Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/b341be4cdee4213f034c8f6707344a/fi_workdir/tih_rna_sample_00576_B23MVV7LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/5614718ee02fc957f5822cd99b4a2b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/5614718ee02fc957f5822cd99b4a2b/.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: 3273
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3273
=> 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:3273
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 1 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
CCDC40--ENPP7 HAVANA gene 1021 12850 . + . FI_gene_label "CCDC40^ENSG00000141519.15" ; ID "CCDC40--ENPP7^CCDC40^ENSG00000141519.15" ; ccdsid "CCDS82212.1" ; exon_id "ENSE00001871814.2" ; exon_number 1 ; gene_id "CCDC40--ENPP7^CCDC40^ENSG00000141519.15" ; gene_name CCDC40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132707.5" ; havana_transcript "OTTHUMT00000437423.1" ; hgnc_id "HGNC:26090" ; level 2 ; orig_coord_info "chr17,80036663,80036691,+" ; protein_id "ENSP00000269318.5" ; tag basic CCDS ; transcript_id "CCDC40--ENPP7^ENST00000269318.9" ; transcript_name "CCDC40-201" ; transcript_support_level 2 ; transcript_type protein_coding
CCDC40--ENPP7 HAVANA mRNA 1021 12850 . + . FI_gene_label "CCDC40^ENSG00000141519.15" ; ID "CCDC40--ENPP7^ENST00000269318.9" ; Parent "CCDC40--ENPP7^CCDC40^ENSG00000141519.15" ; ccdsid "CCDS82212.1" ; exon_id "ENSE00001871814.2" ; exon_number 1 ; gene_id "CCDC40--ENPP7^CCDC40^ENSG00000141519.15" ; gene_name CCDC40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132707.5" ; havana_transcript "OTTHUMT00000437423.1" ; hgnc_id "HGNC:26090" ; level 2 ; orig_coord_info "chr17,80036663,80036691,+" ; protein_id "ENSP00000269318.5" ; tag basic CCDS ; transcript_id "CCDC40--ENPP7^ENST00000269318.9" ; transcript_name "CCDC40-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
CCDC40--ENPP7 HAVANA gene 30384 38560 . + . FI_gene_label "ENPP7^ENSG00000182156.10" ; ID "CCDC40--ENPP7^ENPP7^ENSG00000182156.10" ; ccdsid "CCDS11763.1" ; exon_id "ENSE00001297319.6" ; exon_number 1 ; gene_id "CCDC40--ENPP7^ENPP7^ENSG00000182156.10" ; gene_name ENPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177462.3" ; havana_transcript "OTTHUMT00000437038.3" ; hgnc_id "HGNC:23764" ; level 2 ; orig_coord_info "chr17,79731140,79731392,+" ; protein_id "ENSP00000332656.5" ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC40--ENPP7^ENST00000328313.10" ; transcript_name "ENPP7-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC40--ENPP7 HAVANA mRNA 30384 38560 . + . FI_gene_label "ENPP7^ENSG00000182156.10" ; ID "CCDC40--ENPP7^ENST00000328313.10" ; Parent "CCDC40--ENPP7^ENPP7^ENSG00000182156.10" ; ccdsid "CCDS11763.1" ; exon_id "ENSE00001297319.6" ; exon_number 1 ; gene_id "CCDC40--ENPP7^ENPP7^ENSG00000182156.10" ; gene_name ENPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177462.3" ; havana_transcript "OTTHUMT00000437038.3" ; hgnc_id "HGNC:23764" ; level 2 ; orig_coord_info "chr17,79731140,79731392,+" ; protein_id "ENSP00000332656.5" ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC40--ENPP7^ENST00000328313.10" ; transcript_name "ENPP7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CU104787.1--KMT2C HAVANA gene 5927 79546 . + . FI_gene_label "KMT2C^ENSG00000055609.20" ; ID "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20" ; ccdsid "CCDS5931.1" ; exon_id "ENSE00003850683.1" ; exon_number 1 ; gene_id "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20" ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7" ; havana_transcript "OTTHUMT00000318887.4" ; hgnc_id "HGNC:13726" ; level 2 ; orig_coord_info "chr7,152435626,152435786,-" ; protein_id "ENSP00000262189.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CU104787.1--KMT2C^ENST00000262189.11" ; transcript_name "KMT2C-201" ; transcript_support_level 1 ; transcript_type protein_coding
CU104787.1--KMT2C HAVANA mRNA 5927 79546 . + . FI_gene_label "KMT2C^ENSG00000055609.20" ; ID "CU104787.1--KMT2C^ENST00000262189.11" ; Parent "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20" ; ccdsid "CCDS5931.1" ; exon_id "ENSE00003850683.1" ; exon_number 1 ; gene_id "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20" ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7" ; havana_transcript "OTTHUMT00000318887.4" ; hgnc_id "HGNC:13726" ; level 2 ; orig_coord_info "chr7,152435626,152435786,-" ; protein_id "ENSP00000262189.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CU104787.1--KMT2C^ENST00000262189.11" ; transcript_name "KMT2C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO42--OSTCP2 HAVANA gene 1001 17155 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--OSTCP2^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--OSTCP2 HAVANA mRNA 1001 17155 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "FBXO42--OSTCP2^ENST00000375592.8" ; Parent "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--OSTCP2^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO42--TRNP1 HAVANA gene 1001 17155 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "FBXO42--TRNP1^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "FBXO42--TRNP1^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--TRNP1 HAVANA mRNA 1001 17155 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "FBXO42--TRNP1^ENST00000375592.8" ; Parent "FBXO42--TRNP1^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "FBXO42--TRNP1^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO42--TRNP1 HAVANA gene 20156 23134 . + . FI_gene_label "TRNP1^ENSG00000253368.4" ; ID "FBXO42--TRNP1^TRNP1^ENSG00000253368.4" ; ccdsid "CCDS41289.1" ; exon_id "ENSE00002107275.2" ; exon_number 1 ; gene_id "FBXO42--TRNP1^TRNP1^ENSG00000253368.4" ; gene_name TRNP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004277.5" ; havana_transcript "OTTHUMT00000012346.4" ; hgnc_id "HGNC:34348" ; level 2 ; orig_coord_info "chr1,26993787,26994467,+" ; protein_id "ENSP00000429216.2" ; tag NMD_exception basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000522111.3" ; transcript_name "TRNP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--TRNP1 HAVANA mRNA 20156 23134 . + . FI_gene_label "TRNP1^ENSG00000253368.4" ; ID "FBXO42--TRNP1^ENST00000522111.3" ; Parent "FBXO42--TRNP1^TRNP1^ENSG00000253368.4" ; ccdsid "CCDS41289.1" ; exon_id "ENSE00002107275.2" ; exon_number 1 ; gene_id "FBXO42--TRNP1^TRNP1^ENSG00000253368.4" ; gene_name TRNP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004277.5" ; havana_transcript "OTTHUMT00000012346.4" ; hgnc_id "HGNC:34348" ; level 2 ; orig_coord_info "chr1,26993787,26994467,+" ; protein_id "ENSP00000429216.2" ; tag NMD_exception basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000522111.3" ; transcript_name "TRNP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KHDRBS3--ZFAT HAVANA gene 1001 18198 . + . FI_gene_label "KHDRBS3^ENSG00000131773.14" ; ID "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14" ; ccdsid "CCDS6374.1" ; exon_id "ENSE00001722982.2" ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14" ; gene_name KHDRBS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164164.5" ; havana_transcript "OTTHUMT00000377529.2" ; hgnc_id "HGNC:18117" ; level 2 ; orig_coord_info "chr8,135457867,135457954,+" ; protein_id "ENSP00000348108.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000355849.10" ; transcript_name "KHDRBS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
KHDRBS3--ZFAT HAVANA mRNA 1001 18198 . + . FI_gene_label "KHDRBS3^ENSG00000131773.14" ; ID "KHDRBS3--ZFAT^ENST00000355849.10" ; Parent "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14" ; ccdsid "CCDS6374.1" ; exon_id "ENSE00001722982.2" ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14" ; gene_name KHDRBS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164164.5" ; havana_transcript "OTTHUMT00000377529.2" ; hgnc_id "HGNC:18117" ; level 2 ; orig_coord_info "chr8,135457867,135457954,+" ; protein_id "ENSP00000348108.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000355849.10" ; transcript_name "KHDRBS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KHDRBS3--ZFAT HAVANA gene 23702 52396 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding
KHDRBS3--ZFAT HAVANA mRNA 23702 52396 . + . FI_gene_label "ZFAT^ENSG00000066827.16" ; ID "KHDRBS3--ZFAT^ENST00000377838.8" ; Parent "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16" ; ccdsid "CCDS47924.1" ; exon_id "ENSE00003841474.1" ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16" ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3" ; havana_transcript "OTTHUMT00000378272.2" ; hgnc_id "HGNC:19899" ; level 2 ; orig_coord_info "chr8,134712845,134712863,-" ; protein_id "ENSP00000367069.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000377838.8" ; transcript_name "ZFAT-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PAFAH1B3--GSK3A HAVANA gene 8325 18727 . + . FI_gene_label "GSK3A^ENSG00000105723.13" ; ID "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13" ; ccdsid "CCDS12599.1" ; exon_id "ENSE00001053028.4" ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13" ; gene_name GSK3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150722.3" ; havana_transcript "OTTHUMT00000319782.3" ; hgnc_id "HGNC:4616" ; level 2 ; orig_coord_info "chr19,42242183,42242465,-" ; protein_id "ENSP00000222330.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000222330.8" ; transcript_name "GSK3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
PAFAH1B3--GSK3A HAVANA mRNA 8325 18727 . + . FI_gene_label "GSK3A^ENSG00000105723.13" ; ID "PAFAH1B3--GSK3A^ENST00000222330.8" ; Parent "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13" ; ccdsid "CCDS12599.1" ; exon_id "ENSE00001053028.4" ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13" ; gene_name GSK3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150722.3" ; havana_transcript "OTTHUMT00000319782.3" ; hgnc_id "HGNC:4616" ; level 2 ; orig_coord_info "chr19,42242183,42242465,-" ; protein_id "ENSP00000222330.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000222330.8" ; transcript_name "GSK3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PAFAH1B3--GSK3A HAVANA gene 1923 5299 . + . FI_gene_label "PAFAH1B3^ENSG00000079462.8" ; ID "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8" ; ccdsid "CCDS12602.1" ; exon_id "ENSE00000897478.4" ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8" ; gene_name PAFAH1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182795.2" ; havana_transcript "OTTHUMT00000463726.1" ; hgnc_id "HGNC:8576" ; level 2 ; orig_coord_info "chr19,42302232,42302309,-" ; protein_id "ENSP00000262890.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000262890.8" ; transcript_name "PAFAH1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PAFAH1B3--GSK3A HAVANA mRNA 1923 5299 . + . FI_gene_label "PAFAH1B3^ENSG00000079462.8" ; ID "PAFAH1B3--GSK3A^ENST00000262890.8" ; Parent "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8" ; ccdsid "CCDS12602.1" ; exon_id "ENSE00000897478.4" ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8" ; gene_name PAFAH1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182795.2" ; havana_transcript "OTTHUMT00000463726.1" ; hgnc_id "HGNC:8576" ; level 2 ; orig_coord_info "chr19,42302232,42302309,-" ; protein_id "ENSP00000262890.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000262890.8" ; transcript_name "PAFAH1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SAMD12--XKR6 HAVANA gene 32877 35426 . + . FI_gene_label "XKR6^ENSG00000171044.11" ; ID "SAMD12--XKR6^XKR6^ENSG00000171044.11" ; exon_id "ENSE00001492174.1" ; exon_number 1 ; gene_id "SAMD12--XKR6^XKR6^ENSG00000171044.11" ; gene_name XKR6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129351.6" ; havana_transcript "OTTHUMT00000383960.2" ; hgnc_id "HGNC:27806" ; level 1 ; orig_coord_info "chr8,11200576,11201339,-" ; protein_id "ENSP00000297303.4" ; tag basic exp_conf ; transcript_id "SAMD12--XKR6^ENST00000297303.4" ; transcript_name "XKR6-201" ; transcript_support_level 1 ; transcript_type protein_coding
SAMD12--XKR6 HAVANA mRNA 32877 35426 . + . FI_gene_label "XKR6^ENSG00000171044.11" ; ID "SAMD12--XKR6^ENST00000297303.4" ; Parent "SAMD12--XKR6^XKR6^ENSG00000171044.11" ; exon_id "ENSE00001492174.1" ; exon_number 1 ; gene_id "SAMD12--XKR6^XKR6^ENSG00000171044.11" ; gene_name XKR6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129351.6" ; havana_transcript "OTTHUMT00000383960.2" ; hgnc_id "HGNC:27806" ; level 1 ; orig_coord_info "chr8,11200576,11201339,-" ; protein_id "ENSP00000297303.4" ; tag basic exp_conf ; transcript_id "SAMD12--XKR6^ENST00000297303.4" ; transcript_name "XKR6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SAMD12--XKR6 HAVANA gene 1150 12162 . + . FI_gene_label "SAMD12^ENSG00000177570.15" ; ID "SAMD12--XKR6^SAMD12^ENSG00000177570.15" ; ccdsid "CCDS6325.1" ; exon_id "ENSE00002146278.2" ; exon_number 1 ; gene_id "SAMD12--XKR6^SAMD12^ENSG00000177570.15" ; gene_name SAMD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059817.6" ; havana_transcript "OTTHUMT00000132989.3" ; hgnc_id "HGNC:31750" ; level 2 ; orig_coord_info "chr8,118621804,118621816,-" ; protein_id "ENSP00000314173.4" ; tag basic MANE_Select CCDS ; transcript_id "SAMD12--XKR6^ENST00000314727.9" ; transcript_name "SAMD12-201" ; transcript_support_level 1 ; transcript_type protein_coding
SAMD12--XKR6 HAVANA mRNA 1150 12162 . + . FI_gene_label "SAMD12^ENSG00000177570.15" ; ID "SAMD12--XKR6^ENST00000314727.9" ; Parent "SAMD12--XKR6^SAMD12^ENSG00000177570.15" ; ccdsid "CCDS6325.1" ; exon_id "ENSE00002146278.2" ; exon_number 1 ; gene_id "SAMD12--XKR6^SAMD12^ENSG00000177570.15" ; gene_name SAMD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059817.6" ; havana_transcript "OTTHUMT00000132989.3" ; hgnc_id "HGNC:31750" ; level 2 ; orig_coord_info "chr8,118621804,118621816,-" ; protein_id "ENSP00000314173.4" ; tag basic MANE_Select CCDS ; transcript_id "SAMD12--XKR6^ENST00000314727.9" ; transcript_name "SAMD12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SSU72--FBXO42 HAVANA gene 1001 11569 . + . FI_gene_label "SSU72^ENSG00000160075.12" ; ID "SSU72--FBXO42^SSU72^ENSG00000160075.12" ; ccdsid "CCDS32.1" ; exon_id "ENSE00001478524.4" ; exon_number 1 ; gene_id "SSU72--FBXO42^SSU72^ENSG00000160075.12" ; gene_name SSU72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000000576.6" ; havana_transcript "OTTHUMT00000001366.2" ; hgnc_id "HGNC:25016" ; level 2 ; orig_coord_info "chr1,1574478,1574557,-" ; protein_id "ENSP00000291386.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000291386.4" ; transcript_name "SSU72-201" ; transcript_support_level 1 ; transcript_type protein_coding
SSU72--FBXO42 HAVANA mRNA 1001 11569 . + . FI_gene_label "SSU72^ENSG00000160075.12" ; ID "SSU72--FBXO42^ENST00000291386.4" ; Parent "SSU72--FBXO42^SSU72^ENSG00000160075.12" ; ccdsid "CCDS32.1" ; exon_id "ENSE00001478524.4" ; exon_number 1 ; gene_id "SSU72--FBXO42^SSU72^ENSG00000160075.12" ; gene_name SSU72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000000576.6" ; havana_transcript "OTTHUMT00000001366.2" ; hgnc_id "HGNC:25016" ; level 2 ; orig_coord_info "chr1,1574478,1574557,-" ; protein_id "ENSP00000291386.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000291386.4" ; transcript_name "SSU72-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SSU72--FBXO42 HAVANA gene 14570 30724 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "SSU72--FBXO42^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "SSU72--FBXO42^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
SSU72--FBXO42 HAVANA mRNA 14570 30724 . + . FI_gene_label "FBXO42^ENSG00000037637.11" ; ID "SSU72--FBXO42^ENST00000375592.8" ; Parent "SSU72--FBXO42^FBXO42^ENSG00000037637.11" ; ccdsid "CCDS30613.1" ; exon_id "ENSE00001467565.1" ; exon_number 2 ; gene_id "SSU72--FBXO42^FBXO42^ENSG00000037637.11" ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3" ; havana_transcript "OTTHUMT00000006285.2" ; hgnc_id "HGNC:29249" ; level 2 ; orig_coord_info "chr1,16315169,16315418,-" ; protein_id "ENSP00000364742.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000375592.8" ; transcript_name "FBXO42-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TEX2--AC105021.1 HAVANA gene 1034 24053 . + . FI_gene_label "TEX2^ENSG00000136478.8" ; ID "TEX2--AC105021.1^TEX2^ENSG00000136478.8" ; ccdsid "CCDS11658.1" ; exon_id "ENSE00001324420.1" ; exon_number 2 ; gene_id "TEX2--AC105021.1^TEX2^ENSG00000136478.8" ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2" ; havana_transcript "OTTHUMT00000443743.1" ; hgnc_id "HGNC:30884" ; level 2 ; orig_coord_info "chr17,64212574,64214217,-" ; protein_id "ENSP00000258991.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--AC105021.1^ENST00000258991.7" ; transcript_name "TEX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--AC105021.1 HAVANA mRNA 1034 24053 . + . FI_gene_label "TEX2^ENSG00000136478.8" ; ID "TEX2--AC105021.1^ENST00000258991.7" ; Parent "TEX2--AC105021.1^TEX2^ENSG00000136478.8" ; ccdsid "CCDS11658.1" ; exon_id "ENSE00001324420.1" ; exon_number 2 ; gene_id "TEX2--AC105021.1^TEX2^ENSG00000136478.8" ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2" ; havana_transcript "OTTHUMT00000443743.1" ; hgnc_id "HGNC:30884" ; level 2 ; orig_coord_info "chr17,64212574,64214217,-" ; protein_id "ENSP00000258991.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--AC105021.1^ENST00000258991.7" ; transcript_name "TEX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TEX2--TMEM100 HAVANA gene 1034 24053 . + . FI_gene_label "TEX2^ENSG00000136478.8" ; ID "TEX2--TMEM100^TEX2^ENSG00000136478.8" ; ccdsid "CCDS11658.1" ; exon_id "ENSE00001324420.1" ; exon_number 2 ; gene_id "TEX2--TMEM100^TEX2^ENSG00000136478.8" ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2" ; havana_transcript "OTTHUMT00000443743.1" ; hgnc_id "HGNC:30884" ; level 2 ; orig_coord_info "chr17,64212574,64214217,-" ; protein_id "ENSP00000258991.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--TMEM100^ENST00000258991.7" ; transcript_name "TEX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--TMEM100 HAVANA mRNA 1034 24053 . + . FI_gene_label "TEX2^ENSG00000136478.8" ; ID "TEX2--TMEM100^ENST00000258991.7" ; Parent "TEX2--TMEM100^TEX2^ENSG00000136478.8" ; ccdsid "CCDS11658.1" ; exon_id "ENSE00001324420.1" ; exon_number 2 ; gene_id "TEX2--TMEM100^TEX2^ENSG00000136478.8" ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2" ; havana_transcript "OTTHUMT00000443743.1" ; hgnc_id "HGNC:30884" ; level 2 ; orig_coord_info "chr17,64212574,64214217,-" ; protein_id "ENSP00000258991.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--TMEM100^ENST00000258991.7" ; transcript_name "TEX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TEX2--TMEM100 HAVANA gene 29847 33084 . + . FI_gene_label "TMEM100^ENSG00000166292.12" ; ID "TEX2--TMEM100^TMEM100^ENSG00000166292.12" ; ccdsid "CCDS11587.1" ; exon_id "ENSE00002683681.1" ; exon_number 2 ; gene_id "TEX2--TMEM100^TMEM100^ENSG00000166292.12" ; gene_name TMEM100 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177858.5" ; havana_transcript "OTTHUMT00000439265.2" ; hgnc_id "HGNC:25607" ; level 2 ; orig_coord_info "chr17,55720669,55721070,-" ; protein_id "ENSP00000395328.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TEX2--TMEM100^ENST00000424486.3" ; transcript_name "TMEM100-201" ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--TMEM100 HAVANA mRNA 29847 33084 . + . FI_gene_label "TMEM100^ENSG00000166292.12" ; ID "TEX2--TMEM100^ENST00000424486.3" ; Parent "TEX2--TMEM100^TMEM100^ENSG00000166292.12" ; ccdsid "CCDS11587.1" ; exon_id "ENSE00002683681.1" ; exon_number 2 ; gene_id "TEX2--TMEM100^TMEM100^ENSG00000166292.12" ; gene_name TMEM100 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177858.5" ; havana_transcript "OTTHUMT00000439265.2" ; hgnc_id "HGNC:25607" ; level 2 ; orig_coord_info "chr17,55720669,55721070,-" ; protein_id "ENSP00000395328.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TEX2--TMEM100^ENST00000424486.3" ; transcript_name "TMEM100-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^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--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^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--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TPTE--AL356585.3 HAVANA gene 1023 23850 . + . FI_gene_label "TPTE^ENSG00000274391.5" ; ID "TPTE--AL356585.3^TPTE^ENSG00000274391.5" ; ccdsid "CCDS74773.1" ; exon_id "ENSE00003735534.1" ; exon_number 4 ; gene_id "TPTE--AL356585.3^TPTE^ENSG00000274391.5" ; gene_name TPTE ; gene_type protein_coding ; havana_gene "OTTHUMG00000074127.15" ; havana_transcript "OTTHUMT00000157414.2" ; hgnc_id "HGNC:12023" ; level 2 ; orig_coord_info "chr21,10538724,10538734,+" ; protein_id "ENSP00000482488.1" ; tag basic appris_alternative_2 CCDS ; transcript_id "TPTE--AL356585.3^ENST00000427445.6" ; transcript_name "TPTE-201" ; transcript_support_level 1 ; transcript_type protein_coding
TPTE--AL356585.3 HAVANA mRNA 1023 23850 . + . FI_gene_label "TPTE^ENSG00000274391.5" ; ID "TPTE--AL356585.3^ENST00000427445.6" ; Parent "TPTE--AL356585.3^TPTE^ENSG00000274391.5" ; ccdsid "CCDS74773.1" ; exon_id "ENSE00003735534.1" ; exon_number 4 ; gene_id "TPTE--AL356585.3^TPTE^ENSG00000274391.5" ; gene_name TPTE ; gene_type protein_coding ; havana_gene "OTTHUMG00000074127.15" ; havana_transcript "OTTHUMT00000157414.2" ; hgnc_id "HGNC:12023" ; level 2 ; orig_coord_info "chr21,10538724,10538734,+" ; protein_id "ENSP00000482488.1" ; tag basic appris_alternative_2 CCDS ; transcript_id "TPTE--AL356585.3^ENST00000427445.6" ; transcript_name "TPTE-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:
AC008443.2--BAGE2 HAVANA gene 1001 2549 . + . FI_gene_label "AC008443.2^ENSG00000248103.1" ; ID "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1" ; exon_id "ENSE00002038514.1" ; exon_number 1 ; gene_id "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1" ; gene_name "AC008443.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163377.1" ; havana_transcript "OTTHUMT00000372940.1" ; level 1 ; orig_coord_info "chr5,181281375,181281612,+" ; tag basic exp_conf ; transcript_id "AC008443.2--BAGE2^ENST00000412295.2" ; transcript_name "AC008443.2-201" ; transcript_support_level 4 ; transcript_type lncRNA
AC008443.2--BAGE2 HAVANA RNA 1001 2549 . + . FI_gene_label "AC008443.2^ENSG00000248103.1" ; ID "AC008443.2--BAGE2^ENST00000412295.2" ; Parent "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1" ; exon_id "ENSE00002038514.1" ; exon_number 1 ; gene_id "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1" ; gene_name "AC008443.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163377.1" ; havana_transcript "OTTHUMT00000372940.1" ; level 1 ; orig_coord_info "chr5,181281375,181281612,+" ; tag basic exp_conf ; transcript_id "AC008443.2--BAGE2^ENST00000412295.2" ; transcript_name "AC008443.2-201" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
AC008443.2--BAGE2 HAVANA gene 5605 17808 . + . FI_gene_label "BAGE2^ENSG00000187172.15" ; ID "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15" ; exon_id "ENSE00001647801.1" ; exon_number 1 ; gene_id "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15" ; gene_name BAGE2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074128.5" ; havana_transcript "OTTHUMT00000157417.3" ; hgnc_id "HGNC:15723" ; level 2 ; orig_coord_info "chr21,10413532,10413754,+" ; tag mRNA_end_NF ; transcript_id "AC008443.2--BAGE2^ENST00000470054.5" ; transcript_name "BAGE2-201" ; transcript_support_level 1 ; transcript_type processed_transcript
AC008443.2--BAGE2 HAVANA RNA 5605 17808 . + . FI_gene_label "BAGE2^ENSG00000187172.15" ; ID "AC008443.2--BAGE2^ENST00000470054.5" ; Parent "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15" ; exon_id "ENSE00001647801.1" ; exon_number 1 ; gene_id "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15" ; gene_name BAGE2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074128.5" ; havana_transcript "OTTHUMT00000157417.3" ; hgnc_id "HGNC:15723" ; level 2 ; orig_coord_info "chr21,10413532,10413754,+" ; tag mRNA_end_NF ; transcript_id "AC008443.2--BAGE2^ENST00000470054.5" ; transcript_name "BAGE2-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
CU104787.1--KMT2C HAVANA gene 1001 2288 . + . FI_gene_label "CU104787.1^ENSG00000279973.2" ; ID "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2" ; exon_id "ENSE00003758096.2" ; exon_number 1 ; gene_id "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2" ; gene_name "CU104787.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192006.1" ; havana_transcript "OTTHUMT00000491988.1" ; level 2 ; orig_coord_info "chr22,11066418,11066515,+" ; tag basic ; transcript_id "CU104787.1--KMT2C^ENST00000624155.2" ; transcript_name "CU104787.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
CU104787.1--KMT2C HAVANA RNA 1001 2288 . + . FI_gene_label "CU104787.1^ENSG00000279973.2" ; ID "CU104787.1--KMT2C^ENST00000624155.2" ; Parent "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2" ; exon_id "ENSE00003758096.2" ; exon_number 1 ; gene_id "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2" ; gene_name "CU104787.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192006.1" ; havana_transcript "OTTHUMT00000491988.1" ; level 2 ; orig_coord_info "chr22,11066418,11066515,+" ; tag basic ; transcript_id "CU104787.1--KMT2C^ENST00000624155.2" ; transcript_name "CU104787.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
FBXO42--OSTCP2 HAVANA gene 20156 20599 . + . FI_gene_label "OSTCP2^ENSG00000225294.1" ; ID "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1" ; exon_id "ENSE00001720295.1" ; exon_number 1 ; gene_id "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1" ; gene_name OSTCP2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000004276.1" ; havana_transcript "OTTHUMT00000012345.1" ; hgnc_id "HGNC:42864" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,26985897,26986340,-" ; tag pseudo_consens basic ; transcript_id "FBXO42--OSTCP2^ENST00000437956.1" ; transcript_name "OSTCP2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
FBXO42--OSTCP2 HAVANA RNA 20156 20599 . + . FI_gene_label "OSTCP2^ENSG00000225294.1" ; ID "FBXO42--OSTCP2^ENST00000437956.1" ; Parent "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1" ; exon_id "ENSE00001720295.1" ; exon_number 1 ; gene_id "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1" ; gene_name OSTCP2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000004276.1" ; havana_transcript "OTTHUMT00000012345.1" ; hgnc_id "HGNC:42864" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr1,26985897,26986340,-" ; tag pseudo_consens basic ; transcript_id "FBXO42--OSTCP2^ENST00000437956.1" ; transcript_name "OSTCP2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TEX2--AC105021.1 HAVANA gene 27540 29841 . + . FI_gene_label "AC105021.1^ENSG00000236319.2" ; ID "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2" ; exon_id "ENSE00001598631.1" ; exon_number 1 ; gene_id "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2" ; gene_name "AC105021.1" ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000177856.1" ; havana_transcript "OTTHUMT00000439262.1" ; level 2 ; orig_coord_info "chr17,55560957,55561091,-" ; tag basic ; transcript_id "TEX2--AC105021.1^ENST00000455347.1" ; transcript_name "AC105021.1-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TEX2--AC105021.1 HAVANA RNA 27540 29841 . + . FI_gene_label "AC105021.1^ENSG00000236319.2" ; ID "TEX2--AC105021.1^ENST00000455347.1" ; Parent "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2" ; exon_id "ENSE00001598631.1" ; exon_number 1 ; gene_id "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2" ; gene_name "AC105021.1" ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000177856.1" ; havana_transcript "OTTHUMT00000439262.1" ; level 2 ; orig_coord_info "chr17,55560957,55561091,-" ; tag basic ; transcript_id "TEX2--AC105021.1^ENST00000455347.1" ; transcript_name "AC105021.1-201" ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
TPTE--AL356585.3 HAVANA gene 27275 34055 . + . FI_gene_label "AL356585.3^ENSG00000279231.1" ; ID "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1" ; exon_id "ENSE00003757265.1" ; exon_number 1 ; gene_id "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1" ; gene_name "AL356585.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189384.1" ; havana_transcript "OTTHUMT00000479525.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr13,18331933,18332052,+" ; tag basic ; transcript_id "TPTE--AL356585.3^ENST00000625196.1" ; transcript_name "AL356585.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
TPTE--AL356585.3 HAVANA RNA 27275 34055 . + . FI_gene_label "AL356585.3^ENSG00000279231.1" ; ID "TPTE--AL356585.3^ENST00000625196.1" ; Parent "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1" ; exon_id "ENSE00003757265.1" ; exon_number 1 ; gene_id "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1" ; gene_name "AL356585.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189384.1" ; havana_transcript "OTTHUMT00000479525.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr13,18331933,18332052,+" ; tag basic ; transcript_id "TPTE--AL356585.3^ENST00000625196.1" ; transcript_name "AL356585.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
259 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 ------------------------------
475 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 19 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