Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/a2fb34b4dc93c11ed6d5667530d98b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/eded6786c4a93711ae5f62ac14aef4/fi_workdir/aih-tih-sc-69be7e-R1_A23YTGFLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/a2fb34b4dc93c11ed6d5667530d98b/.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: 5981
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5981
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:5981
=> 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:
AC005993.1--RGS6 ENSEMBL gene 16301 50680 . + . FI_gene_label "RGS6^ENSG00000182732.18" ; ID "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; exon_id "ENSE00003732696.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; gene_name RGS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171340.6" ; hgnc_id "HGNC:10002" ; level 3 ; orig_coord_info "chr14,72352116,72352194,+" ; protein_id "ENSP00000341199.7" ; tag basic ; transcript_id "AC005993.1--RGS6^ENST00000343854.10" ; transcript_name "RGS6-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC005993.1--RGS6 ENSEMBL mRNA 16301 50680 . + . FI_gene_label "RGS6^ENSG00000182732.18" ; ID "AC005993.1--RGS6^ENST00000343854.10" ; Parent "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; exon_id "ENSE00003732696.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; gene_name RGS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171340.6" ; hgnc_id "HGNC:10002" ; level 3 ; orig_coord_info "chr14,72352116,72352194,+" ; protein_id "ENSP00000341199.7" ; tag basic ; transcript_id "AC005993.1--RGS6^ENST00000343854.10" ; transcript_name "RGS6-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ANO6--ARID2 HAVANA gene 1109 32557 . + . FI_gene_label "ANO6^ENSG00000177119.17" ; ID "ANO6--ARID2^ANO6^ENSG00000177119.17" ; ccdsid "CCDS31782.1" ; exon_id "ENSE00003849088.1" ; exon_number 1 ; gene_id "ANO6--ARID2^ANO6^ENSG00000177119.17" ; gene_name ANO6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169564.2" ; havana_transcript "OTTHUMT00000404822.2" ; hgnc_id "HGNC:25240" ; level 2 ; orig_coord_info "chr12,45216322,45216391,+" ; protein_id "ENSP00000320087.8" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ANO6--ARID2^ENST00000320560.13" ; transcript_name "ANO6-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANO6--ARID2 HAVANA mRNA 1109 32557 . + . FI_gene_label "ANO6^ENSG00000177119.17" ; ID "ANO6--ARID2^ENST00000320560.13" ; Parent "ANO6--ARID2^ANO6^ENSG00000177119.17" ; ccdsid "CCDS31782.1" ; exon_id "ENSE00003849088.1" ; exon_number 1 ; gene_id "ANO6--ARID2^ANO6^ENSG00000177119.17" ; gene_name ANO6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169564.2" ; havana_transcript "OTTHUMT00000404822.2" ; hgnc_id "HGNC:25240" ; level 2 ; orig_coord_info "chr12,45216322,45216391,+" ; protein_id "ENSP00000320087.8" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ANO6--ARID2^ENST00000320560.13" ; transcript_name "ANO6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ANO6--ARID2 HAVANA gene 38735 67704 . + . FI_gene_label "ARID2^ENSG00000189079.17" ; ID "ANO6--ARID2^ARID2^ENSG00000189079.17" ; ccdsid "CCDS31783.1" ; exon_id "ENSE00002363600.2" ; exon_number 1 ; gene_id "ANO6--ARID2^ARID2^ENSG00000189079.17" ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6" ; havana_transcript "OTTHUMT00000318380.3" ; hgnc_id "HGNC:18037" ; level 2 ; orig_coord_info "chr12,45729837,45729928,+" ; protein_id "ENSP00000335044.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANO6--ARID2^ENST00000334344.11" ; transcript_name "ARID2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANO6--ARID2 HAVANA mRNA 38735 67704 . + . FI_gene_label "ARID2^ENSG00000189079.17" ; ID "ANO6--ARID2^ENST00000334344.11" ; Parent "ANO6--ARID2^ARID2^ENSG00000189079.17" ; ccdsid "CCDS31783.1" ; exon_id "ENSE00002363600.2" ; exon_number 1 ; gene_id "ANO6--ARID2^ARID2^ENSG00000189079.17" ; gene_name ARID2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150487.6" ; havana_transcript "OTTHUMT00000318380.3" ; hgnc_id "HGNC:18037" ; level 2 ; orig_coord_info "chr12,45729837,45729928,+" ; protein_id "ENSP00000335044.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANO6--ARID2^ENST00000334344.11" ; transcript_name "ARID2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AP000347.1--IGLL1 HAVANA gene 21739 24573 . + . FI_gene_label "IGLL1^ENSG00000128322.7" ; ID "AP000347.1--IGLL1^IGLL1^ENSG00000128322.7" ; ccdsid "CCDS13810.1" ; exon_id "ENSE00001912592.1" ; exon_number 1 ; gene_id "AP000347.1--IGLL1^IGLL1^ENSG00000128322.7" ; gene_name IGLL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150673.3" ; havana_transcript "OTTHUMT00000319568.1" ; hgnc_id "HGNC:5870" ; level 2 ; orig_coord_info "chr22,23579985,23580190,-" ; protein_id "ENSP00000249053.3" ; tag basic CCDS ; transcript_id "AP000347.1--IGLL1^ENST00000249053.3" ; transcript_name "IGLL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AP000347.1--IGLL1 HAVANA mRNA 21739 24573 . + . FI_gene_label "IGLL1^ENSG00000128322.7" ; ID "AP000347.1--IGLL1^ENST00000249053.3" ; Parent "AP000347.1--IGLL1^IGLL1^ENSG00000128322.7" ; ccdsid "CCDS13810.1" ; exon_id "ENSE00001912592.1" ; exon_number 1 ; gene_id "AP000347.1--IGLL1^IGLL1^ENSG00000128322.7" ; gene_name IGLL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150673.3" ; havana_transcript "OTTHUMT00000319568.1" ; hgnc_id "HGNC:5870" ; level 2 ; orig_coord_info "chr22,23579985,23580190,-" ; protein_id "ENSP00000249053.3" ; tag basic CCDS ; transcript_id "AP000347.1--IGLL1^ENST00000249053.3" ; transcript_name "IGLL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARID1B--AFDN HAVANA gene 9425 59032 . + . FI_gene_label "ARID1B^ENSG00000049618.24" ; ID "ARID1B--AFDN^ARID1B^ENSG00000049618.24" ; exon_id "ENSE00002535311.1" ; exon_number 1 ; gene_id "ARID1B--AFDN^ARID1B^ENSG00000049618.24" ; gene_name ARID1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000015890.14" ; havana_transcript "OTTHUMT00000042830.3" ; hgnc_id "HGNC:18040" ; level 1 ; orig_coord_info "chr6,156901376,156901525,+" ; protein_id "ENSP00000313006.7" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "ARID1B--AFDN^ENST00000319584.11" ; transcript_name "ARID1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
ARID1B--AFDN HAVANA mRNA 9425 59032 . + . FI_gene_label "ARID1B^ENSG00000049618.24" ; ID "ARID1B--AFDN^ENST00000319584.11" ; Parent "ARID1B--AFDN^ARID1B^ENSG00000049618.24" ; exon_id "ENSE00002535311.1" ; exon_number 1 ; gene_id "ARID1B--AFDN^ARID1B^ENSG00000049618.24" ; gene_name ARID1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000015890.14" ; havana_transcript "OTTHUMT00000042830.3" ; hgnc_id "HGNC:18040" ; level 1 ; orig_coord_info "chr6,156901376,156901525,+" ; protein_id "ENSP00000313006.7" ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "ARID1B--AFDN^ENST00000319584.11" ; transcript_name "ARID1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ARID1B--AFDN HAVANA gene 78791 113692 . + . FI_gene_label "AFDN^ENSG00000130396.20" ; ID "ARID1B--AFDN^AFDN^ENSG00000130396.20" ; exon_id "ENSE00002039523.1" ; exon_number 1 ; gene_id "ARID1B--AFDN^AFDN^ENSG00000130396.20" ; gene_name AFDN ; gene_type protein_coding ; havana_gene "OTTHUMG00000016031.9" ; havana_transcript "OTTHUMT00000043149.2" ; hgnc_id "HGNC:7137" ; level 2 ; orig_coord_info "chr6,167827133,167827237,+" ; protein_id "ENSP00000341118.4" ; tag not_organism_supported basic ; transcript_id "ARID1B--AFDN^ENST00000344191.8" ; transcript_name "AFDN-201" ; transcript_support_level 5 ; transcript_type protein_coding
ARID1B--AFDN HAVANA mRNA 78791 113692 . + . FI_gene_label "AFDN^ENSG00000130396.20" ; ID "ARID1B--AFDN^ENST00000344191.8" ; Parent "ARID1B--AFDN^AFDN^ENSG00000130396.20" ; exon_id "ENSE00002039523.1" ; exon_number 1 ; gene_id "ARID1B--AFDN^AFDN^ENSG00000130396.20" ; gene_name AFDN ; gene_type protein_coding ; havana_gene "OTTHUMG00000016031.9" ; havana_transcript "OTTHUMT00000043149.2" ; hgnc_id "HGNC:7137" ; level 2 ; orig_coord_info "chr6,167827133,167827237,+" ; protein_id "ENSP00000341118.4" ; tag not_organism_supported basic ; transcript_id "ARID1B--AFDN^ENST00000344191.8" ; transcript_name "AFDN-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
BRPF1--ATG7 HAVANA gene 17136 52174 . + . FI_gene_label "ATG7^ENSG00000197548.12" ; ID "BRPF1--ATG7^ATG7^ENSG00000197548.12" ; ccdsid "CCDS2605.1" ; exon_id "ENSE00003638636.1" ; exon_number 2 ; gene_id "BRPF1--ATG7^ATG7^ENSG00000197548.12" ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21" ; havana_transcript "OTTHUMT00000251951.3" ; hgnc_id "HGNC:16935" ; level 2 ; orig_coord_info "chr3,11298696,11298855,+" ; protein_id "ENSP00000346437.3" ; tag basic appris_principal_1 CCDS ; transcript_id "BRPF1--ATG7^ENST00000354449.7" ; transcript_name "ATG7-201" ; transcript_support_level 1 ; transcript_type protein_coding
BRPF1--ATG7 HAVANA mRNA 17136 52174 . + . FI_gene_label "ATG7^ENSG00000197548.12" ; ID "BRPF1--ATG7^ENST00000354449.7" ; Parent "BRPF1--ATG7^ATG7^ENSG00000197548.12" ; ccdsid "CCDS2605.1" ; exon_id "ENSE00003638636.1" ; exon_number 2 ; gene_id "BRPF1--ATG7^ATG7^ENSG00000197548.12" ; gene_name ATG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129740.21" ; havana_transcript "OTTHUMT00000251951.3" ; hgnc_id "HGNC:16935" ; level 2 ; orig_coord_info "chr3,11298696,11298855,+" ; protein_id "ENSP00000346437.3" ; tag basic appris_principal_1 CCDS ; transcript_id "BRPF1--ATG7^ENST00000354449.7" ; transcript_name "ATG7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BRPF1--ATG7 HAVANA gene 1007 14028 . + . FI_gene_label "BRPF1^ENSG00000156983.16" ; ID "BRPF1--ATG7^BRPF1^ENSG00000156983.16" ; ccdsid "CCDS33692.1" ; exon_id "ENSE00001330625.4" ; exon_number 2 ; gene_id "BRPF1--ATG7^BRPF1^ENSG00000156983.16" ; gene_name BRPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097033.8" ; havana_transcript "OTTHUMT00000214130.3" ; hgnc_id "HGNC:14255" ; level 2 ; orig_coord_info "chr3,9734141,9734739,+" ; protein_id "ENSP00000373340.2" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "BRPF1--ATG7^ENST00000383829.7" ; transcript_name "BRPF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
BRPF1--ATG7 HAVANA mRNA 1007 14028 . + . FI_gene_label "BRPF1^ENSG00000156983.16" ; ID "BRPF1--ATG7^ENST00000383829.7" ; Parent "BRPF1--ATG7^BRPF1^ENSG00000156983.16" ; ccdsid "CCDS33692.1" ; exon_id "ENSE00001330625.4" ; exon_number 2 ; gene_id "BRPF1--ATG7^BRPF1^ENSG00000156983.16" ; gene_name BRPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097033.8" ; havana_transcript "OTTHUMT00000214130.3" ; hgnc_id "HGNC:14255" ; level 2 ; orig_coord_info "chr3,9734141,9734739,+" ; protein_id "ENSP00000373340.2" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "BRPF1--ATG7^ENST00000383829.7" ; transcript_name "BRPF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CCDC169--SOHLH2 HAVANA gene 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^ENST00000239859.8" ; Parent "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CCDC169--SOHLH2 HAVANA gene 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^ENST00000317764.6" ; Parent "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DHRS2--GSTM2 HAVANA gene 14174 20563 . + . FI_gene_label "GSTM2^ENSG00000213366.13" ; ID "DHRS2--GSTM2^GSTM2^ENSG00000213366.13" ; ccdsid "CCDS808.1" ; exon_id "ENSE00002597187.2" ; exon_number 1 ; gene_id "DHRS2--GSTM2^GSTM2^ENSG00000213366.13" ; gene_name GSTM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011638.8" ; havana_transcript "OTTHUMT00000032167.3" ; hgnc_id "HGNC:4634" ; level 2 ; orig_coord_info "chr1,109668116,109668151,+" ; protein_id "ENSP00000241337.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHRS2--GSTM2^ENST00000241337.9" ; transcript_name "GSTM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHRS2--GSTM2 HAVANA mRNA 14174 20563 . + . FI_gene_label "GSTM2^ENSG00000213366.13" ; ID "DHRS2--GSTM2^ENST00000241337.9" ; Parent "DHRS2--GSTM2^GSTM2^ENSG00000213366.13" ; ccdsid "CCDS808.1" ; exon_id "ENSE00002597187.2" ; exon_number 1 ; gene_id "DHRS2--GSTM2^GSTM2^ENSG00000213366.13" ; gene_name GSTM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011638.8" ; havana_transcript "OTTHUMT00000032167.3" ; hgnc_id "HGNC:4634" ; level 2 ; orig_coord_info "chr1,109668116,109668151,+" ; protein_id "ENSP00000241337.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHRS2--GSTM2^ENST00000241337.9" ; transcript_name "GSTM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DHRS2--GSTM2 HAVANA gene 2122 11138 . + . FI_gene_label "DHRS2^ENSG00000100867.15" ; ID "DHRS2--GSTM2^DHRS2^ENSG00000100867.15" ; ccdsid "CCDS9604.1" ; exon_id "ENSE00003512286.1" ; exon_number 2 ; gene_id "DHRS2--GSTM2^DHRS2^ENSG00000100867.15" ; gene_name DHRS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028771.5" ; havana_transcript "OTTHUMT00000071842.2" ; hgnc_id "HGNC:18349" ; level 2 ; orig_coord_info "chr14,23638865,23639004,+" ; protein_id "ENSP00000250383.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DHRS2--GSTM2^ENST00000250383.11" ; transcript_name "DHRS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHRS2--GSTM2 HAVANA mRNA 2122 11138 . + . FI_gene_label "DHRS2^ENSG00000100867.15" ; ID "DHRS2--GSTM2^ENST00000250383.11" ; Parent "DHRS2--GSTM2^DHRS2^ENSG00000100867.15" ; ccdsid "CCDS9604.1" ; exon_id "ENSE00003512286.1" ; exon_number 2 ; gene_id "DHRS2--GSTM2^DHRS2^ENSG00000100867.15" ; gene_name DHRS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000028771.5" ; havana_transcript "OTTHUMT00000071842.2" ; hgnc_id "HGNC:18349" ; level 2 ; orig_coord_info "chr14,23638865,23639004,+" ; protein_id "ENSP00000250383.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DHRS2--GSTM2^ENST00000250383.11" ; transcript_name "DHRS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1 HAVANA mRNA 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^ENST00000276326.9" ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HNRNPR--TCEA3 HAVANA gene 1053 18148 . + . FI_gene_label "HNRNPR^ENSG00000125944.21" ; ID "HNRNPR--TCEA3^HNRNPR^ENSG00000125944.21" ; ccdsid "CCDS232.1" ; exon_id "ENSE00003690057.1" ; exon_number 2 ; gene_id "HNRNPR--TCEA3^HNRNPR^ENSG00000125944.21" ; gene_name HNRNPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000003224.6" ; havana_transcript "OTTHUMT00000008887.2" ; hgnc_id "HGNC:5047" ; level 2 ; orig_coord_info "chr1,23340852,23341008,-" ; protein_id "ENSP00000304405.6" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "HNRNPR--TCEA3^ENST00000302271.11" ; transcript_name "HNRNPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
HNRNPR--TCEA3 HAVANA mRNA 1053 18148 . + . FI_gene_label "HNRNPR^ENSG00000125944.21" ; ID "HNRNPR--TCEA3^ENST00000302271.11" ; Parent "HNRNPR--TCEA3^HNRNPR^ENSG00000125944.21" ; ccdsid "CCDS232.1" ; exon_id "ENSE00003690057.1" ; exon_number 2 ; gene_id "HNRNPR--TCEA3^HNRNPR^ENSG00000125944.21" ; gene_name HNRNPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000003224.6" ; havana_transcript "OTTHUMT00000008887.2" ; hgnc_id "HGNC:5047" ; level 2 ; orig_coord_info "chr1,23340852,23341008,-" ; protein_id "ENSP00000304405.6" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "HNRNPR--TCEA3^ENST00000302271.11" ; transcript_name "HNRNPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HNRNPR--TCEA3 HAVANA gene 22107 28234 . + . FI_gene_label "TCEA3^ENSG00000204219.11" ; ID "HNRNPR--TCEA3^TCEA3^ENSG00000204219.11" ; exon_id "ENSE00001463953.2" ; exon_number 1 ; gene_id "HNRNPR--TCEA3^TCEA3^ENSG00000204219.11" ; gene_name TCEA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003233.6" ; havana_transcript "OTTHUMT00000470075.1" ; hgnc_id "HGNC:11615" ; level 2 ; orig_coord_info "chr1,23424565,23424633,-" ; protein_id "ENSP00000363729.3" ; tag basic ; transcript_id "HNRNPR--TCEA3^ENST00000374601.7" ; transcript_name "TCEA3-201" ; transcript_support_level 1 ; transcript_type protein_coding
HNRNPR--TCEA3 HAVANA mRNA 22107 28234 . + . FI_gene_label "TCEA3^ENSG00000204219.11" ; ID "HNRNPR--TCEA3^ENST00000374601.7" ; Parent "HNRNPR--TCEA3^TCEA3^ENSG00000204219.11" ; exon_id "ENSE00001463953.2" ; exon_number 1 ; gene_id "HNRNPR--TCEA3^TCEA3^ENSG00000204219.11" ; gene_name TCEA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003233.6" ; havana_transcript "OTTHUMT00000470075.1" ; hgnc_id "HGNC:11615" ; level 2 ; orig_coord_info "chr1,23424565,23424633,-" ; protein_id "ENSP00000363729.3" ; tag basic ; transcript_id "HNRNPR--TCEA3^ENST00000374601.7" ; transcript_name "TCEA3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP4K3--CRHR2 HAVANA gene 1017 37121 . + . FI_gene_label "MAP4K3^ENSG00000011566.15" ; ID "MAP4K3--CRHR2^MAP4K3^ENSG00000011566.15" ; ccdsid "CCDS1803.1" ; exon_id "ENSE00001922471.2" ; exon_number 1 ; gene_id "MAP4K3--CRHR2^MAP4K3^ENSG00000011566.15" ; gene_name MAP4K3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000102127.5" ; havana_transcript "OTTHUMT00000219966.3" ; hgnc_id "HGNC:6865" ; level 2 ; orig_coord_info "chr2,39436892,39436987,-" ; protein_id "ENSP00000263881.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP4K3--CRHR2^ENST00000263881.8" ; transcript_name "MAP4K3-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP4K3--CRHR2 HAVANA mRNA 1017 37121 . + . FI_gene_label "MAP4K3^ENSG00000011566.15" ; ID "MAP4K3--CRHR2^ENST00000263881.8" ; Parent "MAP4K3--CRHR2^MAP4K3^ENSG00000011566.15" ; ccdsid "CCDS1803.1" ; exon_id "ENSE00001922471.2" ; exon_number 1 ; gene_id "MAP4K3--CRHR2^MAP4K3^ENSG00000011566.15" ; gene_name MAP4K3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000102127.5" ; havana_transcript "OTTHUMT00000219966.3" ; hgnc_id "HGNC:6865" ; level 2 ; orig_coord_info "chr2,39436892,39436987,-" ; protein_id "ENSP00000263881.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP4K3--CRHR2^ENST00000263881.8" ; transcript_name "MAP4K3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP4K3--CRHR2 ENSEMBL gene 40148 55010 . + . FI_gene_label "CRHR2^ENSG00000106113.19" ; ID "MAP4K3--CRHR2^CRHR2^ENSG00000106113.19" ; ccdsid "CCDS56477.1" ; exon_id "ENSE00001372886.4" ; exon_number 3 ; gene_id "MAP4K3--CRHR2^CRHR2^ENSG00000106113.19" ; gene_name CRHR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023218.6" ; hgnc_id "HGNC:2358" ; level 3 ; orig_coord_info "chr7,30686389,30686449,-" ; protein_id "ENSP00000344304.4" ; tag basic CCDS ; transcript_id "MAP4K3--CRHR2^ENST00000341843.8" ; transcript_name "CRHR2-201" ; transcript_support_level 5 ; transcript_type protein_coding
MAP4K3--CRHR2 ENSEMBL mRNA 40148 55010 . + . FI_gene_label "CRHR2^ENSG00000106113.19" ; ID "MAP4K3--CRHR2^ENST00000341843.8" ; Parent "MAP4K3--CRHR2^CRHR2^ENSG00000106113.19" ; ccdsid "CCDS56477.1" ; exon_id "ENSE00001372886.4" ; exon_number 3 ; gene_id "MAP4K3--CRHR2^CRHR2^ENSG00000106113.19" ; gene_name CRHR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023218.6" ; hgnc_id "HGNC:2358" ; level 3 ; orig_coord_info "chr7,30686389,30686449,-" ; protein_id "ENSP00000344304.4" ; tag basic CCDS ; transcript_id "MAP4K3--CRHR2^ENST00000341843.8" ; transcript_name "CRHR2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SLBP--LETM1 HAVANA gene 11305 33090 . + . FI_gene_label "LETM1^ENSG00000168924.15" ; ID "SLBP--LETM1^LETM1^ENSG00000168924.15" ; ccdsid "CCDS3355.1" ; exon_id "ENSE00001164778.2" ; exon_number 1 ; gene_id "SLBP--LETM1^LETM1^ENSG00000168924.15" ; gene_name LETM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121149.5" ; havana_transcript "OTTHUMT00000241634.2" ; hgnc_id "HGNC:6556" ; level 2 ; orig_coord_info "chr4,1855869,1855950,-" ; protein_id "ENSP00000305653.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLBP--LETM1^ENST00000302787.3" ; transcript_name "LETM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLBP--LETM1 HAVANA mRNA 11305 33090 . + . FI_gene_label "LETM1^ENSG00000168924.15" ; ID "SLBP--LETM1^ENST00000302787.3" ; Parent "SLBP--LETM1^LETM1^ENSG00000168924.15" ; ccdsid "CCDS3355.1" ; exon_id "ENSE00001164778.2" ; exon_number 1 ; gene_id "SLBP--LETM1^LETM1^ENSG00000168924.15" ; gene_name LETM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121149.5" ; havana_transcript "OTTHUMT00000241634.2" ; hgnc_id "HGNC:6556" ; level 2 ; orig_coord_info "chr4,1855869,1855950,-" ; protein_id "ENSP00000305653.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLBP--LETM1^ENST00000302787.3" ; transcript_name "LETM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLBP--LETM1 HAVANA gene 1095 8177 . + . FI_gene_label "SLBP^ENSG00000163950.13" ; ID "SLBP--LETM1^SLBP^ENSG00000163950.13" ; exon_id "ENSE00001888468.1" ; exon_number 1 ; gene_id "SLBP--LETM1^SLBP^ENSG00000163950.13" ; gene_name SLBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000089349.7" ; havana_transcript "OTTHUMT00000357833.1" ; hgnc_id "HGNC:10904" ; level 2 ; orig_coord_info "chr4,1712130,1712188,-" ; protein_id "ENSP00000316490.4" ; tag basic appris_alternative_2 ; transcript_id "SLBP--LETM1^ENST00000318386.8" ; transcript_name "SLBP-201" ; transcript_support_level 3 ; transcript_type protein_coding
SLBP--LETM1 HAVANA mRNA 1095 8177 . + . FI_gene_label "SLBP^ENSG00000163950.13" ; ID "SLBP--LETM1^ENST00000318386.8" ; Parent "SLBP--LETM1^SLBP^ENSG00000163950.13" ; exon_id "ENSE00001888468.1" ; exon_number 1 ; gene_id "SLBP--LETM1^SLBP^ENSG00000163950.13" ; gene_name SLBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000089349.7" ; havana_transcript "OTTHUMT00000357833.1" ; hgnc_id "HGNC:10904" ; level 2 ; orig_coord_info "chr4,1712130,1712188,-" ; protein_id "ENSP00000316490.4" ; tag basic appris_alternative_2 ; transcript_id "SLBP--LETM1^ENST00000318386.8" ; transcript_name "SLBP-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
SLBP--NSD2 HAVANA gene 14324 54755 . + . FI_gene_label "NSD2^ENSG00000109685.19" ; ID "SLBP--NSD2^NSD2^ENSG00000109685.19" ; ccdsid "CCDS3356.1" ; exon_id "ENSE00003801156.1" ; exon_number 4 ; gene_id "SLBP--NSD2^NSD2^ENSG00000109685.19" ; gene_name NSD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121147.15" ; havana_transcript "OTTHUMT00000366268.1" ; hgnc_id "HGNC:12766" ; level 2 ; orig_coord_info "chr4,1900655,1901251,+" ; protein_id "ENSP00000308780.6" ; tag CCDS ; transcript_id "SLBP--NSD2^ENST00000312087.10" ; transcript_name "NSD2-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
SLBP--NSD2 HAVANA mRNA 14324 54755 . + . FI_gene_label "NSD2^ENSG00000109685.19" ; ID "SLBP--NSD2^ENST00000312087.10" ; Parent "SLBP--NSD2^NSD2^ENSG00000109685.19" ; ccdsid "CCDS3356.1" ; exon_id "ENSE00003801156.1" ; exon_number 4 ; gene_id "SLBP--NSD2^NSD2^ENSG00000109685.19" ; gene_name NSD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121147.15" ; havana_transcript "OTTHUMT00000366268.1" ; hgnc_id "HGNC:12766" ; level 2 ; orig_coord_info "chr4,1900655,1901251,+" ; protein_id "ENSP00000308780.6" ; tag CCDS ; transcript_id "SLBP--NSD2^ENST00000312087.10" ; transcript_name "NSD2-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
SLBP--NSD2 HAVANA gene 1095 8177 . + . FI_gene_label "SLBP^ENSG00000163950.13" ; ID "SLBP--NSD2^SLBP^ENSG00000163950.13" ; exon_id "ENSE00001888468.1" ; exon_number 1 ; gene_id "SLBP--NSD2^SLBP^ENSG00000163950.13" ; gene_name SLBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000089349.7" ; havana_transcript "OTTHUMT00000357833.1" ; hgnc_id "HGNC:10904" ; level 2 ; orig_coord_info "chr4,1712130,1712188,-" ; protein_id "ENSP00000316490.4" ; tag basic appris_alternative_2 ; transcript_id "SLBP--NSD2^ENST00000318386.8" ; transcript_name "SLBP-201" ; transcript_support_level 3 ; transcript_type protein_coding
SLBP--NSD2 HAVANA mRNA 1095 8177 . + . FI_gene_label "SLBP^ENSG00000163950.13" ; ID "SLBP--NSD2^ENST00000318386.8" ; Parent "SLBP--NSD2^SLBP^ENSG00000163950.13" ; exon_id "ENSE00001888468.1" ; exon_number 1 ; gene_id "SLBP--NSD2^SLBP^ENSG00000163950.13" ; gene_name SLBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000089349.7" ; havana_transcript "OTTHUMT00000357833.1" ; hgnc_id "HGNC:10904" ; level 2 ; orig_coord_info "chr4,1712130,1712188,-" ; protein_id "ENSP00000316490.4" ; tag basic appris_alternative_2 ; transcript_id "SLBP--NSD2^ENST00000318386.8" ; transcript_name "SLBP-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
SPPL2B--PSPN HAVANA gene 23548 24103 . + . FI_gene_label "PSPN^ENSG00000125650.4" ; ID "SPPL2B--PSPN^PSPN^ENSG00000125650.4" ; ccdsid "CCDS12164.1" ; exon_id "ENSE00000666075.1" ; exon_number 1 ; gene_id "SPPL2B--PSPN^PSPN^ENSG00000125650.4" ; gene_name PSPN ; gene_type protein_coding ; havana_gene "OTTHUMG00000168086.3" ; havana_transcript "OTTHUMT00000398032.2" ; hgnc_id "HGNC:9579" ; level 2 ; orig_coord_info "chr19,6375702,6375849,-" ; protein_id "ENSP00000245810.1" ; tag basic appris_principal_1 CCDS ; transcript_id "SPPL2B--PSPN^ENST00000245810.1" ; transcript_name "PSPN-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPPL2B--PSPN HAVANA mRNA 23548 24103 . + . FI_gene_label "PSPN^ENSG00000125650.4" ; ID "SPPL2B--PSPN^ENST00000245810.1" ; Parent "SPPL2B--PSPN^PSPN^ENSG00000125650.4" ; ccdsid "CCDS12164.1" ; exon_id "ENSE00000666075.1" ; exon_number 1 ; gene_id "SPPL2B--PSPN^PSPN^ENSG00000125650.4" ; gene_name PSPN ; gene_type protein_coding ; havana_gene "OTTHUMG00000168086.3" ; havana_transcript "OTTHUMT00000398032.2" ; hgnc_id "HGNC:9579" ; level 2 ; orig_coord_info "chr19,6375702,6375849,-" ; protein_id "ENSP00000245810.1" ; tag basic appris_principal_1 CCDS ; transcript_id "SPPL2B--PSPN^ENST00000245810.1" ; transcript_name "PSPN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPPL2B--PSPN HAVANA gene 1045 5116 . + . FI_gene_label "SPPL2B^ENSG00000005206.17" ; ID "SPPL2B--PSPN^SPPL2B^ENSG00000005206.17" ; exon_id "ENSE00002951294.1" ; exon_number 1 ; gene_id "SPPL2B--PSPN^SPPL2B^ENSG00000005206.17" ; gene_name SPPL2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000180443.10" ; havana_transcript "OTTHUMT00000451379.2" ; hgnc_id "HGNC:30627" ; level 2 ; orig_coord_info "chr19,2328710,2328775,+" ; protein_id "ENSP00000480311.1" ; transcript_id "SPPL2B--PSPN^ENST00000586332.5" ; transcript_name "SPPL2B-203" ; transcript_support_level 3 ; transcript_type nonsense_mediated_decay
SPPL2B--PSPN HAVANA mRNA 1045 5116 . + . FI_gene_label "SPPL2B^ENSG00000005206.17" ; ID "SPPL2B--PSPN^ENST00000586332.5" ; Parent "SPPL2B--PSPN^SPPL2B^ENSG00000005206.17" ; exon_id "ENSE00002951294.1" ; exon_number 1 ; gene_id "SPPL2B--PSPN^SPPL2B^ENSG00000005206.17" ; gene_name SPPL2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000180443.10" ; havana_transcript "OTTHUMT00000451379.2" ; hgnc_id "HGNC:30627" ; level 2 ; orig_coord_info "chr19,2328710,2328775,+" ; protein_id "ENSP00000480311.1" ; transcript_id "SPPL2B--PSPN^ENST00000586332.5" ; transcript_name "SPPL2B-203" ; transcript_support_level 3 ; transcript_type nonsense_mediated_decay
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:
TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; 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:
VOPP1--TNS3 HAVANA gene 1487 20610 . + . FI_gene_label "VOPP1^ENSG00000154978.13" ; ID "VOPP1--TNS3^VOPP1^ENSG00000154978.13" ; ccdsid "CCDS47588.1" ; exon_id "ENSE00001122599.5" ; exon_number 1 ; gene_id "VOPP1--TNS3^VOPP1^ENSG00000154978.13" ; gene_name VOPP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156124.5" ; havana_transcript "OTTHUMT00000343074.2" ; hgnc_id "HGNC:34518" ; level 2 ; orig_coord_info "chr7,55572271,55572324,-" ; protein_id "ENSP00000285279.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VOPP1--TNS3^ENST00000285279.10" ; transcript_name "VOPP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
VOPP1--TNS3 HAVANA mRNA 1487 20610 . + . FI_gene_label "VOPP1^ENSG00000154978.13" ; ID "VOPP1--TNS3^ENST00000285279.10" ; Parent "VOPP1--TNS3^VOPP1^ENSG00000154978.13" ; ccdsid "CCDS47588.1" ; exon_id "ENSE00001122599.5" ; exon_number 1 ; gene_id "VOPP1--TNS3^VOPP1^ENSG00000154978.13" ; gene_name VOPP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156124.5" ; havana_transcript "OTTHUMT00000343074.2" ; hgnc_id "HGNC:34518" ; level 2 ; orig_coord_info "chr7,55572271,55572324,-" ; protein_id "ENSP00000285279.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VOPP1--TNS3^ENST00000285279.10" ; transcript_name "VOPP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VOPP1--TNS3 HAVANA gene 25177 69356 . + . FI_gene_label "TNS3^ENSG00000136205.17" ; ID "VOPP1--TNS3^TNS3^ENSG00000136205.17" ; ccdsid "CCDS5506.2" ; exon_id "ENSE00003480523.1" ; exon_number 6 ; gene_id "VOPP1--TNS3^TNS3^ENSG00000136205.17" ; gene_name TNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074075.4" ; havana_transcript "OTTHUMT00000157253.2" ; hgnc_id "HGNC:21616" ; level 2 ; orig_coord_info "chr7,47439487,47439636,-" ; protein_id "ENSP00000312143.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VOPP1--TNS3^ENST00000311160.14" ; transcript_name "TNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
VOPP1--TNS3 HAVANA mRNA 25177 69356 . + . FI_gene_label "TNS3^ENSG00000136205.17" ; ID "VOPP1--TNS3^ENST00000311160.14" ; Parent "VOPP1--TNS3^TNS3^ENSG00000136205.17" ; ccdsid "CCDS5506.2" ; exon_id "ENSE00003480523.1" ; exon_number 6 ; gene_id "VOPP1--TNS3^TNS3^ENSG00000136205.17" ; gene_name TNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074075.4" ; havana_transcript "OTTHUMT00000157253.2" ; hgnc_id "HGNC:21616" ; level 2 ; orig_coord_info "chr7,47439487,47439636,-" ; protein_id "ENSP00000312143.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VOPP1--TNS3^ENST00000311160.14" ; transcript_name "TNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWTR1--AC079841.2 HAVANA gene 10616 24379 . + . FI_gene_label "WWTR1^ENSG00000018408.15" ; ID "WWTR1--AC079841.2^WWTR1^ENSG00000018408.15" ; ccdsid "CCDS3144.1" ; exon_id "ENSE00001078038.4" ; exon_number 2 ; gene_id "WWTR1--AC079841.2^WWTR1^ENSG00000018408.15" ; gene_name WWTR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159614.13" ; havana_transcript "OTTHUMT00000356501.1" ; hgnc_id "HGNC:24042" ; level 2 ; orig_coord_info "chr3,149656876,149657306,-" ; protein_id "ENSP00000353847.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWTR1--AC079841.2^ENST00000360632.8" ; transcript_name "WWTR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWTR1--AC079841.2 HAVANA mRNA 10616 24379 . + . FI_gene_label "WWTR1^ENSG00000018408.15" ; ID "WWTR1--AC079841.2^ENST00000360632.8" ; Parent "WWTR1--AC079841.2^WWTR1^ENSG00000018408.15" ; ccdsid "CCDS3144.1" ; exon_id "ENSE00001078038.4" ; exon_number 2 ; gene_id "WWTR1--AC079841.2^WWTR1^ENSG00000018408.15" ; gene_name WWTR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159614.13" ; havana_transcript "OTTHUMT00000356501.1" ; hgnc_id "HGNC:24042" ; level 2 ; orig_coord_info "chr3,149656876,149657306,-" ; protein_id "ENSP00000353847.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWTR1--AC079841.2^ENST00000360632.8" ; transcript_name "WWTR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC005993.1--RGS6 HAVANA gene 1001 4837 . + . FI_gene_label "AC005993.1^ENSG00000266869.2" ; ID "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; exon_id "ENSE00002516676.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; gene_name "AC005993.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179238.4" ; havana_transcript "OTTHUMT00000445384.1" ; level 2 ; orig_coord_info "chr14,71848606,71848736,+" ; transcript_id "AC005993.1--RGS6^ENST00000555581.1" ; transcript_name "AC005993.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
AC005993.1--RGS6 HAVANA RNA 1001 4837 . + . FI_gene_label "AC005993.1^ENSG00000266869.2" ; ID "AC005993.1--RGS6^ENST00000555581.1" ; Parent "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; exon_id "ENSE00002516676.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; gene_name "AC005993.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179238.4" ; havana_transcript "OTTHUMT00000445384.1" ; level 2 ; orig_coord_info "chr14,71848606,71848736,+" ; transcript_id "AC005993.1--RGS6^ENST00000555581.1" ; transcript_name "AC005993.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
AP000347.1--IGLL1 HAVANA gene 8244 18675 . + . FI_gene_label "AP000347.1^ENSG00000272578.5" ; ID "AP000347.1--IGLL1^AP000347.1^ENSG00000272578.5" ; exon_id "ENSE00001748689.1" ; exon_number 1 ; gene_id "AP000347.1--IGLL1^AP000347.1^ENSG00000272578.5" ; gene_name "AP000347.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000186353.2" ; havana_transcript "OTTHUMT00000471975.1" ; level 2 ; orig_coord_info "chr22,23690232,23693185,-" ; tag basic ; transcript_id "AP000347.1--IGLL1^ENST00000417194.5" ; transcript_name "AP000347.1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
AP000347.1--IGLL1 HAVANA RNA 8244 18675 . + . FI_gene_label "AP000347.1^ENSG00000272578.5" ; ID "AP000347.1--IGLL1^ENST00000417194.5" ; Parent "AP000347.1--IGLL1^AP000347.1^ENSG00000272578.5" ; exon_id "ENSE00001748689.1" ; exon_number 1 ; gene_id "AP000347.1--IGLL1^AP000347.1^ENSG00000272578.5" ; gene_name "AP000347.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000186353.2" ; havana_transcript "OTTHUMT00000471975.1" ; level 2 ; orig_coord_info "chr22,23690232,23693185,-" ; tag basic ; transcript_id "AP000347.1--IGLL1^ENST00000417194.5" ; transcript_name "AP000347.1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1 HAVANA RNA 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^ENST00000624936.2" ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
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:
WWTR1--AC079841.2 HAVANA gene 27380 30425 . + . FI_gene_label "AC079841.2^ENSG00000287022.1" ; ID "WWTR1--AC079841.2^AC079841.2^ENSG00000287022.1" ; exon_id "ENSE00003857933.1" ; exon_number 1 ; gene_id "WWTR1--AC079841.2^AC079841.2^ENSG00000287022.1" ; gene_name "AC079841.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195424.1" ; havana_transcript "OTTHUMT00000526845.1" ; level 2 ; orig_coord_info "chr3,121430389,121431198,-" ; tag basic TAGENE ; transcript_id "WWTR1--AC079841.2^ENST00000666486.1" ; transcript_name "AC079841.2-201" ; transcript_type lncRNA
WWTR1--AC079841.2 HAVANA RNA 27380 30425 . + . FI_gene_label "AC079841.2^ENSG00000287022.1" ; ID "WWTR1--AC079841.2^ENST00000666486.1" ; Parent "WWTR1--AC079841.2^AC079841.2^ENSG00000287022.1" ; exon_id "ENSE00003857933.1" ; exon_number 1 ; gene_id "WWTR1--AC079841.2^AC079841.2^ENSG00000287022.1" ; gene_name "AC079841.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195424.1" ; havana_transcript "OTTHUMT00000526845.1" ; level 2 ; orig_coord_info "chr3,121430389,121431198,-" ; tag basic TAGENE ; transcript_id "WWTR1--AC079841.2^ENST00000666486.1" ; transcript_name "AC079841.2-201" ; transcript_type lncRNA
419 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 ------------------------------
789 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 33 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