Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/1dd728cae3591450f7f8bd2ebfd481/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/d33bb0b0acb150e4e7a18b58dcebcd/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/1dd728cae3591450f7f8bd2ebfd481/.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: 7970
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 7970
=> 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:7970
=> 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:
ANKRD24--KEAP1 HAVANA gene 22888 31039 . + . FI_gene_label "KEAP1^ENSG00000079999.14" ; ID "ANKRD24--KEAP1^KEAP1^ENSG00000079999.14" ; ccdsid "CCDS12239.1" ; exon_id "ENSE00003799100.1" ; exon_number 2 ; gene_id "ANKRD24--KEAP1^KEAP1^ENSG00000079999.14" ; gene_name KEAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180579.5" ; havana_transcript "OTTHUMT00000452000.2" ; hgnc_id "HGNC:23177" ; level 2 ; orig_coord_info "chr19,10499395,10500033,-" ; protein_id "ENSP00000171111.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANKRD24--KEAP1^ENST00000171111.10" ; transcript_name "KEAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANKRD24--KEAP1 HAVANA mRNA 22888 31039 . + . FI_gene_label "KEAP1^ENSG00000079999.14" ; ID "ANKRD24--KEAP1^ENST00000171111.10" ; Parent "ANKRD24--KEAP1^KEAP1^ENSG00000079999.14" ; ccdsid "CCDS12239.1" ; exon_id "ENSE00003799100.1" ; exon_number 2 ; gene_id "ANKRD24--KEAP1^KEAP1^ENSG00000079999.14" ; gene_name KEAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180579.5" ; havana_transcript "OTTHUMT00000452000.2" ; hgnc_id "HGNC:23177" ; level 2 ; orig_coord_info "chr19,10499395,10500033,-" ; protein_id "ENSP00000171111.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANKRD24--KEAP1^ENST00000171111.10" ; transcript_name "KEAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ANKRD24--KEAP1 HAVANA gene 3317 19376 . + . FI_gene_label "ANKRD24^ENSG00000089847.12" ; ID "ANKRD24--KEAP1^ANKRD24^ENSG00000089847.12" ; exon_id "ENSE00001146379.2" ; exon_number 1 ; gene_id "ANKRD24--KEAP1^ANKRD24^ENSG00000089847.12" ; gene_name ANKRD24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181865.3" ; havana_transcript "OTTHUMT00000458004.3" ; hgnc_id "HGNC:29424" ; level 2 ; orig_coord_info "chr19,4198140,4198532,+" ; protein_id "ENSP00000262970.4" ; tag basic appris_principal_1 ; transcript_id "ANKRD24--KEAP1^ENST00000262970.9" ; transcript_name "ANKRD24-201" ; transcript_support_level 5 ; transcript_type protein_coding
ANKRD24--KEAP1 HAVANA mRNA 3317 19376 . + . FI_gene_label "ANKRD24^ENSG00000089847.12" ; ID "ANKRD24--KEAP1^ENST00000262970.9" ; Parent "ANKRD24--KEAP1^ANKRD24^ENSG00000089847.12" ; exon_id "ENSE00001146379.2" ; exon_number 1 ; gene_id "ANKRD24--KEAP1^ANKRD24^ENSG00000089847.12" ; gene_name ANKRD24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181865.3" ; havana_transcript "OTTHUMT00000458004.3" ; hgnc_id "HGNC:29424" ; level 2 ; orig_coord_info "chr19,4198140,4198532,+" ; protein_id "ENSP00000262970.4" ; tag basic appris_principal_1 ; transcript_id "ANKRD24--KEAP1^ENST00000262970.9" ; transcript_name "ANKRD24-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
DLG5--CTSLP1 HAVANA gene 1001 37468 . + . FI_gene_label "DLG5^ENSG00000151208.17" ; ID "DLG5--CTSLP1^DLG5^ENSG00000151208.17" ; ccdsid "CCDS7353.2" ; exon_id "ENSE00001942599.2" ; exon_number 1 ; gene_id "DLG5--CTSLP1^DLG5^ENSG00000151208.17" ; gene_name DLG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018548.5" ; havana_transcript "OTTHUMT00000048900.3" ; hgnc_id "HGNC:2904" ; level 2 ; orig_coord_info "chr10,77926217,77926520,-" ; protein_id "ENSP00000361467.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DLG5--CTSLP1^ENST00000372391.7" ; transcript_name "DLG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
DLG5--CTSLP1 HAVANA mRNA 1001 37468 . + . FI_gene_label "DLG5^ENSG00000151208.17" ; ID "DLG5--CTSLP1^ENST00000372391.7" ; Parent "DLG5--CTSLP1^DLG5^ENSG00000151208.17" ; ccdsid "CCDS7353.2" ; exon_id "ENSE00001942599.2" ; exon_number 1 ; gene_id "DLG5--CTSLP1^DLG5^ENSG00000151208.17" ; gene_name DLG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018548.5" ; havana_transcript "OTTHUMT00000048900.3" ; hgnc_id "HGNC:2904" ; level 2 ; orig_coord_info "chr10,77926217,77926520,-" ; protein_id "ENSP00000361467.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DLG5--CTSLP1^ENST00000372391.7" ; transcript_name "DLG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DLG5--KCNMA1 HAVANA gene 40936 120071 . + . FI_gene_label "KCNMA1^ENSG00000156113.24" ; ID "DLG5--KCNMA1^KCNMA1^ENSG00000156113.24" ; ccdsid "CCDS7352.1" ; exon_id "ENSE00003806997.1" ; exon_number 1 ; gene_id "DLG5--KCNMA1^KCNMA1^ENSG00000156113.24" ; gene_name KCNMA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018543.33" ; havana_transcript "OTTHUMT00000048877.5" ; hgnc_id "HGNC:6284" ; level 2 ; orig_coord_info "chr10,77637265,77637642,-" ; protein_id "ENSP00000286627.5" ; tag basic appris_principal_4 CCDS ; transcript_id "DLG5--KCNMA1^ENST00000286627.10" ; transcript_name "KCNMA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DLG5--KCNMA1 HAVANA mRNA 40936 120071 . + . FI_gene_label "KCNMA1^ENSG00000156113.24" ; ID "DLG5--KCNMA1^ENST00000286627.10" ; Parent "DLG5--KCNMA1^KCNMA1^ENSG00000156113.24" ; ccdsid "CCDS7352.1" ; exon_id "ENSE00003806997.1" ; exon_number 1 ; gene_id "DLG5--KCNMA1^KCNMA1^ENSG00000156113.24" ; gene_name KCNMA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018543.33" ; havana_transcript "OTTHUMT00000048877.5" ; hgnc_id "HGNC:6284" ; level 2 ; orig_coord_info "chr10,77637265,77637642,-" ; protein_id "ENSP00000286627.5" ; tag basic appris_principal_4 CCDS ; transcript_id "DLG5--KCNMA1^ENST00000286627.10" ; transcript_name "KCNMA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DLG5--KCNMA1 HAVANA gene 1001 37468 . + . FI_gene_label "DLG5^ENSG00000151208.17" ; ID "DLG5--KCNMA1^DLG5^ENSG00000151208.17" ; ccdsid "CCDS7353.2" ; exon_id "ENSE00001942599.2" ; exon_number 1 ; gene_id "DLG5--KCNMA1^DLG5^ENSG00000151208.17" ; gene_name DLG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018548.5" ; havana_transcript "OTTHUMT00000048900.3" ; hgnc_id "HGNC:2904" ; level 2 ; orig_coord_info "chr10,77926217,77926520,-" ; protein_id "ENSP00000361467.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DLG5--KCNMA1^ENST00000372391.7" ; transcript_name "DLG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
DLG5--KCNMA1 HAVANA mRNA 1001 37468 . + . FI_gene_label "DLG5^ENSG00000151208.17" ; ID "DLG5--KCNMA1^ENST00000372391.7" ; Parent "DLG5--KCNMA1^DLG5^ENSG00000151208.17" ; ccdsid "CCDS7353.2" ; exon_id "ENSE00001942599.2" ; exon_number 1 ; gene_id "DLG5--KCNMA1^DLG5^ENSG00000151208.17" ; gene_name DLG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018548.5" ; havana_transcript "OTTHUMT00000048900.3" ; hgnc_id "HGNC:2904" ; level 2 ; orig_coord_info "chr10,77926217,77926520,-" ; protein_id "ENSP00000361467.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DLG5--KCNMA1^ENST00000372391.7" ; transcript_name "DLG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPRC5A--RFC1 HAVANA gene 1004 10972 . + . FI_gene_label "GPRC5A^ENSG00000013588.9" ; ID "GPRC5A--RFC1^GPRC5A^ENSG00000013588.9" ; ccdsid "CCDS8657.1" ; exon_id "ENSE00000822076.3" ; exon_number 2 ; gene_id "GPRC5A--RFC1^GPRC5A^ENSG00000013588.9" ; gene_name GPRC5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168710.4" ; havana_transcript "OTTHUMT00000400682.1" ; hgnc_id "HGNC:9836" ; level 2 ; orig_coord_info "chr12,12908250,12909171,+" ; protein_id "ENSP00000014914.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GPRC5A--RFC1^ENST00000014914.6" ; transcript_name "GPRC5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPRC5A--RFC1 HAVANA mRNA 1004 10972 . + . FI_gene_label "GPRC5A^ENSG00000013588.9" ; ID "GPRC5A--RFC1^ENST00000014914.6" ; Parent "GPRC5A--RFC1^GPRC5A^ENSG00000013588.9" ; ccdsid "CCDS8657.1" ; exon_id "ENSE00000822076.3" ; exon_number 2 ; gene_id "GPRC5A--RFC1^GPRC5A^ENSG00000013588.9" ; gene_name GPRC5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168710.4" ; havana_transcript "OTTHUMT00000400682.1" ; hgnc_id "HGNC:9836" ; level 2 ; orig_coord_info "chr12,12908250,12909171,+" ; protein_id "ENSP00000014914.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GPRC5A--RFC1^ENST00000014914.6" ; transcript_name "GPRC5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPRC5A--RFC1 HAVANA gene 13986 44161 . + . FI_gene_label "RFC1^ENSG00000035928.16" ; ID "GPRC5A--RFC1^RFC1^ENSG00000035928.16" ; ccdsid "CCDS3450.1" ; exon_id "ENSE00002063495.2" ; exon_number 1 ; gene_id "GPRC5A--RFC1^RFC1^ENSG00000035928.16" ; gene_name RFC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099363.4" ; havana_transcript "OTTHUMT00000361001.2" ; hgnc_id "HGNC:9969" ; level 2 ; orig_coord_info "chr4,39366239,39366241,-" ; protein_id "ENSP00000261424.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GPRC5A--RFC1^ENST00000349703.7" ; transcript_name "RFC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPRC5A--RFC1 HAVANA mRNA 13986 44161 . + . FI_gene_label "RFC1^ENSG00000035928.16" ; ID "GPRC5A--RFC1^ENST00000349703.7" ; Parent "GPRC5A--RFC1^RFC1^ENSG00000035928.16" ; ccdsid "CCDS3450.1" ; exon_id "ENSE00002063495.2" ; exon_number 1 ; gene_id "GPRC5A--RFC1^RFC1^ENSG00000035928.16" ; gene_name RFC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099363.4" ; havana_transcript "OTTHUMT00000361001.2" ; hgnc_id "HGNC:9969" ; level 2 ; orig_coord_info "chr4,39366239,39366241,-" ; protein_id "ENSP00000261424.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GPRC5A--RFC1^ENST00000349703.7" ; transcript_name "RFC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
JMJD1C--AL137026.2 HAVANA gene 14813 30669 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "JMJD1C--AL137026.2^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "JMJD1C--AL137026.2^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--AL137026.2^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding
JMJD1C--AL137026.2 HAVANA mRNA 14813 30669 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "JMJD1C--AL137026.2^ENST00000327520.7" ; Parent "JMJD1C--AL137026.2^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "JMJD1C--AL137026.2^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--AL137026.2^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
JMJD1C--LINC00841 HAVANA gene 14813 30669 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "JMJD1C--LINC00841^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "JMJD1C--LINC00841^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--LINC00841^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding
JMJD1C--LINC00841 HAVANA mRNA 14813 30669 . + . FI_gene_label "JMJD1C^ENSG00000171988.19" ; ID "JMJD1C--LINC00841^ENST00000327520.7" ; Parent "JMJD1C--LINC00841^JMJD1C^ENSG00000171988.19" ; exon_id "ENSE00001605128.1" ; exon_number 1 ; gene_id "JMJD1C--LINC00841^JMJD1C^ENSG00000171988.19" ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7" ; havana_transcript "OTTHUMT00000048250.1" ; hgnc_id "HGNC:12313" ; level 1 ; orig_coord_info "chr10,63206595,63207725,-" ; protein_id "ENSP00000335929.5" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--LINC00841^ENST00000327520.7" ; transcript_name "JMJD1C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
MRPS6--RUNX1 HAVANA gene 31747 52807 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "MRPS6--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "MRPS6--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "MRPS6--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MRPS6--RUNX1 HAVANA mRNA 31747 52807 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "MRPS6--RUNX1^ENST00000300305.7" ; Parent "MRPS6--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "MRPS6--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "MRPS6--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MRPS6--RUNX1 HAVANA gene 1355 9137 . + . FI_gene_label "MRPS6^ENSG00000243927.6" ; ID "MRPS6--RUNX1^MRPS6^ENSG00000243927.6" ; ccdsid "CCDS33548.1" ; exon_id "ENSE00001537488.3" ; exon_number 1 ; gene_id "MRPS6--RUNX1^MRPS6^ENSG00000243927.6" ; gene_name MRPS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000065820.3" ; havana_transcript "OTTHUMT00000141033.2" ; hgnc_id "HGNC:14051" ; level 2 ; orig_coord_info "chr21,34073701,34073745,+" ; protein_id "ENSP00000382250.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS6--RUNX1^ENST00000399312.3" ; transcript_name "MRPS6-201" ; transcript_support_level 1 ; transcript_type protein_coding
MRPS6--RUNX1 HAVANA mRNA 1355 9137 . + . FI_gene_label "MRPS6^ENSG00000243927.6" ; ID "MRPS6--RUNX1^ENST00000399312.3" ; Parent "MRPS6--RUNX1^MRPS6^ENSG00000243927.6" ; ccdsid "CCDS33548.1" ; exon_id "ENSE00001537488.3" ; exon_number 1 ; gene_id "MRPS6--RUNX1^MRPS6^ENSG00000243927.6" ; gene_name MRPS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000065820.3" ; havana_transcript "OTTHUMT00000141033.2" ; hgnc_id "HGNC:14051" ; level 2 ; orig_coord_info "chr21,34073701,34073745,+" ; protein_id "ENSP00000382250.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRPS6--RUNX1^ENST00000399312.3" ; transcript_name "MRPS6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PKP2--ASS1P14 HAVANA gene 1022 20050 . + . FI_gene_label "PKP2^ENSG00000057294.15" ; ID "PKP2--ASS1P14^PKP2^ENSG00000057294.15" ; ccdsid "CCDS8731.1" ; exon_id "ENSE00002372317.1" ; exon_number 1 ; gene_id "PKP2--ASS1P14^PKP2^ENSG00000057294.15" ; gene_name PKP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169500.3" ; havana_transcript "OTTHUMT00000404449.1" ; hgnc_id "HGNC:9024" ; level 2 ; orig_coord_info "chr12,32896509,32896731,-" ; protein_id "ENSP00000070846.6" ; tag basic CCDS ; transcript_id "PKP2--ASS1P14^ENST00000070846.10" ; transcript_name "PKP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PKP2--ASS1P14 HAVANA mRNA 1022 20050 . + . FI_gene_label "PKP2^ENSG00000057294.15" ; ID "PKP2--ASS1P14^ENST00000070846.10" ; Parent "PKP2--ASS1P14^PKP2^ENSG00000057294.15" ; ccdsid "CCDS8731.1" ; exon_id "ENSE00002372317.1" ; exon_number 1 ; gene_id "PKP2--ASS1P14^PKP2^ENSG00000057294.15" ; gene_name PKP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169500.3" ; havana_transcript "OTTHUMT00000404449.1" ; hgnc_id "HGNC:9024" ; level 2 ; orig_coord_info "chr12,32896509,32896731,-" ; protein_id "ENSP00000070846.6" ; tag basic CCDS ; transcript_id "PKP2--ASS1P14^ENST00000070846.10" ; transcript_name "PKP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POLR2E--KEAP1 HAVANA gene 12627 20778 . + . FI_gene_label "KEAP1^ENSG00000079999.14" ; ID "POLR2E--KEAP1^KEAP1^ENSG00000079999.14" ; ccdsid "CCDS12239.1" ; exon_id "ENSE00003799100.1" ; exon_number 2 ; gene_id "POLR2E--KEAP1^KEAP1^ENSG00000079999.14" ; gene_name KEAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180579.5" ; havana_transcript "OTTHUMT00000452000.2" ; hgnc_id "HGNC:23177" ; level 2 ; orig_coord_info "chr19,10499395,10500033,-" ; protein_id "ENSP00000171111.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POLR2E--KEAP1^ENST00000171111.10" ; transcript_name "KEAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
POLR2E--KEAP1 HAVANA mRNA 12627 20778 . + . FI_gene_label "KEAP1^ENSG00000079999.14" ; ID "POLR2E--KEAP1^ENST00000171111.10" ; Parent "POLR2E--KEAP1^KEAP1^ENSG00000079999.14" ; ccdsid "CCDS12239.1" ; exon_id "ENSE00003799100.1" ; exon_number 2 ; gene_id "POLR2E--KEAP1^KEAP1^ENSG00000079999.14" ; gene_name KEAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180579.5" ; havana_transcript "OTTHUMT00000452000.2" ; hgnc_id "HGNC:23177" ; level 2 ; orig_coord_info "chr19,10499395,10500033,-" ; protein_id "ENSP00000171111.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POLR2E--KEAP1^ENST00000171111.10" ; transcript_name "KEAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POLR2E--KEAP1 HAVANA gene 1007 7835 . + . FI_gene_label "POLR2E^ENSG00000099817.12" ; ID "POLR2E--KEAP1^POLR2E^ENSG00000099817.12" ; exon_id "ENSE00002835191.2" ; exon_number 1 ; gene_id "POLR2E--KEAP1^POLR2E^ENSG00000099817.12" ; gene_name POLR2E ; gene_type protein_coding ; havana_gene "OTTHUMG00000181873.6" ; havana_transcript "OTTHUMT00000473949.1" ; hgnc_id "HGNC:9192" ; level 2 ; orig_coord_info "chr19,1095259,1095315,-" ; protein_id "ENSP00000215587.7" ; transcript_id "POLR2E--KEAP1^ENST00000215587.11" ; transcript_name "POLR2E-201" ; transcript_support_level 3 ; transcript_type nonsense_mediated_decay
POLR2E--KEAP1 HAVANA mRNA 1007 7835 . + . FI_gene_label "POLR2E^ENSG00000099817.12" ; ID "POLR2E--KEAP1^ENST00000215587.11" ; Parent "POLR2E--KEAP1^POLR2E^ENSG00000099817.12" ; exon_id "ENSE00002835191.2" ; exon_number 1 ; gene_id "POLR2E--KEAP1^POLR2E^ENSG00000099817.12" ; gene_name POLR2E ; gene_type protein_coding ; havana_gene "OTTHUMG00000181873.6" ; havana_transcript "OTTHUMT00000473949.1" ; hgnc_id "HGNC:9192" ; level 2 ; orig_coord_info "chr19,1095259,1095315,-" ; protein_id "ENSP00000215587.7" ; transcript_id "POLR2E--KEAP1^ENST00000215587.11" ; transcript_name "POLR2E-201" ; transcript_support_level 3 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^ENST00000356698.9" ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^ENST00000368207.7" ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RFC1--GPRC5A HAVANA gene 34193 44161 . + . FI_gene_label "GPRC5A^ENSG00000013588.9" ; ID "RFC1--GPRC5A^GPRC5A^ENSG00000013588.9" ; ccdsid "CCDS8657.1" ; exon_id "ENSE00000822076.3" ; exon_number 2 ; gene_id "RFC1--GPRC5A^GPRC5A^ENSG00000013588.9" ; gene_name GPRC5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168710.4" ; havana_transcript "OTTHUMT00000400682.1" ; hgnc_id "HGNC:9836" ; level 2 ; orig_coord_info "chr12,12908250,12909171,+" ; protein_id "ENSP00000014914.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RFC1--GPRC5A^ENST00000014914.6" ; transcript_name "GPRC5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
RFC1--GPRC5A HAVANA mRNA 34193 44161 . + . FI_gene_label "GPRC5A^ENSG00000013588.9" ; ID "RFC1--GPRC5A^ENST00000014914.6" ; Parent "RFC1--GPRC5A^GPRC5A^ENSG00000013588.9" ; ccdsid "CCDS8657.1" ; exon_id "ENSE00000822076.3" ; exon_number 2 ; gene_id "RFC1--GPRC5A^GPRC5A^ENSG00000013588.9" ; gene_name GPRC5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168710.4" ; havana_transcript "OTTHUMT00000400682.1" ; hgnc_id "HGNC:9836" ; level 2 ; orig_coord_info "chr12,12908250,12909171,+" ; protein_id "ENSP00000014914.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RFC1--GPRC5A^ENST00000014914.6" ; transcript_name "GPRC5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RFC1--GPRC5A HAVANA gene 1014 31189 . + . FI_gene_label "RFC1^ENSG00000035928.16" ; ID "RFC1--GPRC5A^RFC1^ENSG00000035928.16" ; ccdsid "CCDS3450.1" ; exon_id "ENSE00002063495.2" ; exon_number 1 ; gene_id "RFC1--GPRC5A^RFC1^ENSG00000035928.16" ; gene_name RFC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099363.4" ; havana_transcript "OTTHUMT00000361001.2" ; hgnc_id "HGNC:9969" ; level 2 ; orig_coord_info "chr4,39366239,39366241,-" ; protein_id "ENSP00000261424.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "RFC1--GPRC5A^ENST00000349703.7" ; transcript_name "RFC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RFC1--GPRC5A HAVANA mRNA 1014 31189 . + . FI_gene_label "RFC1^ENSG00000035928.16" ; ID "RFC1--GPRC5A^ENST00000349703.7" ; Parent "RFC1--GPRC5A^RFC1^ENSG00000035928.16" ; ccdsid "CCDS3450.1" ; exon_id "ENSE00002063495.2" ; exon_number 1 ; gene_id "RFC1--GPRC5A^RFC1^ENSG00000035928.16" ; gene_name RFC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099363.4" ; havana_transcript "OTTHUMT00000361001.2" ; hgnc_id "HGNC:9969" ; level 2 ; orig_coord_info "chr4,39366239,39366241,-" ; protein_id "ENSP00000261424.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "RFC1--GPRC5A^ENST00000349703.7" ; transcript_name "RFC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC5A3--RUNX1 HAVANA gene 36172 57232 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "SLC5A3--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "SLC5A3--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC5A3--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC5A3--RUNX1 HAVANA mRNA 36172 57232 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "SLC5A3--RUNX1^ENST00000300305.7" ; Parent "SLC5A3--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "SLC5A3--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC5A3--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC5A3--RUNX1 HAVANA gene 1001 13566 . + . FI_gene_label "SLC5A3^ENSG00000198743.7" ; ID "SLC5A3--RUNX1^SLC5A3^ENSG00000198743.7" ; ccdsid "CCDS33549.1" ; exon_id "ENSE00001487667.5" ; exon_number 2 ; gene_id "SLC5A3--RUNX1^SLC5A3^ENSG00000198743.7" ; gene_name SLC5A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000065821.4" ; havana_transcript "OTTHUMT00000141037.4" ; hgnc_id "HGNC:11038" ; level 2 ; orig_coord_info "chr21,34095199,34097352,+" ; protein_id "ENSP00000370543.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC5A3--RUNX1^ENST00000381151.5" ; transcript_name "SLC5A3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC5A3--RUNX1 HAVANA mRNA 1001 13566 . + . FI_gene_label "SLC5A3^ENSG00000198743.7" ; ID "SLC5A3--RUNX1^ENST00000381151.5" ; Parent "SLC5A3--RUNX1^SLC5A3^ENSG00000198743.7" ; ccdsid "CCDS33549.1" ; exon_id "ENSE00001487667.5" ; exon_number 2 ; gene_id "SLC5A3--RUNX1^SLC5A3^ENSG00000198743.7" ; gene_name SLC5A3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000065821.4" ; havana_transcript "OTTHUMT00000141037.4" ; hgnc_id "HGNC:11038" ; level 2 ; orig_coord_info "chr21,34095199,34097352,+" ; protein_id "ENSP00000370543.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC5A3--RUNX1^ENST00000381151.5" ; transcript_name "SLC5A3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SULT1B1--AC098680.2 HAVANA gene 3199 16368 . + . FI_gene_label "SULT1B1^ENSG00000173597.9" ; ID "SULT1B1--AC098680.2^SULT1B1^ENSG00000173597.9" ; ccdsid "CCDS3530.1" ; exon_id "ENSE00001180407.3" ; exon_number 2 ; gene_id "SULT1B1--AC098680.2^SULT1B1^ENSG00000173597.9" ; gene_name SULT1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129407.7" ; havana_transcript "OTTHUMT00000251563.3" ; hgnc_id "HGNC:17845" ; level 2 ; orig_coord_info "chr4,69755070,69755217,-" ; protein_id "ENSP00000308770.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--AC098680.2^ENST00000310613.8" ; transcript_name "SULT1B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SULT1B1--AC098680.2 HAVANA mRNA 3199 16368 . + . FI_gene_label "SULT1B1^ENSG00000173597.9" ; ID "SULT1B1--AC098680.2^ENST00000310613.8" ; Parent "SULT1B1--AC098680.2^SULT1B1^ENSG00000173597.9" ; ccdsid "CCDS3530.1" ; exon_id "ENSE00001180407.3" ; exon_number 2 ; gene_id "SULT1B1--AC098680.2^SULT1B1^ENSG00000173597.9" ; gene_name SULT1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129407.7" ; havana_transcript "OTTHUMT00000251563.3" ; hgnc_id "HGNC:17845" ; level 2 ; orig_coord_info "chr4,69755070,69755217,-" ; protein_id "ENSP00000308770.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--AC098680.2^ENST00000310613.8" ; transcript_name "SULT1B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SULT1B1--TBC1D1 HAVANA gene 19369 56736 . + . FI_gene_label "TBC1D1^ENSG00000065882.16" ; ID "SULT1B1--TBC1D1^TBC1D1^ENSG00000065882.16" ; ccdsid "CCDS33972.1" ; exon_id "ENSE00001340229.1" ; exon_number 2 ; gene_id "SULT1B1--TBC1D1^TBC1D1^ENSG00000065882.16" ; gene_name TBC1D1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150302.10" ; havana_transcript "OTTHUMT00000317443.3" ; hgnc_id "HGNC:11578" ; level 2 ; orig_coord_info "chr4,37902096,37902512,+" ; protein_id "ENSP00000261439.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--TBC1D1^ENST00000261439.9" ; transcript_name "TBC1D1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SULT1B1--TBC1D1 HAVANA mRNA 19369 56736 . + . FI_gene_label "TBC1D1^ENSG00000065882.16" ; ID "SULT1B1--TBC1D1^ENST00000261439.9" ; Parent "SULT1B1--TBC1D1^TBC1D1^ENSG00000065882.16" ; ccdsid "CCDS33972.1" ; exon_id "ENSE00001340229.1" ; exon_number 2 ; gene_id "SULT1B1--TBC1D1^TBC1D1^ENSG00000065882.16" ; gene_name TBC1D1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150302.10" ; havana_transcript "OTTHUMT00000317443.3" ; hgnc_id "HGNC:11578" ; level 2 ; orig_coord_info "chr4,37902096,37902512,+" ; protein_id "ENSP00000261439.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--TBC1D1^ENST00000261439.9" ; transcript_name "TBC1D1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SULT1B1--TBC1D1 HAVANA gene 3199 16368 . + . FI_gene_label "SULT1B1^ENSG00000173597.9" ; ID "SULT1B1--TBC1D1^SULT1B1^ENSG00000173597.9" ; ccdsid "CCDS3530.1" ; exon_id "ENSE00001180407.3" ; exon_number 2 ; gene_id "SULT1B1--TBC1D1^SULT1B1^ENSG00000173597.9" ; gene_name SULT1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129407.7" ; havana_transcript "OTTHUMT00000251563.3" ; hgnc_id "HGNC:17845" ; level 2 ; orig_coord_info "chr4,69755070,69755217,-" ; protein_id "ENSP00000308770.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--TBC1D1^ENST00000310613.8" ; transcript_name "SULT1B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SULT1B1--TBC1D1 HAVANA mRNA 3199 16368 . + . FI_gene_label "SULT1B1^ENSG00000173597.9" ; ID "SULT1B1--TBC1D1^ENST00000310613.8" ; Parent "SULT1B1--TBC1D1^SULT1B1^ENSG00000173597.9" ; ccdsid "CCDS3530.1" ; exon_id "ENSE00001180407.3" ; exon_number 2 ; gene_id "SULT1B1--TBC1D1^SULT1B1^ENSG00000173597.9" ; gene_name SULT1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129407.7" ; havana_transcript "OTTHUMT00000251563.3" ; hgnc_id "HGNC:17845" ; level 2 ; orig_coord_info "chr4,69755070,69755217,-" ; protein_id "ENSP00000308770.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SULT1B1--TBC1D1^ENST00000310613.8" ; transcript_name "SULT1B1-201" ; 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:
TYK2--SBNO2 ENSEMBL gene 2959 20504 . + . FI_gene_label "TYK2^ENSG00000105397.14" ; ID "TYK2--SBNO2^TYK2^ENSG00000105397.14" ; ccdsid "CCDS12236.1" ; exon_id "ENSE00001223242.9" ; exon_number 1 ; gene_id "TYK2--SBNO2^TYK2^ENSG00000105397.14" ; gene_name TYK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166373.4" ; hgnc_id "HGNC:12440" ; level 3 ; orig_coord_info "chr19,10378214,10378406,-" ; protein_id "ENSP00000264818.6" ; tag basic appris_principal_1 CCDS ; transcript_id "TYK2--SBNO2^ENST00000264818.10" ; transcript_name "TYK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TYK2--SBNO2 ENSEMBL mRNA 2959 20504 . + . FI_gene_label "TYK2^ENSG00000105397.14" ; ID "TYK2--SBNO2^ENST00000264818.10" ; Parent "TYK2--SBNO2^TYK2^ENSG00000105397.14" ; ccdsid "CCDS12236.1" ; exon_id "ENSE00001223242.9" ; exon_number 1 ; gene_id "TYK2--SBNO2^TYK2^ENSG00000105397.14" ; gene_name TYK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166373.4" ; hgnc_id "HGNC:12440" ; level 3 ; orig_coord_info "chr19,10378214,10378406,-" ; protein_id "ENSP00000264818.6" ; tag basic appris_principal_1 CCDS ; transcript_id "TYK2--SBNO2^ENST00000264818.10" ; transcript_name "TYK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TYK2--SBNO2 HAVANA gene 23505 47799 . + . FI_gene_label "SBNO2^ENSG00000064932.16" ; ID "TYK2--SBNO2^SBNO2^ENSG00000064932.16" ; ccdsid "CCDS45894.1" ; exon_id "ENSE00002286470.1" ; exon_number 2 ; gene_id "TYK2--SBNO2^SBNO2^ENSG00000064932.16" ; gene_name SBNO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181875.7" ; havana_transcript "OTTHUMT00000458065.4" ; hgnc_id "HGNC:29158" ; level 2 ; orig_coord_info "chr19,1154184,1154276,-" ; protein_id "ENSP00000354733.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TYK2--SBNO2^ENST00000361757.8" ; transcript_name "SBNO2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TYK2--SBNO2 HAVANA mRNA 23505 47799 . + . FI_gene_label "SBNO2^ENSG00000064932.16" ; ID "TYK2--SBNO2^ENST00000361757.8" ; Parent "TYK2--SBNO2^SBNO2^ENSG00000064932.16" ; ccdsid "CCDS45894.1" ; exon_id "ENSE00002286470.1" ; exon_number 2 ; gene_id "TYK2--SBNO2^SBNO2^ENSG00000064932.16" ; gene_name SBNO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181875.7" ; havana_transcript "OTTHUMT00000458065.4" ; hgnc_id "HGNC:29158" ; level 2 ; orig_coord_info "chr19,1154184,1154276,-" ; protein_id "ENSP00000354733.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TYK2--SBNO2^ENST00000361757.8" ; transcript_name "SBNO2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WDR19--ATP8A1 HAVANA gene 42428 87835 . + . FI_gene_label "ATP8A1^ENSG00000124406.16" ; ID "WDR19--ATP8A1^ATP8A1^ENSG00000124406.16" ; ccdsid "CCDS47049.1" ; exon_id "ENSE00001809509.1" ; exon_number 1 ; gene_id "WDR19--ATP8A1^ATP8A1^ENSG00000124406.16" ; gene_name ATP8A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099403.3" ; havana_transcript "OTTHUMT00000363531.1" ; hgnc_id "HGNC:13531" ; level 2 ; orig_coord_info "chr4,42656825,42656873,-" ; protein_id "ENSP00000264449.10" ; tag basic appris_principal_3 CCDS ; transcript_id "WDR19--ATP8A1^ENST00000264449.14" ; transcript_name "ATP8A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
WDR19--ATP8A1 HAVANA mRNA 42428 87835 . + . FI_gene_label "ATP8A1^ENSG00000124406.16" ; ID "WDR19--ATP8A1^ENST00000264449.14" ; Parent "WDR19--ATP8A1^ATP8A1^ENSG00000124406.16" ; ccdsid "CCDS47049.1" ; exon_id "ENSE00001809509.1" ; exon_number 1 ; gene_id "WDR19--ATP8A1^ATP8A1^ENSG00000124406.16" ; gene_name ATP8A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099403.3" ; havana_transcript "OTTHUMT00000363531.1" ; hgnc_id "HGNC:13531" ; level 2 ; orig_coord_info "chr4,42656825,42656873,-" ; protein_id "ENSP00000264449.10" ; tag basic appris_principal_3 CCDS ; transcript_id "WDR19--ATP8A1^ENST00000264449.14" ; transcript_name "ATP8A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WDR19--ATP8A1 HAVANA gene 1026 39415 . + . FI_gene_label "WDR19^ENSG00000157796.18" ; ID "WDR19--ATP8A1^WDR19^ENSG00000157796.18" ; ccdsid "CCDS47042.1" ; exon_id "ENSE00003539935.1" ; exon_number 1 ; gene_id "WDR19--ATP8A1^WDR19^ENSG00000157796.18" ; gene_name WDR19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160466.5" ; havana_transcript "OTTHUMT00000360689.2" ; hgnc_id "HGNC:18340" ; level 2 ; orig_coord_info "chr4,39182558,39182563,+" ; protein_id "ENSP00000382717.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR19--ATP8A1^ENST00000399820.8" ; transcript_name "WDR19-201" ; transcript_support_level 1 ; transcript_type protein_coding
WDR19--ATP8A1 HAVANA mRNA 1026 39415 . + . FI_gene_label "WDR19^ENSG00000157796.18" ; ID "WDR19--ATP8A1^ENST00000399820.8" ; Parent "WDR19--ATP8A1^WDR19^ENSG00000157796.18" ; ccdsid "CCDS47042.1" ; exon_id "ENSE00003539935.1" ; exon_number 1 ; gene_id "WDR19--ATP8A1^WDR19^ENSG00000157796.18" ; gene_name WDR19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160466.5" ; havana_transcript "OTTHUMT00000360689.2" ; hgnc_id "HGNC:18340" ; level 2 ; orig_coord_info "chr4,39182558,39182563,+" ; protein_id "ENSP00000382717.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WDR19--ATP8A1^ENST00000399820.8" ; transcript_name "WDR19-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DLG5--CTSLP1 HAVANA gene 40469 43987 . + . FI_gene_label "CTSLP1^ENSG00000236417.2" ; ID "DLG5--CTSLP1^CTSLP1^ENSG00000236417.2" ; exon_id "ENSE00002436926.1" ; exon_number 1 ; gene_id "DLG5--CTSLP1^CTSLP1^ENSG00000236417.2" ; gene_name CTSLP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000018677.1" ; havana_transcript "OTTHUMT00000049220.1" ; hgnc_id "HGNC:2539" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr10,87390078,87390203,-" ; tag basic ; transcript_id "DLG5--CTSLP1^ENST00000457530.1" ; transcript_name "CTSLP1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
DLG5--CTSLP1 HAVANA RNA 40469 43987 . + . FI_gene_label "CTSLP1^ENSG00000236417.2" ; ID "DLG5--CTSLP1^ENST00000457530.1" ; Parent "DLG5--CTSLP1^CTSLP1^ENSG00000236417.2" ; exon_id "ENSE00002436926.1" ; exon_number 1 ; gene_id "DLG5--CTSLP1^CTSLP1^ENSG00000236417.2" ; gene_name CTSLP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000018677.1" ; havana_transcript "OTTHUMT00000049220.1" ; hgnc_id "HGNC:2539" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr10,87390078,87390203,-" ; tag basic ; transcript_id "DLG5--CTSLP1^ENST00000457530.1" ; transcript_name "CTSLP1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
JMJD1C--AL137026.2 HAVANA gene 36519 38359 . + . FI_gene_label "AL137026.2^ENSG00000237590.1" ; ID "JMJD1C--AL137026.2^AL137026.2^ENSG00000237590.1" ; exon_id "ENSE00001778540.1" ; exon_number 1 ; gene_id "JMJD1C--AL137026.2^AL137026.2^ENSG00000237590.1" ; gene_name "AL137026.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000018055.1" ; havana_transcript "OTTHUMT00000047740.1" ; level 1 ; orig_coord_info "chr10,44261517,44261813,-" ; tag basic exp_conf ; transcript_id "JMJD1C--AL137026.2^ENST00000437014.1" ; transcript_name "AL137026.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
JMJD1C--AL137026.2 HAVANA RNA 36519 38359 . + . FI_gene_label "AL137026.2^ENSG00000237590.1" ; ID "JMJD1C--AL137026.2^ENST00000437014.1" ; Parent "JMJD1C--AL137026.2^AL137026.2^ENSG00000237590.1" ; exon_id "ENSE00001778540.1" ; exon_number 1 ; gene_id "JMJD1C--AL137026.2^AL137026.2^ENSG00000237590.1" ; gene_name "AL137026.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000018055.1" ; havana_transcript "OTTHUMT00000047740.1" ; level 1 ; orig_coord_info "chr10,44261517,44261813,-" ; tag basic exp_conf ; transcript_id "JMJD1C--AL137026.2^ENST00000437014.1" ; transcript_name "AL137026.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
JMJD1C--LINC00841 HAVANA gene 41069 45417 . + . FI_gene_label "LINC00841^ENSG00000233395.2" ; ID "JMJD1C--LINC00841^LINC00841^ENSG00000233395.2" ; exon_id "ENSE00001629556.1" ; exon_number 1 ; gene_id "JMJD1C--LINC00841^LINC00841^ENSG00000233395.2" ; gene_name LINC00841 ; gene_type lncRNA ; havana_gene "OTTHUMG00000018053.10" ; havana_transcript "OTTHUMT00000047736.1" ; hgnc_id "HGNC:27430" ; level 2 ; orig_coord_info "chr10,43939003,43940542,+" ; tag basic ; transcript_id "JMJD1C--LINC00841^ENST00000451929.1" ; transcript_name "LINC00841-201" ; transcript_support_level 2 ; transcript_type lncRNA
JMJD1C--LINC00841 HAVANA RNA 41069 45417 . + . FI_gene_label "LINC00841^ENSG00000233395.2" ; ID "JMJD1C--LINC00841^ENST00000451929.1" ; Parent "JMJD1C--LINC00841^LINC00841^ENSG00000233395.2" ; exon_id "ENSE00001629556.1" ; exon_number 1 ; gene_id "JMJD1C--LINC00841^LINC00841^ENSG00000233395.2" ; gene_name LINC00841 ; gene_type lncRNA ; havana_gene "OTTHUMG00000018053.10" ; havana_transcript "OTTHUMT00000047736.1" ; hgnc_id "HGNC:27430" ; level 2 ; orig_coord_info "chr10,43939003,43940542,+" ; tag basic ; transcript_id "JMJD1C--LINC00841^ENST00000451929.1" ; transcript_name "LINC00841-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
PKP2--ASS1P14 HAVANA gene 23150 24382 . + . FI_gene_label "ASS1P14^ENSG00000257316.1" ; ID "PKP2--ASS1P14^ASS1P14^ENSG00000257316.1" ; exon_id "ENSE00001698226.3" ; exon_number 1 ; gene_id "PKP2--ASS1P14^ASS1P14^ENSG00000257316.1" ; gene_name ASS1P14 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169504.1" ; havana_transcript "OTTHUMT00000404497.1" ; hgnc_id "HGNC:764" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,32985838,32987070,+" ; tag pseudo_consens basic ; transcript_id "PKP2--ASS1P14^ENST00000553060.1" ; transcript_name "ASS1P14-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
PKP2--ASS1P14 HAVANA RNA 23150 24382 . + . FI_gene_label "ASS1P14^ENSG00000257316.1" ; ID "PKP2--ASS1P14^ENST00000553060.1" ; Parent "PKP2--ASS1P14^ASS1P14^ENSG00000257316.1" ; exon_id "ENSE00001698226.3" ; exon_number 1 ; gene_id "PKP2--ASS1P14^ASS1P14^ENSG00000257316.1" ; gene_name ASS1P14 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169504.1" ; havana_transcript "OTTHUMT00000404497.1" ; hgnc_id "HGNC:764" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,32985838,32987070,+" ; tag pseudo_consens basic ; transcript_id "PKP2--ASS1P14^ENST00000553060.1" ; transcript_name "ASS1P14-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
SULT1B1--AC098680.2 HAVANA gene 19369 21035 . + . FI_gene_label "AC098680.2^ENSG00000287659.1" ; ID "SULT1B1--AC098680.2^AC098680.2^ENSG00000287659.1" ; exon_id "ENSE00003859334.1" ; exon_number 1 ; gene_id "SULT1B1--AC098680.2^AC098680.2^ENSG00000287659.1" ; gene_name "AC098680.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194583.1" ; havana_transcript "OTTHUMT00000519167.1" ; level 2 ; orig_coord_info "chr4,38279671,38279880,-" ; tag basic TAGENE ; transcript_id "SULT1B1--AC098680.2^ENST00000670635.1" ; transcript_name "AC098680.2-201" ; transcript_type lncRNA
SULT1B1--AC098680.2 HAVANA RNA 19369 21035 . + . FI_gene_label "AC098680.2^ENSG00000287659.1" ; ID "SULT1B1--AC098680.2^ENST00000670635.1" ; Parent "SULT1B1--AC098680.2^AC098680.2^ENSG00000287659.1" ; exon_id "ENSE00003859334.1" ; exon_number 1 ; gene_id "SULT1B1--AC098680.2^AC098680.2^ENSG00000287659.1" ; gene_name "AC098680.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194583.1" ; havana_transcript "OTTHUMT00000519167.1" ; level 2 ; orig_coord_info "chr4,38279671,38279880,-" ; tag basic TAGENE ; transcript_id "SULT1B1--AC098680.2^ENST00000670635.1" ; transcript_name "AC098680.2-201" ; transcript_type lncRNA
408 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 1 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
766 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 26 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed