Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/9a4b072f7a0020c8d0c03ee84893a1/fi_workdir/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/d3dc47203225964c062e175e71207b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/d3dc47203225964c062e175e71207b/.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: 2196
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2196
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:2196
=> 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:
AC079610.2--IKZF2 HAVANA gene 7237 23374 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "AC079610.2--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC079610.2--IKZF2 HAVANA mRNA 7237 23374 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "AC079610.2--IKZF2^ENST00000342002.6" ; Parent "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "AC079610.2--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTTN--AC136759.1 HAVANA gene 1126 21252 . + . FI_gene_label "CTTN^ENSG00000085733.16" ; ID "CTTN--AC136759.1^CTTN^ENSG00000085733.16" ; ccdsid "CCDS41680.1" ; exon_id "ENSE00003684603.1" ; exon_number 3 ; gene_id "CTTN--AC136759.1^CTTN^ENSG00000085733.16" ; gene_name CTTN ; gene_type protein_coding ; havana_gene "OTTHUMG00000134307.4" ; havana_transcript "OTTHUMT00000259233.3" ; hgnc_id "HGNC:3338" ; level 2 ; orig_coord_info "chr11,70407298,70407384,+" ; protein_id "ENSP00000301843.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTTN--AC136759.1^ENST00000301843.13" ; transcript_name "CTTN-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTTN--AC136759.1 HAVANA mRNA 1126 21252 . + . FI_gene_label "CTTN^ENSG00000085733.16" ; ID "CTTN--AC136759.1^ENST00000301843.13" ; Parent "CTTN--AC136759.1^CTTN^ENSG00000085733.16" ; ccdsid "CCDS41680.1" ; exon_id "ENSE00003684603.1" ; exon_number 3 ; gene_id "CTTN--AC136759.1^CTTN^ENSG00000085733.16" ; gene_name CTTN ; gene_type protein_coding ; havana_gene "OTTHUMG00000134307.4" ; havana_transcript "OTTHUMT00000259233.3" ; hgnc_id "HGNC:3338" ; level 2 ; orig_coord_info "chr11,70407298,70407384,+" ; protein_id "ENSP00000301843.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTTN--AC136759.1^ENST00000301843.13" ; transcript_name "CTTN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
IKZF2--LINC01953 HAVANA gene 3090 19227 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "IKZF2--LINC01953^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "IKZF2--LINC01953^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "IKZF2--LINC01953^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
IKZF2--LINC01953 HAVANA mRNA 3090 19227 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "IKZF2--LINC01953^ENST00000342002.6" ; Parent "IKZF2--LINC01953^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "IKZF2--LINC01953^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "IKZF2--LINC01953^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LINC01953--IKZF2 HAVANA gene 7807 23944 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "LINC01953--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
LINC01953--IKZF2 HAVANA mRNA 7807 23944 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "LINC01953--IKZF2^ENST00000342002.6" ; Parent "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "LINC01953--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHA13 HAVANA gene 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHA13 HAVANA mRNA 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^ENST00000289272.3" ; Parent "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHA13 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHA13 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^ENST00000532566.3" ; Parent "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC1 HAVANA gene 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHAC1 HAVANA mRNA 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC1 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHAC1 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC2 HAVANA gene 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHAC2 HAVANA mRNA 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC2 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHAC2 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--AC136759.1 HAVANA gene 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC136759.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC136759.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC136759.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--AC136759.1 HAVANA mRNA 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC136759.1^ENST00000338508.8" ; Parent "SHANK2--AC136759.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC136759.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC136759.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; 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:
THBS1--AC013652.1 HAVANA gene 1001 18558 . + . FI_gene_label "THBS1^ENSG00000137801.11" ; ID "THBS1--AC013652.1^THBS1^ENSG00000137801.11" ; ccdsid "CCDS32194.1" ; exon_id "ENSE00002289128.1" ; exon_number 2 ; gene_id "THBS1--AC013652.1^THBS1^ENSG00000137801.11" ; gene_name THBS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133665.3" ; havana_transcript "OTTHUMT00000257831.2" ; hgnc_id "HGNC:11785" ; level 2 ; orig_coord_info "chr15,39581858,39581924,+" ; protein_id "ENSP00000260356.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "THBS1--AC013652.1^ENST00000260356.6" ; transcript_name "THBS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
THBS1--AC013652.1 HAVANA mRNA 1001 18558 . + . FI_gene_label "THBS1^ENSG00000137801.11" ; ID "THBS1--AC013652.1^ENST00000260356.6" ; Parent "THBS1--AC013652.1^THBS1^ENSG00000137801.11" ; ccdsid "CCDS32194.1" ; exon_id "ENSE00002289128.1" ; exon_number 2 ; gene_id "THBS1--AC013652.1^THBS1^ENSG00000137801.11" ; gene_name THBS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133665.3" ; havana_transcript "OTTHUMT00000257831.2" ; hgnc_id "HGNC:11785" ; level 2 ; orig_coord_info "chr15,39581858,39581924,+" ; protein_id "ENSP00000260356.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "THBS1--AC013652.1^ENST00000260356.6" ; transcript_name "THBS1-201" ; 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:
UBE2D3--AC098487.1 HAVANA gene 2789 15049 . + . FI_gene_label "UBE2D3^ENSG00000109332.20" ; ID "UBE2D3--AC098487.1^UBE2D3^ENSG00000109332.20" ; ccdsid "CCDS3660.1" ; exon_id "ENSE00001519643.1" ; exon_number 2 ; gene_id "UBE2D3--AC098487.1^UBE2D3^ENSG00000109332.20" ; gene_name UBE2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131119.17" ; havana_transcript "OTTHUMT00000363398.1" ; hgnc_id "HGNC:12476" ; level 2 ; orig_coord_info "chr4,102826485,102826508,-" ; protein_id "ENSP00000318494.7" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "UBE2D3--AC098487.1^ENST00000321805.11" ; transcript_name "UBE2D3-201" ; transcript_support_level 5 ; transcript_type protein_coding
UBE2D3--AC098487.1 HAVANA mRNA 2789 15049 . + . FI_gene_label "UBE2D3^ENSG00000109332.20" ; ID "UBE2D3--AC098487.1^ENST00000321805.11" ; Parent "UBE2D3--AC098487.1^UBE2D3^ENSG00000109332.20" ; ccdsid "CCDS3660.1" ; exon_id "ENSE00001519643.1" ; exon_number 2 ; gene_id "UBE2D3--AC098487.1^UBE2D3^ENSG00000109332.20" ; gene_name UBE2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131119.17" ; havana_transcript "OTTHUMT00000363398.1" ; hgnc_id "HGNC:12476" ; level 2 ; orig_coord_info "chr4,102826485,102826508,-" ; protein_id "ENSP00000318494.7" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "UBE2D3--AC098487.1^ENST00000321805.11" ; transcript_name "UBE2D3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AC079610.2--IKZF2 HAVANA gene 1001 2147 . + . FI_gene_label "AC079610.2^ENSG00000272519.1" ; ID "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; exon_id "ENSE00003699505.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; gene_name "AC079610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000185531.1" ; havana_transcript "OTTHUMT00000470662.1" ; level 2 ; orig_coord_info "chr2,213276072,213276152,-" ; tag basic ; transcript_id "AC079610.2--IKZF2^ENST00000606960.1" ; transcript_name "AC079610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC079610.2--IKZF2 HAVANA RNA 1001 2147 . + . FI_gene_label "AC079610.2^ENSG00000272519.1" ; ID "AC079610.2--IKZF2^ENST00000606960.1" ; Parent "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; exon_id "ENSE00003699505.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; gene_name "AC079610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000185531.1" ; havana_transcript "OTTHUMT00000470662.1" ; level 2 ; orig_coord_info "chr2,213276072,213276152,-" ; tag basic ; transcript_id "AC079610.2--IKZF2^ENST00000606960.1" ; transcript_name "AC079610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
CTTN--AC136759.1 HAVANA gene 25432 33487 . + . FI_gene_label "AC136759.1^ENSG00000205035.8" ; ID "CTTN--AC136759.1^AC136759.1^ENSG00000205035.8" ; exon_id "ENSE00002173855.1" ; exon_number 1 ; gene_id "CTTN--AC136759.1^AC136759.1^ENSG00000205035.8" ; gene_name "AC136759.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166650.5" ; havana_transcript "OTTHUMT00000391378.2" ; level 2 ; orig_coord_info "chr11,49560818,49561018,+" ; tag basic ; transcript_id "CTTN--AC136759.1^ENST00000527477.1" ; transcript_name "AC136759.1-203" ; transcript_support_level 1 ; transcript_type processed_transcript
CTTN--AC136759.1 HAVANA RNA 25432 33487 . + . FI_gene_label "AC136759.1^ENSG00000205035.8" ; ID "CTTN--AC136759.1^ENST00000527477.1" ; Parent "CTTN--AC136759.1^AC136759.1^ENSG00000205035.8" ; exon_id "ENSE00002173855.1" ; exon_number 1 ; gene_id "CTTN--AC136759.1^AC136759.1^ENSG00000205035.8" ; gene_name "AC136759.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166650.5" ; havana_transcript "OTTHUMT00000391378.2" ; level 2 ; orig_coord_info "chr11,49560818,49561018,+" ; tag basic ; transcript_id "CTTN--AC136759.1^ENST00000527477.1" ; transcript_name "AC136759.1-203" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
IKZF2--LINC01953 HAVANA gene 27900 29616 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "IKZF2--LINC01953^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "IKZF2--LINC01953^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "IKZF2--LINC01953^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
IKZF2--LINC01953 HAVANA RNA 27900 29616 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "IKZF2--LINC01953^ENST00000426870.1" ; Parent "IKZF2--LINC01953^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "IKZF2--LINC01953^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "IKZF2--LINC01953^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
LINC01953--IKZF2 HAVANA gene 1001 2717 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "LINC01953--IKZF2^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
LINC01953--IKZF2 HAVANA RNA 1001 2717 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "LINC01953--IKZF2^ENST00000426870.1" ; Parent "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "LINC01953--IKZF2^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
SHANK2--AC136759.1 HAVANA gene 63115 71170 . + . FI_gene_label "AC136759.1^ENSG00000205035.8" ; ID "SHANK2--AC136759.1^AC136759.1^ENSG00000205035.8" ; exon_id "ENSE00002173855.1" ; exon_number 1 ; gene_id "SHANK2--AC136759.1^AC136759.1^ENSG00000205035.8" ; gene_name "AC136759.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166650.5" ; havana_transcript "OTTHUMT00000391378.2" ; level 2 ; orig_coord_info "chr11,49560818,49561018,+" ; tag basic ; transcript_id "SHANK2--AC136759.1^ENST00000527477.1" ; transcript_name "AC136759.1-203" ; transcript_support_level 1 ; transcript_type processed_transcript
SHANK2--AC136759.1 HAVANA RNA 63115 71170 . + . FI_gene_label "AC136759.1^ENSG00000205035.8" ; ID "SHANK2--AC136759.1^ENST00000527477.1" ; Parent "SHANK2--AC136759.1^AC136759.1^ENSG00000205035.8" ; exon_id "ENSE00002173855.1" ; exon_number 1 ; gene_id "SHANK2--AC136759.1^AC136759.1^ENSG00000205035.8" ; gene_name "AC136759.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166650.5" ; havana_transcript "OTTHUMT00000391378.2" ; level 2 ; orig_coord_info "chr11,49560818,49561018,+" ; tag basic ; transcript_id "SHANK2--AC136759.1^ENST00000527477.1" ; transcript_name "AC136759.1-203" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
THBS1--AC013652.1 HAVANA gene 21559 36999 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "THBS1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "THBS1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "THBS1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
THBS1--AC013652.1 HAVANA RNA 21559 36999 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "THBS1--AC013652.1^ENST00000558209.1" ; Parent "THBS1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "THBS1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "THBS1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; 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:
UBE2D3--AC098487.1 HAVANA gene 22023 25068 . + . FI_gene_label "AC098487.1^ENSG00000248161.5" ; ID "UBE2D3--AC098487.1^AC098487.1^ENSG00000248161.5" ; exon_id "ENSE00002028515.1" ; exon_number 1 ; gene_id "UBE2D3--AC098487.1^AC098487.1^ENSG00000248161.5" ; gene_name "AC098487.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10" ; havana_transcript "OTTHUMT00000363754.1" ; level 2 ; orig_coord_info "chr4,102431062,102431249,-" ; tag dotter_confirmed ; transcript_id "UBE2D3--AC098487.1^ENST00000502883.5" ; transcript_name "AC098487.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
UBE2D3--AC098487.1 HAVANA RNA 22023 25068 . + . FI_gene_label "AC098487.1^ENSG00000248161.5" ; ID "UBE2D3--AC098487.1^ENST00000502883.5" ; Parent "UBE2D3--AC098487.1^AC098487.1^ENSG00000248161.5" ; exon_id "ENSE00002028515.1" ; exon_number 1 ; gene_id "UBE2D3--AC098487.1^AC098487.1^ENSG00000248161.5" ; gene_name "AC098487.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10" ; havana_transcript "OTTHUMT00000363754.1" ; level 2 ; orig_coord_info "chr4,102431062,102431249,-" ; tag dotter_confirmed ; transcript_id "UBE2D3--AC098487.1^ENST00000502883.5" ; transcript_name "AC098487.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
243 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 ------------------------------
456 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 22 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