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test.gtf
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chr1 HAVANA gene 11869 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 ENSEMBL transcript 11872 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 11872 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 1; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 12613 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 2; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 13225 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 3; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL transcript 11874 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 11874 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 1; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 12595 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 2; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 13403 13655 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 3; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 ENSEMBL exon 13661 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 4; level 3; havana_gene "OTTHUMG00000000961.2";
chr1 HAVANA transcript 12010 13670 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 12010 12057 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 12179 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 12613 12697 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 12975 13052 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 13221 13374 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 5; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1 HAVANA exon 13453 13670 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 6; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";