Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/b29a0893d1339a2aff669b84a95407/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/9373d85ab0aed754f8fd93fa988503/fi_workdir/tih_rna_sample_00096_23H5VFLT4_s11.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/b29a0893d1339a2aff669b84a95407/.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: 7018
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 7018
=> 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:7018
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 2 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AL049555.1--LLGL2 HAVANA gene 6580 28403 . + . FI_gene_label "LLGL2^ENSG00000073350.14" ; ID "AL049555.1--LLGL2^LLGL2^ENSG00000073350.14" ; ccdsid "CCDS11725.1" ; exon_id "ENSE00001687800.1" ; exon_number 2 ; gene_id "AL049555.1--LLGL2^LLGL2^ENSG00000073350.14" ; gene_name LLGL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179685.3" ; havana_transcript "OTTHUMT00000447631.1" ; hgnc_id "HGNC:6629" ; level 2 ; orig_coord_info "chr17,75543427,75543501,+" ; protein_id "ENSP00000167462.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "AL049555.1--LLGL2^ENST00000167462.9" ; transcript_name "LLGL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AL049555.1--LLGL2 HAVANA mRNA 6580 28403 . + . FI_gene_label "LLGL2^ENSG00000073350.14" ; ID "AL049555.1--LLGL2^ENST00000167462.9" ; Parent "AL049555.1--LLGL2^LLGL2^ENSG00000073350.14" ; ccdsid "CCDS11725.1" ; exon_id "ENSE00001687800.1" ; exon_number 2 ; gene_id "AL049555.1--LLGL2^LLGL2^ENSG00000073350.14" ; gene_name LLGL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179685.3" ; havana_transcript "OTTHUMT00000447631.1" ; hgnc_id "HGNC:6629" ; level 2 ; orig_coord_info "chr17,75543427,75543501,+" ; protein_id "ENSP00000167462.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "AL049555.1--LLGL2^ENST00000167462.9" ; transcript_name "LLGL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARHGEF17--CCS HAVANA gene 1001 21369 . + . FI_gene_label "ARHGEF17^ENSG00000110237.5" ; ID "ARHGEF17--CCS^ARHGEF17^ENSG00000110237.5" ; ccdsid "CCDS8221.1" ; exon_id "ENSE00001155082.6" ; exon_number 1 ; gene_id "ARHGEF17--CCS^ARHGEF17^ENSG00000110237.5" ; gene_name ARHGEF17 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167971.4" ; havana_transcript "OTTHUMT00000397365.2" ; hgnc_id "HGNC:21726" ; level 2 ; orig_coord_info "chr11,73308639,73311830,+" ; protein_id "ENSP00000263674.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ARHGEF17--CCS^ENST00000263674.4" ; transcript_name "ARHGEF17-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARHGEF17--CCS HAVANA mRNA 1001 21369 . + . FI_gene_label "ARHGEF17^ENSG00000110237.5" ; ID "ARHGEF17--CCS^ENST00000263674.4" ; Parent "ARHGEF17--CCS^ARHGEF17^ENSG00000110237.5" ; ccdsid "CCDS8221.1" ; exon_id "ENSE00001155082.6" ; exon_number 1 ; gene_id "ARHGEF17--CCS^ARHGEF17^ENSG00000110237.5" ; gene_name ARHGEF17 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167971.4" ; havana_transcript "OTTHUMT00000397365.2" ; hgnc_id "HGNC:21726" ; level 2 ; orig_coord_info "chr11,73308639,73311830,+" ; protein_id "ENSP00000263674.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ARHGEF17--CCS^ENST00000263674.4" ; transcript_name "ARHGEF17-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARHGEF17--CCS HAVANA gene 24458 29131 . + . FI_gene_label "CCS^ENSG00000173992.9" ; ID "ARHGEF17--CCS^CCS^ENSG00000173992.9" ; exon_id "ENSE00002197662.1" ; exon_number 2 ; gene_id "ARHGEF17--CCS^CCS^ENSG00000173992.9" ; gene_name CCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000167238.3" ; havana_transcript "OTTHUMT00000393832.1" ; hgnc_id "HGNC:1613" ; level 2 ; orig_coord_info "chr11,66593660,66593714,+" ; protein_id "ENSP00000307870.4" ; tag not_organism_supported basic ; transcript_id "ARHGEF17--CCS^ENST00000310190.8" ; transcript_name "CCS-201" ; transcript_support_level 5 ; transcript_type protein_coding
ARHGEF17--CCS HAVANA mRNA 24458 29131 . + . FI_gene_label "CCS^ENSG00000173992.9" ; ID "ARHGEF17--CCS^ENST00000310190.8" ; Parent "ARHGEF17--CCS^CCS^ENSG00000173992.9" ; exon_id "ENSE00002197662.1" ; exon_number 2 ; gene_id "ARHGEF17--CCS^CCS^ENSG00000173992.9" ; gene_name CCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000167238.3" ; havana_transcript "OTTHUMT00000393832.1" ; hgnc_id "HGNC:1613" ; level 2 ; orig_coord_info "chr11,66593660,66593714,+" ; protein_id "ENSP00000307870.4" ; tag not_organism_supported basic ; transcript_id "ARHGEF17--CCS^ENST00000310190.8" ; transcript_name "CCS-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CCDC169--SOHLH2 HAVANA gene 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^ENST00000239859.8" ; Parent "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CCDC169--SOHLH2 HAVANA gene 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^ENST00000317764.6" ; Parent "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CCS--ACTN3 HAVANA gene 1089 5762 . + . FI_gene_label "CCS^ENSG00000173992.9" ; ID "CCS--ACTN3^CCS^ENSG00000173992.9" ; exon_id "ENSE00002197662.1" ; exon_number 2 ; gene_id "CCS--ACTN3^CCS^ENSG00000173992.9" ; gene_name CCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000167238.3" ; havana_transcript "OTTHUMT00000393832.1" ; hgnc_id "HGNC:1613" ; level 2 ; orig_coord_info "chr11,66593660,66593714,+" ; protein_id "ENSP00000307870.4" ; tag not_organism_supported basic ; transcript_id "CCS--ACTN3^ENST00000310190.8" ; transcript_name "CCS-201" ; transcript_support_level 5 ; transcript_type protein_coding
CCS--ACTN3 HAVANA mRNA 1089 5762 . + . FI_gene_label "CCS^ENSG00000173992.9" ; ID "CCS--ACTN3^ENST00000310190.8" ; Parent "CCS--ACTN3^CCS^ENSG00000173992.9" ; exon_id "ENSE00002197662.1" ; exon_number 2 ; gene_id "CCS--ACTN3^CCS^ENSG00000173992.9" ; gene_name CCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000167238.3" ; havana_transcript "OTTHUMT00000393832.1" ; hgnc_id "HGNC:1613" ; level 2 ; orig_coord_info "chr11,66593660,66593714,+" ; protein_id "ENSP00000307870.4" ; tag not_organism_supported basic ; transcript_id "CCS--ACTN3^ENST00000310190.8" ; transcript_name "CCS-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CCS--ACTN3 HAVANA gene 8863 21368 . + . FI_gene_label "ACTN3^ENSG00000248746.6" ; ID "CCS--ACTN3^ACTN3^ENSG00000248746.6" ; ccdsid "CCDS76439.1" ; exon_id "ENSE00002085197.1" ; exon_number 1 ; gene_id "CCS--ACTN3^ACTN3^ENSG00000248746.6" ; gene_name ACTN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160815.4" ; havana_transcript "OTTHUMT00000362465.2" ; hgnc_id "HGNC:165" ; level 2 ; orig_coord_info "chr11,66546511,66546786,+" ; protein_id "ENSP00000422007.1" ; tag basic CCDS ; transcript_id "CCS--ACTN3^ENST00000502692.5" ; transcript_name "ACTN3-201" ; transcript_support_level 2 ; transcript_type protein_coding
CCS--ACTN3 HAVANA mRNA 8863 21368 . + . FI_gene_label "ACTN3^ENSG00000248746.6" ; ID "CCS--ACTN3^ENST00000502692.5" ; Parent "CCS--ACTN3^ACTN3^ENSG00000248746.6" ; ccdsid "CCDS76439.1" ; exon_id "ENSE00002085197.1" ; exon_number 1 ; gene_id "CCS--ACTN3^ACTN3^ENSG00000248746.6" ; gene_name ACTN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160815.4" ; havana_transcript "OTTHUMT00000362465.2" ; hgnc_id "HGNC:165" ; level 2 ; orig_coord_info "chr11,66546511,66546786,+" ; protein_id "ENSP00000422007.1" ; tag basic CCDS ; transcript_id "CCS--ACTN3^ENST00000502692.5" ; transcript_name "ACTN3-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
CHERP--OR2Z1 HAVANA gene 1023 17056 . + . FI_gene_label "CHERP^ENSG00000085872.15" ; ID "CHERP--OR2Z1^CHERP^ENSG00000085872.15" ; exon_id "ENSE00002213748.2" ; exon_number 1 ; gene_id "CHERP--OR2Z1^CHERP^ENSG00000085872.15" ; gene_name CHERP ; gene_type protein_coding ; havana_gene "OTTHUMG00000169304.3" ; havana_transcript "OTTHUMT00000403372.1" ; hgnc_id "HGNC:16930" ; level 1 ; orig_coord_info "chr19,16542354,16542378,-" ; protein_id "ENSP00000198939.6" ; tag not_organism_supported basic appris_alternative_1 exp_conf ; transcript_id "CHERP--OR2Z1^ENST00000198939.6" ; transcript_name "CHERP-201" ; transcript_support_level 5 ; transcript_type protein_coding
CHERP--OR2Z1 HAVANA mRNA 1023 17056 . + . FI_gene_label "CHERP^ENSG00000085872.15" ; ID "CHERP--OR2Z1^ENST00000198939.6" ; Parent "CHERP--OR2Z1^CHERP^ENSG00000085872.15" ; exon_id "ENSE00002213748.2" ; exon_number 1 ; gene_id "CHERP--OR2Z1^CHERP^ENSG00000085872.15" ; gene_name CHERP ; gene_type protein_coding ; havana_gene "OTTHUMG00000169304.3" ; havana_transcript "OTTHUMT00000403372.1" ; hgnc_id "HGNC:16930" ; level 1 ; orig_coord_info "chr19,16542354,16542378,-" ; protein_id "ENSP00000198939.6" ; tag not_organism_supported basic appris_alternative_1 exp_conf ; transcript_id "CHERP--OR2Z1^ENST00000198939.6" ; transcript_name "CHERP-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CHERP--OR2Z1 HAVANA gene 20059 23813 . + . FI_gene_label "OR2Z1^ENSG00000181733.4" ; ID "CHERP--OR2Z1^OR2Z1^ENSG00000181733.4" ; ccdsid "CCDS32895.1" ; exon_id "ENSE00003814100.1" ; exon_number 3 ; gene_id "CHERP--OR2Z1^OR2Z1^ENSG00000181733.4" ; gene_name OR2Z1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182195.3" ; havana_transcript "OTTHUMT00000459954.3" ; hgnc_id "HGNC:15391" ; level 2 ; orig_coord_info "chr19,8731029,8731970,+" ; protein_id "ENSP00000493322.1" ; tag RNA_Seq_supported_partial basic appris_principal_1 CCDS ; transcript_id "CHERP--OR2Z1^ENST00000641125.1" ; transcript_name "OR2Z1-201" ; transcript_type protein_coding
CHERP--OR2Z1 HAVANA mRNA 20059 23813 . + . FI_gene_label "OR2Z1^ENSG00000181733.4" ; ID "CHERP--OR2Z1^ENST00000641125.1" ; Parent "CHERP--OR2Z1^OR2Z1^ENSG00000181733.4" ; ccdsid "CCDS32895.1" ; exon_id "ENSE00003814100.1" ; exon_number 3 ; gene_id "CHERP--OR2Z1^OR2Z1^ENSG00000181733.4" ; gene_name OR2Z1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182195.3" ; havana_transcript "OTTHUMT00000459954.3" ; hgnc_id "HGNC:15391" ; level 2 ; orig_coord_info "chr19,8731029,8731970,+" ; protein_id "ENSP00000493322.1" ; tag RNA_Seq_supported_partial basic appris_principal_1 CCDS ; transcript_id "CHERP--OR2Z1^ENST00000641125.1" ; transcript_name "OR2Z1-201" ; transcript_type protein_coding
L1 and L2 created:
CLPB--AP001107.5 HAVANA gene 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--AP001107.5^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--AP001107.5^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--AP001107.5^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
CLPB--AP001107.5 HAVANA mRNA 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--AP001107.5^ENST00000294053.9" ; Parent "CLPB--AP001107.5^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--AP001107.5^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--AP001107.5^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CLPB--RNU1-84P HAVANA gene 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--RNU1-84P^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--RNU1-84P^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--RNU1-84P^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
CLPB--RNU1-84P HAVANA mRNA 1150 35473 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "CLPB--RNU1-84P^ENST00000294053.9" ; Parent "CLPB--RNU1-84P^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "CLPB--RNU1-84P^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "CLPB--RNU1-84P^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTTN--SPCS2 HAVANA gene 24281 31962 . + . FI_gene_label "SPCS2^ENSG00000118363.12" ; ID "CTTN--SPCS2^SPCS2^ENSG00000118363.12" ; ccdsid "CCDS44681.1" ; exon_id "ENSE00003846827.1" ; exon_number 1 ; gene_id "CTTN--SPCS2^SPCS2^ENSG00000118363.12" ; gene_name SPCS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165517.3" ; havana_transcript "OTTHUMT00000384587.2" ; hgnc_id "HGNC:28962" ; level 2 ; orig_coord_info "chr11,74949286,74949399,+" ; protein_id "ENSP00000263672.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CTTN--SPCS2^ENST00000263672.11" ; transcript_name "SPCS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTTN--SPCS2 HAVANA mRNA 24281 31962 . + . FI_gene_label "SPCS2^ENSG00000118363.12" ; ID "CTTN--SPCS2^ENST00000263672.11" ; Parent "CTTN--SPCS2^SPCS2^ENSG00000118363.12" ; ccdsid "CCDS44681.1" ; exon_id "ENSE00003846827.1" ; exon_number 1 ; gene_id "CTTN--SPCS2^SPCS2^ENSG00000118363.12" ; gene_name SPCS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165517.3" ; havana_transcript "OTTHUMT00000384587.2" ; hgnc_id "HGNC:28962" ; level 2 ; orig_coord_info "chr11,74949286,74949399,+" ; protein_id "ENSP00000263672.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CTTN--SPCS2^ENST00000263672.11" ; transcript_name "SPCS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTTN--SPCS2 HAVANA gene 1126 21252 . + . FI_gene_label "CTTN^ENSG00000085733.16" ; ID "CTTN--SPCS2^CTTN^ENSG00000085733.16" ; ccdsid "CCDS41680.1" ; exon_id "ENSE00003684603.1" ; exon_number 3 ; gene_id "CTTN--SPCS2^CTTN^ENSG00000085733.16" ; gene_name CTTN ; gene_type protein_coding ; havana_gene "OTTHUMG00000134307.4" ; havana_transcript "OTTHUMT00000259233.3" ; hgnc_id "HGNC:3338" ; level 2 ; orig_coord_info "chr11,70407298,70407384,+" ; protein_id "ENSP00000301843.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTTN--SPCS2^ENST00000301843.13" ; transcript_name "CTTN-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTTN--SPCS2 HAVANA mRNA 1126 21252 . + . FI_gene_label "CTTN^ENSG00000085733.16" ; ID "CTTN--SPCS2^ENST00000301843.13" ; Parent "CTTN--SPCS2^CTTN^ENSG00000085733.16" ; ccdsid "CCDS41680.1" ; exon_id "ENSE00003684603.1" ; exon_number 3 ; gene_id "CTTN--SPCS2^CTTN^ENSG00000085733.16" ; gene_name CTTN ; gene_type protein_coding ; havana_gene "OTTHUMG00000134307.4" ; havana_transcript "OTTHUMT00000259233.3" ; hgnc_id "HGNC:3338" ; level 2 ; orig_coord_info "chr11,70407298,70407384,+" ; protein_id "ENSP00000301843.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTTN--SPCS2^ENST00000301843.13" ; transcript_name "CTTN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GOLGA6L10--GOLGA2P6 HAVANA gene 1001 9781 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
GOLGA6L10--GOLGA2P6 HAVANA mRNA 1001 9781 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; Parent "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
GRPEL2--HSPA9 HAVANA gene 11696 26933 . + . FI_gene_label "HSPA9^ENSG00000113013.16" ; ID "GRPEL2--HSPA9^HSPA9^ENSG00000113013.16" ; ccdsid "CCDS4208.1" ; exon_id "ENSE00003548889.1" ; exon_number 1 ; gene_id "GRPEL2--HSPA9^HSPA9^ENSG00000113013.16" ; gene_name HSPA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129206.7" ; havana_transcript "OTTHUMT00000501296.3" ; hgnc_id "HGNC:5244" ; level 2 ; orig_coord_info "chr5,138575238,138575318,-" ; protein_id "ENSP00000297185.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRPEL2--HSPA9^ENST00000297185.9" ; transcript_name "HSPA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
GRPEL2--HSPA9 HAVANA mRNA 11696 26933 . + . FI_gene_label "HSPA9^ENSG00000113013.16" ; ID "GRPEL2--HSPA9^ENST00000297185.9" ; Parent "GRPEL2--HSPA9^HSPA9^ENSG00000113013.16" ; ccdsid "CCDS4208.1" ; exon_id "ENSE00003548889.1" ; exon_number 1 ; gene_id "GRPEL2--HSPA9^HSPA9^ENSG00000113013.16" ; gene_name HSPA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129206.7" ; havana_transcript "OTTHUMT00000501296.3" ; hgnc_id "HGNC:5244" ; level 2 ; orig_coord_info "chr5,138575238,138575318,-" ; protein_id "ENSP00000297185.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRPEL2--HSPA9^ENST00000297185.9" ; transcript_name "HSPA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GRPEL2--HSPA9 HAVANA gene 1070 8421 . + . FI_gene_label "GRPEL2^ENSG00000164284.15" ; ID "GRPEL2--HSPA9^GRPEL2^ENSG00000164284.15" ; ccdsid "CCDS4295.1" ; exon_id "ENSE00003842982.1" ; exon_number 1 ; gene_id "GRPEL2--HSPA9^GRPEL2^ENSG00000164284.15" ; gene_name GRPEL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130048.3" ; havana_transcript "OTTHUMT00000252327.2" ; hgnc_id "HGNC:21060" ; level 2 ; orig_coord_info "chr5,149345540,149345616,+" ; protein_id "ENSP00000329558.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRPEL2--HSPA9^ENST00000329271.8" ; transcript_name "GRPEL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GRPEL2--HSPA9 HAVANA mRNA 1070 8421 . + . FI_gene_label "GRPEL2^ENSG00000164284.15" ; ID "GRPEL2--HSPA9^ENST00000329271.8" ; Parent "GRPEL2--HSPA9^GRPEL2^ENSG00000164284.15" ; ccdsid "CCDS4295.1" ; exon_id "ENSE00003842982.1" ; exon_number 1 ; gene_id "GRPEL2--HSPA9^GRPEL2^ENSG00000164284.15" ; gene_name GRPEL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130048.3" ; havana_transcript "OTTHUMT00000252327.2" ; hgnc_id "HGNC:21060" ; level 2 ; orig_coord_info "chr5,149345540,149345616,+" ; protein_id "ENSP00000329558.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRPEL2--HSPA9^ENST00000329271.8" ; transcript_name "GRPEL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC12--HOXC10 HAVANA gene 1001 5054 . + . FI_gene_label "HOXC12^ENSG00000123407.4" ; ID "HOXC12--HOXC10^HOXC12^ENSG00000123407.4" ; ccdsid "CCDS8866.1" ; exon_id "ENSE00001059266.3" ; exon_number 1 ; gene_id "HOXC12--HOXC10^HOXC12^ENSG00000123407.4" ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3" ; havana_transcript "OTTHUMT00000358868.3" ; hgnc_id "HGNC:5124" ; level 2 ; orig_coord_info "chr12,53954930,53955539,+" ; protein_id "ENSP00000243103.3" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC10^ENST00000243103.4" ; transcript_name "HOXC12-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC12--HOXC10 HAVANA mRNA 1001 5054 . + . FI_gene_label "HOXC12^ENSG00000123407.4" ; ID "HOXC12--HOXC10^ENST00000243103.4" ; Parent "HOXC12--HOXC10^HOXC12^ENSG00000123407.4" ; ccdsid "CCDS8866.1" ; exon_id "ENSE00001059266.3" ; exon_number 1 ; gene_id "HOXC12--HOXC10^HOXC12^ENSG00000123407.4" ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3" ; havana_transcript "OTTHUMT00000358868.3" ; hgnc_id "HGNC:5124" ; level 2 ; orig_coord_info "chr12,53954930,53955539,+" ; protein_id "ENSP00000243103.3" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC10^ENST00000243103.4" ; transcript_name "HOXC12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC12--HOXC10 HAVANA gene 8136 11787 . + . FI_gene_label "HOXC10^ENSG00000180818.5" ; ID "HOXC12--HOXC10^HOXC10^ENSG00000180818.5" ; ccdsid "CCDS8868.1" ; exon_id "ENSE00001151648.5" ; exon_number 1 ; gene_id "HOXC12--HOXC10^HOXC10^ENSG00000180818.5" ; gene_name HOXC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160031.3" ; havana_transcript "OTTHUMT00000358952.3" ; hgnc_id "HGNC:5122" ; level 2 ; orig_coord_info "chr12,53985260,53986010,+" ; protein_id "ENSP00000307321.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC10^ENST00000303460.5" ; transcript_name "HOXC10-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC12--HOXC10 HAVANA mRNA 8136 11787 . + . FI_gene_label "HOXC10^ENSG00000180818.5" ; ID "HOXC12--HOXC10^ENST00000303460.5" ; Parent "HOXC12--HOXC10^HOXC10^ENSG00000180818.5" ; ccdsid "CCDS8868.1" ; exon_id "ENSE00001151648.5" ; exon_number 1 ; gene_id "HOXC12--HOXC10^HOXC10^ENSG00000180818.5" ; gene_name HOXC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160031.3" ; havana_transcript "OTTHUMT00000358952.3" ; hgnc_id "HGNC:5122" ; level 2 ; orig_coord_info "chr12,53985260,53986010,+" ; protein_id "ENSP00000307321.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC10^ENST00000303460.5" ; transcript_name "HOXC10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC12--HOXC11 HAVANA gene 8057 11095 . + . FI_gene_label "HOXC11^ENSG00000123388.4" ; ID "HOXC12--HOXC11^HOXC11^ENSG00000123388.4" ; exon_id "ENSE00002374295.1" ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC11^ENSG00000123388.4" ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3" ; havana_transcript "OTTHUMT00000407429.2" ; hgnc_id "HGNC:5123" ; level 1 ; orig_coord_info "chr12,53973242,53973927,+" ; protein_id "ENSP00000243082.4" ; tag basic exp_conf ; transcript_id "HOXC12--HOXC11^ENST00000243082.4" ; transcript_name "HOXC11-201" ; transcript_support_level 3 ; transcript_type protein_coding
HOXC12--HOXC11 HAVANA mRNA 8057 11095 . + . FI_gene_label "HOXC11^ENSG00000123388.4" ; ID "HOXC12--HOXC11^ENST00000243082.4" ; Parent "HOXC12--HOXC11^HOXC11^ENSG00000123388.4" ; exon_id "ENSE00002374295.1" ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC11^ENSG00000123388.4" ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3" ; havana_transcript "OTTHUMT00000407429.2" ; hgnc_id "HGNC:5123" ; level 1 ; orig_coord_info "chr12,53973242,53973927,+" ; protein_id "ENSP00000243082.4" ; tag basic exp_conf ; transcript_id "HOXC12--HOXC11^ENST00000243082.4" ; transcript_name "HOXC11-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
HOXC12--HOXC11 HAVANA gene 1001 5054 . + . FI_gene_label "HOXC12^ENSG00000123407.4" ; ID "HOXC12--HOXC11^HOXC12^ENSG00000123407.4" ; ccdsid "CCDS8866.1" ; exon_id "ENSE00001059266.3" ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC12^ENSG00000123407.4" ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3" ; havana_transcript "OTTHUMT00000358868.3" ; hgnc_id "HGNC:5124" ; level 2 ; orig_coord_info "chr12,53954930,53955539,+" ; protein_id "ENSP00000243103.3" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC11^ENST00000243103.4" ; transcript_name "HOXC12-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC12--HOXC11 HAVANA mRNA 1001 5054 . + . FI_gene_label "HOXC12^ENSG00000123407.4" ; ID "HOXC12--HOXC11^ENST00000243103.4" ; Parent "HOXC12--HOXC11^HOXC12^ENSG00000123407.4" ; ccdsid "CCDS8866.1" ; exon_id "ENSE00001059266.3" ; exon_number 1 ; gene_id "HOXC12--HOXC11^HOXC12^ENSG00000123407.4" ; gene_name HOXC12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160010.3" ; havana_transcript "OTTHUMT00000358868.3" ; hgnc_id "HGNC:5124" ; level 2 ; orig_coord_info "chr12,53954930,53955539,+" ; protein_id "ENSP00000243103.3" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC12--HOXC11^ENST00000243103.4" ; transcript_name "HOXC12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC13--HOXC10 HAVANA gene 1001 4357 . + . FI_gene_label "HOXC13^ENSG00000123364.5" ; ID "HOXC13--HOXC10^HOXC13^ENSG00000123364.5" ; ccdsid "CCDS8865.1" ; exon_id "ENSE00000838327.5" ; exon_number 1 ; gene_id "HOXC13--HOXC10^HOXC13^ENSG00000123364.5" ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4" ; havana_transcript "OTTHUMT00000358865.4" ; hgnc_id "HGNC:5125" ; level 2 ; orig_coord_info "chr12,53938907,53939642,+" ; protein_id "ENSP00000243056.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC10^ENST00000243056.5" ; transcript_name "HOXC13-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC13--HOXC10 HAVANA mRNA 1001 4357 . + . FI_gene_label "HOXC13^ENSG00000123364.5" ; ID "HOXC13--HOXC10^ENST00000243056.5" ; Parent "HOXC13--HOXC10^HOXC13^ENSG00000123364.5" ; ccdsid "CCDS8865.1" ; exon_id "ENSE00000838327.5" ; exon_number 1 ; gene_id "HOXC13--HOXC10^HOXC13^ENSG00000123364.5" ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4" ; havana_transcript "OTTHUMT00000358865.4" ; hgnc_id "HGNC:5125" ; level 2 ; orig_coord_info "chr12,53938907,53939642,+" ; protein_id "ENSP00000243056.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC10^ENST00000243056.5" ; transcript_name "HOXC13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC13--HOXC10 HAVANA gene 7439 11090 . + . FI_gene_label "HOXC10^ENSG00000180818.5" ; ID "HOXC13--HOXC10^HOXC10^ENSG00000180818.5" ; ccdsid "CCDS8868.1" ; exon_id "ENSE00001151648.5" ; exon_number 1 ; gene_id "HOXC13--HOXC10^HOXC10^ENSG00000180818.5" ; gene_name HOXC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160031.3" ; havana_transcript "OTTHUMT00000358952.3" ; hgnc_id "HGNC:5122" ; level 2 ; orig_coord_info "chr12,53985260,53986010,+" ; protein_id "ENSP00000307321.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC10^ENST00000303460.5" ; transcript_name "HOXC10-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC13--HOXC10 HAVANA mRNA 7439 11090 . + . FI_gene_label "HOXC10^ENSG00000180818.5" ; ID "HOXC13--HOXC10^ENST00000303460.5" ; Parent "HOXC13--HOXC10^HOXC10^ENSG00000180818.5" ; ccdsid "CCDS8868.1" ; exon_id "ENSE00001151648.5" ; exon_number 1 ; gene_id "HOXC13--HOXC10^HOXC10^ENSG00000180818.5" ; gene_name HOXC10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160031.3" ; havana_transcript "OTTHUMT00000358952.3" ; hgnc_id "HGNC:5122" ; level 2 ; orig_coord_info "chr12,53985260,53986010,+" ; protein_id "ENSP00000307321.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC10^ENST00000303460.5" ; transcript_name "HOXC10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC13--HOXC11 HAVANA gene 1001 4357 . + . FI_gene_label "HOXC13^ENSG00000123364.5" ; ID "HOXC13--HOXC11^HOXC13^ENSG00000123364.5" ; ccdsid "CCDS8865.1" ; exon_id "ENSE00000838327.5" ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC13^ENSG00000123364.5" ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4" ; havana_transcript "OTTHUMT00000358865.4" ; hgnc_id "HGNC:5125" ; level 2 ; orig_coord_info "chr12,53938907,53939642,+" ; protein_id "ENSP00000243056.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC11^ENST00000243056.5" ; transcript_name "HOXC13-201" ; transcript_support_level 1 ; transcript_type protein_coding
HOXC13--HOXC11 HAVANA mRNA 1001 4357 . + . FI_gene_label "HOXC13^ENSG00000123364.5" ; ID "HOXC13--HOXC11^ENST00000243056.5" ; Parent "HOXC13--HOXC11^HOXC13^ENSG00000123364.5" ; ccdsid "CCDS8865.1" ; exon_id "ENSE00000838327.5" ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC13^ENSG00000123364.5" ; gene_name HOXC13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160008.4" ; havana_transcript "OTTHUMT00000358865.4" ; hgnc_id "HGNC:5125" ; level 2 ; orig_coord_info "chr12,53938907,53939642,+" ; protein_id "ENSP00000243056.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HOXC13--HOXC11^ENST00000243056.5" ; transcript_name "HOXC13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HOXC13--HOXC11 HAVANA gene 7360 10398 . + . FI_gene_label "HOXC11^ENSG00000123388.4" ; ID "HOXC13--HOXC11^HOXC11^ENSG00000123388.4" ; exon_id "ENSE00002374295.1" ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC11^ENSG00000123388.4" ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3" ; havana_transcript "OTTHUMT00000407429.2" ; hgnc_id "HGNC:5123" ; level 1 ; orig_coord_info "chr12,53973242,53973927,+" ; protein_id "ENSP00000243082.4" ; tag basic exp_conf ; transcript_id "HOXC13--HOXC11^ENST00000243082.4" ; transcript_name "HOXC11-201" ; transcript_support_level 3 ; transcript_type protein_coding
HOXC13--HOXC11 HAVANA mRNA 7360 10398 . + . FI_gene_label "HOXC11^ENSG00000123388.4" ; ID "HOXC13--HOXC11^ENST00000243082.4" ; Parent "HOXC13--HOXC11^HOXC11^ENSG00000123388.4" ; exon_id "ENSE00002374295.1" ; exon_number 1 ; gene_id "HOXC13--HOXC11^HOXC11^ENSG00000123388.4" ; gene_name HOXC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160011.3" ; havana_transcript "OTTHUMT00000407429.2" ; hgnc_id "HGNC:5123" ; level 1 ; orig_coord_info "chr12,53973242,53973927,+" ; protein_id "ENSP00000243082.4" ; tag basic exp_conf ; transcript_id "HOXC13--HOXC11^ENST00000243082.4" ; transcript_name "HOXC11-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
KDM4B--NFIC HAVANA gene 1001 37721 . + . FI_gene_label "KDM4B^ENSG00000127663.15" ; ID "KDM4B--NFIC^KDM4B^ENSG00000127663.15" ; ccdsid "CCDS12138.1" ; exon_id "ENSE00000874797.2" ; exon_number 3 ; gene_id "KDM4B--NFIC^KDM4B^ENSG00000127663.15" ; gene_name KDM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000180281.5" ; havana_transcript "OTTHUMT00000450558.3" ; hgnc_id "HGNC:29136" ; level 2 ; orig_coord_info "chr19,5032891,5033031,+" ; protein_id "ENSP00000159111.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KDM4B--NFIC^ENST00000159111.9" ; transcript_name "KDM4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
KDM4B--NFIC HAVANA mRNA 1001 37721 . + . FI_gene_label "KDM4B^ENSG00000127663.15" ; ID "KDM4B--NFIC^ENST00000159111.9" ; Parent "KDM4B--NFIC^KDM4B^ENSG00000127663.15" ; ccdsid "CCDS12138.1" ; exon_id "ENSE00000874797.2" ; exon_number 3 ; gene_id "KDM4B--NFIC^KDM4B^ENSG00000127663.15" ; gene_name KDM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000180281.5" ; havana_transcript "OTTHUMT00000450558.3" ; hgnc_id "HGNC:29136" ; level 2 ; orig_coord_info "chr19,5032891,5033031,+" ; protein_id "ENSP00000159111.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KDM4B--NFIC^ENST00000159111.9" ; transcript_name "KDM4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KDM4B--NFIC HAVANA gene 43299 57601 . + . FI_gene_label "NFIC^ENSG00000141905.19" ; ID "KDM4B--NFIC^NFIC^ENSG00000141905.19" ; ccdsid "CCDS12107.1" ; exon_id "ENSE00002938816.1" ; exon_number 1 ; gene_id "KDM4B--NFIC^NFIC^ENSG00000141905.19" ; gene_name NFIC ; gene_type protein_coding ; havana_gene "OTTHUMG00000180731.8" ; havana_transcript "OTTHUMT00000452832.1" ; hgnc_id "HGNC:7786" ; level 2 ; orig_coord_info "chr19,3366637,3366666,+" ; protein_id "ENSP00000342194.2" ; tag basic CCDS ; transcript_id "KDM4B--NFIC^ENST00000341919.7" ; transcript_name "NFIC-201" ; transcript_support_level 1 ; transcript_type protein_coding
KDM4B--NFIC HAVANA mRNA 43299 57601 . + . FI_gene_label "NFIC^ENSG00000141905.19" ; ID "KDM4B--NFIC^ENST00000341919.7" ; Parent "KDM4B--NFIC^NFIC^ENSG00000141905.19" ; ccdsid "CCDS12107.1" ; exon_id "ENSE00002938816.1" ; exon_number 1 ; gene_id "KDM4B--NFIC^NFIC^ENSG00000141905.19" ; gene_name NFIC ; gene_type protein_coding ; havana_gene "OTTHUMG00000180731.8" ; havana_transcript "OTTHUMT00000452832.1" ; hgnc_id "HGNC:7786" ; level 2 ; orig_coord_info "chr19,3366637,3366666,+" ; protein_id "ENSP00000342194.2" ; tag basic CCDS ; transcript_id "KDM4B--NFIC^ENST00000341919.7" ; transcript_name "NFIC-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LSP1--AC013734.1 HAVANA gene 2937 20432 . + . FI_gene_label "LSP1^ENSG00000130592.17" ; ID "LSP1--AC013734.1^LSP1^ENSG00000130592.17" ; ccdsid "CCDS31334.1" ; exon_id "ENSE00002286022.2" ; exon_number 1 ; gene_id "LSP1--AC013734.1^LSP1^ENSG00000130592.17" ; gene_name LSP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012252.24" ; havana_transcript "OTTHUMT00000034045.3" ; hgnc_id "HGNC:6707" ; level 2 ; orig_coord_info "chr11,1853145,1853197,+" ; protein_id "ENSP00000308383.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_3 CCDS ; transcript_id "LSP1--AC013734.1^ENST00000311604.8" ; transcript_name "LSP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
LSP1--AC013734.1 HAVANA mRNA 2937 20432 . + . FI_gene_label "LSP1^ENSG00000130592.17" ; ID "LSP1--AC013734.1^ENST00000311604.8" ; Parent "LSP1--AC013734.1^LSP1^ENSG00000130592.17" ; ccdsid "CCDS31334.1" ; exon_id "ENSE00002286022.2" ; exon_number 1 ; gene_id "LSP1--AC013734.1^LSP1^ENSG00000130592.17" ; gene_name LSP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012252.24" ; havana_transcript "OTTHUMT00000034045.3" ; hgnc_id "HGNC:6707" ; level 2 ; orig_coord_info "chr11,1853145,1853197,+" ; protein_id "ENSP00000308383.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_3 CCDS ; transcript_id "LSP1--AC013734.1^ENST00000311604.8" ; transcript_name "LSP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NCOA6--AHCY HAVANA gene 36701 47580 . + . FI_gene_label "AHCY^ENSG00000101444.13" ; ID "NCOA6--AHCY^AHCY^ENSG00000101444.13" ; ccdsid "CCDS13233.1" ; exon_id "ENSE00001152081.5" ; exon_number 1 ; gene_id "NCOA6--AHCY^AHCY^ENSG00000101444.13" ; gene_name AHCY ; gene_type protein_coding ; havana_gene "OTTHUMG00000140098.4" ; havana_transcript "OTTHUMT00000078773.3" ; hgnc_id "HGNC:343" ; level 2 ; orig_coord_info "chr20,34303243,34303270,-" ; protein_id "ENSP00000217426.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NCOA6--AHCY^ENST00000217426.7" ; transcript_name "AHCY-201" ; transcript_support_level 1 ; transcript_type protein_coding
NCOA6--AHCY HAVANA mRNA 36701 47580 . + . FI_gene_label "AHCY^ENSG00000101444.13" ; ID "NCOA6--AHCY^ENST00000217426.7" ; Parent "NCOA6--AHCY^AHCY^ENSG00000101444.13" ; ccdsid "CCDS13233.1" ; exon_id "ENSE00001152081.5" ; exon_number 1 ; gene_id "NCOA6--AHCY^AHCY^ENSG00000101444.13" ; gene_name AHCY ; gene_type protein_coding ; havana_gene "OTTHUMG00000140098.4" ; havana_transcript "OTTHUMT00000078773.3" ; hgnc_id "HGNC:343" ; level 2 ; orig_coord_info "chr20,34303243,34303270,-" ; protein_id "ENSP00000217426.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NCOA6--AHCY^ENST00000217426.7" ; transcript_name "AHCY-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NCOA6--AHCY HAVANA gene 1001 27599 . + . FI_gene_label "NCOA6^ENSG00000198646.14" ; ID "NCOA6--AHCY^NCOA6^ENSG00000198646.14" ; ccdsid "CCDS13241.1" ; exon_id "ENSE00001311630.2" ; exon_number 3 ; gene_id "NCOA6--AHCY^NCOA6^ENSG00000198646.14" ; gene_name NCOA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032311.9" ; havana_transcript "OTTHUMT00000078812.5" ; hgnc_id "HGNC:15936" ; level 2 ; orig_coord_info "chr20,34782121,34782355,-" ; protein_id "ENSP00000351894.2" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "NCOA6--AHCY^ENST00000359003.7" ; transcript_name "NCOA6-201" ; transcript_support_level 1 ; transcript_type protein_coding
NCOA6--AHCY HAVANA mRNA 1001 27599 . + . FI_gene_label "NCOA6^ENSG00000198646.14" ; ID "NCOA6--AHCY^ENST00000359003.7" ; Parent "NCOA6--AHCY^NCOA6^ENSG00000198646.14" ; ccdsid "CCDS13241.1" ; exon_id "ENSE00001311630.2" ; exon_number 3 ; gene_id "NCOA6--AHCY^NCOA6^ENSG00000198646.14" ; gene_name NCOA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032311.9" ; havana_transcript "OTTHUMT00000078812.5" ; hgnc_id "HGNC:15936" ; level 2 ; orig_coord_info "chr20,34782121,34782355,-" ; protein_id "ENSP00000351894.2" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "NCOA6--AHCY^ENST00000359003.7" ; transcript_name "NCOA6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^ENST00000289272.3" ; Parent "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^ENST00000562220.2" ; Parent "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4 HAVANA gene 15043 21268 . + . FI_gene_label "RBM4^ENSG00000173933.21" ; ID "RBM14--RBM4^RBM4^ENSG00000173933.21" ; ccdsid "CCDS41676.1" ; exon_id "ENSE00003513724.1" ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21" ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7" ; havana_transcript "OTTHUMT00000334210.2" ; hgnc_id "HGNC:9901" ; level 2 ; orig_coord_info "chr11,66639712,66640123,+" ; protein_id "ENSP00000309166.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12" ; transcript_name "RBM4-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4 HAVANA mRNA 15043 21268 . + . FI_gene_label "RBM4^ENSG00000173933.21" ; ID "RBM14--RBM4^ENST00000310092.12" ; Parent "RBM14--RBM4^RBM4^ENSG00000173933.21" ; ccdsid "CCDS41676.1" ; exon_id "ENSE00003513724.1" ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21" ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7" ; havana_transcript "OTTHUMT00000334210.2" ; hgnc_id "HGNC:9901" ; level 2 ; orig_coord_info "chr11,66639712,66640123,+" ; protein_id "ENSP00000309166.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12" ; transcript_name "RBM4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4 HAVANA gene 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4 HAVANA mRNA 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4^ENST00000310137.5" ; Parent "RBM14--RBM4^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--DLG2 HAVANA gene 80843 123160 . + . FI_gene_label "DLG2^ENSG00000150672.18" ; ID "SHANK2--DLG2^DLG2^ENSG00000150672.18" ; ccdsid "CCDS55782.1" ; exon_id "ENSE00001532570.2" ; exon_number 1 ; gene_id "SHANK2--DLG2^DLG2^ENSG00000150672.18" ; gene_name DLG2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134309.9" ; hgnc_id "HGNC:2901" ; level 2 ; orig_coord_info "chr11,84316825,84317145,-" ; protein_id "ENSP00000280241.8" ; tag basic CCDS ; transcript_id "SHANK2--DLG2^ENST00000280241.12" ; transcript_name "DLG2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--DLG2 HAVANA mRNA 80843 123160 . + . FI_gene_label "DLG2^ENSG00000150672.18" ; ID "SHANK2--DLG2^ENST00000280241.12" ; Parent "SHANK2--DLG2^DLG2^ENSG00000150672.18" ; ccdsid "CCDS55782.1" ; exon_id "ENSE00001532570.2" ; exon_number 1 ; gene_id "SHANK2--DLG2^DLG2^ENSG00000150672.18" ; gene_name DLG2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134309.9" ; hgnc_id "HGNC:2901" ; level 2 ; orig_coord_info "chr11,84316825,84317145,-" ; protein_id "ENSP00000280241.8" ; tag basic CCDS ; transcript_id "SHANK2--DLG2^ENST00000280241.12" ; transcript_name "DLG2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--DLG2 HAVANA gene 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--DLG2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--DLG2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--DLG2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--DLG2 HAVANA mRNA 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--DLG2^ENST00000338508.8" ; Parent "SHANK2--DLG2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--DLG2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--DLG2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SSRP1--BDNF HAVANA gene 1001 10905 . + . FI_gene_label "SSRP1^ENSG00000149136.9" ; ID "SSRP1--BDNF^SSRP1^ENSG00000149136.9" ; ccdsid "CCDS7952.1" ; exon_id "ENSE00001027126.1" ; exon_number 2 ; gene_id "SSRP1--BDNF^SSRP1^ENSG00000149136.9" ; gene_name SSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167024.5" ; havana_transcript "OTTHUMT00000392460.2" ; hgnc_id "HGNC:11327" ; level 2 ; orig_coord_info "chr11,57335068,57335121,-" ; protein_id "ENSP00000278412.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSRP1--BDNF^ENST00000278412.7" ; transcript_name "SSRP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SSRP1--BDNF HAVANA mRNA 1001 10905 . + . FI_gene_label "SSRP1^ENSG00000149136.9" ; ID "SSRP1--BDNF^ENST00000278412.7" ; Parent "SSRP1--BDNF^SSRP1^ENSG00000149136.9" ; ccdsid "CCDS7952.1" ; exon_id "ENSE00001027126.1" ; exon_number 2 ; gene_id "SSRP1--BDNF^SSRP1^ENSG00000149136.9" ; gene_name SSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167024.5" ; havana_transcript "OTTHUMT00000392460.2" ; hgnc_id "HGNC:11327" ; level 2 ; orig_coord_info "chr11,57335068,57335121,-" ; protein_id "ENSP00000278412.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSRP1--BDNF^ENST00000278412.7" ; transcript_name "SSRP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SSRP1--BDNF HAVANA gene 13908 27370 . + . FI_gene_label "BDNF^ENSG00000176697.20" ; ID "SSRP1--BDNF^BDNF^ENSG00000176697.20" ; ccdsid "CCDS7865.1" ; exon_id "ENSE00001412786.2" ; exon_number 1 ; gene_id "SSRP1--BDNF^BDNF^ENSG00000176697.20" ; gene_name BDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000178797.3" ; havana_transcript "OTTHUMT00000388138.1" ; hgnc_id "HGNC:1033" ; level 2 ; orig_coord_info "chr11,27721412,27721414,-" ; protein_id "ENSP00000320002.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "SSRP1--BDNF^ENST00000314915.6" ; transcript_name "BDNF-201" ; transcript_support_level 1 ; transcript_type protein_coding
SSRP1--BDNF HAVANA mRNA 13908 27370 . + . FI_gene_label "BDNF^ENSG00000176697.20" ; ID "SSRP1--BDNF^ENST00000314915.6" ; Parent "SSRP1--BDNF^BDNF^ENSG00000176697.20" ; ccdsid "CCDS7865.1" ; exon_id "ENSE00001412786.2" ; exon_number 1 ; gene_id "SSRP1--BDNF^BDNF^ENSG00000176697.20" ; gene_name BDNF ; gene_type protein_coding ; havana_gene "OTTHUMG00000178797.3" ; havana_transcript "OTTHUMT00000388138.1" ; hgnc_id "HGNC:1033" ; level 2 ; orig_coord_info "chr11,27721412,27721414,-" ; protein_id "ENSP00000320002.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "SSRP1--BDNF^ENST00000314915.6" ; transcript_name "BDNF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ST3GAL1--NDRG1 HAVANA gene 29778 61281 . + . FI_gene_label "NDRG1^ENSG00000104419.17" ; ID "ST3GAL1--NDRG1^NDRG1^ENSG00000104419.17" ; ccdsid "CCDS34945.1" ; exon_id "ENSE00003667452.1" ; exon_number 2 ; gene_id "ST3GAL1--NDRG1^NDRG1^ENSG00000104419.17" ; gene_name NDRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164441.4" ; havana_transcript "OTTHUMT00000378799.2" ; hgnc_id "HGNC:7679" ; level 2 ; orig_coord_info "chr8,133284249,133284311,-" ; protein_id "ENSP00000319977.8" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "ST3GAL1--NDRG1^ENST00000323851.13" ; transcript_name "NDRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ST3GAL1--NDRG1 HAVANA mRNA 29778 61281 . + . FI_gene_label "NDRG1^ENSG00000104419.17" ; ID "ST3GAL1--NDRG1^ENST00000323851.13" ; Parent "ST3GAL1--NDRG1^NDRG1^ENSG00000104419.17" ; ccdsid "CCDS34945.1" ; exon_id "ENSE00003667452.1" ; exon_number 2 ; gene_id "ST3GAL1--NDRG1^NDRG1^ENSG00000104419.17" ; gene_name NDRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164441.4" ; havana_transcript "OTTHUMT00000378799.2" ; hgnc_id "HGNC:7679" ; level 2 ; orig_coord_info "chr8,133284249,133284311,-" ; protein_id "ENSP00000319977.8" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "ST3GAL1--NDRG1^ENST00000323851.13" ; transcript_name "NDRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ST3GAL1--NDRG1 ENSEMBL gene 1001 24536 . + . FI_gene_label "ST3GAL1^ENSG00000008513.16" ; ID "ST3GAL1--NDRG1^ST3GAL1^ENSG00000008513.16" ; ccdsid "CCDS6373.1" ; exon_id "ENSE00001521347.1" ; exon_number 5 ; gene_id "ST3GAL1--NDRG1^ST3GAL1^ENSG00000008513.16" ; gene_name ST3GAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164534.6" ; hgnc_id "HGNC:10862" ; level 3 ; orig_coord_info "chr8,133475719,133476024,-" ; protein_id "ENSP00000414073.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ST3GAL1--NDRG1^ENST00000399640.3" ; transcript_name "ST3GAL1-201" ; transcript_support_level 5 ; transcript_type protein_coding
ST3GAL1--NDRG1 ENSEMBL mRNA 1001 24536 . + . FI_gene_label "ST3GAL1^ENSG00000008513.16" ; ID "ST3GAL1--NDRG1^ENST00000399640.3" ; Parent "ST3GAL1--NDRG1^ST3GAL1^ENSG00000008513.16" ; ccdsid "CCDS6373.1" ; exon_id "ENSE00001521347.1" ; exon_number 5 ; gene_id "ST3GAL1--NDRG1^ST3GAL1^ENSG00000008513.16" ; gene_name ST3GAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164534.6" ; hgnc_id "HGNC:10862" ; level 3 ; orig_coord_info "chr8,133475719,133476024,-" ; protein_id "ENSP00000414073.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ST3GAL1--NDRG1^ENST00000399640.3" ; transcript_name "ST3GAL1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
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:
TMEM138--AP001107.6 HAVANA gene 1031 8166 . + . FI_gene_label "TMEM138^ENSG00000149483.12" ; ID "TMEM138--AP001107.6^TMEM138^ENSG00000149483.12" ; ccdsid "CCDS8005.1" ; exon_id "ENSE00003556955.1" ; exon_number 2 ; gene_id "TMEM138--AP001107.6^TMEM138^ENSG00000149483.12" ; gene_name TMEM138 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168145.4" ; havana_transcript "OTTHUMT00000398399.3" ; hgnc_id "HGNC:26944" ; level 2 ; orig_coord_info "chr11,61364391,61364518,+" ; protein_id "ENSP00000278826.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM138--AP001107.6^ENST00000278826.11" ; transcript_name "TMEM138-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM138--AP001107.6 HAVANA mRNA 1031 8166 . + . FI_gene_label "TMEM138^ENSG00000149483.12" ; ID "TMEM138--AP001107.6^ENST00000278826.11" ; Parent "TMEM138--AP001107.6^TMEM138^ENSG00000149483.12" ; ccdsid "CCDS8005.1" ; exon_id "ENSE00003556955.1" ; exon_number 2 ; gene_id "TMEM138--AP001107.6^TMEM138^ENSG00000149483.12" ; gene_name TMEM138 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168145.4" ; havana_transcript "OTTHUMT00000398399.3" ; hgnc_id "HGNC:26944" ; level 2 ; orig_coord_info "chr11,61364391,61364518,+" ; protein_id "ENSP00000278826.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM138--AP001107.6^ENST00000278826.11" ; transcript_name "TMEM138-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TSG101--CLPB HAVANA gene 1010 13888 . + . FI_gene_label "TSG101^ENSG00000074319.13" ; ID "TSG101--CLPB^TSG101^ENSG00000074319.13" ; ccdsid "CCDS7842.1" ; exon_id "ENSE00002295781.2" ; exon_number 1 ; gene_id "TSG101--CLPB^TSG101^ENSG00000074319.13" ; gene_name TSG101 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167725.4" ; havana_transcript "OTTHUMT00000395906.2" ; hgnc_id "HGNC:15971" ; level 2 ; orig_coord_info "chr11,18526775,18526816,-" ; protein_id "ENSP00000251968.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSG101--CLPB^ENST00000251968.4" ; transcript_name "TSG101-201" ; transcript_support_level 1 ; transcript_type protein_coding
TSG101--CLPB HAVANA mRNA 1010 13888 . + . FI_gene_label "TSG101^ENSG00000074319.13" ; ID "TSG101--CLPB^ENST00000251968.4" ; Parent "TSG101--CLPB^TSG101^ENSG00000074319.13" ; ccdsid "CCDS7842.1" ; exon_id "ENSE00002295781.2" ; exon_number 1 ; gene_id "TSG101--CLPB^TSG101^ENSG00000074319.13" ; gene_name TSG101 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167725.4" ; havana_transcript "OTTHUMT00000395906.2" ; hgnc_id "HGNC:15971" ; level 2 ; orig_coord_info "chr11,18526775,18526816,-" ; protein_id "ENSP00000251968.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSG101--CLPB^ENST00000251968.4" ; transcript_name "TSG101-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TSG101--CLPB HAVANA gene 20827 55150 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "TSG101--CLPB^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "TSG101--CLPB^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "TSG101--CLPB^ENST00000294053.9" ; transcript_name "CLPB-201" ; transcript_support_level 1 ; transcript_type protein_coding
TSG101--CLPB HAVANA mRNA 20827 55150 . + . FI_gene_label "CLPB^ENSG00000162129.14" ; ID "TSG101--CLPB^ENST00000294053.9" ; Parent "TSG101--CLPB^CLPB^ENSG00000162129.14" ; ccdsid "CCDS8215.1" ; exon_id "ENSE00002302745.2" ; exon_number 1 ; gene_id "TSG101--CLPB^CLPB^ENSG00000162129.14" ; gene_name CLPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167902.11" ; havana_transcript "OTTHUMT00000396889.3" ; hgnc_id "HGNC:30664" ; level 2 ; orig_coord_info "chr11,72434072,72434474,-" ; protein_id "ENSP00000294053.3" ; tag CAGE_supported_TSS basic appris_alternative_2 CCDS ; transcript_id "TSG101--CLPB^ENST00000294053.9" ; transcript_name "CLPB-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:
UVRAG--KDM2A ENSEMBL gene 34190 60523 . + . FI_gene_label "KDM2A^ENSG00000173120.15" ; ID "UVRAG--KDM2A^KDM2A^ENSG00000173120.15" ; exon_id "ENSE00003741868.1" ; exon_number 3 ; gene_id "UVRAG--KDM2A^KDM2A^ENSG00000173120.15" ; gene_name KDM2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000167103.3" ; hgnc_id "HGNC:13606" ; level 3 ; orig_coord_info "chr11,67180088,67180217,+" ; protein_id "ENSP00000309302.6" ; tag basic ; transcript_id "UVRAG--KDM2A^ENST00000308783.9" ; transcript_name "KDM2A-201" ; transcript_support_level 1 ; transcript_type protein_coding
UVRAG--KDM2A ENSEMBL mRNA 34190 60523 . + . FI_gene_label "KDM2A^ENSG00000173120.15" ; ID "UVRAG--KDM2A^ENST00000308783.9" ; Parent "UVRAG--KDM2A^KDM2A^ENSG00000173120.15" ; exon_id "ENSE00003741868.1" ; exon_number 3 ; gene_id "UVRAG--KDM2A^KDM2A^ENSG00000173120.15" ; gene_name KDM2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000167103.3" ; hgnc_id "HGNC:13606" ; level 3 ; orig_coord_info "chr11,67180088,67180217,+" ; protein_id "ENSP00000309302.6" ; tag basic ; transcript_id "UVRAG--KDM2A^ENST00000308783.9" ; transcript_name "KDM2A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
UVRAG--KDM2A HAVANA gene 1001 29367 . + . FI_gene_label "UVRAG^ENSG00000198382.9" ; ID "UVRAG--KDM2A^UVRAG^ENSG00000198382.9" ; ccdsid "CCDS8241.1" ; exon_id "ENSE00001153107.8" ; exon_number 1 ; gene_id "UVRAG--KDM2A^UVRAG^ENSG00000198382.9" ; gene_name UVRAG ; gene_type protein_coding ; havana_gene "OTTHUMG00000165319.3" ; havana_transcript "OTTHUMT00000383430.2" ; hgnc_id "HGNC:12640" ; level 2 ; orig_coord_info "chr11,75815408,75815524,+" ; protein_id "ENSP00000348455.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UVRAG--KDM2A^ENST00000356136.8" ; transcript_name "UVRAG-201" ; transcript_support_level 1 ; transcript_type protein_coding
UVRAG--KDM2A HAVANA mRNA 1001 29367 . + . FI_gene_label "UVRAG^ENSG00000198382.9" ; ID "UVRAG--KDM2A^ENST00000356136.8" ; Parent "UVRAG--KDM2A^UVRAG^ENSG00000198382.9" ; ccdsid "CCDS8241.1" ; exon_id "ENSE00001153107.8" ; exon_number 1 ; gene_id "UVRAG--KDM2A^UVRAG^ENSG00000198382.9" ; gene_name UVRAG ; gene_type protein_coding ; havana_gene "OTTHUMG00000165319.3" ; havana_transcript "OTTHUMT00000383430.2" ; hgnc_id "HGNC:12640" ; level 2 ; orig_coord_info "chr11,75815408,75815524,+" ; protein_id "ENSP00000348455.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UVRAG--KDM2A^ENST00000356136.8" ; transcript_name "UVRAG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
AL049555.1--LLGL2 HAVANA gene 1001 2933 . + . FI_gene_label "AL049555.1^ENSG00000261116.1" ; ID "AL049555.1--LLGL2^AL049555.1^ENSG00000261116.1" ; exon_id "ENSE00002584090.1" ; exon_number 1 ; gene_id "AL049555.1--LLGL2^AL049555.1^ENSG00000261116.1" ; gene_name "AL049555.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000175921.1" ; havana_transcript "OTTHUMT00000431275.1" ; level 2 ; orig_coord_info "chr6,54943167,54945099,+" ; tag basic ; transcript_id "AL049555.1--LLGL2^ENST00000562834.1" ; transcript_name "AL049555.1-201" ; transcript_support_level NA ; transcript_type lncRNA
AL049555.1--LLGL2 HAVANA RNA 1001 2933 . + . FI_gene_label "AL049555.1^ENSG00000261116.1" ; ID "AL049555.1--LLGL2^ENST00000562834.1" ; Parent "AL049555.1--LLGL2^AL049555.1^ENSG00000261116.1" ; exon_id "ENSE00002584090.1" ; exon_number 1 ; gene_id "AL049555.1--LLGL2^AL049555.1^ENSG00000261116.1" ; gene_name "AL049555.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000175921.1" ; havana_transcript "OTTHUMT00000431275.1" ; level 2 ; orig_coord_info "chr6,54943167,54945099,+" ; tag basic ; transcript_id "AL049555.1--LLGL2^ENST00000562834.1" ; transcript_name "AL049555.1-201" ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created:
CLPB--AP001107.5 HAVANA gene 39988 41624 . + . FI_gene_label "AP001107.5^ENSG00000254510.2" ; ID "CLPB--AP001107.5^AP001107.5^ENSG00000254510.2" ; exon_id "ENSE00002200667.1" ; exon_number 1 ; gene_id "CLPB--AP001107.5^AP001107.5^ENSG00000254510.2" ; gene_name "AP001107.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166924.2" ; havana_transcript "OTTHUMT00000391914.1" ; level 2 ; orig_coord_info "chr11,66410672,66410973,+" ; tag basic ; transcript_id "CLPB--AP001107.5^ENST00000526186.1" ; transcript_name "AP001107.5-204" ; transcript_support_level 2 ; transcript_type lncRNA
CLPB--AP001107.5 HAVANA RNA 39988 41624 . + . FI_gene_label "AP001107.5^ENSG00000254510.2" ; ID "CLPB--AP001107.5^ENST00000526186.1" ; Parent "CLPB--AP001107.5^AP001107.5^ENSG00000254510.2" ; exon_id "ENSE00002200667.1" ; exon_number 1 ; gene_id "CLPB--AP001107.5^AP001107.5^ENSG00000254510.2" ; gene_name "AP001107.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166924.2" ; havana_transcript "OTTHUMT00000391914.1" ; level 2 ; orig_coord_info "chr11,66410672,66410973,+" ; tag basic ; transcript_id "CLPB--AP001107.5^ENST00000526186.1" ; transcript_name "AP001107.5-204" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
CLPB--RNU1-84P ENSEMBL gene 38474 38637 . + . FI_gene_label "RNU1-84P^ENSG00000202317.1" ; ID "CLPB--RNU1-84P^RNU1-84P^ENSG00000202317.1" ; exon_id "ENSE00001440210.1" ; exon_number 1 ; gene_id "CLPB--RNU1-84P^RNU1-84P^ENSG00000202317.1" ; gene_name "RNU1-84P" ; gene_type snRNA ; hgnc_id "HGNC:48426" ; level 3 ; orig_coord_info "chr11,66393449,66393612,+" ; tag basic ; transcript_id "CLPB--RNU1-84P^ENST00000365447.1" ; transcript_name "RNU1-84P-201" ; transcript_support_level NA ; transcript_type snRNA
CLPB--RNU1-84P ENSEMBL RNA 38474 38637 . + . FI_gene_label "RNU1-84P^ENSG00000202317.1" ; ID "CLPB--RNU1-84P^ENST00000365447.1" ; Parent "CLPB--RNU1-84P^RNU1-84P^ENSG00000202317.1" ; exon_id "ENSE00001440210.1" ; exon_number 1 ; gene_id "CLPB--RNU1-84P^RNU1-84P^ENSG00000202317.1" ; gene_name "RNU1-84P" ; gene_type snRNA ; hgnc_id "HGNC:48426" ; level 3 ; orig_coord_info "chr11,66393449,66393612,+" ; tag basic ; transcript_id "CLPB--RNU1-84P^ENST00000365447.1" ; transcript_name "RNU1-84P-201" ; transcript_support_level NA ; transcript_type snRNA
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
GOLGA6L10--GOLGA2P6 HAVANA gene 12782 20364 . + . FI_gene_label "GOLGA2P6^ENSG00000241621.1" ; ID "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; exon_id "ENSE00001603136.1" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1" ; havana_transcript "OTTHUMT00000047421.1" ; hgnc_id "HGNC:44948" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr10,30374327,30374386,-" ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; transcript_name "GOLGA2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GOLGA6L10--GOLGA2P6 HAVANA RNA 12782 20364 . + . FI_gene_label "GOLGA2P6^ENSG00000241621.1" ; ID "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; Parent "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; exon_id "ENSE00001603136.1" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1" ; havana_transcript "OTTHUMT00000047421.1" ; hgnc_id "HGNC:44948" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr10,30374327,30374386,-" ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; transcript_name "GOLGA2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
LSP1--AC013734.1 HAVANA gene 23437 23547 . + . FI_gene_label "AC013734.1^ENSG00000277146.1" ; ID "LSP1--AC013734.1^AC013734.1^ENSG00000277146.1" ; exon_id "ENSE00003713380.1" ; exon_number 1 ; gene_id "LSP1--AC013734.1^AC013734.1^ENSG00000277146.1" ; gene_name "AC013734.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000188106.1" ; havana_transcript "OTTHUMT00000475889.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chrY,26453982,26454092,+" ; tag basic ; transcript_id "LSP1--AC013734.1^ENST00000619329.1" ; transcript_name "AC013734.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
LSP1--AC013734.1 HAVANA RNA 23437 23547 . + . FI_gene_label "AC013734.1^ENSG00000277146.1" ; ID "LSP1--AC013734.1^ENST00000619329.1" ; Parent "LSP1--AC013734.1^AC013734.1^ENSG00000277146.1" ; exon_id "ENSE00003713380.1" ; exon_number 1 ; gene_id "LSP1--AC013734.1^AC013734.1^ENSG00000277146.1" ; gene_name "AC013734.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000188106.1" ; havana_transcript "OTTHUMT00000475889.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chrY,26453982,26454092,+" ; tag basic ; transcript_id "LSP1--AC013734.1^ENST00000619329.1" ; transcript_name "AC013734.1-201" ; 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:
TMEM138--AP001107.6 HAVANA gene 11167 13682 . + . FI_gene_label "AP001107.6^ENSG00000254756.1" ; ID "TMEM138--AP001107.6^AP001107.6^ENSG00000254756.1" ; exon_id "ENSE00002199713.1" ; exon_number 1 ; gene_id "TMEM138--AP001107.6^AP001107.6^ENSG00000254756.1" ; gene_name "AP001107.6" ; gene_type lncRNA ; havana_gene "OTTHUMG00000167074.1" ; havana_transcript "OTTHUMT00000392923.1" ; level 1 ; orig_coord_info "chr11,66334494,66334781,+" ; tag basic exp_conf ; transcript_id "TMEM138--AP001107.6^ENST00000526655.1" ; transcript_name "AP001107.6-201" ; transcript_support_level 3 ; transcript_type lncRNA
TMEM138--AP001107.6 HAVANA RNA 11167 13682 . + . FI_gene_label "AP001107.6^ENSG00000254756.1" ; ID "TMEM138--AP001107.6^ENST00000526655.1" ; Parent "TMEM138--AP001107.6^AP001107.6^ENSG00000254756.1" ; exon_id "ENSE00002199713.1" ; exon_number 1 ; gene_id "TMEM138--AP001107.6^AP001107.6^ENSG00000254756.1" ; gene_name "AP001107.6" ; gene_type lncRNA ; havana_gene "OTTHUMG00000167074.1" ; havana_transcript "OTTHUMT00000392923.1" ; level 1 ; orig_coord_info "chr11,66334494,66334781,+" ; tag basic exp_conf ; transcript_id "TMEM138--AP001107.6^ENST00000526655.1" ; transcript_name "AP001107.6-201" ; transcript_support_level 3 ; transcript_type lncRNA
616 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
1130 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 46 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 1 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed