Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/4cbdeb72ca28ac3d73768b57355eba/fi_workdir/aih-tih-sc-3eb8dd-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/c4fdf3eab246f311145f863c126175/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/c4fdf3eab246f311145f863c126175/.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: 10722
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 10722
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:10722
=> 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:
CBFA2T2--WFDC2 HAVANA gene 29348 32319 . + . FI_gene_label "WFDC2^ENSG00000101443.18" ; ID "CBFA2T2--WFDC2^WFDC2^ENSG00000101443.18" ; exon_id "ENSE00001627595.1" ; exon_number 1 ; gene_id "CBFA2T2--WFDC2^WFDC2^ENSG00000101443.18" ; gene_name WFDC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032594.6" ; havana_transcript "OTTHUMT00000079477.4" ; hgnc_id "HGNC:15939" ; level 1 ; orig_coord_info "chr20,45469782,45469860,+" ; protein_id "ENSP00000217425.5" ; tag basic exp_conf ; transcript_id "CBFA2T2--WFDC2^ENST00000217425.9" ; transcript_name "WFDC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CBFA2T2--WFDC2 HAVANA mRNA 29348 32319 . + . FI_gene_label "WFDC2^ENSG00000101443.18" ; ID "CBFA2T2--WFDC2^ENST00000217425.9" ; Parent "CBFA2T2--WFDC2^WFDC2^ENSG00000101443.18" ; exon_id "ENSE00001627595.1" ; exon_number 1 ; gene_id "CBFA2T2--WFDC2^WFDC2^ENSG00000101443.18" ; gene_name WFDC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032594.6" ; havana_transcript "OTTHUMT00000079477.4" ; hgnc_id "HGNC:15939" ; level 1 ; orig_coord_info "chr20,45469782,45469860,+" ; protein_id "ENSP00000217425.5" ; tag basic exp_conf ; transcript_id "CBFA2T2--WFDC2^ENST00000217425.9" ; transcript_name "WFDC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CBFA2T2--WFDC2 HAVANA gene 1022 26338 . + . FI_gene_label "CBFA2T2^ENSG00000078699.22" ; ID "CBFA2T2--WFDC2^CBFA2T2^ENSG00000078699.22" ; ccdsid "CCDS46590.1" ; exon_id "ENSE00001750956.3" ; exon_number 1 ; gene_id "CBFA2T2--WFDC2^CBFA2T2^ENSG00000078699.22" ; gene_name CBFA2T2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032261.6" ; havana_transcript "OTTHUMT00000471953.1" ; hgnc_id "HGNC:1536" ; level 2 ; orig_coord_info "chr20,33490268,33490301,+" ; protein_id "ENSP00000345810.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CBFA2T2--WFDC2^ENST00000342704.11" ; transcript_name "CBFA2T2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CBFA2T2--WFDC2 HAVANA mRNA 1022 26338 . + . FI_gene_label "CBFA2T2^ENSG00000078699.22" ; ID "CBFA2T2--WFDC2^ENST00000342704.11" ; Parent "CBFA2T2--WFDC2^CBFA2T2^ENSG00000078699.22" ; ccdsid "CCDS46590.1" ; exon_id "ENSE00001750956.3" ; exon_number 1 ; gene_id "CBFA2T2--WFDC2^CBFA2T2^ENSG00000078699.22" ; gene_name CBFA2T2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032261.6" ; havana_transcript "OTTHUMT00000471953.1" ; hgnc_id "HGNC:1536" ; level 2 ; orig_coord_info "chr20,33490268,33490301,+" ; protein_id "ENSP00000345810.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CBFA2T2--WFDC2^ENST00000342704.11" ; transcript_name "CBFA2T2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COPS3--AC005323.2 HAVANA gene 1028 13830 . + . FI_gene_label "COPS3^ENSG00000141030.13" ; ID "COPS3--AC005323.2^COPS3^ENSG00000141030.13" ; ccdsid "CCDS11183.1" ; exon_id "ENSE00001901824.1" ; exon_number 1 ; gene_id "COPS3--AC005323.2^COPS3^ENSG00000141030.13" ; gene_name COPS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059281.7" ; havana_transcript "OTTHUMT00000131603.3" ; hgnc_id "HGNC:2239" ; level 2 ; orig_coord_info "chr17,17281132,17281186,-" ; protein_id "ENSP00000268717.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--AC005323.2^ENST00000268717.10" ; transcript_name "COPS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
COPS3--AC005323.2 HAVANA mRNA 1028 13830 . + . FI_gene_label "COPS3^ENSG00000141030.13" ; ID "COPS3--AC005323.2^ENST00000268717.10" ; Parent "COPS3--AC005323.2^COPS3^ENSG00000141030.13" ; ccdsid "CCDS11183.1" ; exon_id "ENSE00001901824.1" ; exon_number 1 ; gene_id "COPS3--AC005323.2^COPS3^ENSG00000141030.13" ; gene_name COPS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059281.7" ; havana_transcript "OTTHUMT00000131603.3" ; hgnc_id "HGNC:2239" ; level 2 ; orig_coord_info "chr17,17281132,17281186,-" ; protein_id "ENSP00000268717.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--AC005323.2^ENST00000268717.10" ; transcript_name "COPS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COPS3--MYH2 HAVANA gene 16873 39998 . + . FI_gene_label "MYH2^ENSG00000125414.19" ; ID "COPS3--MYH2^MYH2^ENSG00000125414.19" ; ccdsid "CCDS11156.1" ; exon_id "ENSE00000855382.3" ; exon_number 3 ; gene_id "COPS3--MYH2^MYH2^ENSG00000125414.19" ; gene_name MYH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130363.60" ; havana_transcript "OTTHUMT00000252726.4" ; hgnc_id "HGNC:7572" ; level 2 ; orig_coord_info "chr17,10547717,10547920,-" ; protein_id "ENSP00000245503.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--MYH2^ENST00000245503.10" ; transcript_name "MYH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
COPS3--MYH2 HAVANA mRNA 16873 39998 . + . FI_gene_label "MYH2^ENSG00000125414.19" ; ID "COPS3--MYH2^ENST00000245503.10" ; Parent "COPS3--MYH2^MYH2^ENSG00000125414.19" ; ccdsid "CCDS11156.1" ; exon_id "ENSE00000855382.3" ; exon_number 3 ; gene_id "COPS3--MYH2^MYH2^ENSG00000125414.19" ; gene_name MYH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130363.60" ; havana_transcript "OTTHUMT00000252726.4" ; hgnc_id "HGNC:7572" ; level 2 ; orig_coord_info "chr17,10547717,10547920,-" ; protein_id "ENSP00000245503.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--MYH2^ENST00000245503.10" ; transcript_name "MYH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COPS3--MYH2 HAVANA gene 1028 13830 . + . FI_gene_label "COPS3^ENSG00000141030.13" ; ID "COPS3--MYH2^COPS3^ENSG00000141030.13" ; ccdsid "CCDS11183.1" ; exon_id "ENSE00001901824.1" ; exon_number 1 ; gene_id "COPS3--MYH2^COPS3^ENSG00000141030.13" ; gene_name COPS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059281.7" ; havana_transcript "OTTHUMT00000131603.3" ; hgnc_id "HGNC:2239" ; level 2 ; orig_coord_info "chr17,17281132,17281186,-" ; protein_id "ENSP00000268717.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--MYH2^ENST00000268717.10" ; transcript_name "COPS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
COPS3--MYH2 HAVANA mRNA 1028 13830 . + . FI_gene_label "COPS3^ENSG00000141030.13" ; ID "COPS3--MYH2^ENST00000268717.10" ; Parent "COPS3--MYH2^COPS3^ENSG00000141030.13" ; ccdsid "CCDS11183.1" ; exon_id "ENSE00001901824.1" ; exon_number 1 ; gene_id "COPS3--MYH2^COPS3^ENSG00000141030.13" ; gene_name COPS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059281.7" ; havana_transcript "OTTHUMT00000131603.3" ; hgnc_id "HGNC:2239" ; level 2 ; orig_coord_info "chr17,17281132,17281186,-" ; protein_id "ENSP00000268717.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COPS3--MYH2^ENST00000268717.10" ; transcript_name "COPS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNM1L--AK6P1 HAVANA gene 1104 23928 . + . FI_gene_label "DNM1L^ENSG00000087470.19" ; ID "DNM1L--AK6P1^DNM1L^ENSG00000087470.19" ; ccdsid "CCDS8728.1" ; exon_id "ENSE00002365308.1" ; exon_number 1 ; gene_id "DNM1L--AK6P1^DNM1L^ENSG00000087470.19" ; gene_name DNM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000169451.3" ; havana_transcript "OTTHUMT00000404127.1" ; hgnc_id "HGNC:2973" ; level 2 ; orig_coord_info "chr12,32679364,32679465,+" ; protein_id "ENSP00000266481.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNM1L--AK6P1^ENST00000266481.10" ; transcript_name "DNM1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNM1L--AK6P1 HAVANA mRNA 1104 23928 . + . FI_gene_label "DNM1L^ENSG00000087470.19" ; ID "DNM1L--AK6P1^ENST00000266481.10" ; Parent "DNM1L--AK6P1^DNM1L^ENSG00000087470.19" ; ccdsid "CCDS8728.1" ; exon_id "ENSE00002365308.1" ; exon_number 1 ; gene_id "DNM1L--AK6P1^DNM1L^ENSG00000087470.19" ; gene_name DNM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000169451.3" ; havana_transcript "OTTHUMT00000404127.1" ; hgnc_id "HGNC:2973" ; level 2 ; orig_coord_info "chr12,32679364,32679465,+" ; protein_id "ENSP00000266481.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNM1L--AK6P1^ENST00000266481.10" ; transcript_name "DNM1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNM1L--ZNF970P HAVANA gene 1104 23928 . + . FI_gene_label "DNM1L^ENSG00000087470.19" ; ID "DNM1L--ZNF970P^DNM1L^ENSG00000087470.19" ; ccdsid "CCDS8728.1" ; exon_id "ENSE00002365308.1" ; exon_number 1 ; gene_id "DNM1L--ZNF970P^DNM1L^ENSG00000087470.19" ; gene_name DNM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000169451.3" ; havana_transcript "OTTHUMT00000404127.1" ; hgnc_id "HGNC:2973" ; level 2 ; orig_coord_info "chr12,32679364,32679465,+" ; protein_id "ENSP00000266481.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNM1L--ZNF970P^ENST00000266481.10" ; transcript_name "DNM1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNM1L--ZNF970P HAVANA mRNA 1104 23928 . + . FI_gene_label "DNM1L^ENSG00000087470.19" ; ID "DNM1L--ZNF970P^ENST00000266481.10" ; Parent "DNM1L--ZNF970P^DNM1L^ENSG00000087470.19" ; ccdsid "CCDS8728.1" ; exon_id "ENSE00002365308.1" ; exon_number 1 ; gene_id "DNM1L--ZNF970P^DNM1L^ENSG00000087470.19" ; gene_name DNM1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000169451.3" ; havana_transcript "OTTHUMT00000404127.1" ; hgnc_id "HGNC:2973" ; level 2 ; orig_coord_info "chr12,32679364,32679465,+" ; protein_id "ENSP00000266481.6" ; tag basic appris_alternative_1 CCDS ; transcript_id "DNM1L--ZNF970P^ENST00000266481.10" ; transcript_name "DNM1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DST--FARS2 HAVANA gene 22073 129360 . + . FI_gene_label "DST^ENSG00000151914.21" ; ID "DST--FARS2^DST^ENSG00000151914.21" ; ccdsid "CCDS47443.1" ; exon_id "ENSE00002133064.1" ; exon_number 1 ; gene_id "DST--FARS2^DST^ENSG00000151914.21" ; gene_name DST ; gene_type protein_coding ; havana_gene "OTTHUMG00000014913.26" ; havana_transcript "OTTHUMT00000041022.4" ; hgnc_id "HGNC:1090" ; level 2 ; orig_coord_info "chr6,56642622,56642788,-" ; protein_id "ENSP00000244364.6" ; tag basic CCDS ; transcript_id "DST--FARS2^ENST00000244364.10" ; transcript_name "DST-201" ; transcript_support_level 1 ; transcript_type protein_coding
DST--FARS2 HAVANA mRNA 22073 129360 . + . FI_gene_label "DST^ENSG00000151914.21" ; ID "DST--FARS2^ENST00000244364.10" ; Parent "DST--FARS2^DST^ENSG00000151914.21" ; ccdsid "CCDS47443.1" ; exon_id "ENSE00002133064.1" ; exon_number 1 ; gene_id "DST--FARS2^DST^ENSG00000151914.21" ; gene_name DST ; gene_type protein_coding ; havana_gene "OTTHUMG00000014913.26" ; havana_transcript "OTTHUMT00000041022.4" ; hgnc_id "HGNC:1090" ; level 2 ; orig_coord_info "chr6,56642622,56642788,-" ; protein_id "ENSP00000244364.6" ; tag basic CCDS ; transcript_id "DST--FARS2^ENST00000244364.10" ; transcript_name "DST-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DST--FARS2 HAVANA gene 132830 142210 . + . FI_gene_label "FARS2^ENSG00000145982.13" ; ID "DST--FARS2^FARS2^ENSG00000145982.13" ; ccdsid "CCDS4494.1" ; exon_id "ENSE00001125682.3" ; exon_number 2 ; gene_id "DST--FARS2^FARS2^ENSG00000145982.13" ; gene_name FARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014178.6" ; havana_transcript "OTTHUMT00000039746.2" ; hgnc_id "HGNC:21062" ; level 2 ; orig_coord_info "chr6,5368571,5369182,+" ; protein_id "ENSP00000274680.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DST--FARS2^ENST00000274680.9" ; transcript_name "FARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DST--FARS2 HAVANA mRNA 132830 142210 . + . FI_gene_label "FARS2^ENSG00000145982.13" ; ID "DST--FARS2^ENST00000274680.9" ; Parent "DST--FARS2^FARS2^ENSG00000145982.13" ; ccdsid "CCDS4494.1" ; exon_id "ENSE00001125682.3" ; exon_number 2 ; gene_id "DST--FARS2^FARS2^ENSG00000145982.13" ; gene_name FARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014178.6" ; havana_transcript "OTTHUMT00000039746.2" ; hgnc_id "HGNC:21062" ; level 2 ; orig_coord_info "chr6,5368571,5369182,+" ; protein_id "ENSP00000274680.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DST--FARS2^ENST00000274680.9" ; transcript_name "FARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DUSP15--TRPC4AP HAVANA gene 15244 34977 . + . FI_gene_label "TRPC4AP^ENSG00000100991.12" ; ID "DUSP15--TRPC4AP^TRPC4AP^ENSG00000100991.12" ; ccdsid "CCDS13246.1" ; exon_id "ENSE00002254384.1" ; exon_number 1 ; gene_id "DUSP15--TRPC4AP^TRPC4AP^ENSG00000100991.12" ; gene_name TRPC4AP ; gene_type protein_coding ; havana_gene "OTTHUMG00000032319.3" ; havana_transcript "OTTHUMT00000078832.2" ; hgnc_id "HGNC:16181" ; level 2 ; orig_coord_info "chr20,35092614,35092781,-" ; protein_id "ENSP00000252015.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "DUSP15--TRPC4AP^ENST00000252015.3" ; transcript_name "TRPC4AP-201" ; transcript_support_level 1 ; transcript_type protein_coding
DUSP15--TRPC4AP HAVANA mRNA 15244 34977 . + . FI_gene_label "TRPC4AP^ENSG00000100991.12" ; ID "DUSP15--TRPC4AP^ENST00000252015.3" ; Parent "DUSP15--TRPC4AP^TRPC4AP^ENSG00000100991.12" ; ccdsid "CCDS13246.1" ; exon_id "ENSE00002254384.1" ; exon_number 1 ; gene_id "DUSP15--TRPC4AP^TRPC4AP^ENSG00000100991.12" ; gene_name TRPC4AP ; gene_type protein_coding ; havana_gene "OTTHUMG00000032319.3" ; havana_transcript "OTTHUMT00000078832.2" ; hgnc_id "HGNC:16181" ; level 2 ; orig_coord_info "chr20,35092614,35092781,-" ; protein_id "ENSP00000252015.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "DUSP15--TRPC4AP^ENST00000252015.3" ; transcript_name "TRPC4AP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DUSP15--TRPC4AP HAVANA gene 1084 12243 . + . FI_gene_label "DUSP15^ENSG00000149599.15" ; ID "DUSP15--TRPC4AP^DUSP15^ENSG00000149599.15" ; ccdsid "CCDS82606.1" ; exon_id "ENSE00001404816.1" ; exon_number 1 ; gene_id "DUSP15--TRPC4AP^DUSP15^ENSG00000149599.15" ; gene_name DUSP15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032182.7" ; havana_transcript "OTTHUMT00000078555.3" ; hgnc_id "HGNC:16236" ; level 2 ; orig_coord_info "chr20,31870576,31870587,-" ; protein_id "ENSP00000278979.3" ; tag basic CCDS ; transcript_id "DUSP15--TRPC4AP^ENST00000278979.7" ; transcript_name "DUSP15-201" ; transcript_support_level 2 ; transcript_type protein_coding
DUSP15--TRPC4AP HAVANA mRNA 1084 12243 . + . FI_gene_label "DUSP15^ENSG00000149599.15" ; ID "DUSP15--TRPC4AP^ENST00000278979.7" ; Parent "DUSP15--TRPC4AP^DUSP15^ENSG00000149599.15" ; ccdsid "CCDS82606.1" ; exon_id "ENSE00001404816.1" ; exon_number 1 ; gene_id "DUSP15--TRPC4AP^DUSP15^ENSG00000149599.15" ; gene_name DUSP15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032182.7" ; havana_transcript "OTTHUMT00000078555.3" ; hgnc_id "HGNC:16236" ; level 2 ; orig_coord_info "chr20,31870576,31870587,-" ; protein_id "ENSP00000278979.3" ; tag basic CCDS ; transcript_id "DUSP15--TRPC4AP^ENST00000278979.7" ; transcript_name "DUSP15-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
EPB41L1--PREX1 HAVANA gene 1001 37968 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "EPB41L1--PREX1^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "EPB41L1--PREX1^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--PREX1^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPB41L1--PREX1 HAVANA mRNA 1001 37968 . + . FI_gene_label "EPB41L1^ENSG00000088367.23" ; ID "EPB41L1--PREX1^ENST00000202028.9" ; Parent "EPB41L1--PREX1^EPB41L1^ENSG00000088367.23" ; ccdsid "CCDS13272.1" ; exon_id "ENSE00003546773.1" ; exon_number 3 ; gene_id "EPB41L1--PREX1^EPB41L1^ENSG00000088367.23" ; gene_name EPB41L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032378.14" ; havana_transcript "OTTHUMT00000078983.1" ; hgnc_id "HGNC:3378" ; level 2 ; orig_coord_info "chr20,36175560,36175715,+" ; protein_id "ENSP00000202028.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPB41L1--PREX1^ENST00000202028.9" ; transcript_name "EPB41L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPB41L1--PREX1 HAVANA gene 43427 84616 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "EPB41L1--PREX1^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "EPB41L1--PREX1^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPB41L1--PREX1^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPB41L1--PREX1 HAVANA mRNA 43427 84616 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "EPB41L1--PREX1^ENST00000371941.4" ; Parent "EPB41L1--PREX1^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "EPB41L1--PREX1^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPB41L1--PREX1^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FARS2--DST HAVANA gene 39569 146856 . + . FI_gene_label "DST^ENSG00000151914.21" ; ID "FARS2--DST^DST^ENSG00000151914.21" ; ccdsid "CCDS47443.1" ; exon_id "ENSE00002133064.1" ; exon_number 1 ; gene_id "FARS2--DST^DST^ENSG00000151914.21" ; gene_name DST ; gene_type protein_coding ; havana_gene "OTTHUMG00000014913.26" ; havana_transcript "OTTHUMT00000041022.4" ; hgnc_id "HGNC:1090" ; level 2 ; orig_coord_info "chr6,56642622,56642788,-" ; protein_id "ENSP00000244364.6" ; tag basic CCDS ; transcript_id "FARS2--DST^ENST00000244364.10" ; transcript_name "DST-201" ; transcript_support_level 1 ; transcript_type protein_coding
FARS2--DST HAVANA mRNA 39569 146856 . + . FI_gene_label "DST^ENSG00000151914.21" ; ID "FARS2--DST^ENST00000244364.10" ; Parent "FARS2--DST^DST^ENSG00000151914.21" ; ccdsid "CCDS47443.1" ; exon_id "ENSE00002133064.1" ; exon_number 1 ; gene_id "FARS2--DST^DST^ENSG00000151914.21" ; gene_name DST ; gene_type protein_coding ; havana_gene "OTTHUMG00000014913.26" ; havana_transcript "OTTHUMT00000041022.4" ; hgnc_id "HGNC:1090" ; level 2 ; orig_coord_info "chr6,56642622,56642788,-" ; protein_id "ENSP00000244364.6" ; tag basic CCDS ; transcript_id "FARS2--DST^ENST00000244364.10" ; transcript_name "DST-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FARS2--DST HAVANA gene 1470 10850 . + . FI_gene_label "FARS2^ENSG00000145982.13" ; ID "FARS2--DST^FARS2^ENSG00000145982.13" ; ccdsid "CCDS4494.1" ; exon_id "ENSE00001125682.3" ; exon_number 2 ; gene_id "FARS2--DST^FARS2^ENSG00000145982.13" ; gene_name FARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014178.6" ; havana_transcript "OTTHUMT00000039746.2" ; hgnc_id "HGNC:21062" ; level 2 ; orig_coord_info "chr6,5368571,5369182,+" ; protein_id "ENSP00000274680.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FARS2--DST^ENST00000274680.9" ; transcript_name "FARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
FARS2--DST HAVANA mRNA 1470 10850 . + . FI_gene_label "FARS2^ENSG00000145982.13" ; ID "FARS2--DST^ENST00000274680.9" ; Parent "FARS2--DST^FARS2^ENSG00000145982.13" ; ccdsid "CCDS4494.1" ; exon_id "ENSE00001125682.3" ; exon_number 2 ; gene_id "FARS2--DST^FARS2^ENSG00000145982.13" ; gene_name FARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014178.6" ; havana_transcript "OTTHUMT00000039746.2" ; hgnc_id "HGNC:21062" ; level 2 ; orig_coord_info "chr6,5368571,5369182,+" ; protein_id "ENSP00000274680.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FARS2--DST^ENST00000274680.9" ; transcript_name "FARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NLK--SLFN13 HAVANA gene 21638 34806 . + . FI_gene_label "SLFN13^ENSG00000154760.14" ; ID "NLK--SLFN13^SLFN13^ENSG00000154760.14" ; ccdsid "CCDS32620.1" ; exon_id "ENSE00001235446.6" ; exon_number 3 ; gene_id "NLK--SLFN13^SLFN13^ENSG00000154760.14" ; gene_name SLFN13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165108.4" ; havana_transcript "OTTHUMT00000381883.2" ; hgnc_id "HGNC:26481" ; level 2 ; orig_coord_info "chr17,35444615,35445680,-" ; protein_id "ENSP00000285013.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NLK--SLFN13^ENST00000285013.11" ; transcript_name "SLFN13-201" ; transcript_support_level 1 ; transcript_type protein_coding
NLK--SLFN13 HAVANA mRNA 21638 34806 . + . FI_gene_label "SLFN13^ENSG00000154760.14" ; ID "NLK--SLFN13^ENST00000285013.11" ; Parent "NLK--SLFN13^SLFN13^ENSG00000154760.14" ; ccdsid "CCDS32620.1" ; exon_id "ENSE00001235446.6" ; exon_number 3 ; gene_id "NLK--SLFN13^SLFN13^ENSG00000154760.14" ; gene_name SLFN13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165108.4" ; havana_transcript "OTTHUMT00000381883.2" ; hgnc_id "HGNC:26481" ; level 2 ; orig_coord_info "chr17,35444615,35445680,-" ; protein_id "ENSP00000285013.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NLK--SLFN13^ENST00000285013.11" ; transcript_name "SLFN13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NLK--SLFN13 HAVANA gene 1941 18566 . + . FI_gene_label "NLK^ENSG00000087095.13" ; ID "NLK--SLFN13^NLK^ENSG00000087095.13" ; ccdsid "CCDS11224.2" ; exon_id "ENSE00001428262.2" ; exon_number 1 ; gene_id "NLK--SLFN13^NLK^ENSG00000087095.13" ; gene_name NLK ; gene_type protein_coding ; havana_gene "OTTHUMG00000132451.9" ; havana_transcript "OTTHUMT00000255607.4" ; hgnc_id "HGNC:29858" ; level 2 ; orig_coord_info "chr17,28042874,28043331,+" ; protein_id "ENSP00000384625.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NLK--SLFN13^ENST00000407008.8" ; transcript_name "NLK-201" ; transcript_support_level 1 ; transcript_type protein_coding
NLK--SLFN13 HAVANA mRNA 1941 18566 . + . FI_gene_label "NLK^ENSG00000087095.13" ; ID "NLK--SLFN13^ENST00000407008.8" ; Parent "NLK--SLFN13^NLK^ENSG00000087095.13" ; ccdsid "CCDS11224.2" ; exon_id "ENSE00001428262.2" ; exon_number 1 ; gene_id "NLK--SLFN13^NLK^ENSG00000087095.13" ; gene_name NLK ; gene_type protein_coding ; havana_gene "OTTHUMG00000132451.9" ; havana_transcript "OTTHUMT00000255607.4" ; hgnc_id "HGNC:29858" ; level 2 ; orig_coord_info "chr17,28042874,28043331,+" ; protein_id "ENSP00000384625.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NLK--SLFN13^ENST00000407008.8" ; transcript_name "NLK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PDLIM5--BMPR1B HAVANA gene 42813 54534 . + . FI_gene_label "BMPR1B^ENSG00000138696.11" ; ID "PDLIM5--BMPR1B^BMPR1B^ENSG00000138696.11" ; ccdsid "CCDS3642.1" ; exon_id "ENSE00003894599.1" ; exon_number 2 ; gene_id "PDLIM5--BMPR1B^BMPR1B^ENSG00000138696.11" ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6" ; havana_transcript "OTTHUMT00000363051.1" ; hgnc_id "HGNC:1077" ; level 2 ; orig_coord_info "chr4,95104425,95104567,+" ; protein_id "ENSP00000264568.4" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "PDLIM5--BMPR1B^ENST00000264568.8" ; transcript_name "BMPR1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
PDLIM5--BMPR1B HAVANA mRNA 42813 54534 . + . FI_gene_label "BMPR1B^ENSG00000138696.11" ; ID "PDLIM5--BMPR1B^ENST00000264568.8" ; Parent "PDLIM5--BMPR1B^BMPR1B^ENSG00000138696.11" ; ccdsid "CCDS3642.1" ; exon_id "ENSE00003894599.1" ; exon_number 2 ; gene_id "PDLIM5--BMPR1B^BMPR1B^ENSG00000138696.11" ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6" ; havana_transcript "OTTHUMT00000363051.1" ; hgnc_id "HGNC:1077" ; level 2 ; orig_coord_info "chr4,95104425,95104567,+" ; protein_id "ENSP00000264568.4" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "PDLIM5--BMPR1B^ENST00000264568.8" ; transcript_name "BMPR1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PDLIM5--BMPR1B HAVANA gene 1086 32646 . + . FI_gene_label "PDLIM5^ENSG00000163110.15" ; ID "PDLIM5--BMPR1B^PDLIM5^ENSG00000163110.15" ; ccdsid "CCDS3641.1" ; exon_id "ENSE00003692320.1" ; exon_number 2 ; gene_id "PDLIM5--BMPR1B^PDLIM5^ENSG00000163110.15" ; gene_name PDLIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130973.11" ; havana_transcript "OTTHUMT00000253586.2" ; hgnc_id "HGNC:17468" ; level 2 ; orig_coord_info "chr4,94455289,94455384,+" ; protein_id "ENSP00000321746.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PDLIM5--BMPR1B^ENST00000317968.9" ; transcript_name "PDLIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
PDLIM5--BMPR1B HAVANA mRNA 1086 32646 . + . FI_gene_label "PDLIM5^ENSG00000163110.15" ; ID "PDLIM5--BMPR1B^ENST00000317968.9" ; Parent "PDLIM5--BMPR1B^PDLIM5^ENSG00000163110.15" ; ccdsid "CCDS3641.1" ; exon_id "ENSE00003692320.1" ; exon_number 2 ; gene_id "PDLIM5--BMPR1B^PDLIM5^ENSG00000163110.15" ; gene_name PDLIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130973.11" ; havana_transcript "OTTHUMT00000253586.2" ; hgnc_id "HGNC:17468" ; level 2 ; orig_coord_info "chr4,94455289,94455384,+" ; protein_id "ENSP00000321746.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PDLIM5--BMPR1B^ENST00000317968.9" ; transcript_name "PDLIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PREX1--LINC01746 HAVANA gene 1001 42190 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "PREX1--LINC01746^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "PREX1--LINC01746^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PREX1--LINC01746^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PREX1--LINC01746 HAVANA mRNA 1001 42190 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "PREX1--LINC01746^ENST00000371941.4" ; Parent "PREX1--LINC01746^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "PREX1--LINC01746^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PREX1--LINC01746^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PREX1--PPIAP3 HAVANA gene 1001 42190 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "PREX1--PPIAP3^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "PREX1--PPIAP3^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PREX1--PPIAP3^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PREX1--PPIAP3 HAVANA mRNA 1001 42190 . + . FI_gene_label "PREX1^ENSG00000124126.14" ; ID "PREX1--PPIAP3^ENST00000371941.4" ; Parent "PREX1--PPIAP3^PREX1^ENSG00000124126.14" ; ccdsid "CCDS13410.1" ; exon_id "ENSE00001456581.2" ; exon_number 1 ; gene_id "PREX1--PPIAP3^PREX1^ENSG00000124126.14" ; gene_name PREX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032685.5" ; havana_transcript "OTTHUMT00000079623.2" ; hgnc_id "HGNC:32594" ; level 2 ; orig_coord_info "chr20,48827642,48827860,-" ; protein_id "ENSP00000361009.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PREX1--PPIAP3^ENST00000371941.4" ; transcript_name "PREX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RERE--AC118650.1 HAVANA gene 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--AC118650.1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--AC118650.1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--AC118650.1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
RERE--AC118650.1 HAVANA mRNA 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--AC118650.1^ENST00000337907.7" ; Parent "RERE--AC118650.1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--AC118650.1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--AC118650.1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RERE--AC139365.1 HAVANA gene 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--AC139365.1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--AC139365.1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--AC139365.1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
RERE--AC139365.1 HAVANA mRNA 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--AC139365.1^ENST00000337907.7" ; Parent "RERE--AC139365.1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--AC139365.1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--AC139365.1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RERE--KANK4 HAVANA gene 55868 60947 . + . FI_gene_label "KANK4^ENSG00000132854.19" ; ID "RERE--KANK4^KANK4^ENSG00000132854.19" ; exon_id "ENSE00003559773.1" ; exon_number 2 ; gene_id "RERE--KANK4^KANK4^ENSG00000132854.19" ; gene_name KANK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008971.2" ; havana_transcript "OTTHUMT00000024880.1" ; hgnc_id "HGNC:27263" ; level 2 ; orig_coord_info "chr1,62253067,62253162,-" ; protein_id "ENSP00000321161.4" ; tag basic ; transcript_id "RERE--KANK4^ENST00000317477.8" ; transcript_name "KANK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
RERE--KANK4 HAVANA mRNA 55868 60947 . + . FI_gene_label "KANK4^ENSG00000132854.19" ; ID "RERE--KANK4^ENST00000317477.8" ; Parent "RERE--KANK4^KANK4^ENSG00000132854.19" ; exon_id "ENSE00003559773.1" ; exon_number 2 ; gene_id "RERE--KANK4^KANK4^ENSG00000132854.19" ; gene_name KANK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008971.2" ; havana_transcript "OTTHUMT00000024880.1" ; hgnc_id "HGNC:27263" ; level 2 ; orig_coord_info "chr1,62253067,62253162,-" ; protein_id "ENSP00000321161.4" ; tag basic ; transcript_id "RERE--KANK4^ENST00000317477.8" ; transcript_name "KANK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
RERE--KANK4 HAVANA gene 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--KANK4^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--KANK4^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--KANK4^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
RERE--KANK4 HAVANA mRNA 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--KANK4^ENST00000337907.7" ; Parent "RERE--KANK4^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--KANK4^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--KANK4^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RERE--USP1 HAVANA gene 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--USP1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--USP1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--USP1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
RERE--USP1 HAVANA mRNA 4257 43535 . + . FI_gene_label "RERE^ENSG00000142599.19" ; ID "RERE--USP1^ENST00000337907.7" ; Parent "RERE--USP1^RERE^ENSG00000142599.19" ; ccdsid "CCDS95.1" ; exon_id "ENSE00003476162.1" ; exon_number 3 ; gene_id "RERE--USP1^RERE^ENSG00000142599.19" ; gene_name RERE ; gene_type protein_coding ; havana_gene "OTTHUMG00000001765.9" ; havana_transcript "OTTHUMT00000004916.1" ; hgnc_id "HGNC:9965" ; level 2 ; orig_coord_info "chr1,8655973,8656297,-" ; protein_id "ENSP00000338629.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RERE--USP1^ENST00000337907.7" ; transcript_name "RERE-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RERE--USP1 HAVANA gene 47288 58288 . + . FI_gene_label "USP1^ENSG00000162607.13" ; ID "RERE--USP1^USP1^ENSG00000162607.13" ; ccdsid "CCDS621.1" ; exon_id "ENSE00001376175.1" ; exon_number 2 ; gene_id "RERE--USP1^USP1^ENSG00000162607.13" ; gene_name USP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008972.5" ; havana_transcript "OTTHUMT00000024881.2" ; hgnc_id "HGNC:12607" ; level 2 ; orig_coord_info "chr1,62439868,62440037,+" ; protein_id "ENSP00000343526.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RERE--USP1^ENST00000339950.5" ; transcript_name "USP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RERE--USP1 HAVANA mRNA 47288 58288 . + . FI_gene_label "USP1^ENSG00000162607.13" ; ID "RERE--USP1^ENST00000339950.5" ; Parent "RERE--USP1^USP1^ENSG00000162607.13" ; ccdsid "CCDS621.1" ; exon_id "ENSE00001376175.1" ; exon_number 2 ; gene_id "RERE--USP1^USP1^ENSG00000162607.13" ; gene_name USP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008972.5" ; havana_transcript "OTTHUMT00000024881.2" ; hgnc_id "HGNC:12607" ; level 2 ; orig_coord_info "chr1,62439868,62440037,+" ; protein_id "ENSP00000343526.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RERE--USP1^ENST00000339950.5" ; transcript_name "USP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNU13--LLPH HAVANA gene 4331 9276 . + . FI_gene_label "SNU13^ENSG00000100138.15" ; ID "SNU13--LLPH^SNU13^ENSG00000100138.15" ; ccdsid "CCDS14022.1" ; exon_id "ENSE00001388935.4" ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15" ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9" ; havana_transcript "OTTHUMT00000321683.2" ; hgnc_id "HGNC:7819" ; level 2 ; orig_coord_info "chr22,41682356,41682358,-" ; protein_id "ENSP00000215956.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10" ; transcript_name "SNU13-201" ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH HAVANA mRNA 4331 9276 . + . FI_gene_label "SNU13^ENSG00000100138.15" ; ID "SNU13--LLPH^ENST00000215956.10" ; Parent "SNU13--LLPH^SNU13^ENSG00000100138.15" ; ccdsid "CCDS14022.1" ; exon_id "ENSE00001388935.4" ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15" ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9" ; havana_transcript "OTTHUMT00000321683.2" ; hgnc_id "HGNC:7819" ; level 2 ; orig_coord_info "chr22,41682356,41682358,-" ; protein_id "ENSP00000215956.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10" ; transcript_name "SNU13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNU13--LLPH HAVANA gene 13051 23027 . + . FI_gene_label "LLPH^ENSG00000139233.7" ; ID "SNU13--LLPH^LLPH^ENSG00000139233.7" ; ccdsid "CCDS8974.1" ; exon_id "ENSE00003592110.1" ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7" ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4" ; havana_transcript "OTTHUMT00000401752.4" ; hgnc_id "HGNC:28229" ; level 2 ; orig_coord_info "chr12,66128896,66129106,-" ; protein_id "ENSP00000266604.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7" ; transcript_name "LLPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH HAVANA mRNA 13051 23027 . + . FI_gene_label "LLPH^ENSG00000139233.7" ; ID "SNU13--LLPH^ENST00000266604.7" ; Parent "SNU13--LLPH^LLPH^ENSG00000139233.7" ; ccdsid "CCDS8974.1" ; exon_id "ENSE00003592110.1" ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7" ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4" ; havana_transcript "OTTHUMT00000401752.4" ; hgnc_id "HGNC:28229" ; level 2 ; orig_coord_info "chr12,66128896,66129106,-" ; protein_id "ENSP00000266604.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7" ; transcript_name "LLPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STK4--GMEB2 HAVANA gene 26877 38225 . + . FI_gene_label "GMEB2^ENSG00000101216.11" ; ID "STK4--GMEB2^GMEB2^ENSG00000101216.11" ; ccdsid "CCDS13528.1" ; exon_id "ENSE00001109207.1" ; exon_number 1 ; gene_id "STK4--GMEB2^GMEB2^ENSG00000101216.11" ; gene_name GMEB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032988.2" ; havana_transcript "OTTHUMT00000080166.1" ; hgnc_id "HGNC:4371" ; level 2 ; orig_coord_info "chr20,63619267,63619397,-" ; protein_id "ENSP00000266068.1" ; tag basic appris_principal_2 CCDS ; transcript_id "STK4--GMEB2^ENST00000266068.5" ; transcript_name "GMEB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
STK4--GMEB2 HAVANA mRNA 26877 38225 . + . FI_gene_label "GMEB2^ENSG00000101216.11" ; ID "STK4--GMEB2^ENST00000266068.5" ; Parent "STK4--GMEB2^GMEB2^ENSG00000101216.11" ; ccdsid "CCDS13528.1" ; exon_id "ENSE00001109207.1" ; exon_number 1 ; gene_id "STK4--GMEB2^GMEB2^ENSG00000101216.11" ; gene_name GMEB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032988.2" ; havana_transcript "OTTHUMT00000080166.1" ; hgnc_id "HGNC:4371" ; level 2 ; orig_coord_info "chr20,63619267,63619397,-" ; protein_id "ENSP00000266068.1" ; tag basic appris_principal_2 CCDS ; transcript_id "STK4--GMEB2^ENST00000266068.5" ; transcript_name "GMEB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
STK4--GMEB2 HAVANA gene 1044 18317 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "STK4--GMEB2^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "STK4--GMEB2^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "STK4--GMEB2^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
STK4--GMEB2 HAVANA mRNA 1044 18317 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "STK4--GMEB2^ENST00000372801.5" ; Parent "STK4--GMEB2^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "STK4--GMEB2^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "STK4--GMEB2^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; 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:
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:
VAPB--NEURL2 HAVANA gene 20918 23130 . + . FI_gene_label "NEURL2^ENSG00000124257.7" ; ID "VAPB--NEURL2^NEURL2^ENSG00000124257.7" ; ccdsid "CCDS13384.1" ; exon_id "ENSE00001458004.4" ; exon_number 1 ; gene_id "VAPB--NEURL2^NEURL2^ENSG00000124257.7" ; gene_name NEURL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032626.2" ; havana_transcript "OTTHUMT00000079539.2" ; hgnc_id "HGNC:16156" ; level 2 ; orig_coord_info "chr20,45890250,45890991,-" ; protein_id "ENSP00000361596.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VAPB--NEURL2^ENST00000372518.5" ; transcript_name "NEURL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
VAPB--NEURL2 HAVANA mRNA 20918 23130 . + . FI_gene_label "NEURL2^ENSG00000124257.7" ; ID "VAPB--NEURL2^ENST00000372518.5" ; Parent "VAPB--NEURL2^NEURL2^ENSG00000124257.7" ; ccdsid "CCDS13384.1" ; exon_id "ENSE00001458004.4" ; exon_number 1 ; gene_id "VAPB--NEURL2^NEURL2^ENSG00000124257.7" ; gene_name NEURL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032626.2" ; havana_transcript "OTTHUMT00000079539.2" ; hgnc_id "HGNC:16156" ; level 2 ; orig_coord_info "chr20,45890250,45890991,-" ; protein_id "ENSP00000361596.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "VAPB--NEURL2^ENST00000372518.5" ; transcript_name "NEURL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VAPB--NEURL2 HAVANA gene 1085 12368 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "VAPB--NEURL2^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "VAPB--NEURL2^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "VAPB--NEURL2^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
VAPB--NEURL2 HAVANA mRNA 1085 12368 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "VAPB--NEURL2^ENST00000395802.7" ; Parent "VAPB--NEURL2^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "VAPB--NEURL2^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "VAPB--NEURL2^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZHX3--KIZ HAVANA gene 2861 23743 . + . FI_gene_label "ZHX3^ENSG00000174306.21" ; ID "ZHX3--KIZ^ZHX3^ENSG00000174306.21" ; ccdsid "CCDS13315.1" ; exon_id "ENSE00003698803.1" ; exon_number 4 ; gene_id "ZHX3--KIZ^ZHX3^ENSG00000174306.21" ; gene_name ZHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032481.7" ; havana_transcript "OTTHUMT00000079262.3" ; hgnc_id "HGNC:15935" ; level 2 ; orig_coord_info "chr20,41202057,41204916,-" ; protein_id "ENSP00000312222.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ZHX3--KIZ^ENST00000309060.7" ; transcript_name "ZHX3-201" ; transcript_support_level 5 ; transcript_type protein_coding
ZHX3--KIZ HAVANA mRNA 2861 23743 . + . FI_gene_label "ZHX3^ENSG00000174306.21" ; ID "ZHX3--KIZ^ENST00000309060.7" ; Parent "ZHX3--KIZ^ZHX3^ENSG00000174306.21" ; ccdsid "CCDS13315.1" ; exon_id "ENSE00003698803.1" ; exon_number 4 ; gene_id "ZHX3--KIZ^ZHX3^ENSG00000174306.21" ; gene_name ZHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032481.7" ; havana_transcript "OTTHUMT00000079262.3" ; hgnc_id "HGNC:15935" ; level 2 ; orig_coord_info "chr20,41202057,41204916,-" ; protein_id "ENSP00000312222.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ZHX3--KIZ^ENST00000309060.7" ; transcript_name "ZHX3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ZHX3--KIZ HAVANA gene 26800 46109 . + . FI_gene_label "KIZ^ENSG00000088970.16" ; ID "ZHX3--KIZ^KIZ^ENSG00000088970.16" ; exon_id "ENSE00003756607.1" ; exon_number 1 ; gene_id "ZHX3--KIZ^KIZ^ENSG00000088970.16" ; gene_name KIZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000032020.6" ; havana_transcript "OTTHUMT00000478906.1" ; hgnc_id "HGNC:15865" ; level 2 ; orig_coord_info "chr20,21126039,21126204,+" ; protein_id "ENSP00000483644.2" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ZHX3--KIZ^ENST00000611685.4" ; transcript_name "KIZ-205" ; transcript_support_level 2 ; transcript_type protein_coding
ZHX3--KIZ HAVANA mRNA 26800 46109 . + . FI_gene_label "KIZ^ENSG00000088970.16" ; ID "ZHX3--KIZ^ENST00000611685.4" ; Parent "ZHX3--KIZ^KIZ^ENSG00000088970.16" ; exon_id "ENSE00003756607.1" ; exon_number 1 ; gene_id "ZHX3--KIZ^KIZ^ENSG00000088970.16" ; gene_name KIZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000032020.6" ; havana_transcript "OTTHUMT00000478906.1" ; hgnc_id "HGNC:15865" ; level 2 ; orig_coord_info "chr20,21126039,21126204,+" ; protein_id "ENSP00000483644.2" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ZHX3--KIZ^ENST00000611685.4" ; transcript_name "KIZ-205" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ZMYND8--VAPB HAVANA gene 1067 33262 . + . FI_gene_label "ZMYND8^ENSG00000101040.19" ; ID "ZMYND8--VAPB^ZMYND8^ENSG00000101040.19" ; ccdsid "CCDS63301.1" ; exon_id "ENSE00003659831.1" ; exon_number 3 ; gene_id "ZMYND8--VAPB^ZMYND8^ENSG00000101040.19" ; gene_name ZMYND8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032667.11" ; havana_transcript "OTTHUMT00000354390.2" ; hgnc_id "HGNC:9397" ; level 2 ; orig_coord_info "chr20,47347856,47347880,-" ; protein_id "ENSP00000262975.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "ZMYND8--VAPB^ENST00000262975.8" ; transcript_name "ZMYND8-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZMYND8--VAPB HAVANA mRNA 1067 33262 . + . FI_gene_label "ZMYND8^ENSG00000101040.19" ; ID "ZMYND8--VAPB^ENST00000262975.8" ; Parent "ZMYND8--VAPB^ZMYND8^ENSG00000101040.19" ; ccdsid "CCDS63301.1" ; exon_id "ENSE00003659831.1" ; exon_number 3 ; gene_id "ZMYND8--VAPB^ZMYND8^ENSG00000101040.19" ; gene_name ZMYND8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032667.11" ; havana_transcript "OTTHUMT00000354390.2" ; hgnc_id "HGNC:9397" ; level 2 ; orig_coord_info "chr20,47347856,47347880,-" ; protein_id "ENSP00000262975.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "ZMYND8--VAPB^ENST00000262975.8" ; transcript_name "ZMYND8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZMYND8--VAPB HAVANA gene 37546 48829 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "ZMYND8--VAPB^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "ZMYND8--VAPB^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "ZMYND8--VAPB^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
ZMYND8--VAPB HAVANA mRNA 37546 48829 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "ZMYND8--VAPB^ENST00000395802.7" ; Parent "ZMYND8--VAPB^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "ZMYND8--VAPB^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "ZMYND8--VAPB^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COPS3--AC005323.2 HAVANA gene 16831 21599 . + . FI_gene_label "AC005323.2^ENSG00000272736.5" ; ID "COPS3--AC005323.2^AC005323.2^ENSG00000272736.5" ; exon_id "ENSE00002723078.1" ; exon_number 1 ; gene_id "COPS3--AC005323.2^AC005323.2^ENSG00000272736.5" ; gene_name "AC005323.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186178.1" ; havana_transcript "OTTHUMT00000472365.1" ; level 2 ; orig_coord_info "chr17,10383132,10383207,+" ; tag basic ; transcript_id "COPS3--AC005323.2^ENST00000399342.6" ; transcript_name "AC005323.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
COPS3--AC005323.2 HAVANA RNA 16831 21599 . + . FI_gene_label "AC005323.2^ENSG00000272736.5" ; ID "COPS3--AC005323.2^ENST00000399342.6" ; Parent "COPS3--AC005323.2^AC005323.2^ENSG00000272736.5" ; exon_id "ENSE00002723078.1" ; exon_number 1 ; gene_id "COPS3--AC005323.2^AC005323.2^ENSG00000272736.5" ; gene_name "AC005323.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000186178.1" ; havana_transcript "OTTHUMT00000472365.1" ; level 2 ; orig_coord_info "chr17,10383132,10383207,+" ; tag basic ; transcript_id "COPS3--AC005323.2^ENST00000399342.6" ; transcript_name "AC005323.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
DNM1L--AK6P1 HAVANA gene 28229 28706 . + . FI_gene_label "AK6P1^ENSG00000256614.1" ; ID "DNM1L--AK6P1^AK6P1^ENSG00000256614.1" ; exon_id "ENSE00002309684.1" ; exon_number 1 ; gene_id "DNM1L--AK6P1^AK6P1^ENSG00000256614.1" ; gene_name AK6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169291.1" ; havana_transcript "OTTHUMT00000403318.1" ; hgnc_id "HGNC:51678" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,34249481,34249958,+" ; tag pseudo_consens basic ; transcript_id "DNM1L--AK6P1^ENST00000540219.1" ; transcript_name "AK6P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
DNM1L--AK6P1 HAVANA RNA 28229 28706 . + . FI_gene_label "AK6P1^ENSG00000256614.1" ; ID "DNM1L--AK6P1^ENST00000540219.1" ; Parent "DNM1L--AK6P1^AK6P1^ENSG00000256614.1" ; exon_id "ENSE00002309684.1" ; exon_number 1 ; gene_id "DNM1L--AK6P1^AK6P1^ENSG00000256614.1" ; gene_name AK6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169291.1" ; havana_transcript "OTTHUMT00000403318.1" ; hgnc_id "HGNC:51678" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr12,34249481,34249958,+" ; tag pseudo_consens basic ; transcript_id "DNM1L--AK6P1^ENST00000540219.1" ; transcript_name "AK6P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
DNM1L--ZNF970P HAVANA gene 28229 29026 . + . FI_gene_label "ZNF970P^ENSG00000258368.2" ; ID "DNM1L--ZNF970P^ZNF970P^ENSG00000258368.2" ; exon_id "ENSE00002371322.2" ; exon_number 1 ; gene_id "DNM1L--ZNF970P^ZNF970P^ENSG00000258368.2" ; gene_name ZNF970P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000169295.2" ; havana_transcript "OTTHUMT00000403346.2" ; hgnc_id "HGNC:44511" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr12,37575587,37575713,+" ; tag basic ; transcript_id "DNM1L--ZNF970P^ENST00000547456.2" ; transcript_name "ZNF970P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
DNM1L--ZNF970P HAVANA RNA 28229 29026 . + . FI_gene_label "ZNF970P^ENSG00000258368.2" ; ID "DNM1L--ZNF970P^ENST00000547456.2" ; Parent "DNM1L--ZNF970P^ZNF970P^ENSG00000258368.2" ; exon_id "ENSE00002371322.2" ; exon_number 1 ; gene_id "DNM1L--ZNF970P^ZNF970P^ENSG00000258368.2" ; gene_name ZNF970P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000169295.2" ; havana_transcript "OTTHUMT00000403346.2" ; hgnc_id "HGNC:44511" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr12,37575587,37575713,+" ; tag basic ; transcript_id "DNM1L--ZNF970P^ENST00000547456.2" ; transcript_name "ZNF970P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
PREX1--LINC01746 HAVANA gene 45191 48462 . + . FI_gene_label "LINC01746^ENSG00000274469.2" ; ID "PREX1--LINC01746^LINC01746^ENSG00000274469.2" ; exon_id "ENSE00003745253.1" ; exon_number 1 ; gene_id "PREX1--LINC01746^LINC01746^ENSG00000274469.2" ; gene_name LINC01746 ; gene_type lncRNA ; havana_gene "OTTHUMG00000185859.3" ; havana_transcript "OTTHUMT00000473863.1" ; hgnc_id "HGNC:52534" ; level 2 ; orig_coord_info "chr20,37571103,37571298,+" ; transcript_id "PREX1--LINC01746^ENST00000621390.1" ; transcript_name "LINC01746-201" ; transcript_support_level 3 ; transcript_type lncRNA
PREX1--LINC01746 HAVANA RNA 45191 48462 . + . FI_gene_label "LINC01746^ENSG00000274469.2" ; ID "PREX1--LINC01746^ENST00000621390.1" ; Parent "PREX1--LINC01746^LINC01746^ENSG00000274469.2" ; exon_id "ENSE00003745253.1" ; exon_number 1 ; gene_id "PREX1--LINC01746^LINC01746^ENSG00000274469.2" ; gene_name LINC01746 ; gene_type lncRNA ; havana_gene "OTTHUMG00000185859.3" ; havana_transcript "OTTHUMT00000473863.1" ; hgnc_id "HGNC:52534" ; level 2 ; orig_coord_info "chr20,37571103,37571298,+" ; transcript_id "PREX1--LINC01746^ENST00000621390.1" ; transcript_name "LINC01746-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
PREX1--PPIAP3 HAVANA gene 45191 45695 . + . FI_gene_label "PPIAP3^ENSG00000235044.1" ; ID "PREX1--PPIAP3^PPIAP3^ENSG00000235044.1" ; exon_id "ENSE00001664064.1" ; exon_number 1 ; gene_id "PREX1--PPIAP3^PPIAP3^ENSG00000235044.1" ; gene_name PPIAP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032425.1" ; havana_transcript "OTTHUMT00000079122.1" ; hgnc_id "HGNC:16545" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr20,37530039,37530543,+" ; tag pseudo_consens basic ; transcript_id "PREX1--PPIAP3^ENST00000450588.1" ; transcript_name "PPIAP3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
PREX1--PPIAP3 HAVANA RNA 45191 45695 . + . FI_gene_label "PPIAP3^ENSG00000235044.1" ; ID "PREX1--PPIAP3^ENST00000450588.1" ; Parent "PREX1--PPIAP3^PPIAP3^ENSG00000235044.1" ; exon_id "ENSE00001664064.1" ; exon_number 1 ; gene_id "PREX1--PPIAP3^PPIAP3^ENSG00000235044.1" ; gene_name PPIAP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032425.1" ; havana_transcript "OTTHUMT00000079122.1" ; hgnc_id "HGNC:16545" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr20,37530039,37530543,+" ; tag pseudo_consens basic ; transcript_id "PREX1--PPIAP3^ENST00000450588.1" ; transcript_name "PPIAP3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
RERE--AC118650.1 ENSEMBL gene 46536 46624 . + . FI_gene_label "AC118650.1^ENSG00000276685.1" ; ID "RERE--AC118650.1^AC118650.1^ENSG00000276685.1" ; exon_id "ENSE00003715315.1" ; exon_number 1 ; gene_id "RERE--AC118650.1^AC118650.1^ENSG00000276685.1" ; gene_name "AC118650.1" ; gene_type misc_RNA ; level 3 ; orig_coord_info "chr8,46028804,46028892,-" ; tag basic ; transcript_id "RERE--AC118650.1^ENST00000618609.1" ; transcript_name "AC118650.1-201" ; transcript_support_level NA ; transcript_type misc_RNA
RERE--AC118650.1 ENSEMBL RNA 46536 46624 . + . FI_gene_label "AC118650.1^ENSG00000276685.1" ; ID "RERE--AC118650.1^ENST00000618609.1" ; Parent "RERE--AC118650.1^AC118650.1^ENSG00000276685.1" ; exon_id "ENSE00003715315.1" ; exon_number 1 ; gene_id "RERE--AC118650.1^AC118650.1^ENSG00000276685.1" ; gene_name "AC118650.1" ; gene_type misc_RNA ; level 3 ; orig_coord_info "chr8,46028804,46028892,-" ; tag basic ; transcript_id "RERE--AC118650.1^ENST00000618609.1" ; transcript_name "AC118650.1-201" ; transcript_support_level NA ; transcript_type misc_RNA
L1 and L2 created:
RERE--AC139365.1 HAVANA gene 46536 46857 . + . FI_gene_label "AC139365.1^ENSG00000253198.1" ; ID "RERE--AC139365.1^AC139365.1^ENSG00000253198.1" ; exon_id "ENSE00002120320.1" ; exon_number 1 ; gene_id "RERE--AC139365.1^AC139365.1^ENSG00000253198.1" ; gene_name "AC139365.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164120.1" ; havana_transcript "OTTHUMT00000377321.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,43674270,43674591,-" ; tag pseudo_consens basic ; transcript_id "RERE--AC139365.1^ENST00000519417.1" ; transcript_name "AC139365.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
RERE--AC139365.1 HAVANA RNA 46536 46857 . + . FI_gene_label "AC139365.1^ENSG00000253198.1" ; ID "RERE--AC139365.1^ENST00000519417.1" ; Parent "RERE--AC139365.1^AC139365.1^ENSG00000253198.1" ; exon_id "ENSE00002120320.1" ; exon_number 1 ; gene_id "RERE--AC139365.1^AC139365.1^ENSG00000253198.1" ; gene_name "AC139365.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164120.1" ; havana_transcript "OTTHUMT00000377321.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr8,43674270,43674591,-" ; tag pseudo_consens basic ; transcript_id "RERE--AC139365.1^ENST00000519417.1" ; transcript_name "AC139365.1-201" ; 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:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
571 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
1143 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 40 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 1 second) ------
GFF3 file parsed