3" ; hgnc_id "HGNC:4169" ; level 2 ; orig_coord_info "chr17,10039742,10039744,-" ; protein_id "ENSP00000322608.5" ; tag CAGE_supported_TSS basic ; transcript_id "SMG1P1--GAS7^ENST00000323816.8" ; transcript_name "GAS7-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SPNS1--ABCC1 HAVANA gene 1558 9863 . + . FI_gene_label "SPNS1^ENSG00000169682.18" ; ID "SPNS1--ABCC1^SPNS1^ENSG00000169682.18" ; ccdsid "CCDS10646.1" ; exon_id "ENSE00001614308.2" ; exon_number 1 ; gene_id "SPNS1--ABCC1^SPNS1^ENSG00000169682.18" ; gene_name SPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131762.4" ; havana_transcript "OTTHUMT00000254690.3" ; hgnc_id "HGNC:30621" ; level 2 ; orig_coord_info "chr16,28975152,28975392,+" ; protein_id "ENSP00000309945.11" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPNS1--ABCC1^ENST00000311008.16" ; transcript_name "SPNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding SPNS1--ABCC1 HAVANA mRNA 1558 9863 . + . FI_gene_label "SPNS1^ENSG00000169682.18" ; ID "SPNS1--ABCC1^ENST00000311008.16" ; Parent "SPNS1--ABCC1^SPNS1^ENSG00000169682.18" ; ccdsid "CCDS10646.1" ; exon_id "ENSE00001614308.2" ; exon_number 1 ; gene_id "SPNS1--ABCC1^SPNS1^ENSG00000169682.18" ; gene_name SPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131762.4" ; havana_transcript "OTTHUMT00000254690.3" ; hgnc_id "HGNC:30621" ; level 2 ; orig_coord_info "chr16,28975152,28975392,+" ; protein_id "ENSP00000309945.11" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPNS1--ABCC1^ENST00000311008.16" ; transcript_name "SPNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: SPNS1--ABCC1 HAVANA gene 13308 55493 . + . FI_gene_label "ABCC1^ENSG00000103222.20" ; ID "SPNS1--ABCC1^ABCC1^ENSG00000103222.20" ; exon_id "ENSE00003713334.1" ; exon_number 1 ; gene_id "SPNS1--ABCC1^ABCC1^ENSG00000103222.20" ; gene_name ABCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048267.6" ; hgnc_id "HGNC:51" ; level 2 ; orig_coord_info "chr16,15949752,15949799,+" ; protein_id "ENSP00000382340.4" ; tag basic appris_alternative_2 ; transcript_id "SPNS1--ABCC1^ENST00000399408.7" ; transcript_name "ABCC1-201" ; transcript_support_level 5 ; transcript_type protein_coding SPNS1--ABCC1 HAVANA mRNA 13308 55493 . + . FI_gene_label "ABCC1^ENSG00000103222.20" ; ID "SPNS1--ABCC1^ENST00000399408.7" ; Parent "SPNS1--ABCC1^ABCC1^ENSG00000103222.20" ; exon_id "ENSE00003713334.1" ; exon_number 1 ; gene_id "SPNS1--ABCC1^ABCC1^ENSG00000103222.20" ; gene_name ABCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048267.6" ; hgnc_id "HGNC:51" ; level 2 ; orig_coord_info "chr16,15949752,15949799,+" ; protein_id "ENSP00000382340.4" ; tag basic appris_alternative_2 ; transcript_id "SPNS1--ABCC1^ENST00000399408.7" ; transcript_name "ABCC1-201" ; transcript_support_level 5 ; 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: TXNDC11--AC025277.1 HAVANA gene 1001 17381 . + . FI_gene_label "TXNDC11^ENSG00000153066.13" ; ID "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13" ; ccdsid "CCDS32387.1" ; exon_id "ENSE00002633581.2" ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13" ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2" ; havana_transcript "OTTHUMT00000437054.1" ; hgnc_id "HGNC:28030" ; level 2 ; orig_coord_info "chr16,11742477,11742730,-" ; protein_id "ENSP00000283033.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC025277.1^ENST00000283033.10" ; transcript_name "TXNDC11-201" ; transcript_support_level 2 ; transcript_type protein_coding TXNDC11--AC025277.1 HAVANA mRNA 1001 17381 . + . FI_gene_label "TXNDC11^ENSG00000153066.13" ; ID "TXNDC11--AC025277.1^ENST00000283033.10" ; Parent "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13" ; ccdsid "CCDS32387.1" ; exon_id "ENSE00002633581.2" ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13" ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2" ; havana_transcript "OTTHUMT00000437054.1" ; hgnc_id "HGNC:28030" ; level 2 ; orig_coord_info "chr16,11742477,11742730,-" ; protein_id "ENSP00000283033.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC025277.1^ENST00000283033.10" ; transcript_name "TXNDC11-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: TXNDC11--AC109495.1 HAVANA gene 1001 17381 . + . FI_gene_label "TXNDC11^ENSG00000153066.13" ; ID "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13" ; ccdsid "CCDS32387.1" ; exon_id "ENSE00002633581.2" ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13" ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2" ; havana_transcript "OTTHUMT00000437054.1" ; hgnc_id "HGNC:28030" ; level 2 ; orig_coord_info "chr16,11742477,11742730,-" ; protein_id "ENSP00000283033.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC109495.1^ENST00000283033.10" ; transcript_name "TXNDC11-201" ; transcript_support_level 2 ; transcript_type protein_coding TXNDC11--AC109495.1 HAVANA mRNA 1001 17381 . + . FI_gene_label "TXNDC11^ENSG00000153066.13" ; ID "TXNDC11--AC109495.1^ENST00000283033.10" ; Parent "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13" ; ccdsid "CCDS32387.1" ; exon_id "ENSE00002633581.2" ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13" ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2" ; havana_transcript "OTTHUMT00000437054.1" ; hgnc_id "HGNC:28030" ; level 2 ; orig_coord_info "chr16,11742477,11742730,-" ; protein_id "ENSP00000283033.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC109495.1^ENST00000283033.10" ; transcript_name "TXNDC11-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: ULK2--ANKRD30BP1 HAVANA gene 1001 37290 . + . FI_gene_label "ULK2^ENSG00000083290.20" ; ID "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20" ; ccdsid "CCDS11213.1" ; exon_id "ENSE00001415890.1" ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20" ; gene_name ULK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059511.7" ; havana_transcript "OTTHUMT00000132376.2" ; hgnc_id "HGNC:13480" ; level 2 ; orig_coord_info "chr17,19867328,19867417,-" ; protein_id "ENSP00000354877.2" ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "ULK2--ANKRD30BP1^ENST00000361658.6" ; transcript_name "ULK2-201" ; transcript_support_level 1 ; transcript_type protein_coding ULK2--ANKRD30BP1 HAVANA mRNA 1001 37290 . + . FI_gene_label "ULK2^ENSG00000083290.20" ; ID "ULK2--ANKRD30BP1^ENST00000361658.6" ; Parent "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20" ; ccdsid "CCDS11213.1" ; exon_id "ENSE00001415890.1" ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20" ; gene_name ULK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059511.7" ; havana_transcript "OTTHUMT00000132376.2" ; hgnc_id "HGNC:13480" ; level 2 ; orig_coord_info "chr17,19867328,19867417,-" ; protein_id "ENSP00000354877.2" ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "ULK2--ANKRD30BP1^ENST00000361658.6" ; transcript_name "ULK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: CRK--AC004253.2 HAVANA gene 11065 12084 . + . FI_gene_label "AC004253.2^ENSG00000265046.1" ; ID "CRK--AC004253.2^AC004253.2^ENSG00000265046.1" ; exon_id "ENSE00002734663.1" ; exon_number 1 ; gene_id "CRK--AC004253.2^AC004253.2^ENSG00000265046.1" ; gene_name "AC004253.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179321.1" ; havana_transcript "OTTHUMT00000445734.1" ; level 2 ; orig_coord_info "chr17,31830731,31830790,+" ; tag basic ; transcript_id "CRK--AC004253.2^ENST00000585025.1" ; transcript_name "AC004253.2-201" ; transcript_support_level 3 ; transcript_type lncRNA CRK--AC004253.2 HAVANA RNA 11065 12084 . + . FI_gene_label "AC004253.2^ENSG00000265046.1" ; ID "CRK--AC004253.2^ENST00000585025.1" ; Parent "CRK--AC004253.2^AC004253.2^ENSG00000265046.1" ; exon_id "ENSE00002734663.1" ; exon_number 1 ; gene_id "CRK--AC004253.2^AC004253.2^ENSG00000265046.1" ; gene_name "AC004253.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179321.1" ; havana_transcript "OTTHUMT00000445734.1" ; level 2 ; orig_coord_info "chr17,31830731,31830790,+" ; tag basic ; transcript_id "CRK--AC004253.2^ENST00000585025.1" ; transcript_name "AC004253.2-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: POLR3E--BCLAF1P2 HAVANA gene 27641 30249 . + . FI_gene_label "BCLAF1P2^ENSG00000279800.2" ; ID "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2" ; exon_id "ENSE00003755616.2" ; exon_number 1 ; gene_id "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2" ; gene_name BCLAF1P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000191386.1" ; havana_transcript "OTTHUMT00000487743.1" ; hgnc_id "HGNC:51807" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,34266041,34268649,-" ; tag pseudo_consens basic ; transcript_id "POLR3E--BCLAF1P2^ENST00000624956.2" ; transcript_name "BCLAF1P2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene POLR3E--BCLAF1P2 HAVANA RNA 27641 30249 . + . FI_gene_label "BCLAF1P2^ENSG00000279800.2" ; ID "POLR3E--BCLAF1P2^ENST00000624956.2" ; Parent "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2" ; exon_id "ENSE00003755616.2" ; exon_number 1 ; gene_id "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2" ; gene_name BCLAF1P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000191386.1" ; havana_transcript "OTTHUMT00000487743.1" ; hgnc_id "HGNC:51807" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,34266041,34268649,-" ; tag pseudo_consens basic ; transcript_id "POLR3E--BCLAF1P2^ENST00000624956.2" ; transcript_name "BCLAF1P2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: POLR3E--RNA5-8SP2 ENSEMBL gene 27641 27792 . + . FI_gene_label "RNA5-8SP2^ENSG00000200434.1" ; ID "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1" ; exon_id "ENSE00001806843.1" ; exon_number 1 ; gene_id "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1" ; gene_name "RNA5-8SP2" ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41956" ; level 3 ; orig_coord_info "chr16,34162959,34163110,+" ; tag basic ; transcript_id "POLR3E--RNA5-8SP2^ENST00000363564.1" ; transcript_name "RNA5-8SP2-201" ; transcript_support_level NA ; transcript_type rRNA_pseudogene POLR3E--RNA5-8SP2 ENSEMBL RNA 27641 27792 . + . FI_gene_label "RNA5-8SP2^ENSG00000200434.1" ; ID "POLR3E--RNA5-8SP2^ENST00000363564.1" ; Parent "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1" ; exon_id "ENSE00001806843.1" ; exon_number 1 ; gene_id "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1" ; gene_name "RNA5-8SP2" ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41956" ; level 3 ; orig_coord_info "chr16,34162959,34163110,+" ; tag basic ; transcript_id "POLR3E--RNA5-8SP2^ENST00000363564.1" ; transcript_name "RNA5-8SP2-201" ; transcript_support_level NA ; transcript_type rRNA_pseudogene L1 and L2 created: SMG1P1--GAS7 HAVANA gene 1578 10727 . + . FI_gene_label "SMG1P1^ENSG00000237296.9" ; ID "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9" ; exon_id "ENSE00001654077.1" ; exon_number 1 ; gene_id "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9" ; gene_name SMG1P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156797.2" ; havana_transcript "OTTHUMT00000345868.1" ; hgnc_id "HGNC:44186" ; level 2 ; orig_coord_info "chr16,22437585,22437737,+" ; transcript_id "SMG1P1--GAS7^ENST00000308347.10" ; transcript_name "SMG1P1-201" ; transcript_support_level 5 ; transcript_type processed_transcript SMG1P1--GAS7 HAVANA RNA 1578 10727 . + . FI_gene_label "SMG1P1^ENSG00000237296.9" ; ID "SMG1P1--GAS7^ENST00000308347.10" ; Parent "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9" ; exon_id "ENSE00001654077.1" ; exon_number 1 ; gene_id "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9" ; gene_name SMG1P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156797.2" ; havana_transcript "OTTHUMT00000345868.1" ; hgnc_id "HGNC:44186" ; level 2 ; orig_coord_info "chr16,22437585,22437737,+" ; transcript_id "SMG1P1--GAS7^ENST00000308347.10" ; transcript_name "SMG1P1-201" ; transcript_support_level 5 ; transcript_type processed_transcript L1 and L2 created: TXNDC11--AC025277.1 HAVANA gene 20382 22036 . + . FI_gene_label "AC025277.1^ENSG00000261555.1" ; ID "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1" ; exon_id "ENSE00002589454.1" ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1" ; gene_name "AC025277.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177267.1" ; havana_transcript "OTTHUMT00000436068.1" ; level 2 ; orig_coord_info "chr16,17825252,17826906,+" ; tag basic ; transcript_id "TXNDC11--AC025277.1^ENST00000564852.1" ; transcript_name "AC025277.1-201" ; transcript_support_level NA ; transcript_type lncRNA TXNDC11--AC025277.1 HAVANA RNA 20382 22036 . + . FI_gene_label "AC025277.1^ENSG00000261555.1" ; ID "TXNDC11--AC025277.1^ENST00000564852.1" ; Parent "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1" ; exon_id "ENSE00002589454.1" ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1" ; gene_name "AC025277.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177267.1" ; havana_transcript "OTTHUMT00000436068.1" ; level 2 ; orig_coord_info "chr16,17825252,17826906,+" ; tag basic ; transcript_id "TXNDC11--AC025277.1^ENST00000564852.1" ; transcript_name "AC025277.1-201" ; transcript_support_level NA ; transcript_type lncRNA L1 and L2 created: TXNDC11--AC109495.1 HAVANA gene 20382 21036 . + . FI_gene_label "AC109495.1^ENSG00000260945.1" ; ID "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1" ; exon_id "ENSE00002597322.1" ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1" ; gene_name "AC109495.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177266.1" ; havana_transcript "OTTHUMT00000436067.1" ; level 2 ; orig_coord_info "chr16,17540947,17540985,-" ; tag basic ; transcript_id "TXNDC11--AC109495.1^ENST00000568026.1" ; transcript_name "AC109495.1-201" ; transcript_support_level 4 ; transcript_type lncRNA TXNDC11--AC109495.1 HAVANA RNA 20382 21036 . + . FI_gene_label "AC109495.1^ENSG00000260945.1" ; ID "TXNDC11--AC109495.1^ENST00000568026.1" ; Parent "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1" ; exon_id "ENSE00002597322.1" ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1" ; gene_name "AC109495.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177266.1" ; havana_transcript "OTTHUMT00000436067.1" ; level 2 ; orig_coord_info "chr16,17540947,17540985,-" ; tag basic ; transcript_id "TXNDC11--AC109495.1^ENST00000568026.1" ; transcript_name "AC109495.1-201" ; transcript_support_level 4 ; transcript_type lncRNA L1 and L2 created: ULK2--ANKRD30BP1 HAVANA gene 40292 55178 . + . FI_gene_label "ANKRD30BP1^ENSG00000175302.5" ; ID "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5" ; exon_id "ENSE00001690047.1" ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5" ; gene_name ANKRD30BP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000074201.1" ; havana_transcript "OTTHUMT00000157664.1" ; hgnc_id "HGNC:19722" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr21,13427745,13427773,-" ; tag pseudo_consens basic ; transcript_id "ULK2--ANKRD30BP1^ENST00000451052.1" ; transcript_name "ANKRD30BP1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene ULK2--ANKRD30BP1 HAVANA RNA 40292 55178 . + . FI_gene_label "ANKRD30BP1^ENSG00000175302.5" ; ID "ULK2--ANKRD30BP1^ENST00000451052.1" ; Parent "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5" ; exon_id "ENSE00001690047.1" ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5" ; gene_name ANKRD30BP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000074201.1" ; havana_transcript "OTTHUMT00000157664.1" ; hgnc_id "HGNC:19722" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr21,13427745,13427773,-" ; tag pseudo_consens basic ; transcript_id "ULK2--ANKRD30BP1^ENST00000451052.1" ; transcript_name "ANKRD30BP1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene 268 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 ------------------------------ 432 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 21 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