Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/d3e94fe0ae5da3c725f40e2898c872/fi_workdir/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/e99a756be903b40bbc703361a43a8f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/e99a756be903b40bbc703361a43a8f/.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: 5531
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5531
=> 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:5531
=> 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:
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:
CDKAL1--LARP4B HAVANA gene 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--LARP4B^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--LARP4B^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--LARP4B^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDKAL1--LARP4B HAVANA mRNA 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--LARP4B^ENST00000274695.8" ; Parent "CDKAL1--LARP4B^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--LARP4B^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--LARP4B^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDKAL1--LARP4B HAVANA gene 24483 50686 . + . FI_gene_label "LARP4B^ENSG00000107929.15" ; ID "CDKAL1--LARP4B^LARP4B^ENSG00000107929.15" ; ccdsid "CCDS31131.1" ; exon_id "ENSE00003703032.1" ; exon_number 2 ; gene_id "CDKAL1--LARP4B^LARP4B^ENSG00000107929.15" ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8" ; havana_transcript "OTTHUMT00000046395.5" ; hgnc_id "HGNC:28987" ; level 2 ; orig_coord_info "chr10,885641,885721,-" ; protein_id "ENSP00000326128.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--LARP4B^ENST00000316157.8" ; transcript_name "LARP4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDKAL1--LARP4B HAVANA mRNA 24483 50686 . + . FI_gene_label "LARP4B^ENSG00000107929.15" ; ID "CDKAL1--LARP4B^ENST00000316157.8" ; Parent "CDKAL1--LARP4B^LARP4B^ENSG00000107929.15" ; ccdsid "CCDS31131.1" ; exon_id "ENSE00003703032.1" ; exon_number 2 ; gene_id "CDKAL1--LARP4B^LARP4B^ENSG00000107929.15" ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8" ; havana_transcript "OTTHUMT00000046395.5" ; hgnc_id "HGNC:28987" ; level 2 ; orig_coord_info "chr10,885641,885721,-" ; protein_id "ENSP00000326128.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--LARP4B^ENST00000316157.8" ; transcript_name "LARP4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ENTPD6--AL035252.2 HAVANA gene 1001 17877 . + . FI_gene_label "ENTPD6^ENSG00000197586.13" ; ID "ENTPD6--AL035252.2^ENTPD6^ENSG00000197586.13" ; ccdsid "CCDS46586.1" ; exon_id "ENSE00001869951.1" ; exon_number 1 ; gene_id "ENTPD6--AL035252.2^ENTPD6^ENSG00000197586.13" ; gene_name ENTPD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032116.4" ; havana_transcript "OTTHUMT00000078398.2" ; hgnc_id "HGNC:3368" ; level 2 ; orig_coord_info "chr20,25195865,25195867,+" ; protein_id "ENSP00000347084.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "ENTPD6--AL035252.2^ENST00000354989.9" ; transcript_name "ENTPD6-201" ; transcript_support_level 1 ; transcript_type protein_coding
ENTPD6--AL035252.2 HAVANA mRNA 1001 17877 . + . FI_gene_label "ENTPD6^ENSG00000197586.13" ; ID "ENTPD6--AL035252.2^ENST00000354989.9" ; Parent "ENTPD6--AL035252.2^ENTPD6^ENSG00000197586.13" ; ccdsid "CCDS46586.1" ; exon_id "ENSE00001869951.1" ; exon_number 1 ; gene_id "ENTPD6--AL035252.2^ENTPD6^ENSG00000197586.13" ; gene_name ENTPD6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032116.4" ; havana_transcript "OTTHUMT00000078398.2" ; hgnc_id "HGNC:3368" ; level 2 ; orig_coord_info "chr20,25195865,25195867,+" ; protein_id "ENSP00000347084.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "ENTPD6--AL035252.2^ENST00000354989.9" ; transcript_name "ENTPD6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC6B--ATP9A HAVANA gene 1009 34110 . + . FI_gene_label "EXOC6B^ENSG00000144036.16" ; ID "EXOC6B--ATP9A^EXOC6B^ENSG00000144036.16" ; ccdsid "CCDS46333.1" ; exon_id "ENSE00000000137.2" ; exon_number 1 ; gene_id "EXOC6B--ATP9A^EXOC6B^ENSG00000144036.16" ; gene_name EXOC6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152723.3" ; havana_transcript "OTTHUMT00000327558.1" ; hgnc_id "HGNC:17085" ; level 2 ; orig_coord_info "chr2,72825798,72825910,-" ; protein_id "ENSP00000272427.7" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EXOC6B--ATP9A^ENST00000272427.11" ; transcript_name "EXOC6B-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC6B--ATP9A HAVANA mRNA 1009 34110 . + . FI_gene_label "EXOC6B^ENSG00000144036.16" ; ID "EXOC6B--ATP9A^ENST00000272427.11" ; Parent "EXOC6B--ATP9A^EXOC6B^ENSG00000144036.16" ; ccdsid "CCDS46333.1" ; exon_id "ENSE00000000137.2" ; exon_number 1 ; gene_id "EXOC6B--ATP9A^EXOC6B^ENSG00000144036.16" ; gene_name EXOC6B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152723.3" ; havana_transcript "OTTHUMT00000327558.1" ; hgnc_id "HGNC:17085" ; level 2 ; orig_coord_info "chr2,72825798,72825910,-" ; protein_id "ENSP00000272427.7" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EXOC6B--ATP9A^ENST00000272427.11" ; transcript_name "EXOC6B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC6B--ATP9A HAVANA gene 37173 72263 . + . FI_gene_label "ATP9A^ENSG00000054793.14" ; ID "EXOC6B--ATP9A^ATP9A^ENSG00000054793.14" ; exon_id "ENSE00001455504.1" ; exon_number 1 ; gene_id "EXOC6B--ATP9A^ATP9A^ENSG00000054793.14" ; gene_name ATP9A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032751.4" ; havana_transcript "OTTHUMT00000079736.3" ; hgnc_id "HGNC:13540" ; level 2 ; orig_coord_info "chr20,51768302,51768324,-" ; protein_id "ENSP00000309086.5" ; tag basic ; transcript_id "EXOC6B--ATP9A^ENST00000311637.9" ; transcript_name "ATP9A-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC6B--ATP9A HAVANA mRNA 37173 72263 . + . FI_gene_label "ATP9A^ENSG00000054793.14" ; ID "EXOC6B--ATP9A^ENST00000311637.9" ; Parent "EXOC6B--ATP9A^ATP9A^ENSG00000054793.14" ; exon_id "ENSE00001455504.1" ; exon_number 1 ; gene_id "EXOC6B--ATP9A^ATP9A^ENSG00000054793.14" ; gene_name ATP9A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032751.4" ; havana_transcript "OTTHUMT00000079736.3" ; hgnc_id "HGNC:13540" ; level 2 ; orig_coord_info "chr20,51768302,51768324,-" ; protein_id "ENSP00000309086.5" ; tag basic ; transcript_id "EXOC6B--ATP9A^ENST00000311637.9" ; transcript_name "ATP9A-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:
HMG20A--EIF2B3 HAVANA gene 1477 16424 . + . FI_gene_label "HMG20A^ENSG00000140382.15" ; ID "HMG20A--EIF2B3^HMG20A^ENSG00000140382.15" ; ccdsid "CCDS10295.1" ; exon_id "ENSE00003462611.1" ; exon_number 2 ; gene_id "HMG20A--EIF2B3^HMG20A^ENSG00000140382.15" ; gene_name HMG20A ; gene_type protein_coding ; havana_gene "OTTHUMG00000143729.8" ; havana_transcript "OTTHUMT00000289794.4" ; hgnc_id "HGNC:5001" ; level 2 ; orig_coord_info "chr15,77458408,77458496,+" ; protein_id "ENSP00000336856.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HMG20A--EIF2B3^ENST00000336216.9" ; transcript_name "HMG20A-201" ; transcript_support_level 1 ; transcript_type protein_coding
HMG20A--EIF2B3 HAVANA mRNA 1477 16424 . + . FI_gene_label "HMG20A^ENSG00000140382.15" ; ID "HMG20A--EIF2B3^ENST00000336216.9" ; Parent "HMG20A--EIF2B3^HMG20A^ENSG00000140382.15" ; ccdsid "CCDS10295.1" ; exon_id "ENSE00003462611.1" ; exon_number 2 ; gene_id "HMG20A--EIF2B3^HMG20A^ENSG00000140382.15" ; gene_name HMG20A ; gene_type protein_coding ; havana_gene "OTTHUMG00000143729.8" ; havana_transcript "OTTHUMT00000289794.4" ; hgnc_id "HGNC:5001" ; level 2 ; orig_coord_info "chr15,77458408,77458496,+" ; protein_id "ENSP00000336856.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HMG20A--EIF2B3^ENST00000336216.9" ; transcript_name "HMG20A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HMG20A--EIF2B3 HAVANA gene 19556 40369 . + . FI_gene_label "EIF2B3^ENSG00000070785.17" ; ID "HMG20A--EIF2B3^EIF2B3^ENSG00000070785.17" ; ccdsid "CCDS517.1" ; exon_id "ENSE00003470577.1" ; exon_number 2 ; gene_id "HMG20A--EIF2B3^EIF2B3^ENSG00000070785.17" ; gene_name EIF2B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008585.5" ; havana_transcript "OTTHUMT00000023724.2" ; hgnc_id "HGNC:3259" ; level 2 ; orig_coord_info "chr1,44981021,44981168,-" ; protein_id "ENSP00000353575.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HMG20A--EIF2B3^ENST00000360403.7" ; transcript_name "EIF2B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
HMG20A--EIF2B3 HAVANA mRNA 19556 40369 . + . FI_gene_label "EIF2B3^ENSG00000070785.17" ; ID "HMG20A--EIF2B3^ENST00000360403.7" ; Parent "HMG20A--EIF2B3^EIF2B3^ENSG00000070785.17" ; ccdsid "CCDS517.1" ; exon_id "ENSE00003470577.1" ; exon_number 2 ; gene_id "HMG20A--EIF2B3^EIF2B3^ENSG00000070785.17" ; gene_name EIF2B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008585.5" ; havana_transcript "OTTHUMT00000023724.2" ; hgnc_id "HGNC:3259" ; level 2 ; orig_coord_info "chr1,44981021,44981168,-" ; protein_id "ENSP00000353575.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HMG20A--EIF2B3^ENST00000360403.7" ; transcript_name "EIF2B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LARP4B--CDKAL1 HAVANA gene 32564 53045 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "LARP4B--CDKAL1^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "LARP4B--CDKAL1^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--CDKAL1^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
LARP4B--CDKAL1 HAVANA mRNA 32564 53045 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "LARP4B--CDKAL1^ENST00000274695.8" ; Parent "LARP4B--CDKAL1^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "LARP4B--CDKAL1^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--CDKAL1^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LARP4B--CDKAL1 HAVANA gene 1001 27204 . + . FI_gene_label "LARP4B^ENSG00000107929.15" ; ID "LARP4B--CDKAL1^LARP4B^ENSG00000107929.15" ; ccdsid "CCDS31131.1" ; exon_id "ENSE00003703032.1" ; exon_number 2 ; gene_id "LARP4B--CDKAL1^LARP4B^ENSG00000107929.15" ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8" ; havana_transcript "OTTHUMT00000046395.5" ; hgnc_id "HGNC:28987" ; level 2 ; orig_coord_info "chr10,885641,885721,-" ; protein_id "ENSP00000326128.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--CDKAL1^ENST00000316157.8" ; transcript_name "LARP4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
LARP4B--CDKAL1 HAVANA mRNA 1001 27204 . + . FI_gene_label "LARP4B^ENSG00000107929.15" ; ID "LARP4B--CDKAL1^ENST00000316157.8" ; Parent "LARP4B--CDKAL1^LARP4B^ENSG00000107929.15" ; ccdsid "CCDS31131.1" ; exon_id "ENSE00003703032.1" ; exon_number 2 ; gene_id "LARP4B--CDKAL1^LARP4B^ENSG00000107929.15" ; gene_name LARP4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017534.8" ; havana_transcript "OTTHUMT00000046395.5" ; hgnc_id "HGNC:28987" ; level 2 ; orig_coord_info "chr10,885641,885721,-" ; protein_id "ENSP00000326128.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LARP4B--CDKAL1^ENST00000316157.8" ; transcript_name "LARP4B-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:
MOB1B--ACTL6A HAVANA gene 1044 16602 . + . FI_gene_label "MOB1B^ENSG00000173542.9" ; ID "MOB1B--ACTL6A^MOB1B^ENSG00000173542.9" ; ccdsid "CCDS34002.1" ; exon_id "ENSE00002075662.2" ; exon_number 1 ; gene_id "MOB1B--ACTL6A^MOB1B^ENSG00000173542.9" ; gene_name MOB1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000160844.3" ; havana_transcript "OTTHUMT00000362634.1" ; hgnc_id "HGNC:29801" ; level 2 ; orig_coord_info "chr4,70902537,70902550,+" ; protein_id "ENSP00000310189.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MOB1B--ACTL6A^ENST00000309395.7" ; transcript_name "MOB1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
MOB1B--ACTL6A HAVANA mRNA 1044 16602 . + . FI_gene_label "MOB1B^ENSG00000173542.9" ; ID "MOB1B--ACTL6A^ENST00000309395.7" ; Parent "MOB1B--ACTL6A^MOB1B^ENSG00000173542.9" ; ccdsid "CCDS34002.1" ; exon_id "ENSE00002075662.2" ; exon_number 1 ; gene_id "MOB1B--ACTL6A^MOB1B^ENSG00000173542.9" ; gene_name MOB1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000160844.3" ; havana_transcript "OTTHUMT00000362634.1" ; hgnc_id "HGNC:29801" ; level 2 ; orig_coord_info "chr4,70902537,70902550,+" ; protein_id "ENSP00000310189.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MOB1B--ACTL6A^ENST00000309395.7" ; transcript_name "MOB1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MOB1B--ACTL6A ENSEMBL gene 21836 33705 . + . FI_gene_label "ACTL6A^ENSG00000136518.17" ; ID "MOB1B--ACTL6A^ACTL6A^ENSG00000136518.17" ; ccdsid "CCDS43174.1" ; exon_id "ENSE00003797062.1" ; exon_number 3 ; gene_id "MOB1B--ACTL6A^ACTL6A^ENSG00000136518.17" ; gene_name ACTL6A ; gene_type protein_coding ; havana_gene "OTTHUMG00000157782.9" ; hgnc_id "HGNC:24124" ; level 3 ; orig_coord_info "chr3,179570091,179570241,+" ; protein_id "ENSP00000376430.1" ; tag basic CCDS ; transcript_id "MOB1B--ACTL6A^ENST00000392662.5" ; transcript_name "ACTL6A-201" ; transcript_support_level 2 ; transcript_type protein_coding
MOB1B--ACTL6A ENSEMBL mRNA 21836 33705 . + . FI_gene_label "ACTL6A^ENSG00000136518.17" ; ID "MOB1B--ACTL6A^ENST00000392662.5" ; Parent "MOB1B--ACTL6A^ACTL6A^ENSG00000136518.17" ; ccdsid "CCDS43174.1" ; exon_id "ENSE00003797062.1" ; exon_number 3 ; gene_id "MOB1B--ACTL6A^ACTL6A^ENSG00000136518.17" ; gene_name ACTL6A ; gene_type protein_coding ; havana_gene "OTTHUMG00000157782.9" ; hgnc_id "HGNC:24124" ; level 3 ; orig_coord_info "chr3,179570091,179570241,+" ; protein_id "ENSP00000376430.1" ; tag basic CCDS ; transcript_id "MOB1B--ACTL6A^ENST00000392662.5" ; transcript_name "ACTL6A-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PABPC1--VPS13B HAVANA gene 1722 17180 . + . FI_gene_label "PABPC1^ENSG00000070756.17" ; ID "PABPC1--VPS13B^PABPC1^ENSG00000070756.17" ; ccdsid "CCDS6289.1" ; exon_id "ENSE00002107718.2" ; exon_number 1 ; gene_id "PABPC1--VPS13B^PABPC1^ENSG00000070756.17" ; gene_name PABPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164779.4" ; havana_transcript "OTTHUMT00000380217.2" ; hgnc_id "HGNC:8554" ; level 2 ; orig_coord_info "chr8,100721391,100721583,-" ; protein_id "ENSP00000313007.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PABPC1--VPS13B^ENST00000318607.10" ; transcript_name "PABPC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PABPC1--VPS13B HAVANA mRNA 1722 17180 . + . FI_gene_label "PABPC1^ENSG00000070756.17" ; ID "PABPC1--VPS13B^ENST00000318607.10" ; Parent "PABPC1--VPS13B^PABPC1^ENSG00000070756.17" ; ccdsid "CCDS6289.1" ; exon_id "ENSE00002107718.2" ; exon_number 1 ; gene_id "PABPC1--VPS13B^PABPC1^ENSG00000070756.17" ; gene_name PABPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164779.4" ; havana_transcript "OTTHUMT00000380217.2" ; hgnc_id "HGNC:8554" ; level 2 ; orig_coord_info "chr8,100721391,100721583,-" ; protein_id "ENSP00000313007.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PABPC1--VPS13B^ENST00000318607.10" ; transcript_name "PABPC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PABPC1--VPS13B HAVANA gene 22525 40751 . + . FI_gene_label "VPS13B^ENSG00000132549.19" ; ID "PABPC1--VPS13B^VPS13B^ENSG00000132549.19" ; ccdsid "CCDS6283.1" ; exon_id "ENSE00002135952.1" ; exon_number 2 ; gene_id "PABPC1--VPS13B^VPS13B^ENSG00000132549.19" ; gene_name VPS13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000140383.3" ; havana_transcript "OTTHUMT00000277140.1" ; hgnc_id "HGNC:2183" ; level 2 ; orig_coord_info "chr8,99013789,99013935,+" ; protein_id "ENSP00000347281.1" ; tag basic CCDS ; transcript_id "PABPC1--VPS13B^ENST00000355155.5" ; transcript_name "VPS13B-201" ; transcript_support_level 1 ; transcript_type protein_coding
PABPC1--VPS13B HAVANA mRNA 22525 40751 . + . FI_gene_label "VPS13B^ENSG00000132549.19" ; ID "PABPC1--VPS13B^ENST00000355155.5" ; Parent "PABPC1--VPS13B^VPS13B^ENSG00000132549.19" ; ccdsid "CCDS6283.1" ; exon_id "ENSE00002135952.1" ; exon_number 2 ; gene_id "PABPC1--VPS13B^VPS13B^ENSG00000132549.19" ; gene_name VPS13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000140383.3" ; havana_transcript "OTTHUMT00000277140.1" ; hgnc_id "HGNC:2183" ; level 2 ; orig_coord_info "chr8,99013789,99013935,+" ; protein_id "ENSP00000347281.1" ; tag basic CCDS ; transcript_id "PABPC1--VPS13B^ENST00000355155.5" ; transcript_name "VPS13B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PDPK1--ABCA17P HAVANA gene 1025 22708 . + . FI_gene_label "PDPK1^ENSG00000140992.19" ; ID "PDPK1--ABCA17P^PDPK1^ENSG00000140992.19" ; ccdsid "CCDS10473.1" ; exon_id "ENSE00001867541.1" ; exon_number 1 ; gene_id "PDPK1--ABCA17P^PDPK1^ENSG00000140992.19" ; gene_name PDPK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128874.8" ; havana_transcript "OTTHUMT00000250832.2" ; hgnc_id "HGNC:8816" ; level 2 ; orig_coord_info "chr16,2538113,2538136,+" ; protein_id "ENSP00000268673.7" ; tag basic CCDS ; transcript_id "PDPK1--ABCA17P^ENST00000268673.11" ; transcript_name "PDPK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PDPK1--ABCA17P HAVANA mRNA 1025 22708 . + . FI_gene_label "PDPK1^ENSG00000140992.19" ; ID "PDPK1--ABCA17P^ENST00000268673.11" ; Parent "PDPK1--ABCA17P^PDPK1^ENSG00000140992.19" ; ccdsid "CCDS10473.1" ; exon_id "ENSE00001867541.1" ; exon_number 1 ; gene_id "PDPK1--ABCA17P^PDPK1^ENSG00000140992.19" ; gene_name PDPK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128874.8" ; havana_transcript "OTTHUMT00000250832.2" ; hgnc_id "HGNC:8816" ; level 2 ; orig_coord_info "chr16,2538113,2538136,+" ; protein_id "ENSP00000268673.7" ; tag basic CCDS ; transcript_id "PDPK1--ABCA17P^ENST00000268673.11" ; transcript_name "PDPK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PFKL--TRPM2 HAVANA gene 25650 59624 . + . FI_gene_label "TRPM2^ENSG00000142185.16" ; ID "PFKL--TRPM2^TRPM2^ENSG00000142185.16" ; exon_id "ENSE00001877735.1" ; exon_number 1 ; gene_id "PFKL--TRPM2^TRPM2^ENSG00000142185.16" ; gene_name TRPM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040840.5" ; havana_transcript "OTTHUMT00000098087.1" ; hgnc_id "HGNC:12339" ; level 2 ; orig_coord_info "chr21,44353701,44353865,+" ; protein_id "ENSP00000300481.9" ; tag basic ; transcript_id "PFKL--TRPM2^ENST00000300481.13" ; transcript_name "TRPM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PFKL--TRPM2 HAVANA mRNA 25650 59624 . + . FI_gene_label "TRPM2^ENSG00000142185.16" ; ID "PFKL--TRPM2^ENST00000300481.13" ; Parent "PFKL--TRPM2^TRPM2^ENSG00000142185.16" ; exon_id "ENSE00001877735.1" ; exon_number 1 ; gene_id "PFKL--TRPM2^TRPM2^ENSG00000142185.16" ; gene_name TRPM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040840.5" ; havana_transcript "OTTHUMT00000098087.1" ; hgnc_id "HGNC:12339" ; level 2 ; orig_coord_info "chr21,44353701,44353865,+" ; protein_id "ENSP00000300481.9" ; tag basic ; transcript_id "PFKL--TRPM2^ENST00000300481.13" ; transcript_name "TRPM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PFKL--TRPM2 HAVANA gene 1003 21022 . + . FI_gene_label "PFKL^ENSG00000141959.17" ; ID "PFKL--TRPM2^PFKL^ENSG00000141959.17" ; ccdsid "CCDS33582.1" ; exon_id "ENSE00003843359.1" ; exon_number 1 ; gene_id "PFKL--TRPM2^PFKL^ENSG00000141959.17" ; gene_name PFKL ; gene_type protein_coding ; havana_gene "OTTHUMG00000086910.3" ; havana_transcript "OTTHUMT00000195805.2" ; hgnc_id "HGNC:8876" ; level 2 ; orig_coord_info "chr21,44300106,44300190,+" ; protein_id "ENSP00000269848.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PFKL--TRPM2^ENST00000349048.9" ; transcript_name "PFKL-201" ; transcript_support_level 1 ; transcript_type protein_coding
PFKL--TRPM2 HAVANA mRNA 1003 21022 . + . FI_gene_label "PFKL^ENSG00000141959.17" ; ID "PFKL--TRPM2^ENST00000349048.9" ; Parent "PFKL--TRPM2^PFKL^ENSG00000141959.17" ; ccdsid "CCDS33582.1" ; exon_id "ENSE00003843359.1" ; exon_number 1 ; gene_id "PFKL--TRPM2^PFKL^ENSG00000141959.17" ; gene_name PFKL ; gene_type protein_coding ; havana_gene "OTTHUMG00000086910.3" ; havana_transcript "OTTHUMT00000195805.2" ; hgnc_id "HGNC:8876" ; level 2 ; orig_coord_info "chr21,44300106,44300190,+" ; protein_id "ENSP00000269848.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PFKL--TRPM2^ENST00000349048.9" ; transcript_name "PFKL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SH3PXD2A--COL17A1 ENSEMBL gene 1138 28152 . + . FI_gene_label "SH3PXD2A^ENSG00000107957.16" ; ID "SH3PXD2A--COL17A1^SH3PXD2A^ENSG00000107957.16" ; ccdsid "CCDS31278.1" ; exon_id "ENSE00001450855.1" ; exon_number 1 ; gene_id "SH3PXD2A--COL17A1^SH3PXD2A^ENSG00000107957.16" ; gene_name SH3PXD2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000018997.2" ; hgnc_id "HGNC:23664" ; level 3 ; orig_coord_info "chr10,103855195,103855266,-" ; protein_id "ENSP00000348215.2" ; tag basic appris_principal_4 CCDS ; transcript_id "SH3PXD2A--COL17A1^ENST00000355946.6" ; transcript_name "SH3PXD2A-202" ; transcript_support_level 1 ; transcript_type protein_coding
SH3PXD2A--COL17A1 ENSEMBL mRNA 1138 28152 . + . FI_gene_label "SH3PXD2A^ENSG00000107957.16" ; ID "SH3PXD2A--COL17A1^ENST00000355946.6" ; Parent "SH3PXD2A--COL17A1^SH3PXD2A^ENSG00000107957.16" ; ccdsid "CCDS31278.1" ; exon_id "ENSE00001450855.1" ; exon_number 1 ; gene_id "SH3PXD2A--COL17A1^SH3PXD2A^ENSG00000107957.16" ; gene_name SH3PXD2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000018997.2" ; hgnc_id "HGNC:23664" ; level 3 ; orig_coord_info "chr10,103855195,103855266,-" ; protein_id "ENSP00000348215.2" ; tag basic appris_principal_4 CCDS ; transcript_id "SH3PXD2A--COL17A1^ENST00000355946.6" ; transcript_name "SH3PXD2A-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SH3PXD2A--COL17A1 HAVANA gene 32324 72675 . + . FI_gene_label "COL17A1^ENSG00000065618.21" ; ID "SH3PXD2A--COL17A1^COL17A1^ENSG00000065618.21" ; exon_id "ENSE00003834865.1" ; exon_number 1 ; gene_id "SH3PXD2A--COL17A1^COL17A1^ENSG00000065618.21" ; gene_name COL17A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018998.8" ; havana_transcript "OTTHUMT00000050183.3" ; hgnc_id "HGNC:2194" ; level 2 ; orig_coord_info "chr10,104080622,104080673,-" ; protein_id "ENSP00000358748.3" ; tag dotter_confirmed not_organism_supported basic ; transcript_id "SH3PXD2A--COL17A1^ENST00000369733.8" ; transcript_name "COL17A1-201" ; transcript_support_level 5 ; transcript_type protein_coding
SH3PXD2A--COL17A1 HAVANA mRNA 32324 72675 . + . FI_gene_label "COL17A1^ENSG00000065618.21" ; ID "SH3PXD2A--COL17A1^ENST00000369733.8" ; Parent "SH3PXD2A--COL17A1^COL17A1^ENSG00000065618.21" ; exon_id "ENSE00003834865.1" ; exon_number 1 ; gene_id "SH3PXD2A--COL17A1^COL17A1^ENSG00000065618.21" ; gene_name COL17A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018998.8" ; havana_transcript "OTTHUMT00000050183.3" ; hgnc_id "HGNC:2194" ; level 2 ; orig_coord_info "chr10,104080622,104080673,-" ; protein_id "ENSP00000358748.3" ; tag dotter_confirmed not_organism_supported basic ; transcript_id "SH3PXD2A--COL17A1^ENST00000369733.8" ; transcript_name "COL17A1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
U2SURP--RHOA HAVANA gene 41621 51237 . + . FI_gene_label "RHOA^ENSG00000067560.14" ; ID "U2SURP--RHOA^RHOA^ENSG00000067560.14" ; ccdsid "CCDS2795.1" ; exon_id "ENSE00003765190.1" ; exon_number 2 ; gene_id "U2SURP--RHOA^RHOA^ENSG00000067560.14" ; gene_name RHOA ; gene_type protein_coding ; havana_gene "OTTHUMG00000156838.8" ; havana_transcript "OTTHUMT00000346157.4" ; hgnc_id "HGNC:667" ; level 2 ; orig_coord_info "chr3,49375434,49375589,-" ; protein_id "ENSP00000400175.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "U2SURP--RHOA^ENST00000418115.6" ; transcript_name "RHOA-202" ; transcript_support_level 1 ; transcript_type protein_coding
U2SURP--RHOA HAVANA mRNA 41621 51237 . + . FI_gene_label "RHOA^ENSG00000067560.14" ; ID "U2SURP--RHOA^ENST00000418115.6" ; Parent "U2SURP--RHOA^RHOA^ENSG00000067560.14" ; ccdsid "CCDS2795.1" ; exon_id "ENSE00003765190.1" ; exon_number 2 ; gene_id "U2SURP--RHOA^RHOA^ENSG00000067560.14" ; gene_name RHOA ; gene_type protein_coding ; havana_gene "OTTHUMG00000156838.8" ; havana_transcript "OTTHUMT00000346157.4" ; hgnc_id "HGNC:667" ; level 2 ; orig_coord_info "chr3,49375434,49375589,-" ; protein_id "ENSP00000400175.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "U2SURP--RHOA^ENST00000418115.6" ; transcript_name "RHOA-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
U2SURP--RHOA HAVANA gene 4835 34526 . + . FI_gene_label "U2SURP^ENSG00000163714.18" ; ID "U2SURP--RHOA^U2SURP^ENSG00000163714.18" ; exon_id "ENSE00001915399.1" ; exon_number 1 ; gene_id "U2SURP--RHOA^U2SURP^ENSG00000163714.18" ; gene_name U2SURP ; gene_type protein_coding ; havana_gene "OTTHUMG00000159323.19" ; havana_transcript "OTTHUMT00000354606.2" ; hgnc_id "HGNC:30855" ; level 2 ; orig_coord_info "chr3,143001623,143001673,+" ; protein_id "ENSP00000420210.2" ; tag mRNA_start_NF cds_start_NF ; transcript_id "U2SURP--RHOA^ENST00000463563.6" ; transcript_name "U2SURP-203" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
U2SURP--RHOA HAVANA mRNA 4835 34526 . + . FI_gene_label "U2SURP^ENSG00000163714.18" ; ID "U2SURP--RHOA^ENST00000463563.6" ; Parent "U2SURP--RHOA^U2SURP^ENSG00000163714.18" ; exon_id "ENSE00001915399.1" ; exon_number 1 ; gene_id "U2SURP--RHOA^U2SURP^ENSG00000163714.18" ; gene_name U2SURP ; gene_type protein_coding ; havana_gene "OTTHUMG00000159323.19" ; havana_transcript "OTTHUMT00000354606.2" ; hgnc_id "HGNC:30855" ; level 2 ; orig_coord_info "chr3,143001623,143001673,+" ; protein_id "ENSP00000420210.2" ; tag mRNA_start_NF cds_start_NF ; transcript_id "U2SURP--RHOA^ENST00000463563.6" ; transcript_name "U2SURP-203" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
VIRMA--MYO1E HAVANA gene 33114 69605 . + . FI_gene_label "MYO1E^ENSG00000157483.9" ; ID "VIRMA--MYO1E^MYO1E^ENSG00000157483.9" ; ccdsid "CCDS32254.1" ; exon_id "ENSE00002548049.2" ; exon_number 1 ; gene_id "VIRMA--MYO1E^MYO1E^ENSG00000157483.9" ; gene_name MYO1E ; gene_type protein_coding ; havana_gene "OTTHUMG00000171944.4" ; havana_transcript "OTTHUMT00000416024.3" ; hgnc_id "HGNC:7599" ; level 2 ; orig_coord_info "chr15,59372498,59372500,-" ; protein_id "ENSP00000288235.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VIRMA--MYO1E^ENST00000288235.9" ; transcript_name "MYO1E-201" ; transcript_support_level 1 ; transcript_type protein_coding
VIRMA--MYO1E HAVANA mRNA 33114 69605 . + . FI_gene_label "MYO1E^ENSG00000157483.9" ; ID "VIRMA--MYO1E^ENST00000288235.9" ; Parent "VIRMA--MYO1E^MYO1E^ENSG00000157483.9" ; ccdsid "CCDS32254.1" ; exon_id "ENSE00002548049.2" ; exon_number 1 ; gene_id "VIRMA--MYO1E^MYO1E^ENSG00000157483.9" ; gene_name MYO1E ; gene_type protein_coding ; havana_gene "OTTHUMG00000171944.4" ; havana_transcript "OTTHUMT00000416024.3" ; hgnc_id "HGNC:7599" ; level 2 ; orig_coord_info "chr15,59372498,59372500,-" ; protein_id "ENSP00000288235.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VIRMA--MYO1E^ENST00000288235.9" ; transcript_name "MYO1E-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VIRMA--MYO1E HAVANA gene 1061 30113 . + . FI_gene_label "VIRMA^ENSG00000164944.12" ; ID "VIRMA--MYO1E^VIRMA^ENSG00000164944.12" ; ccdsid "CCDS34923.1" ; exon_id "ENSE00002127505.2" ; exon_number 1 ; gene_id "VIRMA--MYO1E^VIRMA^ENSG00000164944.12" ; gene_name VIRMA ; gene_type protein_coding ; havana_gene "OTTHUMG00000164426.3" ; havana_transcript "OTTHUMT00000378720.3" ; hgnc_id "HGNC:24500" ; level 2 ; orig_coord_info "chr8,94553385,94553447,-" ; protein_id "ENSP00000297591.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VIRMA--MYO1E^ENST00000297591.10" ; transcript_name "VIRMA-201" ; transcript_support_level 1 ; transcript_type protein_coding
VIRMA--MYO1E HAVANA mRNA 1061 30113 . + . FI_gene_label "VIRMA^ENSG00000164944.12" ; ID "VIRMA--MYO1E^ENST00000297591.10" ; Parent "VIRMA--MYO1E^VIRMA^ENSG00000164944.12" ; ccdsid "CCDS34923.1" ; exon_id "ENSE00002127505.2" ; exon_number 1 ; gene_id "VIRMA--MYO1E^VIRMA^ENSG00000164944.12" ; gene_name VIRMA ; gene_type protein_coding ; havana_gene "OTTHUMG00000164426.3" ; havana_transcript "OTTHUMT00000378720.3" ; hgnc_id "HGNC:24500" ; level 2 ; orig_coord_info "chr8,94553385,94553447,-" ; protein_id "ENSP00000297591.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VIRMA--MYO1E^ENST00000297591.10" ; transcript_name "VIRMA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VPS13B--TCF12 HAVANA gene 80308 117046 . + . FI_gene_label "TCF12^ENSG00000140262.18" ; ID "VPS13B--TCF12^TCF12^ENSG00000140262.18" ; ccdsid "CCDS10159.1" ; exon_id "ENSE00003647364.1" ; exon_number 2 ; gene_id "VPS13B--TCF12^TCF12^ENSG00000140262.18" ; gene_name TCF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132047.13" ; havana_transcript "OTTHUMT00000255069.3" ; hgnc_id "HGNC:11623" ; level 2 ; orig_coord_info "chr15,56919914,56919988,+" ; protein_id "ENSP00000267811.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "VPS13B--TCF12^ENST00000267811.9" ; transcript_name "TCF12-201" ; transcript_support_level 1 ; transcript_type protein_coding
VPS13B--TCF12 HAVANA mRNA 80308 117046 . + . FI_gene_label "TCF12^ENSG00000140262.18" ; ID "VPS13B--TCF12^ENST00000267811.9" ; Parent "VPS13B--TCF12^TCF12^ENSG00000140262.18" ; ccdsid "CCDS10159.1" ; exon_id "ENSE00003647364.1" ; exon_number 2 ; gene_id "VPS13B--TCF12^TCF12^ENSG00000140262.18" ; gene_name TCF12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132047.13" ; havana_transcript "OTTHUMT00000255069.3" ; hgnc_id "HGNC:11623" ; level 2 ; orig_coord_info "chr15,56919914,56919988,+" ; protein_id "ENSP00000267811.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "VPS13B--TCF12^ENST00000267811.9" ; transcript_name "TCF12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VPS13B--TCF12 HAVANA gene 1001 19227 . + . FI_gene_label "VPS13B^ENSG00000132549.19" ; ID "VPS13B--TCF12^VPS13B^ENSG00000132549.19" ; ccdsid "CCDS6283.1" ; exon_id "ENSE00002135952.1" ; exon_number 2 ; gene_id "VPS13B--TCF12^VPS13B^ENSG00000132549.19" ; gene_name VPS13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000140383.3" ; havana_transcript "OTTHUMT00000277140.1" ; hgnc_id "HGNC:2183" ; level 2 ; orig_coord_info "chr8,99013789,99013935,+" ; protein_id "ENSP00000347281.1" ; tag basic CCDS ; transcript_id "VPS13B--TCF12^ENST00000355155.5" ; transcript_name "VPS13B-201" ; transcript_support_level 1 ; transcript_type protein_coding
VPS13B--TCF12 HAVANA mRNA 1001 19227 . + . FI_gene_label "VPS13B^ENSG00000132549.19" ; ID "VPS13B--TCF12^ENST00000355155.5" ; Parent "VPS13B--TCF12^VPS13B^ENSG00000132549.19" ; ccdsid "CCDS6283.1" ; exon_id "ENSE00002135952.1" ; exon_number 2 ; gene_id "VPS13B--TCF12^VPS13B^ENSG00000132549.19" ; gene_name VPS13B ; gene_type protein_coding ; havana_gene "OTTHUMG00000140383.3" ; havana_transcript "OTTHUMT00000277140.1" ; hgnc_id "HGNC:2183" ; level 2 ; orig_coord_info "chr8,99013789,99013935,+" ; protein_id "ENSP00000347281.1" ; tag basic CCDS ; transcript_id "VPS13B--TCF12^ENST00000355155.5" ; transcript_name "VPS13B-201" ; transcript_support_level 1 ; 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:
ENTPD6--AL035252.2 HAVANA gene 24132 26253 . + . FI_gene_label "AL035252.2^ENSG00000230725.6" ; ID "ENTPD6--AL035252.2^AL035252.2^ENSG00000230725.6" ; exon_id "ENSE00001684929.1" ; exon_number 1 ; gene_id "ENTPD6--AL035252.2^AL035252.2^ENSG00000230725.6" ; gene_name "AL035252.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000032113.7" ; havana_transcript "OTTHUMT00000078390.1" ; level 2 ; orig_coord_info "chr20,25147449,25147464,-" ; tag dotter_confirmed ; transcript_id "ENTPD6--AL035252.2^ENST00000426854.5" ; transcript_name "AL035252.2-209" ; transcript_support_level 5 ; transcript_type lncRNA
ENTPD6--AL035252.2 HAVANA RNA 24132 26253 . + . FI_gene_label "AL035252.2^ENSG00000230725.6" ; ID "ENTPD6--AL035252.2^ENST00000426854.5" ; Parent "ENTPD6--AL035252.2^AL035252.2^ENSG00000230725.6" ; exon_id "ENSE00001684929.1" ; exon_number 1 ; gene_id "ENTPD6--AL035252.2^AL035252.2^ENSG00000230725.6" ; gene_name "AL035252.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000032113.7" ; havana_transcript "OTTHUMT00000078390.1" ; level 2 ; orig_coord_info "chr20,25147449,25147464,-" ; tag dotter_confirmed ; transcript_id "ENTPD6--AL035252.2^ENST00000426854.5" ; transcript_name "AL035252.2-209" ; transcript_support_level 5 ; transcript_type lncRNA
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:
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:
PDPK1--ABCA17P HAVANA gene 30436 33698 . + . FI_gene_label "ABCA17P^ENSG00000238098.9" ; ID "PDPK1--ABCA17P^ABCA17P^ENSG00000238098.9" ; exon_id "ENSE00001916113.1" ; exon_number 1 ; gene_id "PDPK1--ABCA17P^ABCA17P^ENSG00000238098.9" ; gene_name ABCA17P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154348.4" ; havana_transcript "OTTHUMT00000335049.1" ; hgnc_id "HGNC:32972" ; level 2 ; orig_coord_info "chr16,2342979,2343085,+" ; transcript_id "PDPK1--ABCA17P^ENST00000466730.1" ; transcript_name "ABCA17P-201" ; transcript_support_level 3 ; transcript_type processed_transcript
PDPK1--ABCA17P HAVANA RNA 30436 33698 . + . FI_gene_label "ABCA17P^ENSG00000238098.9" ; ID "PDPK1--ABCA17P^ENST00000466730.1" ; Parent "PDPK1--ABCA17P^ABCA17P^ENSG00000238098.9" ; exon_id "ENSE00001916113.1" ; exon_number 1 ; gene_id "PDPK1--ABCA17P^ABCA17P^ENSG00000238098.9" ; gene_name ABCA17P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154348.4" ; havana_transcript "OTTHUMT00000335049.1" ; hgnc_id "HGNC:32972" ; level 2 ; orig_coord_info "chr16,2342979,2343085,+" ; transcript_id "PDPK1--ABCA17P^ENST00000466730.1" ; transcript_name "ABCA17P-201" ; transcript_support_level 3 ; transcript_type processed_transcript
372 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 ------------------------------
680 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 30 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