Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d789ec62ffe21d4e42264d120e8118/fi_workdir/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/da54280d9649deb25f891d82b036d6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/da54280d9649deb25f891d82b036d6/.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: 7025
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 7025
=> 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:7025
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 1 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
AL031767.1--MBOAT1 HAVANA gene 4887 21211 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "AL031767.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "AL031767.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL031767.1--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AL031767.1--MBOAT1 HAVANA mRNA 4887 21211 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "AL031767.1--MBOAT1^ENST00000324607.8" ; Parent "AL031767.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "AL031767.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL031767.1--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AL451080.1--MBOAT1 HAVANA gene 5501 21825 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "AL451080.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "AL451080.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL451080.1--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AL451080.1--MBOAT1 HAVANA mRNA 5501 21825 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "AL451080.1--MBOAT1^ENST00000324607.8" ; Parent "AL451080.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "AL451080.1--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL451080.1--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BIRC6--PKD1L2 ENSEMBL gene 87220 109031 . + . FI_gene_label "PKD1L2^ENSG00000166473.17" ; ID "BIRC6--PKD1L2^PKD1L2^ENSG00000166473.17" ; exon_id "ENSE00003630958.1" ; exon_number 1 ; gene_id "BIRC6--PKD1L2^PKD1L2^ENSG00000166473.17" ; gene_name PKD1L2 ; gene_type polymorphic_pseudogene ; havana_gene "OTTHUMG00000166126.5" ; hgnc_id "HGNC:21715" ; level 3 ; orig_coord_info "chr16,81220070,81220370,-" ; protein_id "ENSP00000337397.4" ; tag basic appris_principal_1 ; transcript_id "BIRC6--PKD1L2^ENST00000337114.8" ; transcript_name "PKD1L2-202" ; transcript_support_level 5 ; transcript_type protein_coding
BIRC6--PKD1L2 ENSEMBL mRNA 87220 109031 . + . FI_gene_label "PKD1L2^ENSG00000166473.17" ; ID "BIRC6--PKD1L2^ENST00000337114.8" ; Parent "BIRC6--PKD1L2^PKD1L2^ENSG00000166473.17" ; exon_id "ENSE00003630958.1" ; exon_number 1 ; gene_id "BIRC6--PKD1L2^PKD1L2^ENSG00000166473.17" ; gene_name PKD1L2 ; gene_type polymorphic_pseudogene ; havana_gene "OTTHUMG00000166126.5" ; hgnc_id "HGNC:21715" ; level 3 ; orig_coord_info "chr16,81220070,81220370,-" ; protein_id "ENSP00000337397.4" ; tag basic appris_principal_1 ; transcript_id "BIRC6--PKD1L2^ENST00000337114.8" ; transcript_name "PKD1L2-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
BIRC6--PKD1L2 HAVANA gene 1001 84219 . + . FI_gene_label "BIRC6^ENSG00000115760.14" ; ID "BIRC6--PKD1L2^BIRC6^ENSG00000115760.14" ; ccdsid "CCDS33175.2" ; exon_id "ENSE00000743520.4" ; exon_number 1 ; gene_id "BIRC6--PKD1L2^BIRC6^ENSG00000115760.14" ; gene_name BIRC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150528.8" ; havana_transcript "OTTHUMT00000318769.4" ; hgnc_id "HGNC:13516" ; level 2 ; orig_coord_info "chr2,32357162,32357486,+" ; protein_id "ENSP00000393596.2" ; tag basic appris_principal_1 CCDS ; transcript_id "BIRC6--PKD1L2^ENST00000421745.6" ; transcript_name "BIRC6-201" ; transcript_support_level 1 ; transcript_type protein_coding
BIRC6--PKD1L2 HAVANA mRNA 1001 84219 . + . FI_gene_label "BIRC6^ENSG00000115760.14" ; ID "BIRC6--PKD1L2^ENST00000421745.6" ; Parent "BIRC6--PKD1L2^BIRC6^ENSG00000115760.14" ; ccdsid "CCDS33175.2" ; exon_id "ENSE00000743520.4" ; exon_number 1 ; gene_id "BIRC6--PKD1L2^BIRC6^ENSG00000115760.14" ; gene_name BIRC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150528.8" ; havana_transcript "OTTHUMT00000318769.4" ; hgnc_id "HGNC:13516" ; level 2 ; orig_coord_info "chr2,32357162,32357486,+" ; protein_id "ENSP00000393596.2" ; tag basic appris_principal_1 CCDS ; transcript_id "BIRC6--PKD1L2^ENST00000421745.6" ; transcript_name "BIRC6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BLACE--PKD1L2 ENSEMBL gene 10494 32305 . + . FI_gene_label "PKD1L2^ENSG00000166473.17" ; ID "BLACE--PKD1L2^PKD1L2^ENSG00000166473.17" ; exon_id "ENSE00003630958.1" ; exon_number 1 ; gene_id "BLACE--PKD1L2^PKD1L2^ENSG00000166473.17" ; gene_name PKD1L2 ; gene_type polymorphic_pseudogene ; havana_gene "OTTHUMG00000166126.5" ; hgnc_id "HGNC:21715" ; level 3 ; orig_coord_info "chr16,81220070,81220370,-" ; protein_id "ENSP00000337397.4" ; tag basic appris_principal_1 ; transcript_id "BLACE--PKD1L2^ENST00000337114.8" ; transcript_name "PKD1L2-202" ; transcript_support_level 5 ; transcript_type protein_coding
BLACE--PKD1L2 ENSEMBL mRNA 10494 32305 . + . FI_gene_label "PKD1L2^ENSG00000166473.17" ; ID "BLACE--PKD1L2^ENST00000337114.8" ; Parent "BLACE--PKD1L2^PKD1L2^ENSG00000166473.17" ; exon_id "ENSE00003630958.1" ; exon_number 1 ; gene_id "BLACE--PKD1L2^PKD1L2^ENSG00000166473.17" ; gene_name PKD1L2 ; gene_type polymorphic_pseudogene ; havana_gene "OTTHUMG00000166126.5" ; hgnc_id "HGNC:21715" ; level 3 ; orig_coord_info "chr16,81220070,81220370,-" ; protein_id "ENSP00000337397.4" ; tag basic appris_principal_1 ; transcript_id "BLACE--PKD1L2^ENST00000337114.8" ; transcript_name "PKD1L2-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CDKAL1--LNC-LBCS HAVANA gene 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--LNC-LBCS^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--LNC-LBCS^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--LNC-LBCS^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDKAL1--LNC-LBCS HAVANA mRNA 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--LNC-LBCS^ENST00000274695.8" ; Parent "CDKAL1--LNC-LBCS^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--LNC-LBCS^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--LNC-LBCS^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COP1--TRAPPC9 HAVANA gene 1309 25254 . + . FI_gene_label "COP1^ENSG00000143207.21" ; ID "COP1--TRAPPC9^COP1^ENSG00000143207.21" ; ccdsid "CCDS44279.1" ; exon_id "ENSE00002179931.1" ; exon_number 1 ; gene_id "COP1--TRAPPC9^COP1^ENSG00000143207.21" ; gene_name COP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034986.7" ; havana_transcript "OTTHUMT00000393314.2" ; hgnc_id "HGNC:17440" ; level 2 ; orig_coord_info "chr1,176206572,176206978,-" ; protein_id "ENSP00000310943.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "COP1--TRAPPC9^ENST00000308769.12" ; transcript_name "COP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
COP1--TRAPPC9 HAVANA mRNA 1309 25254 . + . FI_gene_label "COP1^ENSG00000143207.21" ; ID "COP1--TRAPPC9^ENST00000308769.12" ; Parent "COP1--TRAPPC9^COP1^ENSG00000143207.21" ; ccdsid "CCDS44279.1" ; exon_id "ENSE00002179931.1" ; exon_number 1 ; gene_id "COP1--TRAPPC9^COP1^ENSG00000143207.21" ; gene_name COP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034986.7" ; havana_transcript "OTTHUMT00000393314.2" ; hgnc_id "HGNC:17440" ; level 2 ; orig_coord_info "chr1,176206572,176206978,-" ; protein_id "ENSP00000310943.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "COP1--TRAPPC9^ENST00000308769.12" ; transcript_name "COP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COP1--TRAPPC9 HAVANA gene 29412 70517 . + . FI_gene_label "TRAPPC9^ENSG00000167632.18" ; ID "COP1--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; ccdsid "CCDS55278.1" ; exon_id "ENSE00003610885.1" ; exon_number 2 ; gene_id "COP1--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10" ; havana_transcript "OTTHUMT00000497841.1" ; hgnc_id "HGNC:30832" ; level 2 ; orig_coord_info "chr8,140450790,140451373,-" ; protein_id "ENSP00000405060.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "COP1--TRAPPC9^ENST00000438773.4" ; transcript_name "TRAPPC9-201" ; transcript_support_level 1 ; transcript_type protein_coding
COP1--TRAPPC9 HAVANA mRNA 29412 70517 . + . FI_gene_label "TRAPPC9^ENSG00000167632.18" ; ID "COP1--TRAPPC9^ENST00000438773.4" ; Parent "COP1--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; ccdsid "CCDS55278.1" ; exon_id "ENSE00003610885.1" ; exon_number 2 ; gene_id "COP1--TRAPPC9^TRAPPC9^ENSG00000167632.18" ; gene_name TRAPPC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164187.10" ; havana_transcript "OTTHUMT00000497841.1" ; hgnc_id "HGNC:30832" ; level 2 ; orig_coord_info "chr8,140450790,140451373,-" ; protein_id "ENSP00000405060.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "COP1--TRAPPC9^ENST00000438773.4" ; transcript_name "TRAPPC9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COX16--MIDEAS ENSEMBL gene 13697 34596 . + . FI_gene_label "MIDEAS^ENSG00000156030.13" ; ID "COX16--MIDEAS^MIDEAS^ENSG00000156030.13" ; ccdsid "CCDS9819.1" ; exon_id "ENSE00001382111.1" ; exon_number 2 ; gene_id "COX16--MIDEAS^MIDEAS^ENSG00000156030.13" ; gene_name MIDEAS ; gene_type protein_coding ; havana_gene "OTTHUMG00000150359.3" ; hgnc_id "HGNC:19853" ; level 3 ; orig_coord_info "chr14,73738560,73740008,-" ; protein_id "ENSP00000286523.5" ; tag basic CCDS ; transcript_id "COX16--MIDEAS^ENST00000286523.9" ; transcript_name "MIDEAS-201" ; transcript_support_level 1 ; transcript_type protein_coding
COX16--MIDEAS ENSEMBL mRNA 13697 34596 . + . FI_gene_label "MIDEAS^ENSG00000156030.13" ; ID "COX16--MIDEAS^ENST00000286523.9" ; Parent "COX16--MIDEAS^MIDEAS^ENSG00000156030.13" ; ccdsid "CCDS9819.1" ; exon_id "ENSE00001382111.1" ; exon_number 2 ; gene_id "COX16--MIDEAS^MIDEAS^ENSG00000156030.13" ; gene_name MIDEAS ; gene_type protein_coding ; havana_gene "OTTHUMG00000150359.3" ; hgnc_id "HGNC:19853" ; level 3 ; orig_coord_info "chr14,73738560,73740008,-" ; protein_id "ENSP00000286523.5" ; tag basic CCDS ; transcript_id "COX16--MIDEAS^ENST00000286523.9" ; transcript_name "MIDEAS-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COX16--MIDEAS HAVANA gene 2103 8078 . + . FI_gene_label "COX16^ENSG00000133983.16" ; ID "COX16--MIDEAS^COX16^ENSG00000133983.16" ; ccdsid "CCDS9802.1" ; exon_id "ENSE00001518105.5" ; exon_number 1 ; gene_id "COX16--MIDEAS^COX16^ENSG00000133983.16" ; gene_name COX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171238.5" ; havana_transcript "OTTHUMT00000412470.3" ; hgnc_id "HGNC:20213" ; level 2 ; orig_coord_info "chr14,70359519,70359587,-" ; protein_id "ENSP00000374562.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX16--MIDEAS^ENST00000389912.7" ; transcript_name "COX16-201" ; transcript_support_level 1 ; transcript_type protein_coding
COX16--MIDEAS HAVANA mRNA 2103 8078 . + . FI_gene_label "COX16^ENSG00000133983.16" ; ID "COX16--MIDEAS^ENST00000389912.7" ; Parent "COX16--MIDEAS^COX16^ENSG00000133983.16" ; ccdsid "CCDS9802.1" ; exon_id "ENSE00001518105.5" ; exon_number 1 ; gene_id "COX16--MIDEAS^COX16^ENSG00000133983.16" ; gene_name COX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171238.5" ; havana_transcript "OTTHUMT00000412470.3" ; hgnc_id "HGNC:20213" ; level 2 ; orig_coord_info "chr14,70359519,70359587,-" ; protein_id "ENSP00000374562.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX16--MIDEAS^ENST00000389912.7" ; transcript_name "COX16-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DYRK1A--OSER1 HAVANA gene 50904 57291 . + . FI_gene_label "OSER1^ENSG00000132823.11" ; ID "DYRK1A--OSER1^OSER1^ENSG00000132823.11" ; ccdsid "CCDS13327.1" ; exon_id "ENSE00000906877.1" ; exon_number 2 ; gene_id "DYRK1A--OSER1^OSER1^ENSG00000132823.11" ; gene_name OSER1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032518.3" ; havana_transcript "OTTHUMT00000079333.2" ; hgnc_id "HGNC:16105" ; level 2 ; orig_coord_info "chr20,44206881,44206957,-" ; protein_id "ENSP00000255174.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DYRK1A--OSER1^ENST00000255174.3" ; transcript_name "OSER1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DYRK1A--OSER1 HAVANA mRNA 50904 57291 . + . FI_gene_label "OSER1^ENSG00000132823.11" ; ID "DYRK1A--OSER1^ENST00000255174.3" ; Parent "DYRK1A--OSER1^OSER1^ENSG00000132823.11" ; ccdsid "CCDS13327.1" ; exon_id "ENSE00000906877.1" ; exon_number 2 ; gene_id "DYRK1A--OSER1^OSER1^ENSG00000132823.11" ; gene_name OSER1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032518.3" ; havana_transcript "OTTHUMT00000079333.2" ; hgnc_id "HGNC:16105" ; level 2 ; orig_coord_info "chr20,44206881,44206957,-" ; protein_id "ENSP00000255174.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DYRK1A--OSER1^ENST00000255174.3" ; transcript_name "OSER1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DYRK1A--OSER1 HAVANA gene 2985 36922 . + . FI_gene_label "DYRK1A^ENSG00000157540.22" ; ID "DYRK1A--OSER1^DYRK1A^ENSG00000157540.22" ; ccdsid "CCDS42926.1" ; exon_id "ENSE00003829613.1" ; exon_number 3 ; gene_id "DYRK1A--OSER1^DYRK1A^ENSG00000157540.22" ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9" ; havana_transcript "OTTHUMT00000194799.2" ; hgnc_id "HGNC:3091" ; level 2 ; orig_coord_info "chr21,37420375,37420384,+" ; protein_id "ENSP00000342690.3" ; tag basic CCDS ; transcript_id "DYRK1A--OSER1^ENST00000338785.8" ; transcript_name "DYRK1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
DYRK1A--OSER1 HAVANA mRNA 2985 36922 . + . FI_gene_label "DYRK1A^ENSG00000157540.22" ; ID "DYRK1A--OSER1^ENST00000338785.8" ; Parent "DYRK1A--OSER1^DYRK1A^ENSG00000157540.22" ; ccdsid "CCDS42926.1" ; exon_id "ENSE00003829613.1" ; exon_number 3 ; gene_id "DYRK1A--OSER1^DYRK1A^ENSG00000157540.22" ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9" ; havana_transcript "OTTHUMT00000194799.2" ; hgnc_id "HGNC:3091" ; level 2 ; orig_coord_info "chr21,37420375,37420384,+" ; protein_id "ENSP00000342690.3" ; tag basic CCDS ; transcript_id "DYRK1A--OSER1^ENST00000338785.8" ; transcript_name "DYRK1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
E2F3--AL031767.1 HAVANA gene 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--AL031767.1^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--AL031767.1^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--AL031767.1^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
E2F3--AL031767.1 HAVANA mRNA 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--AL031767.1^ENST00000346618.8" ; Parent "E2F3--AL031767.1^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--AL031767.1^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--AL031767.1^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
E2F3--AL451080.1 HAVANA gene 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--AL451080.1^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--AL451080.1^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--AL451080.1^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
E2F3--AL451080.1 HAVANA mRNA 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--AL451080.1^ENST00000346618.8" ; Parent "E2F3--AL451080.1^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--AL451080.1^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--AL451080.1^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
E2F3--LNC-LBCS HAVANA gene 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--LNC-LBCS^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--LNC-LBCS^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--LNC-LBCS^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
E2F3--LNC-LBCS HAVANA mRNA 1001 13190 . + . FI_gene_label "E2F3^ENSG00000112242.15" ; ID "E2F3--LNC-LBCS^ENST00000346618.8" ; Parent "E2F3--LNC-LBCS^E2F3^ENSG00000112242.15" ; ccdsid "CCDS4545.1" ; exon_id "ENSE00001148453.4" ; exon_number 1 ; gene_id "E2F3--LNC-LBCS^E2F3^ENSG00000112242.15" ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3" ; havana_transcript "OTTHUMT00000043828.3" ; hgnc_id "HGNC:3115" ; level 2 ; orig_coord_info "chr6,20402233,20402625,+" ; protein_id "ENSP00000262904.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--LNC-LBCS^ENST00000346618.8" ; transcript_name "E2F3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC6B--CTNNA2 HAVANA gene 1009 34110 . + . FI_gene_label "EXOC6B^ENSG00000144036.16" ; ID "EXOC6B--CTNNA2^EXOC6B^ENSG00000144036.16" ; ccdsid "CCDS46333.1" ; exon_id "ENSE00000000137.2" ; exon_number 1 ; gene_id "EXOC6B--CTNNA2^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--CTNNA2^ENST00000272427.11" ; transcript_name "EXOC6B-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC6B--CTNNA2 HAVANA mRNA 1009 34110 . + . FI_gene_label "EXOC6B^ENSG00000144036.16" ; ID "EXOC6B--CTNNA2^ENST00000272427.11" ; Parent "EXOC6B--CTNNA2^EXOC6B^ENSG00000144036.16" ; ccdsid "CCDS46333.1" ; exon_id "ENSE00000000137.2" ; exon_number 1 ; gene_id "EXOC6B--CTNNA2^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--CTNNA2^ENST00000272427.11" ; transcript_name "EXOC6B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC6B--CTNNA2 ENSEMBL gene 65086 82329 . + . FI_gene_label "CTNNA2^ENSG00000066032.19" ; ID "EXOC6B--CTNNA2^CTNNA2^ENSG00000066032.19" ; ccdsid "CCDS62945.1" ; exon_id "ENSE00001381057.2" ; exon_number 1 ; gene_id "EXOC6B--CTNNA2^CTNNA2^ENSG00000066032.19" ; gene_name CTNNA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152903.13" ; hgnc_id "HGNC:2510" ; level 3 ; orig_coord_info "chr2,80313562,80313654,+" ; protein_id "ENSP00000341500.3" ; tag basic CCDS ; transcript_id "EXOC6B--CTNNA2^ENST00000343114.7" ; transcript_name "CTNNA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC6B--CTNNA2 ENSEMBL mRNA 65086 82329 . + . FI_gene_label "CTNNA2^ENSG00000066032.19" ; ID "EXOC6B--CTNNA2^ENST00000343114.7" ; Parent "EXOC6B--CTNNA2^CTNNA2^ENSG00000066032.19" ; ccdsid "CCDS62945.1" ; exon_id "ENSE00001381057.2" ; exon_number 1 ; gene_id "EXOC6B--CTNNA2^CTNNA2^ENSG00000066032.19" ; gene_name CTNNA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152903.13" ; hgnc_id "HGNC:2510" ; level 3 ; orig_coord_info "chr2,80313562,80313654,+" ; protein_id "ENSP00000341500.3" ; tag basic CCDS ; transcript_id "EXOC6B--CTNNA2^ENST00000343114.7" ; transcript_name "CTNNA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPAT4--ANK1 HAVANA gene 21601 68558 . + . FI_gene_label "ANK1^ENSG00000029534.21" ; ID "GPAT4--ANK1^ANK1^ENSG00000029534.21" ; ccdsid "CCDS47849.1" ; exon_id "ENSE00001482383.3" ; exon_number 1 ; gene_id "GPAT4--ANK1^ANK1^ENSG00000029534.21" ; gene_name ANK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150281.8" ; havana_transcript "OTTHUMT00000377171.2" ; hgnc_id "HGNC:492" ; level 2 ; orig_coord_info "chr8,41896355,41896480,-" ; protein_id "ENSP00000265709.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "GPAT4--ANK1^ENST00000265709.13" ; transcript_name "ANK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPAT4--ANK1 HAVANA mRNA 21601 68558 . + . FI_gene_label "ANK1^ENSG00000029534.21" ; ID "GPAT4--ANK1^ENST00000265709.13" ; Parent "GPAT4--ANK1^ANK1^ENSG00000029534.21" ; ccdsid "CCDS47849.1" ; exon_id "ENSE00001482383.3" ; exon_number 1 ; gene_id "GPAT4--ANK1^ANK1^ENSG00000029534.21" ; gene_name ANK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150281.8" ; havana_transcript "OTTHUMT00000377171.2" ; hgnc_id "HGNC:492" ; level 2 ; orig_coord_info "chr8,41896355,41896480,-" ; protein_id "ENSP00000265709.8" ; tag basic appris_alternative_2 CCDS ; transcript_id "GPAT4--ANK1^ENST00000265709.13" ; transcript_name "ANK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPAT4--ANK1 HAVANA gene 2014 18600 . + . FI_gene_label "GPAT4^ENSG00000158669.11" ; ID "GPAT4--ANK1^GPAT4^ENSG00000158669.11" ; ccdsid "CCDS6117.1" ; exon_id "ENSE00001526992.1" ; exon_number 2 ; gene_id "GPAT4--ANK1^GPAT4^ENSG00000158669.11" ; gene_name GPAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164082.4" ; havana_transcript "OTTHUMT00000377158.1" ; hgnc_id "HGNC:20880" ; level 2 ; orig_coord_info "chr8,41599140,41599304,+" ; protein_id "ENSP00000380184.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPAT4--ANK1^ENST00000396987.7" ; transcript_name "GPAT4-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPAT4--ANK1 HAVANA mRNA 2014 18600 . + . FI_gene_label "GPAT4^ENSG00000158669.11" ; ID "GPAT4--ANK1^ENST00000396987.7" ; Parent "GPAT4--ANK1^GPAT4^ENSG00000158669.11" ; ccdsid "CCDS6117.1" ; exon_id "ENSE00001526992.1" ; exon_number 2 ; gene_id "GPAT4--ANK1^GPAT4^ENSG00000158669.11" ; gene_name GPAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164082.4" ; havana_transcript "OTTHUMT00000377158.1" ; hgnc_id "HGNC:20880" ; level 2 ; orig_coord_info "chr8,41599140,41599304,+" ; protein_id "ENSP00000380184.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPAT4--ANK1^ENST00000396987.7" ; transcript_name "GPAT4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HERC2--AC024405.1 HAVANA gene 1001 86848 . + . FI_gene_label "HERC2^ENSG00000128731.18" ; ID "HERC2--AC024405.1^HERC2^ENSG00000128731.18" ; ccdsid "CCDS10021.1" ; exon_id "ENSE00003655270.1" ; exon_number 2 ; gene_id "HERC2--AC024405.1^HERC2^ENSG00000128731.18" ; gene_name HERC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129251.7" ; havana_transcript "OTTHUMT00000251358.3" ; hgnc_id "HGNC:4868" ; level 2 ; orig_coord_info "chr15,28321362,28321433,-" ; protein_id "ENSP00000261609.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HERC2--AC024405.1^ENST00000261609.13" ; transcript_name "HERC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
HERC2--AC024405.1 HAVANA mRNA 1001 86848 . + . FI_gene_label "HERC2^ENSG00000128731.18" ; ID "HERC2--AC024405.1^ENST00000261609.13" ; Parent "HERC2--AC024405.1^HERC2^ENSG00000128731.18" ; ccdsid "CCDS10021.1" ; exon_id "ENSE00003655270.1" ; exon_number 2 ; gene_id "HERC2--AC024405.1^HERC2^ENSG00000128731.18" ; gene_name HERC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129251.7" ; havana_transcript "OTTHUMT00000251358.3" ; hgnc_id "HGNC:4868" ; level 2 ; orig_coord_info "chr15,28321362,28321433,-" ; protein_id "ENSP00000261609.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HERC2--AC024405.1^ENST00000261609.13" ; transcript_name "HERC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HERC2--OR4C50P HAVANA gene 1001 86848 . + . FI_gene_label "HERC2^ENSG00000128731.18" ; ID "HERC2--OR4C50P^HERC2^ENSG00000128731.18" ; ccdsid "CCDS10021.1" ; exon_id "ENSE00003655270.1" ; exon_number 2 ; gene_id "HERC2--OR4C50P^HERC2^ENSG00000128731.18" ; gene_name HERC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129251.7" ; havana_transcript "OTTHUMT00000251358.3" ; hgnc_id "HGNC:4868" ; level 2 ; orig_coord_info "chr15,28321362,28321433,-" ; protein_id "ENSP00000261609.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HERC2--OR4C50P^ENST00000261609.13" ; transcript_name "HERC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
HERC2--OR4C50P HAVANA mRNA 1001 86848 . + . FI_gene_label "HERC2^ENSG00000128731.18" ; ID "HERC2--OR4C50P^ENST00000261609.13" ; Parent "HERC2--OR4C50P^HERC2^ENSG00000128731.18" ; ccdsid "CCDS10021.1" ; exon_id "ENSE00003655270.1" ; exon_number 2 ; gene_id "HERC2--OR4C50P^HERC2^ENSG00000128731.18" ; gene_name HERC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129251.7" ; havana_transcript "OTTHUMT00000251358.3" ; hgnc_id "HGNC:4868" ; level 2 ; orig_coord_info "chr15,28321362,28321433,-" ; protein_id "ENSP00000261609.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HERC2--OR4C50P^ENST00000261609.13" ; transcript_name "HERC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
IGFL1P2--HIF3A HAVANA gene 5593 23988 . + . FI_gene_label "HIF3A^ENSG00000124440.16" ; ID "IGFL1P2--HIF3A^HIF3A^ENSG00000124440.16" ; ccdsid "CCDS42580.2" ; exon_id "ENSE00003567095.1" ; exon_number 2 ; gene_id "IGFL1P2--HIF3A^HIF3A^ENSG00000124440.16" ; gene_name HIF3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000141296.6" ; havana_transcript "OTTHUMT00000384749.1" ; hgnc_id "HGNC:15825" ; level 2 ; orig_coord_info "chr19,46303933,46304088,+" ; protein_id "ENSP00000244303.6" ; tag basic CCDS ; transcript_id "IGFL1P2--HIF3A^ENST00000244303.10" ; transcript_name "HIF3A-202" ; transcript_support_level 2 ; transcript_type protein_coding
IGFL1P2--HIF3A HAVANA mRNA 5593 23988 . + . FI_gene_label "HIF3A^ENSG00000124440.16" ; ID "IGFL1P2--HIF3A^ENST00000244303.10" ; Parent "IGFL1P2--HIF3A^HIF3A^ENSG00000124440.16" ; ccdsid "CCDS42580.2" ; exon_id "ENSE00003567095.1" ; exon_number 2 ; gene_id "IGFL1P2--HIF3A^HIF3A^ENSG00000124440.16" ; gene_name HIF3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000141296.6" ; havana_transcript "OTTHUMT00000384749.1" ; hgnc_id "HGNC:15825" ; level 2 ; orig_coord_info "chr19,46303933,46304088,+" ; protein_id "ENSP00000244303.6" ; tag basic CCDS ; transcript_id "IGFL1P2--HIF3A^ENST00000244303.10" ; transcript_name "HIF3A-202" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
MBOAT1--LNC-LBCS HAVANA gene 1001 17325 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "MBOAT1--LNC-LBCS^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "MBOAT1--LNC-LBCS^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MBOAT1--LNC-LBCS^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MBOAT1--LNC-LBCS HAVANA mRNA 1001 17325 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "MBOAT1--LNC-LBCS^ENST00000324607.8" ; Parent "MBOAT1--LNC-LBCS^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "MBOAT1--LNC-LBCS^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MBOAT1--LNC-LBCS^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHA13 HAVANA gene 6923 15363 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA7--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA7--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA7--PCDHA13 HAVANA mRNA 6923 15363 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA7--PCDHA13^ENST00000289272.3" ; Parent "PCDHA7--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA7--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHA13 HAVANA gene 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHA13^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHA13^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHA13^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA7--PCDHA13 HAVANA mRNA 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHA13^ENST00000356878.5" ; Parent "PCDHA7--PCDHA13^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHA13^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHA13^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHAC1 HAVANA gene 6923 16938 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA7--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA7--PCDHAC1 HAVANA mRNA 6923 16938 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA7--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA7--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHAC1 HAVANA gene 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHAC1^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC1^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHAC1^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA7--PCDHAC1 HAVANA mRNA 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHAC1^ENST00000356878.5" ; Parent "PCDHA7--PCDHAC1^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC1^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHAC1^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHAC2 HAVANA gene 6929 17664 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA7--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA7--PCDHAC2 HAVANA mRNA 6929 17664 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA7--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA7--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA7--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA7--PCDHAC2 HAVANA gene 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHAC2^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC2^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHAC2^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA7--PCDHAC2 HAVANA mRNA 1001 3922 . + . FI_gene_label "PCDHA7^ENSG00000204963.6" ; ID "PCDHA7--PCDHAC2^ENST00000356878.5" ; Parent "PCDHA7--PCDHAC2^PCDHA7^ENSG00000204963.6" ; exon_id "ENSE00001519049.3" ; exon_number 1 ; gene_id "PCDHA7--PCDHAC2^PCDHA7^ENSG00000204963.6" ; gene_name PCDHA7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163371.4" ; havana_transcript "OTTHUMT00000477551.1" ; hgnc_id "HGNC:8673" ; level 2 ; orig_coord_info "chr5,140834384,140836750,+" ; protein_id "ENSP00000349344.5" ; tag basic ; transcript_id "PCDHA7--PCDHAC2^ENST00000356878.5" ; transcript_name "PCDHA7-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
RPARP-AS1--SUFU HAVANA gene 11734 24627 . + . FI_gene_label "SUFU^ENSG00000107882.12" ; ID "RPARP-AS1--SUFU^SUFU^ENSG00000107882.12" ; ccdsid "CCDS53571.1" ; exon_id "ENSE00001451217.1" ; exon_number 1 ; gene_id "RPARP-AS1--SUFU^SUFU^ENSG00000107882.12" ; gene_name SUFU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018966.4" ; havana_transcript "OTTHUMT00000050092.2" ; hgnc_id "HGNC:16466" ; level 2 ; orig_coord_info "chr10,102504153,102504334,+" ; protein_id "ENSP00000358915.2" ; tag basic CCDS ; transcript_id "RPARP-AS1--SUFU^ENST00000369899.6" ; transcript_name "SUFU-201" ; transcript_support_level 1 ; transcript_type protein_coding
RPARP-AS1--SUFU HAVANA mRNA 11734 24627 . + . FI_gene_label "SUFU^ENSG00000107882.12" ; ID "RPARP-AS1--SUFU^ENST00000369899.6" ; Parent "RPARP-AS1--SUFU^SUFU^ENSG00000107882.12" ; ccdsid "CCDS53571.1" ; exon_id "ENSE00001451217.1" ; exon_number 1 ; gene_id "RPARP-AS1--SUFU^SUFU^ENSG00000107882.12" ; gene_name SUFU ; gene_type protein_coding ; havana_gene "OTTHUMG00000018966.4" ; havana_transcript "OTTHUMT00000050092.2" ; hgnc_id "HGNC:16466" ; level 2 ; orig_coord_info "chr10,102504153,102504334,+" ; protein_id "ENSP00000358915.2" ; tag basic CCDS ; transcript_id "RPARP-AS1--SUFU^ENST00000369899.6" ; transcript_name "SUFU-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RYK--LINC02000 HAVANA gene 1392 21472 . + . FI_gene_label "RYK^ENSG00000163785.13" ; ID "RYK--LINC02000^RYK^ENSG00000163785.13" ; exon_id "ENSE00001869671.2" ; exon_number 1 ; gene_id "RYK--LINC02000^RYK^ENSG00000163785.13" ; gene_name RYK ; gene_type protein_coding ; havana_gene "OTTHUMG00000159750.4" ; havana_transcript "OTTHUMT00000478908.1" ; hgnc_id "HGNC:10481" ; level 2 ; orig_coord_info "chr3,134250423,134250468,-" ; protein_id "ENSP00000419122.2" ; tag non_canonical_other mRNA_start_NF cds_start_NF ; transcript_id "RYK--LINC02000^ENST00000460933.5" ; transcript_name "RYK-201" ; transcript_support_level 1 ; transcript_type protein_coding
RYK--LINC02000 HAVANA mRNA 1392 21472 . + . FI_gene_label "RYK^ENSG00000163785.13" ; ID "RYK--LINC02000^ENST00000460933.5" ; Parent "RYK--LINC02000^RYK^ENSG00000163785.13" ; exon_id "ENSE00001869671.2" ; exon_number 1 ; gene_id "RYK--LINC02000^RYK^ENSG00000163785.13" ; gene_name RYK ; gene_type protein_coding ; havana_gene "OTTHUMG00000159750.4" ; havana_transcript "OTTHUMT00000478908.1" ; hgnc_id "HGNC:10481" ; level 2 ; orig_coord_info "chr3,134250423,134250468,-" ; protein_id "ENSP00000419122.2" ; tag non_canonical_other mRNA_start_NF cds_start_NF ; transcript_id "RYK--LINC02000^ENST00000460933.5" ; transcript_name "RYK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SAE1--CYP2B7P HAVANA gene 3541 19880 . + . FI_gene_label "SAE1^ENSG00000142230.13" ; ID "SAE1--CYP2B7P^SAE1^ENSG00000142230.13" ; ccdsid "CCDS12696.1" ; exon_id "ENSE00003031595.2" ; exon_number 1 ; gene_id "SAE1--CYP2B7P^SAE1^ENSG00000142230.13" ; gene_name SAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183464.5" ; havana_transcript "OTTHUMT00000466775.2" ; hgnc_id "HGNC:30660" ; level 2 ; orig_coord_info "chr19,47130931,47131028,+" ; protein_id "ENSP00000270225.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAE1--CYP2B7P^ENST00000270225.12" ; transcript_name "SAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SAE1--CYP2B7P HAVANA mRNA 3541 19880 . + . FI_gene_label "SAE1^ENSG00000142230.13" ; ID "SAE1--CYP2B7P^ENST00000270225.12" ; Parent "SAE1--CYP2B7P^SAE1^ENSG00000142230.13" ; ccdsid "CCDS12696.1" ; exon_id "ENSE00003031595.2" ; exon_number 1 ; gene_id "SAE1--CYP2B7P^SAE1^ENSG00000142230.13" ; gene_name SAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183464.5" ; havana_transcript "OTTHUMT00000466775.2" ; hgnc_id "HGNC:30660" ; level 2 ; orig_coord_info "chr19,47130931,47131028,+" ; protein_id "ENSP00000270225.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAE1--CYP2B7P^ENST00000270225.12" ; transcript_name "SAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SMCHD1--LDLRAD4 HAVANA gene 1001 53513 . + . FI_gene_label "SMCHD1^ENSG00000101596.16" ; ID "SMCHD1--LDLRAD4^SMCHD1^ENSG00000101596.16" ; ccdsid "CCDS45822.1" ; exon_id "ENSE00002727195.2" ; exon_number 1 ; gene_id "SMCHD1--LDLRAD4^SMCHD1^ENSG00000101596.16" ; gene_name SMCHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178235.5" ; havana_transcript "OTTHUMT00000441082.2" ; hgnc_id "HGNC:29090" ; level 2 ; orig_coord_info "chr18,2656076,2656261,+" ; protein_id "ENSP00000326603.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SMCHD1--LDLRAD4^ENST00000320876.11" ; transcript_name "SMCHD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
SMCHD1--LDLRAD4 HAVANA mRNA 1001 53513 . + . FI_gene_label "SMCHD1^ENSG00000101596.16" ; ID "SMCHD1--LDLRAD4^ENST00000320876.11" ; Parent "SMCHD1--LDLRAD4^SMCHD1^ENSG00000101596.16" ; ccdsid "CCDS45822.1" ; exon_id "ENSE00002727195.2" ; exon_number 1 ; gene_id "SMCHD1--LDLRAD4^SMCHD1^ENSG00000101596.16" ; gene_name SMCHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178235.5" ; havana_transcript "OTTHUMT00000441082.2" ; hgnc_id "HGNC:29090" ; level 2 ; orig_coord_info "chr18,2656076,2656261,+" ; protein_id "ENSP00000326603.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SMCHD1--LDLRAD4^ENST00000320876.11" ; transcript_name "SMCHD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SMCHD1--LDLRAD4 HAVANA gene 60931 121270 . + . FI_gene_label "LDLRAD4^ENSG00000168675.19" ; ID "SMCHD1--LDLRAD4^LDLRAD4^ENSG00000168675.19" ; ccdsid "CCDS32793.1" ; exon_id "ENSE00001354297.2" ; exon_number 2 ; gene_id "SMCHD1--LDLRAD4^LDLRAD4^ENSG00000168675.19" ; gene_name LDLRAD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181925.5" ; havana_transcript "OTTHUMT00000458326.1" ; hgnc_id "HGNC:1224" ; level 2 ; orig_coord_info "chr18,13387723,13387762,+" ; protein_id "ENSP00000352420.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SMCHD1--LDLRAD4^ENST00000359446.10" ; transcript_name "LDLRAD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
SMCHD1--LDLRAD4 HAVANA mRNA 60931 121270 . + . FI_gene_label "LDLRAD4^ENSG00000168675.19" ; ID "SMCHD1--LDLRAD4^ENST00000359446.10" ; Parent "SMCHD1--LDLRAD4^LDLRAD4^ENSG00000168675.19" ; ccdsid "CCDS32793.1" ; exon_id "ENSE00001354297.2" ; exon_number 2 ; gene_id "SMCHD1--LDLRAD4^LDLRAD4^ENSG00000168675.19" ; gene_name LDLRAD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181925.5" ; havana_transcript "OTTHUMT00000458326.1" ; hgnc_id "HGNC:1224" ; level 2 ; orig_coord_info "chr18,13387723,13387762,+" ; protein_id "ENSP00000352420.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SMCHD1--LDLRAD4^ENST00000359446.10" ; transcript_name "LDLRAD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNX29--CIITA HAVANA gene 42621 74507 . + . FI_gene_label "CIITA^ENSG00000179583.20" ; ID "SNX29--CIITA^CIITA^ENSG00000179583.20" ; ccdsid "CCDS10544.1" ; exon_id "ENSE00003915466.1" ; exon_number 1 ; gene_id "SNX29--CIITA^CIITA^ENSG00000179583.20" ; gene_name CIITA ; gene_type protein_coding ; havana_gene "OTTHUMG00000129753.7" ; havana_transcript "OTTHUMT00000251966.5" ; hgnc_id "HGNC:7067" ; level 2 ; orig_coord_info "chr16,10877331,10877382,+" ; protein_id "ENSP00000316328.8" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "SNX29--CIITA^ENST00000324288.14" ; transcript_name "CIITA-201" ; transcript_support_level 1 ; transcript_type protein_coding
SNX29--CIITA HAVANA mRNA 42621 74507 . + . FI_gene_label "CIITA^ENSG00000179583.20" ; ID "SNX29--CIITA^ENST00000324288.14" ; Parent "SNX29--CIITA^CIITA^ENSG00000179583.20" ; ccdsid "CCDS10544.1" ; exon_id "ENSE00003915466.1" ; exon_number 1 ; gene_id "SNX29--CIITA^CIITA^ENSG00000179583.20" ; gene_name CIITA ; gene_type protein_coding ; havana_gene "OTTHUMG00000129753.7" ; havana_transcript "OTTHUMT00000251966.5" ; hgnc_id "HGNC:7067" ; level 2 ; orig_coord_info "chr16,10877331,10877382,+" ; protein_id "ENSP00000316328.8" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "SNX29--CIITA^ENST00000324288.14" ; transcript_name "CIITA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNX29--CIITA HAVANA gene 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--CIITA^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--CIITA^SNX29^ENSG00000048471.14" ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4" ; havana_transcript "OTTHUMT00000422625.1" ; hgnc_id "HGNC:30542" ; level 2 ; orig_coord_info "chr16,12356253,12356279,+" ; protein_id "ENSP00000455327.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--CIITA^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--CIITA HAVANA mRNA 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--CIITA^ENST00000562510.1" ; Parent "SNX29--CIITA^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--CIITA^SNX29^ENSG00000048471.14" ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4" ; havana_transcript "OTTHUMT00000422625.1" ; hgnc_id "HGNC:30542" ; level 2 ; orig_coord_info "chr16,12356253,12356279,+" ; protein_id "ENSP00000455327.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--CIITA^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
TAF1--RHOG2P HAVANA gene 18778 37959 . + . FI_gene_label "TAF1^ENSG00000147133.16" ; ID "TAF1--RHOG2P^TAF1^ENSG00000147133.16" ; exon_id "ENSE00001652592.1" ; exon_number 1 ; gene_id "TAF1--RHOG2P^TAF1^ENSG00000147133.16" ; gene_name TAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022723.7" ; hgnc_id "HGNC:11535" ; level 2 ; orig_coord_info "chrX,71397253,71397466,+" ; protein_id "ENSP00000276072.4" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAF1--RHOG2P^ENST00000276072.8" ; transcript_name "TAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
TAF1--RHOG2P HAVANA mRNA 18778 37959 . + . FI_gene_label "TAF1^ENSG00000147133.16" ; ID "TAF1--RHOG2P^ENST00000276072.8" ; Parent "TAF1--RHOG2P^TAF1^ENSG00000147133.16" ; exon_id "ENSE00001652592.1" ; exon_number 1 ; gene_id "TAF1--RHOG2P^TAF1^ENSG00000147133.16" ; gene_name TAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022723.7" ; hgnc_id "HGNC:11535" ; level 2 ; orig_coord_info "chrX,71397253,71397466,+" ; protein_id "ENSP00000276072.4" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAF1--RHOG2P^ENST00000276072.8" ; transcript_name "TAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TAF1--ZCRB1P1 HAVANA gene 18778 37959 . + . FI_gene_label "TAF1^ENSG00000147133.16" ; ID "TAF1--ZCRB1P1^TAF1^ENSG00000147133.16" ; exon_id "ENSE00001652592.1" ; exon_number 1 ; gene_id "TAF1--ZCRB1P1^TAF1^ENSG00000147133.16" ; gene_name TAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022723.7" ; hgnc_id "HGNC:11535" ; level 2 ; orig_coord_info "chrX,71397253,71397466,+" ; protein_id "ENSP00000276072.4" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAF1--ZCRB1P1^ENST00000276072.8" ; transcript_name "TAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
TAF1--ZCRB1P1 HAVANA mRNA 18778 37959 . + . FI_gene_label "TAF1^ENSG00000147133.16" ; ID "TAF1--ZCRB1P1^ENST00000276072.8" ; Parent "TAF1--ZCRB1P1^TAF1^ENSG00000147133.16" ; exon_id "ENSE00001652592.1" ; exon_number 1 ; gene_id "TAF1--ZCRB1P1^TAF1^ENSG00000147133.16" ; gene_name TAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022723.7" ; hgnc_id "HGNC:11535" ; level 2 ; orig_coord_info "chrX,71397253,71397466,+" ; protein_id "ENSP00000276072.4" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TAF1--ZCRB1P1^ENST00000276072.8" ; transcript_name "TAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
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:
ZC3H4--AL513478.3 HAVANA gene 1001 19492 . + . FI_gene_label "ZC3H4^ENSG00000130749.10" ; ID "ZC3H4--AL513478.3^ZC3H4^ENSG00000130749.10" ; ccdsid "CCDS42582.1" ; exon_id "ENSE00001207487.1" ; exon_number 2 ; gene_id "ZC3H4--AL513478.3^ZC3H4^ENSG00000130749.10" ; gene_name ZC3H4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183442.2" ; havana_transcript "OTTHUMT00000466667.2" ; hgnc_id "HGNC:17808" ; level 2 ; orig_coord_info "chr19,47112424,47112584,-" ; protein_id "ENSP00000253048.4" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H4--AL513478.3^ENST00000253048.10" ; transcript_name "ZC3H4-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZC3H4--AL513478.3 HAVANA mRNA 1001 19492 . + . FI_gene_label "ZC3H4^ENSG00000130749.10" ; ID "ZC3H4--AL513478.3^ENST00000253048.10" ; Parent "ZC3H4--AL513478.3^ZC3H4^ENSG00000130749.10" ; ccdsid "CCDS42582.1" ; exon_id "ENSE00001207487.1" ; exon_number 2 ; gene_id "ZC3H4--AL513478.3^ZC3H4^ENSG00000130749.10" ; gene_name ZC3H4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183442.2" ; havana_transcript "OTTHUMT00000466667.2" ; hgnc_id "HGNC:17808" ; level 2 ; orig_coord_info "chr19,47112424,47112584,-" ; protein_id "ENSP00000253048.4" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H4--AL513478.3^ENST00000253048.10" ; transcript_name "ZC3H4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZC3H4--CDRT15P12 HAVANA gene 1001 19492 . + . FI_gene_label "ZC3H4^ENSG00000130749.10" ; ID "ZC3H4--CDRT15P12^ZC3H4^ENSG00000130749.10" ; ccdsid "CCDS42582.1" ; exon_id "ENSE00001207487.1" ; exon_number 2 ; gene_id "ZC3H4--CDRT15P12^ZC3H4^ENSG00000130749.10" ; gene_name ZC3H4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183442.2" ; havana_transcript "OTTHUMT00000466667.2" ; hgnc_id "HGNC:17808" ; level 2 ; orig_coord_info "chr19,47112424,47112584,-" ; protein_id "ENSP00000253048.4" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H4--CDRT15P12^ENST00000253048.10" ; transcript_name "ZC3H4-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZC3H4--CDRT15P12 HAVANA mRNA 1001 19492 . + . FI_gene_label "ZC3H4^ENSG00000130749.10" ; ID "ZC3H4--CDRT15P12^ENST00000253048.10" ; Parent "ZC3H4--CDRT15P12^ZC3H4^ENSG00000130749.10" ; ccdsid "CCDS42582.1" ; exon_id "ENSE00001207487.1" ; exon_number 2 ; gene_id "ZC3H4--CDRT15P12^ZC3H4^ENSG00000130749.10" ; gene_name ZC3H4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183442.2" ; havana_transcript "OTTHUMT00000466667.2" ; hgnc_id "HGNC:17808" ; level 2 ; orig_coord_info "chr19,47112424,47112584,-" ; protein_id "ENSP00000253048.4" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H4--CDRT15P12^ENST00000253048.10" ; transcript_name "ZC3H4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AL031767.1--MBOAT1 HAVANA gene 1001 1886 . + . FI_gene_label "AL031767.1^ENSG00000227089.2" ; ID "AL031767.1--MBOAT1^AL031767.1^ENSG00000227089.2" ; exon_id "ENSE00001781271.2" ; exon_number 1 ; gene_id "AL031767.1--MBOAT1^AL031767.1^ENSG00000227089.2" ; gene_name "AL031767.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014341.2" ; havana_transcript "OTTHUMT00000039988.2" ; level 2 ; orig_coord_info "chr6,21355102,21355296,-" ; tag basic ; transcript_id "AL031767.1--MBOAT1^ENST00000426374.2" ; transcript_name "AL031767.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
AL031767.1--MBOAT1 HAVANA RNA 1001 1886 . + . FI_gene_label "AL031767.1^ENSG00000227089.2" ; ID "AL031767.1--MBOAT1^ENST00000426374.2" ; Parent "AL031767.1--MBOAT1^AL031767.1^ENSG00000227089.2" ; exon_id "ENSE00001781271.2" ; exon_number 1 ; gene_id "AL031767.1--MBOAT1^AL031767.1^ENSG00000227089.2" ; gene_name "AL031767.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014341.2" ; havana_transcript "OTTHUMT00000039988.2" ; level 2 ; orig_coord_info "chr6,21355102,21355296,-" ; tag basic ; transcript_id "AL031767.1--MBOAT1^ENST00000426374.2" ; transcript_name "AL031767.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
AL451080.1--MBOAT1 HAVANA gene 1001 2500 . + . FI_gene_label "AL451080.1^ENSG00000287404.1" ; ID "AL451080.1--MBOAT1^AL451080.1^ENSG00000287404.1" ; exon_id "ENSE00003887804.1" ; exon_number 1 ; gene_id "AL451080.1--MBOAT1^AL451080.1^ENSG00000287404.1" ; gene_name "AL451080.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195607.1" ; havana_transcript "OTTHUMT00000527732.1" ; level 2 ; orig_coord_info "chr6,21270837,21271132,-" ; tag basic TAGENE ; transcript_id "AL451080.1--MBOAT1^ENST00000669568.1" ; transcript_name "AL451080.1-201" ; transcript_type lncRNA
AL451080.1--MBOAT1 HAVANA RNA 1001 2500 . + . FI_gene_label "AL451080.1^ENSG00000287404.1" ; ID "AL451080.1--MBOAT1^ENST00000669568.1" ; Parent "AL451080.1--MBOAT1^AL451080.1^ENSG00000287404.1" ; exon_id "ENSE00003887804.1" ; exon_number 1 ; gene_id "AL451080.1--MBOAT1^AL451080.1^ENSG00000287404.1" ; gene_name "AL451080.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195607.1" ; havana_transcript "OTTHUMT00000527732.1" ; level 2 ; orig_coord_info "chr6,21270837,21271132,-" ; tag basic TAGENE ; transcript_id "AL451080.1--MBOAT1^ENST00000669568.1" ; transcript_name "AL451080.1-201" ; transcript_type lncRNA
L1 and L2 created:
BLACE--PKD1L2 HAVANA gene 1001 7493 . + . FI_gene_label "BLACE^ENSG00000204960.7" ; ID "BLACE--PKD1L2^BLACE^ENSG00000204960.7" ; exon_id "ENSE00001552014.3" ; exon_number 1 ; gene_id "BLACE--PKD1L2^BLACE^ENSG00000204960.7" ; gene_name BLACE ; gene_type lncRNA ; havana_gene "OTTHUMG00000151351.1" ; havana_transcript "OTTHUMT00000322333.1" ; hgnc_id "HGNC:20484" ; level 1 ; orig_coord_info "chr7,155367809,155367934,-" ; tag basic exp_conf ; transcript_id "BLACE--PKD1L2^ENST00000378120.5" ; transcript_name "BLACE-201" ; transcript_support_level 1 ; transcript_type lncRNA
BLACE--PKD1L2 HAVANA RNA 1001 7493 . + . FI_gene_label "BLACE^ENSG00000204960.7" ; ID "BLACE--PKD1L2^ENST00000378120.5" ; Parent "BLACE--PKD1L2^BLACE^ENSG00000204960.7" ; exon_id "ENSE00001552014.3" ; exon_number 1 ; gene_id "BLACE--PKD1L2^BLACE^ENSG00000204960.7" ; gene_name BLACE ; gene_type lncRNA ; havana_gene "OTTHUMG00000151351.1" ; havana_transcript "OTTHUMT00000322333.1" ; hgnc_id "HGNC:20484" ; level 1 ; orig_coord_info "chr7,155367809,155367934,-" ; tag basic exp_conf ; transcript_id "BLACE--PKD1L2^ENST00000378120.5" ; transcript_name "BLACE-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
CDKAL1--LNC-LBCS HAVANA gene 33456 35667 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "CDKAL1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "CDKAL1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "CDKAL1--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
CDKAL1--LNC-LBCS HAVANA RNA 33456 35667 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "CDKAL1--LNC-LBCS^ENST00000424083.1" ; Parent "CDKAL1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "CDKAL1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "CDKAL1--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
E2F3--AL031767.1 HAVANA gene 16191 17076 . + . FI_gene_label "AL031767.1^ENSG00000227089.2" ; ID "E2F3--AL031767.1^AL031767.1^ENSG00000227089.2" ; exon_id "ENSE00001781271.2" ; exon_number 1 ; gene_id "E2F3--AL031767.1^AL031767.1^ENSG00000227089.2" ; gene_name "AL031767.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014341.2" ; havana_transcript "OTTHUMT00000039988.2" ; level 2 ; orig_coord_info "chr6,21355102,21355296,-" ; tag basic ; transcript_id "E2F3--AL031767.1^ENST00000426374.2" ; transcript_name "AL031767.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
E2F3--AL031767.1 HAVANA RNA 16191 17076 . + . FI_gene_label "AL031767.1^ENSG00000227089.2" ; ID "E2F3--AL031767.1^ENST00000426374.2" ; Parent "E2F3--AL031767.1^AL031767.1^ENSG00000227089.2" ; exon_id "ENSE00001781271.2" ; exon_number 1 ; gene_id "E2F3--AL031767.1^AL031767.1^ENSG00000227089.2" ; gene_name "AL031767.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014341.2" ; havana_transcript "OTTHUMT00000039988.2" ; level 2 ; orig_coord_info "chr6,21355102,21355296,-" ; tag basic ; transcript_id "E2F3--AL031767.1^ENST00000426374.2" ; transcript_name "AL031767.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
E2F3--AL451080.1 HAVANA gene 16191 17690 . + . FI_gene_label "AL451080.1^ENSG00000287404.1" ; ID "E2F3--AL451080.1^AL451080.1^ENSG00000287404.1" ; exon_id "ENSE00003887804.1" ; exon_number 1 ; gene_id "E2F3--AL451080.1^AL451080.1^ENSG00000287404.1" ; gene_name "AL451080.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195607.1" ; havana_transcript "OTTHUMT00000527732.1" ; level 2 ; orig_coord_info "chr6,21270837,21271132,-" ; tag basic TAGENE ; transcript_id "E2F3--AL451080.1^ENST00000669568.1" ; transcript_name "AL451080.1-201" ; transcript_type lncRNA
E2F3--AL451080.1 HAVANA RNA 16191 17690 . + . FI_gene_label "AL451080.1^ENSG00000287404.1" ; ID "E2F3--AL451080.1^ENST00000669568.1" ; Parent "E2F3--AL451080.1^AL451080.1^ENSG00000287404.1" ; exon_id "ENSE00003887804.1" ; exon_number 1 ; gene_id "E2F3--AL451080.1^AL451080.1^ENSG00000287404.1" ; gene_name "AL451080.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195607.1" ; havana_transcript "OTTHUMT00000527732.1" ; level 2 ; orig_coord_info "chr6,21270837,21271132,-" ; tag basic TAGENE ; transcript_id "E2F3--AL451080.1^ENST00000669568.1" ; transcript_name "AL451080.1-201" ; transcript_type lncRNA
L1 and L2 created:
E2F3--LNC-LBCS HAVANA gene 25164 27375 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "E2F3--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "E2F3--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "E2F3--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
E2F3--LNC-LBCS HAVANA RNA 25164 27375 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "E2F3--LNC-LBCS^ENST00000424083.1" ; Parent "E2F3--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "E2F3--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "E2F3--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
HERC2--AC024405.1 HAVANA gene 89849 95746 . + . FI_gene_label "AC024405.1^ENSG00000214883.4" ; ID "HERC2--AC024405.1^AC024405.1^ENSG00000214883.4" ; exon_id "ENSE00002189224.2" ; exon_number 1 ; gene_id "HERC2--AC024405.1^AC024405.1^ENSG00000214883.4" ; gene_name "AC024405.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166694.3" ; havana_transcript "OTTHUMT00000391123.3" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr11,50409042,50409188,+" ; tag basic ; transcript_id "HERC2--AC024405.1^ENST00000532521.2" ; transcript_name "AC024405.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
HERC2--AC024405.1 HAVANA RNA 89849 95746 . + . FI_gene_label "AC024405.1^ENSG00000214883.4" ; ID "HERC2--AC024405.1^ENST00000532521.2" ; Parent "HERC2--AC024405.1^AC024405.1^ENSG00000214883.4" ; exon_id "ENSE00002189224.2" ; exon_number 1 ; gene_id "HERC2--AC024405.1^AC024405.1^ENSG00000214883.4" ; gene_name "AC024405.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000166694.3" ; havana_transcript "OTTHUMT00000391123.3" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr11,50409042,50409188,+" ; tag basic ; transcript_id "HERC2--AC024405.1^ENST00000532521.2" ; transcript_name "AC024405.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
HERC2--OR4C50P HAVANA gene 89849 90778 . + . FI_gene_label "OR4C50P^ENSG00000237610.1" ; ID "HERC2--OR4C50P^OR4C50P^ENSG00000237610.1" ; exon_id "ENSE00001684660.1" ; exon_number 1 ; gene_id "HERC2--OR4C50P^OR4C50P^ENSG00000237610.1" ; gene_name OR4C50P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000154323.1" ; havana_transcript "OTTHUMT00000334836.1" ; hgnc_id "HGNC:31274" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr11,54591480,54592409,+" ; tag basic ; transcript_id "HERC2--OR4C50P^ENST00000330155.3" ; transcript_name "OR4C50P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
HERC2--OR4C50P HAVANA RNA 89849 90778 . + . FI_gene_label "OR4C50P^ENSG00000237610.1" ; ID "HERC2--OR4C50P^ENST00000330155.3" ; Parent "HERC2--OR4C50P^OR4C50P^ENSG00000237610.1" ; exon_id "ENSE00001684660.1" ; exon_number 1 ; gene_id "HERC2--OR4C50P^OR4C50P^ENSG00000237610.1" ; gene_name OR4C50P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000154323.1" ; havana_transcript "OTTHUMT00000334836.1" ; hgnc_id "HGNC:31274" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr11,54591480,54592409,+" ; tag basic ; transcript_id "HERC2--OR4C50P^ENST00000330155.3" ; transcript_name "OR4C50P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
IGFL1P2--HIF3A HAVANA gene 1001 1439 . + . FI_gene_label "IGFL1P2^ENSG00000268238.1" ; ID "IGFL1P2--HIF3A^IGFL1P2^ENSG00000268238.1" ; exon_id "ENSE00003064899.1" ; exon_number 1 ; gene_id "IGFL1P2--HIF3A^IGFL1P2^ENSG00000268238.1" ; gene_name IGFL1P2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000182502.1" ; havana_transcript "OTTHUMT00000461725.1" ; hgnc_id "HGNC:32957" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr19,46260801,46260858,-" ; tag basic ; transcript_id "IGFL1P2--HIF3A^ENST00000593820.1" ; transcript_name "IGFL1P2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
IGFL1P2--HIF3A HAVANA RNA 1001 1439 . + . FI_gene_label "IGFL1P2^ENSG00000268238.1" ; ID "IGFL1P2--HIF3A^ENST00000593820.1" ; Parent "IGFL1P2--HIF3A^IGFL1P2^ENSG00000268238.1" ; exon_id "ENSE00003064899.1" ; exon_number 1 ; gene_id "IGFL1P2--HIF3A^IGFL1P2^ENSG00000268238.1" ; gene_name IGFL1P2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000182502.1" ; havana_transcript "OTTHUMT00000461725.1" ; hgnc_id "HGNC:32957" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr19,46260801,46260858,-" ; tag basic ; transcript_id "IGFL1P2--HIF3A^ENST00000593820.1" ; transcript_name "IGFL1P2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
MBOAT1--LNC-LBCS HAVANA gene 29299 31510 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "MBOAT1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "MBOAT1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "MBOAT1--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
MBOAT1--LNC-LBCS HAVANA RNA 29299 31510 . + . FI_gene_label "LNC-LBCS^ENSG00000228412.9" ; ID "MBOAT1--LNC-LBCS^ENST00000424083.1" ; Parent "MBOAT1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; exon_id "ENSE00001628312.1" ; exon_number 1 ; gene_id "MBOAT1--LNC-LBCS^LNC-LBCS^ENSG00000228412.9" ; gene_name "LNC-LBCS" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014330.26" ; havana_transcript "OTTHUMT00000039977.1" ; hgnc_id "HGNC:54418" ; level 2 ; orig_coord_info "chr6,19749648,19749693,-" ; transcript_id "MBOAT1--LNC-LBCS^ENST00000424083.1" ; transcript_name "LNC-LBCS-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
RPARP-AS1--SUFU HAVANA gene 1001 7482 . + . FI_gene_label "RPARP-AS1^ENSG00000269609.6" ; ID "RPARP-AS1--SUFU^RPARP-AS1^ENSG00000269609.6" ; exon_id "ENSE00002506774.3" ; exon_number 1 ; gene_id "RPARP-AS1--SUFU^RPARP-AS1^ENSG00000269609.6" ; gene_name "RPARP-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182529.6" ; havana_transcript "OTTHUMT00000462234.2" ; hgnc_id "HGNC:45238" ; level 2 ; orig_coord_info "chr10,102449816,102450022,+" ; tag basic TAGENE ; transcript_id "RPARP-AS1--SUFU^ENST00000473970.3" ; transcript_name "RPARP-AS1-201" ; transcript_support_level 1 ; transcript_type lncRNA
RPARP-AS1--SUFU HAVANA RNA 1001 7482 . + . FI_gene_label "RPARP-AS1^ENSG00000269609.6" ; ID "RPARP-AS1--SUFU^ENST00000473970.3" ; Parent "RPARP-AS1--SUFU^RPARP-AS1^ENSG00000269609.6" ; exon_id "ENSE00002506774.3" ; exon_number 1 ; gene_id "RPARP-AS1--SUFU^RPARP-AS1^ENSG00000269609.6" ; gene_name "RPARP-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182529.6" ; havana_transcript "OTTHUMT00000462234.2" ; hgnc_id "HGNC:45238" ; level 2 ; orig_coord_info "chr10,102449816,102450022,+" ; tag basic TAGENE ; transcript_id "RPARP-AS1--SUFU^ENST00000473970.3" ; transcript_name "RPARP-AS1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
RYK--LINC02000 HAVANA gene 27461 29100 . + . FI_gene_label "LINC02000^ENSG00000243832.1" ; ID "RYK--LINC02000^LINC02000^ENSG00000243832.1" ; exon_id "ENSE00001864387.1" ; exon_number 1 ; gene_id "RYK--LINC02000^LINC02000^ENSG00000243832.1" ; gene_name LINC02000 ; gene_type lncRNA ; havana_gene "OTTHUMG00000159748.1" ; havana_transcript "OTTHUMT00000357151.1" ; hgnc_id "HGNC:52835" ; level 1 ; orig_coord_info "chr3,134057410,134057648,-" ; tag basic exp_conf ; transcript_id "RYK--LINC02000^ENST00000483245.1" ; transcript_name "LINC02000-201" ; transcript_support_level 2 ; transcript_type lncRNA
RYK--LINC02000 HAVANA RNA 27461 29100 . + . FI_gene_label "LINC02000^ENSG00000243832.1" ; ID "RYK--LINC02000^ENST00000483245.1" ; Parent "RYK--LINC02000^LINC02000^ENSG00000243832.1" ; exon_id "ENSE00001864387.1" ; exon_number 1 ; gene_id "RYK--LINC02000^LINC02000^ENSG00000243832.1" ; gene_name LINC02000 ; gene_type lncRNA ; havana_gene "OTTHUMG00000159748.1" ; havana_transcript "OTTHUMT00000357151.1" ; hgnc_id "HGNC:52835" ; level 1 ; orig_coord_info "chr3,134057410,134057648,-" ; tag basic exp_conf ; transcript_id "RYK--LINC02000^ENST00000483245.1" ; transcript_name "LINC02000-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
SAE1--CYP2B7P HAVANA gene 22935 31038 . + . FI_gene_label "CYP2B7P^ENSG00000256612.7" ; ID "SAE1--CYP2B7P^CYP2B7P^ENSG00000256612.7" ; exon_id "ENSE00002320869.3" ; exon_number 1 ; gene_id "SAE1--CYP2B7P^CYP2B7P^ENSG00000256612.7" ; gene_name CYP2B7P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182706.6" ; havana_transcript "OTTHUMT00000465179.3" ; hgnc_id "HGNC:2616" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr19,40924273,40924443,+" ; tag basic ; transcript_id "SAE1--CYP2B7P^ENST00000541697.7" ; transcript_name "CYP2B7P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
SAE1--CYP2B7P HAVANA RNA 22935 31038 . + . FI_gene_label "CYP2B7P^ENSG00000256612.7" ; ID "SAE1--CYP2B7P^ENST00000541697.7" ; Parent "SAE1--CYP2B7P^CYP2B7P^ENSG00000256612.7" ; exon_id "ENSE00002320869.3" ; exon_number 1 ; gene_id "SAE1--CYP2B7P^CYP2B7P^ENSG00000256612.7" ; gene_name CYP2B7P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182706.6" ; havana_transcript "OTTHUMT00000465179.3" ; hgnc_id "HGNC:2616" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr19,40924273,40924443,+" ; tag basic ; transcript_id "SAE1--CYP2B7P^ENST00000541697.7" ; transcript_name "CYP2B7P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
TAF1--RHOG2P HAVANA gene 48350 48920 . + . FI_gene_label "RHOG2P^ENSG00000213706.2" ; ID "TAF1--RHOG2P^RHOG2P^ENSG00000213706.2" ; exon_id "ENSE00001522892.2" ; exon_number 1 ; gene_id "TAF1--RHOG2P^RHOG2P^ENSG00000213706.2" ; gene_name RHOG2P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021792.1" ; havana_transcript "OTTHUMT00000057125.1" ; hgnc_id "HGNC:54953" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,71352418,71352988,+" ; tag pseudo_consens basic ; transcript_id "TAF1--RHOG2P^ENST00000395798.2" ; transcript_name "RHOG2P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TAF1--RHOG2P HAVANA RNA 48350 48920 . + . FI_gene_label "RHOG2P^ENSG00000213706.2" ; ID "TAF1--RHOG2P^ENST00000395798.2" ; Parent "TAF1--RHOG2P^RHOG2P^ENSG00000213706.2" ; exon_id "ENSE00001522892.2" ; exon_number 1 ; gene_id "TAF1--RHOG2P^RHOG2P^ENSG00000213706.2" ; gene_name RHOG2P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021792.1" ; havana_transcript "OTTHUMT00000057125.1" ; hgnc_id "HGNC:54953" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,71352418,71352988,+" ; tag pseudo_consens basic ; transcript_id "TAF1--RHOG2P^ENST00000395798.2" ; transcript_name "RHOG2P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TAF1--ZCRB1P1 HAVANA gene 48350 49317 . + . FI_gene_label "ZCRB1P1^ENSG00000224208.1" ; ID "TAF1--ZCRB1P1^ZCRB1P1^ENSG00000224208.1" ; exon_id "ENSE00001617683.1" ; exon_number 1 ; gene_id "TAF1--ZCRB1P1^ZCRB1P1^ENSG00000224208.1" ; gene_name ZCRB1P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021791.1" ; havana_transcript "OTTHUMT00000057124.1" ; hgnc_id "HGNC:54987" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,71315631,71315879,-" ; tag pseudo_consens basic ; transcript_id "TAF1--ZCRB1P1^ENST00000436372.1" ; transcript_name "ZCRB1P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TAF1--ZCRB1P1 HAVANA RNA 48350 49317 . + . FI_gene_label "ZCRB1P1^ENSG00000224208.1" ; ID "TAF1--ZCRB1P1^ENST00000436372.1" ; Parent "TAF1--ZCRB1P1^ZCRB1P1^ENSG00000224208.1" ; exon_id "ENSE00001617683.1" ; exon_number 1 ; gene_id "TAF1--ZCRB1P1^ZCRB1P1^ENSG00000224208.1" ; gene_name ZCRB1P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021791.1" ; havana_transcript "OTTHUMT00000057124.1" ; hgnc_id "HGNC:54987" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chrX,71315631,71315879,-" ; tag pseudo_consens basic ; transcript_id "TAF1--ZCRB1P1^ENST00000436372.1" ; transcript_name "ZCRB1P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
ZC3H4--AL513478.3 HAVANA gene 22493 25550 . + . FI_gene_label "AL513478.3^ENSG00000284658.1" ; ID "ZC3H4--AL513478.3^AL513478.3^ENSG00000284658.1" ; exon_id "ENSE00003811844.1" ; exon_number 1 ; gene_id "ZC3H4--AL513478.3^AL513478.3^ENSG00000284658.1" ; gene_name "AL513478.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000192337.1" ; havana_transcript "OTTHUMT00000493569.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr9,66208791,66208833,-" ; tag basic ; transcript_id "ZC3H4--AL513478.3^ENST00000641636.1" ; transcript_name "AL513478.3-201" ; transcript_type unprocessed_pseudogene
ZC3H4--AL513478.3 HAVANA RNA 22493 25550 . + . FI_gene_label "AL513478.3^ENSG00000284658.1" ; ID "ZC3H4--AL513478.3^ENST00000641636.1" ; Parent "ZC3H4--AL513478.3^AL513478.3^ENSG00000284658.1" ; exon_id "ENSE00003811844.1" ; exon_number 1 ; gene_id "ZC3H4--AL513478.3^AL513478.3^ENSG00000284658.1" ; gene_name "AL513478.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000192337.1" ; havana_transcript "OTTHUMT00000493569.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr9,66208791,66208833,-" ; tag basic ; transcript_id "ZC3H4--AL513478.3^ENST00000641636.1" ; transcript_name "AL513478.3-201" ; transcript_type unprocessed_pseudogene
L1 and L2 created:
ZC3H4--CDRT15P12 HAVANA gene 22493 23533 . + . FI_gene_label "CDRT15P12^ENSG00000233765.1" ; ID "ZC3H4--CDRT15P12^CDRT15P12^ENSG00000233765.1" ; exon_id "ENSE00001618980.1" ; exon_number 1 ; gene_id "ZC3H4--CDRT15P12^CDRT15P12^ENSG00000233765.1" ; gene_name CDRT15P12 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000067362.1" ; havana_transcript "OTTHUMT00000144093.1" ; hgnc_id "HGNC:54919" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr9,66254174,66254464,-" ; tag basic ; transcript_id "ZC3H4--CDRT15P12^ENST00000417001.1" ; transcript_name "CDRT15P12-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
ZC3H4--CDRT15P12 HAVANA RNA 22493 23533 . + . FI_gene_label "CDRT15P12^ENSG00000233765.1" ; ID "ZC3H4--CDRT15P12^ENST00000417001.1" ; Parent "ZC3H4--CDRT15P12^CDRT15P12^ENSG00000233765.1" ; exon_id "ENSE00001618980.1" ; exon_number 1 ; gene_id "ZC3H4--CDRT15P12^CDRT15P12^ENSG00000233765.1" ; gene_name CDRT15P12 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000067362.1" ; havana_transcript "OTTHUMT00000144093.1" ; hgnc_id "HGNC:54919" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr9,66254174,66254464,-" ; tag basic ; transcript_id "ZC3H4--CDRT15P12^ENST00000417001.1" ; transcript_name "CDRT15P12-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
555 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 1 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 ------------------------------
754 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 29 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed