Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/e3173df81b05778ffc18bad3ebefe6/fi_workdir/659_cB6-T1-TRNA-1_B23MHV2LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/149271eb89f3ec10f16ed8aecfb254/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/149271eb89f3ec10f16ed8aecfb254/.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: 3900
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3900
=> 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:3900
=> 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:
AACS--AC117473.1 HAVANA gene 1002 34599 . + . FI_gene_label "AACS^ENSG00000081760.17" ; ID "AACS--AC117473.1^AACS^ENSG00000081760.17" ; ccdsid "CCDS9263.1" ; exon_id "ENSE00001351954.4" ; exon_number 1 ; gene_id "AACS--AC117473.1^AACS^ENSG00000081760.17" ; gene_name AACS ; gene_type protein_coding ; havana_gene "OTTHUMG00000168550.4" ; havana_transcript "OTTHUMT00000400202.2" ; hgnc_id "HGNC:21298" ; level 2 ; orig_coord_info "chr12,125065585,125065717,+" ; protein_id "ENSP00000324842.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AACS--AC117473.1^ENST00000316519.11" ; transcript_name "AACS-201" ; transcript_support_level 1 ; transcript_type protein_coding
AACS--AC117473.1 HAVANA mRNA 1002 34599 . + . FI_gene_label "AACS^ENSG00000081760.17" ; ID "AACS--AC117473.1^ENST00000316519.11" ; Parent "AACS--AC117473.1^AACS^ENSG00000081760.17" ; ccdsid "CCDS9263.1" ; exon_id "ENSE00001351954.4" ; exon_number 1 ; gene_id "AACS--AC117473.1^AACS^ENSG00000081760.17" ; gene_name AACS ; gene_type protein_coding ; havana_gene "OTTHUMG00000168550.4" ; havana_transcript "OTTHUMT00000400202.2" ; hgnc_id "HGNC:21298" ; level 2 ; orig_coord_info "chr12,125065585,125065717,+" ; protein_id "ENSP00000324842.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AACS--AC117473.1^ENST00000316519.11" ; transcript_name "AACS-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ANKRD11--LIN9 HAVANA gene 1001 45872 . + . FI_gene_label "ANKRD11^ENSG00000167522.16" ; ID "ANKRD11--LIN9^ANKRD11^ENSG00000167522.16" ; ccdsid "CCDS32513.1" ; exon_id "ENSE00003537320.1" ; exon_number 3 ; gene_id "ANKRD11--LIN9^ANKRD11^ENSG00000167522.16" ; gene_name ANKRD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175548.14" ; havana_transcript "OTTHUMT00000430462.6" ; hgnc_id "HGNC:21316" ; level 2 ; orig_coord_info "chr16,89316933,89317019,-" ; protein_id "ENSP00000301030.4" ; tag basic MANE_Select CCDS ; transcript_id "ANKRD11--LIN9^ENST00000301030.10" ; transcript_name "ANKRD11-201" ; transcript_support_level 5 ; transcript_type protein_coding
ANKRD11--LIN9 HAVANA mRNA 1001 45872 . + . FI_gene_label "ANKRD11^ENSG00000167522.16" ; ID "ANKRD11--LIN9^ENST00000301030.10" ; Parent "ANKRD11--LIN9^ANKRD11^ENSG00000167522.16" ; ccdsid "CCDS32513.1" ; exon_id "ENSE00003537320.1" ; exon_number 3 ; gene_id "ANKRD11--LIN9^ANKRD11^ENSG00000167522.16" ; gene_name ANKRD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175548.14" ; havana_transcript "OTTHUMT00000430462.6" ; hgnc_id "HGNC:21316" ; level 2 ; orig_coord_info "chr16,89316933,89317019,-" ; protein_id "ENSP00000301030.4" ; tag basic MANE_Select CCDS ; transcript_id "ANKRD11--LIN9^ENST00000301030.10" ; transcript_name "ANKRD11-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ANKRD11--LIN9 HAVANA gene 49009 65177 . + . FI_gene_label "LIN9^ENSG00000183814.16" ; ID "ANKRD11--LIN9^LIN9^ENSG00000183814.16" ; ccdsid "CCDS1553.1" ; exon_id "ENSE00001851042.1" ; exon_number 1 ; gene_id "ANKRD11--LIN9^LIN9^ENSG00000183814.16" ; gene_name LIN9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037557.4" ; havana_transcript "OTTHUMT00000091523.2" ; hgnc_id "HGNC:30830" ; level 2 ; orig_coord_info "chr1,226309109,226309187,-" ; protein_id "ENSP00000329102.5" ; tag basic appris_principal_2 CCDS ; transcript_id "ANKRD11--LIN9^ENST00000328205.9" ; transcript_name "LIN9-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANKRD11--LIN9 HAVANA mRNA 49009 65177 . + . FI_gene_label "LIN9^ENSG00000183814.16" ; ID "ANKRD11--LIN9^ENST00000328205.9" ; Parent "ANKRD11--LIN9^LIN9^ENSG00000183814.16" ; ccdsid "CCDS1553.1" ; exon_id "ENSE00001851042.1" ; exon_number 1 ; gene_id "ANKRD11--LIN9^LIN9^ENSG00000183814.16" ; gene_name LIN9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037557.4" ; havana_transcript "OTTHUMT00000091523.2" ; hgnc_id "HGNC:30830" ; level 2 ; orig_coord_info "chr1,226309109,226309187,-" ; protein_id "ENSP00000329102.5" ; tag basic appris_principal_2 CCDS ; transcript_id "ANKRD11--LIN9^ENST00000328205.9" ; transcript_name "LIN9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DIP2A--TMEM201 HAVANA gene 44352 52664 . + . FI_gene_label "TMEM201^ENSG00000188807.13" ; ID "DIP2A--TMEM201^TMEM201^ENSG00000188807.13" ; ccdsid "CCDS30579.1" ; exon_id "ENSE00001864591.1" ; exon_number 1 ; gene_id "DIP2A--TMEM201^TMEM201^ENSG00000188807.13" ; gene_name TMEM201 ; gene_type protein_coding ; havana_gene "OTTHUMG00000057457.3" ; havana_transcript "OTTHUMT00000127673.2" ; hgnc_id "HGNC:33719" ; level 2 ; orig_coord_info "chr1,9588931,9589043,+" ; protein_id "ENSP00000344772.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "DIP2A--TMEM201^ENST00000340305.9" ; transcript_name "TMEM201-201" ; transcript_support_level 1 ; transcript_type protein_coding
DIP2A--TMEM201 HAVANA mRNA 44352 52664 . + . FI_gene_label "TMEM201^ENSG00000188807.13" ; ID "DIP2A--TMEM201^ENST00000340305.9" ; Parent "DIP2A--TMEM201^TMEM201^ENSG00000188807.13" ; ccdsid "CCDS30579.1" ; exon_id "ENSE00001864591.1" ; exon_number 1 ; gene_id "DIP2A--TMEM201^TMEM201^ENSG00000188807.13" ; gene_name TMEM201 ; gene_type protein_coding ; havana_gene "OTTHUMG00000057457.3" ; havana_transcript "OTTHUMT00000127673.2" ; hgnc_id "HGNC:33719" ; level 2 ; orig_coord_info "chr1,9588931,9589043,+" ; protein_id "ENSP00000344772.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "DIP2A--TMEM201^ENST00000340305.9" ; transcript_name "TMEM201-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DIP2A--TMEM201 HAVANA gene 1009 41033 . + . FI_gene_label "DIP2A^ENSG00000160305.18" ; ID "DIP2A--TMEM201^DIP2A^ENSG00000160305.18" ; ccdsid "CCDS54490.1" ; exon_id "ENSE00001542216.1" ; exon_number 1 ; gene_id "DIP2A--TMEM201^DIP2A^ENSG00000160305.18" ; gene_name DIP2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000090717.6" ; havana_transcript "OTTHUMT00000207431.1" ; hgnc_id "HGNC:17217" ; level 2 ; orig_coord_info "chr21,46459132,46459222,+" ; protein_id "ENSP00000383133.1" ; tag basic appris_alternative_2 CCDS ; transcript_id "DIP2A--TMEM201^ENST00000400274.5" ; transcript_name "DIP2A-201" ; transcript_support_level 5 ; transcript_type protein_coding
DIP2A--TMEM201 HAVANA mRNA 1009 41033 . + . FI_gene_label "DIP2A^ENSG00000160305.18" ; ID "DIP2A--TMEM201^ENST00000400274.5" ; Parent "DIP2A--TMEM201^DIP2A^ENSG00000160305.18" ; ccdsid "CCDS54490.1" ; exon_id "ENSE00001542216.1" ; exon_number 1 ; gene_id "DIP2A--TMEM201^DIP2A^ENSG00000160305.18" ; gene_name DIP2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000090717.6" ; havana_transcript "OTTHUMT00000207431.1" ; hgnc_id "HGNC:17217" ; level 2 ; orig_coord_info "chr21,46459132,46459222,+" ; protein_id "ENSP00000383133.1" ; tag basic appris_alternative_2 CCDS ; transcript_id "DIP2A--TMEM201^ENST00000400274.5" ; transcript_name "DIP2A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
EPHB2--ZSWIM5 HAVANA gene 35022 52330 . + . FI_gene_label "ZSWIM5^ENSG00000162415.7" ; ID "EPHB2--ZSWIM5^ZSWIM5^ENSG00000162415.7" ; ccdsid "CCDS41319.1" ; exon_id "ENSE00001412591.5" ; exon_number 1 ; gene_id "EPHB2--ZSWIM5^ZSWIM5^ENSG00000162415.7" ; gene_name ZSWIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008950.3" ; havana_transcript "OTTHUMT00000024823.3" ; hgnc_id "HGNC:29299" ; level 2 ; orig_coord_info "chr1,45205756,45206350,-" ; protein_id "ENSP00000352614.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPHB2--ZSWIM5^ENST00000359600.6" ; transcript_name "ZSWIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPHB2--ZSWIM5 HAVANA mRNA 35022 52330 . + . FI_gene_label "ZSWIM5^ENSG00000162415.7" ; ID "EPHB2--ZSWIM5^ENST00000359600.6" ; Parent "EPHB2--ZSWIM5^ZSWIM5^ENSG00000162415.7" ; ccdsid "CCDS41319.1" ; exon_id "ENSE00001412591.5" ; exon_number 1 ; gene_id "EPHB2--ZSWIM5^ZSWIM5^ENSG00000162415.7" ; gene_name ZSWIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008950.3" ; havana_transcript "OTTHUMT00000024823.3" ; hgnc_id "HGNC:29299" ; level 2 ; orig_coord_info "chr1,45205756,45206350,-" ; protein_id "ENSP00000352614.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPHB2--ZSWIM5^ENST00000359600.6" ; transcript_name "ZSWIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPHB2--ZSWIM5 HAVANA gene 2206 22046 . + . FI_gene_label "EPHB2^ENSG00000133216.17" ; ID "EPHB2--ZSWIM5^EPHB2^ENSG00000133216.17" ; exon_id "ENSE00001464053.1" ; exon_number 1 ; gene_id "EPHB2--ZSWIM5^EPHB2^ENSG00000133216.17" ; gene_name EPHB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002881.4" ; havana_transcript "OTTHUMT00000008062.2" ; hgnc_id "HGNC:3393" ; level 2 ; orig_coord_info "chr1,22775202,22775244,+" ; protein_id "ENSP00000363758.1" ; tag non_canonical_polymorphism dotter_confirmed basic ; transcript_id "EPHB2--ZSWIM5^ENST00000374627.1" ; transcript_name "EPHB2-201" ; transcript_support_level 5 ; transcript_type protein_coding
EPHB2--ZSWIM5 HAVANA mRNA 2206 22046 . + . FI_gene_label "EPHB2^ENSG00000133216.17" ; ID "EPHB2--ZSWIM5^ENST00000374627.1" ; Parent "EPHB2--ZSWIM5^EPHB2^ENSG00000133216.17" ; exon_id "ENSE00001464053.1" ; exon_number 1 ; gene_id "EPHB2--ZSWIM5^EPHB2^ENSG00000133216.17" ; gene_name EPHB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002881.4" ; havana_transcript "OTTHUMT00000008062.2" ; hgnc_id "HGNC:3393" ; level 2 ; orig_coord_info "chr1,22775202,22775244,+" ; protein_id "ENSP00000363758.1" ; tag non_canonical_polymorphism dotter_confirmed basic ; transcript_id "EPHB2--ZSWIM5^ENST00000374627.1" ; transcript_name "EPHB2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ETNK1--AC022513.1 HAVANA gene 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--AC022513.1^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--AC022513.1^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--AC022513.1^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ETNK1--AC022513.1 HAVANA mRNA 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--AC022513.1^ENST00000266517.9" ; Parent "ETNK1--AC022513.1^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--AC022513.1^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--AC022513.1^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ETNK1--LINC01479 HAVANA gene 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--LINC01479^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--LINC01479^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--LINC01479^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ETNK1--LINC01479 HAVANA mRNA 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--LINC01479^ENST00000266517.9" ; Parent "ETNK1--LINC01479^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--LINC01479^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--LINC01479^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ETNK1--LINC02421 HAVANA gene 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--LINC02421^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--LINC02421^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--LINC02421^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ETNK1--LINC02421 HAVANA mRNA 1097 25041 . + . FI_gene_label "ETNK1^ENSG00000139163.16" ; ID "ETNK1--LINC02421^ENST00000266517.9" ; Parent "ETNK1--LINC02421^ETNK1^ENSG00000139163.16" ; exon_id "ENSE00003895506.1" ; exon_number 1 ; gene_id "ETNK1--LINC02421^ETNK1^ENSG00000139163.16" ; gene_name ETNK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169008.9" ; havana_transcript "OTTHUMT00000401926.4" ; hgnc_id "HGNC:24649" ; level 2 ; orig_coord_info "chr12,22625431,22625586,+" ; protein_id "ENSP00000266517.4" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "ETNK1--LINC02421^ENST00000266517.9" ; transcript_name "ETNK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LCORL--AC106894.1 HAVANA gene 1001 30717 . + . FI_gene_label "LCORL^ENSG00000178177.16" ; ID "LCORL--AC106894.1^LCORL^ENSG00000178177.16" ; ccdsid "CCDS3425.1" ; exon_id "ENSE00001918802.1" ; exon_number 1 ; gene_id "LCORL--AC106894.1^LCORL^ENSG00000178177.16" ; gene_name LCORL ; gene_type protein_coding ; havana_gene "OTTHUMG00000128538.6" ; havana_transcript "OTTHUMT00000250373.3" ; hgnc_id "HGNC:30776" ; level 2 ; orig_coord_info "chr4,18021598,18021751,-" ; protein_id "ENSP00000317566.3" ; tag basic CCDS ; transcript_id "LCORL--AC106894.1^ENST00000326877.8" ; transcript_name "LCORL-201" ; transcript_support_level 1 ; transcript_type protein_coding
LCORL--AC106894.1 HAVANA mRNA 1001 30717 . + . FI_gene_label "LCORL^ENSG00000178177.16" ; ID "LCORL--AC106894.1^ENST00000326877.8" ; Parent "LCORL--AC106894.1^LCORL^ENSG00000178177.16" ; ccdsid "CCDS3425.1" ; exon_id "ENSE00001918802.1" ; exon_number 1 ; gene_id "LCORL--AC106894.1^LCORL^ENSG00000178177.16" ; gene_name LCORL ; gene_type protein_coding ; havana_gene "OTTHUMG00000128538.6" ; havana_transcript "OTTHUMT00000250373.3" ; hgnc_id "HGNC:30776" ; level 2 ; orig_coord_info "chr4,18021598,18021751,-" ; protein_id "ENSP00000317566.3" ; tag basic CCDS ; transcript_id "LCORL--AC106894.1^ENST00000326877.8" ; transcript_name "LCORL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LCORL--LDB2 HAVANA gene 33751 58654 . + . FI_gene_label "LDB2^ENSG00000169744.13" ; ID "LCORL--LDB2^LDB2^ENSG00000169744.13" ; ccdsid "CCDS3420.1" ; exon_id "ENSE00002064728.2" ; exon_number 1 ; gene_id "LCORL--LDB2^LDB2^ENSG00000169744.13" ; gene_name LDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048212.5" ; havana_transcript "OTTHUMT00000250321.3" ; hgnc_id "HGNC:6533" ; level 2 ; orig_coord_info "chr4,16898354,16898485,-" ; protein_id "ENSP00000306772.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LCORL--LDB2^ENST00000304523.10" ; transcript_name "LDB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
LCORL--LDB2 HAVANA mRNA 33751 58654 . + . FI_gene_label "LDB2^ENSG00000169744.13" ; ID "LCORL--LDB2^ENST00000304523.10" ; Parent "LCORL--LDB2^LDB2^ENSG00000169744.13" ; ccdsid "CCDS3420.1" ; exon_id "ENSE00002064728.2" ; exon_number 1 ; gene_id "LCORL--LDB2^LDB2^ENSG00000169744.13" ; gene_name LDB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048212.5" ; havana_transcript "OTTHUMT00000250321.3" ; hgnc_id "HGNC:6533" ; level 2 ; orig_coord_info "chr4,16898354,16898485,-" ; protein_id "ENSP00000306772.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LCORL--LDB2^ENST00000304523.10" ; transcript_name "LDB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LCORL--LDB2 HAVANA gene 1001 30717 . + . FI_gene_label "LCORL^ENSG00000178177.16" ; ID "LCORL--LDB2^LCORL^ENSG00000178177.16" ; ccdsid "CCDS3425.1" ; exon_id "ENSE00001918802.1" ; exon_number 1 ; gene_id "LCORL--LDB2^LCORL^ENSG00000178177.16" ; gene_name LCORL ; gene_type protein_coding ; havana_gene "OTTHUMG00000128538.6" ; havana_transcript "OTTHUMT00000250373.3" ; hgnc_id "HGNC:30776" ; level 2 ; orig_coord_info "chr4,18021598,18021751,-" ; protein_id "ENSP00000317566.3" ; tag basic CCDS ; transcript_id "LCORL--LDB2^ENST00000326877.8" ; transcript_name "LCORL-201" ; transcript_support_level 1 ; transcript_type protein_coding
LCORL--LDB2 HAVANA mRNA 1001 30717 . + . FI_gene_label "LCORL^ENSG00000178177.16" ; ID "LCORL--LDB2^ENST00000326877.8" ; Parent "LCORL--LDB2^LCORL^ENSG00000178177.16" ; ccdsid "CCDS3425.1" ; exon_id "ENSE00001918802.1" ; exon_number 1 ; gene_id "LCORL--LDB2^LCORL^ENSG00000178177.16" ; gene_name LCORL ; gene_type protein_coding ; havana_gene "OTTHUMG00000128538.6" ; havana_transcript "OTTHUMT00000250373.3" ; hgnc_id "HGNC:30776" ; level 2 ; orig_coord_info "chr4,18021598,18021751,-" ; protein_id "ENSP00000317566.3" ; tag basic CCDS ; transcript_id "LCORL--LDB2^ENST00000326877.8" ; transcript_name "LCORL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MTAP--SNX29 HAVANA gene 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--SNX29^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--SNX29^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--SNX29^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--SNX29 HAVANA mRNA 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--SNX29^ENST00000419385.5" ; Parent "MTAP--SNX29^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--SNX29^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--SNX29^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
MTAP--SNX29 HAVANA gene 52514 56049 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "MTAP--SNX29^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "MTAP--SNX29^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 "MTAP--SNX29^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
MTAP--SNX29 HAVANA mRNA 52514 56049 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "MTAP--SNX29^ENST00000562510.1" ; Parent "MTAP--SNX29^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "MTAP--SNX29^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 "MTAP--SNX29^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA10 HAVANA gene 6881 16334 . + . FI_gene_label "PCDHGA10^ENSG00000253846.2" ; ID "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2" ; ccdsid "CCDS47292.1" ; exon_id "ENSE00001792208.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2" ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2" ; havana_transcript "OTTHUMT00000374747.1" ; hgnc_id "HGNC:8697" ; level 2 ; orig_coord_info "chr5,141413176,141415611,+" ; protein_id "ENSP00000381611.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2" ; transcript_name "PCDHGA10-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA10 HAVANA mRNA 6881 16334 . + . FI_gene_label "PCDHGA10^ENSG00000253846.2" ; ID "PCDHGA4--PCDHGA10^ENST00000398610.2" ; Parent "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2" ; ccdsid "CCDS47292.1" ; exon_id "ENSE00001792208.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2" ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2" ; havana_transcript "OTTHUMT00000374747.1" ; hgnc_id "HGNC:8697" ; level 2 ; orig_coord_info "chr5,141413176,141415611,+" ; protein_id "ENSP00000381611.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2" ; transcript_name "PCDHGA10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA10 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA10 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA10^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA11 HAVANA gene 6696 15501 . + . FI_gene_label "PCDHGA11^ENSG00000253873.6" ; ID "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6" ; ccdsid "CCDS47294.1" ; exon_id "ENSE00001533810.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6" ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3" ; havana_transcript "OTTHUMT00000376974.3" ; hgnc_id "HGNC:8698" ; level 2 ; orig_coord_info "chr5,141421228,141423660,+" ; protein_id "ENSP00000381589.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7" ; transcript_name "PCDHGA11-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA11 HAVANA mRNA 6696 15501 . + . FI_gene_label "PCDHGA11^ENSG00000253873.6" ; ID "PCDHGA4--PCDHGA11^ENST00000398587.7" ; Parent "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6" ; ccdsid "CCDS47294.1" ; exon_id "ENSE00001533810.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6" ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3" ; havana_transcript "OTTHUMT00000376974.3" ; hgnc_id "HGNC:8698" ; level 2 ; orig_coord_info "chr5,141421228,141423660,+" ; protein_id "ENSP00000381589.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7" ; transcript_name "PCDHGA11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA11 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA11 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA11^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA12 HAVANA gene 6692 14584 . + . FI_gene_label "PCDHGA12^ENSG00000253159.3" ; ID "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3" ; ccdsid "CCDS4260.1" ; exon_id "ENSE00000814269.5" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3" ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6" ; havana_transcript "OTTHUMT00000251806.3" ; hgnc_id "HGNC:8699" ; level 2 ; orig_coord_info "chr5,141430760,141433183,+" ; protein_id "ENSP00000252085.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4" ; transcript_name "PCDHGA12-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA12 HAVANA mRNA 6692 14584 . + . FI_gene_label "PCDHGA12^ENSG00000253159.3" ; ID "PCDHGA4--PCDHGA12^ENST00000252085.4" ; Parent "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3" ; ccdsid "CCDS4260.1" ; exon_id "ENSE00000814269.5" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3" ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6" ; havana_transcript "OTTHUMT00000251806.3" ; hgnc_id "HGNC:8699" ; level 2 ; orig_coord_info "chr5,141430760,141433183,+" ; protein_id "ENSP00000252085.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4" ; transcript_name "PCDHGA12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA12 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA12 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA12^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA8 HAVANA gene 9168 18348 . + . FI_gene_label "PCDHGA8^ENSG00000253767.3" ; ID "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3" ; ccdsid "CCDS47291.1" ; exon_id "ENSE00001533882.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3" ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2" ; havana_transcript "OTTHUMT00000376972.1" ; hgnc_id "HGNC:8706" ; level 2 ; orig_coord_info "chr5,141392814,141395237,+" ; protein_id "ENSP00000381605.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3" ; transcript_name "PCDHGA8-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA8 HAVANA mRNA 9168 18348 . + . FI_gene_label "PCDHGA8^ENSG00000253767.3" ; ID "PCDHGA4--PCDHGA8^ENST00000398604.3" ; Parent "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3" ; ccdsid "CCDS47291.1" ; exon_id "ENSE00001533882.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3" ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2" ; havana_transcript "OTTHUMT00000376972.1" ; hgnc_id "HGNC:8706" ; level 2 ; orig_coord_info "chr5,141392814,141395237,+" ; protein_id "ENSP00000381605.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3" ; transcript_name "PCDHGA8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA8 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA8 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA8^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA9 HAVANA gene 6713 14440 . + . FI_gene_label "PCDHGA9^ENSG00000261934.2" ; ID "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2" ; ccdsid "CCDS58981.1" ; exon_id "ENSE00002639131.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2" ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2" ; havana_transcript "OTTHUMT00000437105.1" ; hgnc_id "HGNC:8707" ; level 2 ; orig_coord_info "chr5,141402953,141405376,+" ; protein_id "ENSP00000460274.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1" ; transcript_name "PCDHGA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA9 HAVANA mRNA 6713 14440 . + . FI_gene_label "PCDHGA9^ENSG00000261934.2" ; ID "PCDHGA4--PCDHGA9^ENST00000573521.1" ; Parent "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2" ; ccdsid "CCDS58981.1" ; exon_id "ENSE00002639131.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2" ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2" ; havana_transcript "OTTHUMT00000437105.1" ; hgnc_id "HGNC:8707" ; level 2 ; orig_coord_info "chr5,141402953,141405376,+" ; protein_id "ENSP00000460274.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1" ; transcript_name "PCDHGA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGA9 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA9 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGA9^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGB6 HAVANA gene 6874 16473 . + . FI_gene_label "PCDHGB6^ENSG00000253305.2" ; ID "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2" ; ccdsid "CCDS54929.1" ; exon_id "ENSE00002122685.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2" ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2" ; havana_transcript "OTTHUMT00000374746.1" ; hgnc_id "HGNC:8713" ; level 2 ; orig_coord_info "chr5,141408203,141410620,+" ; protein_id "ENSP00000428603.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1" ; transcript_name "PCDHGB6-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB6 HAVANA mRNA 6874 16473 . + . FI_gene_label "PCDHGB6^ENSG00000253305.2" ; ID "PCDHGA4--PCDHGB6^ENST00000520790.1" ; Parent "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2" ; ccdsid "CCDS54929.1" ; exon_id "ENSE00002122685.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2" ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2" ; havana_transcript "OTTHUMT00000374746.1" ; hgnc_id "HGNC:8713" ; level 2 ; orig_coord_info "chr5,141408203,141410620,+" ; protein_id "ENSP00000428603.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1" ; transcript_name "PCDHGB6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGB6 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB6 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGB6^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGB7 HAVANA gene 6724 14653 . + . FI_gene_label "PCDHGB7^ENSG00000254122.3" ; ID "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3" ; ccdsid "CCDS47293.1" ; exon_id "ENSE00001533845.4" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3" ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2" ; havana_transcript "OTTHUMT00000376973.2" ; hgnc_id "HGNC:8714" ; level 2 ; orig_coord_info "chr5,141417860,141420274,+" ; protein_id "ENSP00000381594.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4" ; transcript_name "PCDHGB7-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB7 HAVANA mRNA 6724 14653 . + . FI_gene_label "PCDHGB7^ENSG00000254122.3" ; ID "PCDHGA4--PCDHGB7^ENST00000398594.4" ; Parent "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3" ; ccdsid "CCDS47293.1" ; exon_id "ENSE00001533845.4" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3" ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2" ; havana_transcript "OTTHUMT00000376973.2" ; hgnc_id "HGNC:8714" ; level 2 ; orig_coord_info "chr5,141417860,141420274,+" ; protein_id "ENSP00000381594.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4" ; transcript_name "PCDHGB7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGB7 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB7 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGB7^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC3 HAVANA gene 6711 16897 . + . FI_gene_label "PCDHGC3^ENSG00000240184.7" ; ID "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7" ; ccdsid "CCDS4261.1" ; exon_id "ENSE00001199459.7" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7" ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8" ; havana_transcript "OTTHUMT00000251808.5" ; hgnc_id "HGNC:8716" ; level 2 ; orig_coord_info "chr5,141476117,141478546,+" ; protein_id "ENSP00000312070.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5" ; transcript_name "PCDHGC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC3 HAVANA mRNA 6711 16897 . + . FI_gene_label "PCDHGC3^ENSG00000240184.7" ; ID "PCDHGA4--PCDHGC3^ENST00000308177.5" ; Parent "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7" ; ccdsid "CCDS4261.1" ; exon_id "ENSE00001199459.7" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7" ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8" ; havana_transcript "OTTHUMT00000251808.5" ; hgnc_id "HGNC:8716" ; level 2 ; orig_coord_info "chr5,141476117,141478546,+" ; protein_id "ENSP00000312070.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5" ; transcript_name "PCDHGC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC3 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC3 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC3^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC4 HAVANA gene 6869 14665 . + . FI_gene_label "PCDHGC4^ENSG00000242419.5" ; ID "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5" ; ccdsid "CCDS4262.1" ; exon_id "ENSE00001162305.2" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5" ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4" ; havana_transcript "OTTHUMT00000251820.2" ; hgnc_id "HGNC:8717" ; level 2 ; orig_coord_info "chr5,141485174,141487615,+" ; protein_id "ENSP00000306918.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1" ; transcript_name "PCDHGC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC4 HAVANA mRNA 6869 14665 . + . FI_gene_label "PCDHGC4^ENSG00000242419.5" ; ID "PCDHGA4--PCDHGC4^ENST00000306593.1" ; Parent "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5" ; ccdsid "CCDS4262.1" ; exon_id "ENSE00001162305.2" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5" ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4" ; havana_transcript "OTTHUMT00000251820.2" ; hgnc_id "HGNC:8717" ; level 2 ; orig_coord_info "chr5,141485174,141487615,+" ; protein_id "ENSP00000306918.1" ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1" ; transcript_name "PCDHGC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC4 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC4 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC4^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC5 HAVANA gene 6692 14717 . + . FI_gene_label "PCDHGC5^ENSG00000240764.4" ; ID "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4" ; ccdsid "CCDS4263.1" ; exon_id "ENSE00000766474.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4" ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2" ; havana_transcript "OTTHUMT00000251819.2" ; hgnc_id "HGNC:8718" ; level 2 ; orig_coord_info "chr5,141489241,141491700,+" ; protein_id "ENSP00000252087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3" ; transcript_name "PCDHGC5-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC5 HAVANA mRNA 6692 14717 . + . FI_gene_label "PCDHGC5^ENSG00000240764.4" ; ID "PCDHGA4--PCDHGC5^ENST00000252087.3" ; Parent "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4" ; ccdsid "CCDS4263.1" ; exon_id "ENSE00000766474.3" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4" ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2" ; havana_transcript "OTTHUMT00000251819.2" ; hgnc_id "HGNC:8718" ; level 2 ; orig_coord_info "chr5,141489241,141491700,+" ; protein_id "ENSP00000252087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3" ; transcript_name "PCDHGC5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHGA4--PCDHGC5 HAVANA gene 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC5 HAVANA mRNA 1001 3691 . + . FI_gene_label "PCDHGA4^ENSG00000262576.3" ; ID "PCDHGA4--PCDHGC5^ENST00000612927.1" ; Parent "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3" ; ccdsid "CCDS75331.1" ; exon_id "ENSE00003715198.1" ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3" ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4" ; havana_transcript "OTTHUMT00000476684.1" ; hgnc_id "HGNC:8702" ; level 2 ; orig_coord_info "chr5,141355108,141357660,+" ; protein_id "ENSP00000477894.1" ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1" ; transcript_name "PCDHGA4-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PDXDC1--NPIPB5 ENSEMBL gene 1610 14305 . + . FI_gene_label "PDXDC1^ENSG00000179889.19" ; ID "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19" ; exon_id "ENSE00002269182.2" ; exon_number 1 ; gene_id "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19" ; gene_name PDXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166304.6" ; hgnc_id "HGNC:28995" ; level 3 ; orig_coord_info "chr16,14975200,14975220,+" ; protein_id "ENSP00000322807.8" ; tag basic ; transcript_id "PDXDC1--NPIPB5^ENST00000325823.11" ; transcript_name "PDXDC1-201" ; transcript_support_level 5 ; transcript_type protein_coding
PDXDC1--NPIPB5 ENSEMBL mRNA 1610 14305 . + . FI_gene_label "PDXDC1^ENSG00000179889.19" ; ID "PDXDC1--NPIPB5^ENST00000325823.11" ; Parent "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19" ; exon_id "ENSE00002269182.2" ; exon_number 1 ; gene_id "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19" ; gene_name PDXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166304.6" ; hgnc_id "HGNC:28995" ; level 3 ; orig_coord_info "chr16,14975200,14975220,+" ; protein_id "ENSP00000322807.8" ; tag basic ; transcript_id "PDXDC1--NPIPB5^ENST00000325823.11" ; transcript_name "PDXDC1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PDXDC1--NPIPB5 HAVANA gene 43624 46955 . + . FI_gene_label "NPIPB5^ENSG00000243716.10" ; ID "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10" ; exon_id "ENSE00002265272.1" ; exon_number 3 ; gene_id "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10" ; gene_name NPIPB5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163573.6" ; havana_transcript "OTTHUMT00000403183.2" ; hgnc_id "HGNC:37233" ; level 2 ; orig_coord_info "chr16,22513802,22513834,+" ; protein_id "ENSP00000440137.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "PDXDC1--NPIPB5^ENST00000356156.7" ; transcript_name "NPIPB5-201" ; transcript_support_level 4 ; transcript_type protein_coding
PDXDC1--NPIPB5 HAVANA mRNA 43624 46955 . + . FI_gene_label "NPIPB5^ENSG00000243716.10" ; ID "PDXDC1--NPIPB5^ENST00000356156.7" ; Parent "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10" ; exon_id "ENSE00002265272.1" ; exon_number 3 ; gene_id "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10" ; gene_name NPIPB5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163573.6" ; havana_transcript "OTTHUMT00000403183.2" ; hgnc_id "HGNC:37233" ; level 2 ; orig_coord_info "chr16,22513802,22513834,+" ; protein_id "ENSP00000440137.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "PDXDC1--NPIPB5^ENST00000356156.7" ; transcript_name "NPIPB5-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
SLC9A8--SLC44A5 HAVANA gene 1116 22876 . + . FI_gene_label "SLC9A8^ENSG00000197818.12" ; ID "SLC9A8--SLC44A5^SLC9A8^ENSG00000197818.12" ; ccdsid "CCDS13421.1" ; exon_id "ENSE00001958508.2" ; exon_number 1 ; gene_id "SLC9A8--SLC44A5^SLC9A8^ENSG00000197818.12" ; gene_name SLC9A8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032710.4" ; havana_transcript "OTTHUMT00000106483.3" ; hgnc_id "HGNC:20728" ; level 2 ; orig_coord_info "chr20,49812923,49812948,+" ; protein_id "ENSP00000354966.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC9A8--SLC44A5^ENST00000361573.3" ; transcript_name "SLC9A8-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC9A8--SLC44A5 HAVANA mRNA 1116 22876 . + . FI_gene_label "SLC9A8^ENSG00000197818.12" ; ID "SLC9A8--SLC44A5^ENST00000361573.3" ; Parent "SLC9A8--SLC44A5^SLC9A8^ENSG00000197818.12" ; ccdsid "CCDS13421.1" ; exon_id "ENSE00001958508.2" ; exon_number 1 ; gene_id "SLC9A8--SLC44A5^SLC9A8^ENSG00000197818.12" ; gene_name SLC9A8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032710.4" ; havana_transcript "OTTHUMT00000106483.3" ; hgnc_id "HGNC:20728" ; level 2 ; orig_coord_info "chr20,49812923,49812948,+" ; protein_id "ENSP00000354966.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC9A8--SLC44A5^ENST00000361573.3" ; transcript_name "SLC9A8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC9A8--SLC44A5 HAVANA gene 25909 52524 . + . FI_gene_label "SLC44A5^ENSG00000137968.16" ; ID "SLC9A8--SLC44A5^SLC44A5^ENSG00000137968.16" ; ccdsid "CCDS667.1" ; exon_id "ENSE00003460645.1" ; exon_number 2 ; gene_id "SLC9A8--SLC44A5^SLC44A5^ENSG00000137968.16" ; gene_name SLC44A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009721.3" ; havana_transcript "OTTHUMT00000026921.1" ; hgnc_id "HGNC:28524" ; level 2 ; orig_coord_info "chr1,75541435,75541447,-" ; protein_id "ENSP00000359892.5" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC9A8--SLC44A5^ENST00000370855.5" ; transcript_name "SLC44A5-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC9A8--SLC44A5 HAVANA mRNA 25909 52524 . + . FI_gene_label "SLC44A5^ENSG00000137968.16" ; ID "SLC9A8--SLC44A5^ENST00000370855.5" ; Parent "SLC9A8--SLC44A5^SLC44A5^ENSG00000137968.16" ; ccdsid "CCDS667.1" ; exon_id "ENSE00003460645.1" ; exon_number 2 ; gene_id "SLC9A8--SLC44A5^SLC44A5^ENSG00000137968.16" ; gene_name SLC44A5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009721.3" ; havana_transcript "OTTHUMT00000026921.1" ; hgnc_id "HGNC:28524" ; level 2 ; orig_coord_info "chr1,75541435,75541447,-" ; protein_id "ENSP00000359892.5" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC9A8--SLC44A5^ENST00000370855.5" ; transcript_name "SLC44A5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNX29--AL353684.1 HAVANA gene 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--AL353684.1^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--AL353684.1^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--AL353684.1^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--AL353684.1 HAVANA mRNA 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--AL353684.1^ENST00000562510.1" ; Parent "SNX29--AL353684.1^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--AL353684.1^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--AL353684.1^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
SNX29--AL354676.1 HAVANA gene 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--AL354676.1^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--AL354676.1^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--AL354676.1^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--AL354676.1 HAVANA mRNA 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--AL354676.1^ENST00000562510.1" ; Parent "SNX29--AL354676.1^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--AL354676.1^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--AL354676.1^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AACS--AC117473.1 HAVANA gene 37617 41008 . + . FI_gene_label "AC117473.1^ENSG00000251088.1" ; ID "AACS--AC117473.1^AC117473.1^ENSG00000251088.1" ; exon_id "ENSE00002078572.1" ; exon_number 1 ; gene_id "AACS--AC117473.1^AC117473.1^ENSG00000251088.1" ; gene_name "AC117473.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000160119.1" ; havana_transcript "OTTHUMT00000359282.1" ; level 2 ; orig_coord_info "chr3,98233651,98233676,+" ; tag basic ; transcript_id "AACS--AC117473.1^ENST00000508616.1" ; transcript_name "AC117473.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
AACS--AC117473.1 HAVANA RNA 37617 41008 . + . FI_gene_label "AC117473.1^ENSG00000251088.1" ; ID "AACS--AC117473.1^ENST00000508616.1" ; Parent "AACS--AC117473.1^AC117473.1^ENSG00000251088.1" ; exon_id "ENSE00002078572.1" ; exon_number 1 ; gene_id "AACS--AC117473.1^AC117473.1^ENSG00000251088.1" ; gene_name "AC117473.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000160119.1" ; havana_transcript "OTTHUMT00000359282.1" ; level 2 ; orig_coord_info "chr3,98233651,98233676,+" ; tag basic ; transcript_id "AACS--AC117473.1^ENST00000508616.1" ; transcript_name "AC117473.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
ETNK1--AC022513.1 HAVANA gene 28042 28158 . + . FI_gene_label "AC022513.1^ENSG00000279505.1" ; ID "ETNK1--AC022513.1^AC022513.1^ENSG00000279505.1" ; exon_id "ENSE00003758015.1" ; exon_number 1 ; gene_id "ETNK1--AC022513.1^AC022513.1^ENSG00000279505.1" ; gene_name "AC022513.1" ; gene_type TEC ; havana_gene "OTTHUMG00000172893.1" ; havana_transcript "OTTHUMT00000421195.1" ; level 2 ; orig_coord_info "chr12,67753701,67753817,+" ; tag basic ; transcript_id "ETNK1--AC022513.1^ENST00000624512.1" ; transcript_name "AC022513.1-201" ; transcript_support_level NA ; transcript_type TEC
ETNK1--AC022513.1 HAVANA RNA 28042 28158 . + . FI_gene_label "AC022513.1^ENSG00000279505.1" ; ID "ETNK1--AC022513.1^ENST00000624512.1" ; Parent "ETNK1--AC022513.1^AC022513.1^ENSG00000279505.1" ; exon_id "ENSE00003758015.1" ; exon_number 1 ; gene_id "ETNK1--AC022513.1^AC022513.1^ENSG00000279505.1" ; gene_name "AC022513.1" ; gene_type TEC ; havana_gene "OTTHUMG00000172893.1" ; havana_transcript "OTTHUMT00000421195.1" ; level 2 ; orig_coord_info "chr12,67753701,67753817,+" ; tag basic ; transcript_id "ETNK1--AC022513.1^ENST00000624512.1" ; transcript_name "AC022513.1-201" ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created:
ETNK1--LINC01479 HAVANA gene 28042 29866 . + . FI_gene_label "LINC01479^ENSG00000255772.5" ; ID "ETNK1--LINC01479^LINC01479^ENSG00000255772.5" ; exon_id "ENSE00002285526.1" ; exon_number 1 ; gene_id "ETNK1--LINC01479^LINC01479^ENSG00000255772.5" ; gene_name LINC01479 ; gene_type lncRNA ; havana_gene "OTTHUMG00000169106.1" ; havana_transcript "OTTHUMT00000402291.1" ; hgnc_id "HGNC:51123" ; level 1 ; orig_coord_info "chr12,67929235,67929387,+" ; tag basic exp_conf ; transcript_id "ETNK1--LINC01479^ENST00000545520.5" ; transcript_name "LINC01479-201" ; transcript_support_level 2 ; transcript_type lncRNA
ETNK1--LINC01479 HAVANA RNA 28042 29866 . + . FI_gene_label "LINC01479^ENSG00000255772.5" ; ID "ETNK1--LINC01479^ENST00000545520.5" ; Parent "ETNK1--LINC01479^LINC01479^ENSG00000255772.5" ; exon_id "ENSE00002285526.1" ; exon_number 1 ; gene_id "ETNK1--LINC01479^LINC01479^ENSG00000255772.5" ; gene_name LINC01479 ; gene_type lncRNA ; havana_gene "OTTHUMG00000169106.1" ; havana_transcript "OTTHUMT00000402291.1" ; hgnc_id "HGNC:51123" ; level 1 ; orig_coord_info "chr12,67929235,67929387,+" ; tag basic exp_conf ; transcript_id "ETNK1--LINC01479^ENST00000545520.5" ; transcript_name "LINC01479-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
ETNK1--LINC02421 HAVANA gene 28042 35176 . + . FI_gene_label "LINC02421^ENSG00000255970.1" ; ID "ETNK1--LINC02421^LINC02421^ENSG00000255970.1" ; exon_id "ENSE00002292701.1" ; exon_number 1 ; gene_id "ETNK1--LINC02421^LINC02421^ENSG00000255970.1" ; gene_name LINC02421 ; gene_type lncRNA ; havana_gene "OTTHUMG00000169091.1" ; havana_transcript "OTTHUMT00000402224.1" ; hgnc_id "HGNC:53351" ; level 2 ; orig_coord_info "chr12,67729396,67729475,-" ; tag basic ; transcript_id "ETNK1--LINC02421^ENST00000542219.1" ; transcript_name "LINC02421-201" ; transcript_support_level 1 ; transcript_type lncRNA
ETNK1--LINC02421 HAVANA RNA 28042 35176 . + . FI_gene_label "LINC02421^ENSG00000255970.1" ; ID "ETNK1--LINC02421^ENST00000542219.1" ; Parent "ETNK1--LINC02421^LINC02421^ENSG00000255970.1" ; exon_id "ENSE00002292701.1" ; exon_number 1 ; gene_id "ETNK1--LINC02421^LINC02421^ENSG00000255970.1" ; gene_name LINC02421 ; gene_type lncRNA ; havana_gene "OTTHUMG00000169091.1" ; havana_transcript "OTTHUMT00000402224.1" ; hgnc_id "HGNC:53351" ; level 2 ; orig_coord_info "chr12,67729396,67729475,-" ; tag basic ; transcript_id "ETNK1--LINC02421^ENST00000542219.1" ; transcript_name "LINC02421-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
LCORL--AC106894.1 HAVANA gene 33718 36168 . + . FI_gene_label "AC106894.1^ENSG00000249998.1" ; ID "LCORL--AC106894.1^AC106894.1^ENSG00000249998.1" ; exon_id "ENSE00002028380.1" ; exon_number 1 ; gene_id "LCORL--AC106894.1^AC106894.1^ENSG00000249998.1" ; gene_name "AC106894.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000160229.1" ; havana_transcript "OTTHUMT00000359779.1" ; level 2 ; orig_coord_info "chr4,17073849,17073903,-" ; tag dotter_confirmed basic ; transcript_id "LCORL--AC106894.1^ENST00000511735.1" ; transcript_name "AC106894.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
LCORL--AC106894.1 HAVANA RNA 33718 36168 . + . FI_gene_label "AC106894.1^ENSG00000249998.1" ; ID "LCORL--AC106894.1^ENST00000511735.1" ; Parent "LCORL--AC106894.1^AC106894.1^ENSG00000249998.1" ; exon_id "ENSE00002028380.1" ; exon_number 1 ; gene_id "LCORL--AC106894.1^AC106894.1^ENSG00000249998.1" ; gene_name "AC106894.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000160229.1" ; havana_transcript "OTTHUMT00000359779.1" ; level 2 ; orig_coord_info "chr4,17073849,17073903,-" ; tag dotter_confirmed basic ; transcript_id "LCORL--AC106894.1^ENST00000511735.1" ; transcript_name "AC106894.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
SNX29--AL353684.1 HAVANA gene 41266 42385 . + . FI_gene_label "AL353684.1^ENSG00000277646.1" ; ID "SNX29--AL353684.1^AL353684.1^ENSG00000277646.1" ; exon_id "ENSE00003748492.1" ; exon_number 1 ; gene_id "SNX29--AL353684.1^AL353684.1^ENSG00000277646.1" ; gene_name "AL353684.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000187736.1" ; havana_transcript "OTTHUMT00000475500.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,29317833,29318952,+" ; tag pseudo_consens basic ; transcript_id "SNX29--AL353684.1^ENST00000622677.1" ; transcript_name "AL353684.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
SNX29--AL353684.1 HAVANA RNA 41266 42385 . + . FI_gene_label "AL353684.1^ENSG00000277646.1" ; ID "SNX29--AL353684.1^ENST00000622677.1" ; Parent "SNX29--AL353684.1^AL353684.1^ENSG00000277646.1" ; exon_id "ENSE00003748492.1" ; exon_number 1 ; gene_id "SNX29--AL353684.1^AL353684.1^ENSG00000277646.1" ; gene_name "AL353684.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000187736.1" ; havana_transcript "OTTHUMT00000475500.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,29317833,29318952,+" ; tag pseudo_consens basic ; transcript_id "SNX29--AL353684.1^ENST00000622677.1" ; transcript_name "AL353684.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
SNX29--AL354676.1 HAVANA gene 41266 41633 . + . FI_gene_label "AL354676.1^ENSG00000229834.1" ; ID "SNX29--AL354676.1^AL354676.1^ENSG00000229834.1" ; exon_id "ENSE00001734848.1" ; exon_number 1 ; gene_id "SNX29--AL354676.1^AL354676.1^ENSG00000229834.1" ; gene_name "AL354676.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019723.1" ; havana_transcript "OTTHUMT00000051981.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,29636486,29636853,+" ; tag pseudo_consens basic ; transcript_id "SNX29--AL354676.1^ENST00000458047.1" ; transcript_name "AL354676.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
SNX29--AL354676.1 HAVANA RNA 41266 41633 . + . FI_gene_label "AL354676.1^ENSG00000229834.1" ; ID "SNX29--AL354676.1^ENST00000458047.1" ; Parent "SNX29--AL354676.1^AL354676.1^ENSG00000229834.1" ; exon_id "ENSE00001734848.1" ; exon_number 1 ; gene_id "SNX29--AL354676.1^AL354676.1^ENSG00000229834.1" ; gene_name "AL354676.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019723.1" ; havana_transcript "OTTHUMT00000051981.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr9,29636486,29636853,+" ; tag pseudo_consens basic ; transcript_id "SNX29--AL354676.1^ENST00000458047.1" ; transcript_name "AL354676.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
339 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
617 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 31 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed