Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/aeb5d9d5a3c5f28bd55d0b68ee7376/fi_workdir/aih-tih-sc-606237-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/40aa337ef01ebe1172ed1c401e8692/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/40aa337ef01ebe1172ed1c401e8692/.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: 4418
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4418
=> 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:4418
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 1 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
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:
ADAM9--ZMAT4 HAVANA gene 42020 55703 . + . FI_gene_label "ZMAT4^ENSG00000165061.15" ; ID "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15" ; ccdsid "CCDS34885.1" ; exon_id "ENSE00003606486.1" ; exon_number 2 ; gene_id "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15" ; gene_name ZMAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164049.3" ; havana_transcript "OTTHUMT00000376950.2" ; hgnc_id "HGNC:25844" ; level 2 ; orig_coord_info "chr8,40825575,40825676,-" ; protein_id "ENSP00000297737.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--ZMAT4^ENST00000297737.11" ; transcript_name "ZMAT4-201" ; transcript_support_level 2 ; transcript_type protein_coding
ADAM9--ZMAT4 HAVANA mRNA 42020 55703 . + . FI_gene_label "ZMAT4^ENSG00000165061.15" ; ID "ADAM9--ZMAT4^ENST00000297737.11" ; Parent "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15" ; ccdsid "CCDS34885.1" ; exon_id "ENSE00003606486.1" ; exon_number 2 ; gene_id "ADAM9--ZMAT4^ZMAT4^ENSG00000165061.15" ; gene_name ZMAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164049.3" ; havana_transcript "OTTHUMT00000376950.2" ; hgnc_id "HGNC:25844" ; level 2 ; orig_coord_info "chr8,40825575,40825676,-" ; protein_id "ENSP00000297737.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--ZMAT4^ENST00000297737.11" ; transcript_name "ZMAT4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ADAM9--ZMAT4 HAVANA gene 1273 38711 . + . FI_gene_label "ADAM9^ENSG00000168615.13" ; ID "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13" ; exon_id "ENSE00001854428.1" ; exon_number 1 ; gene_id "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13" ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5" ; havana_transcript "OTTHUMT00000357297.1" ; hgnc_id "HGNC:216" ; level 2 ; orig_coord_info "chr8,38997064,38997160,+" ; protein_id "ENSP00000369249.3" ; transcript_id "ADAM9--ZMAT4^ENST00000379917.7" ; transcript_name "ADAM9-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ADAM9--ZMAT4 HAVANA mRNA 1273 38711 . + . FI_gene_label "ADAM9^ENSG00000168615.13" ; ID "ADAM9--ZMAT4^ENST00000379917.7" ; Parent "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13" ; exon_id "ENSE00001854428.1" ; exon_number 1 ; gene_id "ADAM9--ZMAT4^ADAM9^ENSG00000168615.13" ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5" ; havana_transcript "OTTHUMT00000357297.1" ; hgnc_id "HGNC:216" ; level 2 ; orig_coord_info "chr8,38997064,38997160,+" ; protein_id "ENSP00000369249.3" ; transcript_id "ADAM9--ZMAT4^ENST00000379917.7" ; transcript_name "ADAM9-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
AXIN1--GGA2 HAVANA gene 1001 16032 . + . FI_gene_label "AXIN1^ENSG00000103126.15" ; ID "AXIN1--GGA2^AXIN1^ENSG00000103126.15" ; ccdsid "CCDS10405.1" ; exon_id "ENSE00001331290.2" ; exon_number 2 ; gene_id "AXIN1--GGA2^AXIN1^ENSG00000103126.15" ; gene_name AXIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000064930.5" ; havana_transcript "OTTHUMT00000139441.4" ; hgnc_id "HGNC:903" ; level 2 ; orig_coord_info "chr16,346148,347025,-" ; protein_id "ENSP00000262320.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AXIN1--GGA2^ENST00000262320.8" ; transcript_name "AXIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AXIN1--GGA2 HAVANA mRNA 1001 16032 . + . FI_gene_label "AXIN1^ENSG00000103126.15" ; ID "AXIN1--GGA2^ENST00000262320.8" ; Parent "AXIN1--GGA2^AXIN1^ENSG00000103126.15" ; ccdsid "CCDS10405.1" ; exon_id "ENSE00001331290.2" ; exon_number 2 ; gene_id "AXIN1--GGA2^AXIN1^ENSG00000103126.15" ; gene_name AXIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000064930.5" ; havana_transcript "OTTHUMT00000139441.4" ; hgnc_id "HGNC:903" ; level 2 ; orig_coord_info "chr16,346148,347025,-" ; protein_id "ENSP00000262320.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AXIN1--GGA2^ENST00000262320.8" ; transcript_name "AXIN1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AXIN1--GGA2 HAVANA gene 21289 41972 . + . FI_gene_label "GGA2^ENSG00000103365.15" ; ID "AXIN1--GGA2^GGA2^ENSG00000103365.15" ; ccdsid "CCDS10611.1" ; exon_id "ENSE00003495136.1" ; exon_number 1 ; gene_id "AXIN1--GGA2^GGA2^ENSG00000103365.15" ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5" ; havana_transcript "OTTHUMT00000214019.1" ; hgnc_id "HGNC:16064" ; level 2 ; orig_coord_info "chr16,23510321,23510411,-" ; protein_id "ENSP00000311962.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AXIN1--GGA2^ENST00000309859.8" ; transcript_name "GGA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AXIN1--GGA2 HAVANA mRNA 21289 41972 . + . FI_gene_label "GGA2^ENSG00000103365.15" ; ID "AXIN1--GGA2^ENST00000309859.8" ; Parent "AXIN1--GGA2^GGA2^ENSG00000103365.15" ; ccdsid "CCDS10611.1" ; exon_id "ENSE00003495136.1" ; exon_number 1 ; gene_id "AXIN1--GGA2^GGA2^ENSG00000103365.15" ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5" ; havana_transcript "OTTHUMT00000214019.1" ; hgnc_id "HGNC:16064" ; level 2 ; orig_coord_info "chr16,23510321,23510411,-" ; protein_id "ENSP00000311962.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AXIN1--GGA2^ENST00000309859.8" ; transcript_name "GGA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COX6CP1--COX6C HAVANA gene 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding
COX6CP1--COX6C HAVANA mRNA 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^ENST00000297564.6" ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; 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:
DCTN5--MRPL28 HAVANA gene 23801 27370 . + . FI_gene_label "MRPL28^ENSG00000086504.17" ; ID "DCTN5--MRPL28^MRPL28^ENSG00000086504.17" ; ccdsid "CCDS32349.1" ; exon_id "ENSE00003622338.1" ; exon_number 2 ; gene_id "DCTN5--MRPL28^MRPL28^ENSG00000086504.17" ; gene_name MRPL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047994.9" ; havana_transcript "OTTHUMT00000139285.3" ; hgnc_id "HGNC:14484" ; level 2 ; orig_coord_info "chr16,369931,370218,-" ; protein_id "ENSP00000199706.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000199706.13" ; transcript_name "MRPL28-201" ; transcript_support_level 1 ; transcript_type protein_coding
DCTN5--MRPL28 HAVANA mRNA 23801 27370 . + . FI_gene_label "MRPL28^ENSG00000086504.17" ; ID "DCTN5--MRPL28^ENST00000199706.13" ; Parent "DCTN5--MRPL28^MRPL28^ENSG00000086504.17" ; ccdsid "CCDS32349.1" ; exon_id "ENSE00003622338.1" ; exon_number 2 ; gene_id "DCTN5--MRPL28^MRPL28^ENSG00000086504.17" ; gene_name MRPL28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047994.9" ; havana_transcript "OTTHUMT00000139285.3" ; hgnc_id "HGNC:14484" ; level 2 ; orig_coord_info "chr16,369931,370218,-" ; protein_id "ENSP00000199706.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000199706.13" ; transcript_name "MRPL28-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DCTN5--MRPL28 HAVANA gene 1001 20049 . + . FI_gene_label "DCTN5^ENSG00000166847.10" ; ID "DCTN5--MRPL28^DCTN5^ENSG00000166847.10" ; ccdsid "CCDS10615.1" ; exon_id "ENSE00001830153.2" ; exon_number 1 ; gene_id "DCTN5--MRPL28^DCTN5^ENSG00000166847.10" ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7" ; havana_transcript "OTTHUMT00000254497.3" ; hgnc_id "HGNC:24594" ; level 2 ; orig_coord_info "chr16,23641543,23641590,+" ; protein_id "ENSP00000300087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000300087.7" ; transcript_name "DCTN5-201" ; transcript_support_level 1 ; transcript_type protein_coding
DCTN5--MRPL28 HAVANA mRNA 1001 20049 . + . FI_gene_label "DCTN5^ENSG00000166847.10" ; ID "DCTN5--MRPL28^ENST00000300087.7" ; Parent "DCTN5--MRPL28^DCTN5^ENSG00000166847.10" ; ccdsid "CCDS10615.1" ; exon_id "ENSE00001830153.2" ; exon_number 1 ; gene_id "DCTN5--MRPL28^DCTN5^ENSG00000166847.10" ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7" ; havana_transcript "OTTHUMT00000254497.3" ; hgnc_id "HGNC:24594" ; level 2 ; orig_coord_info "chr16,23641543,23641590,+" ; protein_id "ENSP00000300087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DCTN5--MRPL28^ENST00000300087.7" ; transcript_name "DCTN5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GGA2--WARS2-AS1 HAVANA gene 3257 23940 . + . FI_gene_label "GGA2^ENSG00000103365.15" ; ID "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15" ; ccdsid "CCDS10611.1" ; exon_id "ENSE00003495136.1" ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15" ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5" ; havana_transcript "OTTHUMT00000214019.1" ; hgnc_id "HGNC:16064" ; level 2 ; orig_coord_info "chr16,23510321,23510411,-" ; protein_id "ENSP00000311962.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA2--WARS2-AS1^ENST00000309859.8" ; transcript_name "GGA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GGA2--WARS2-AS1 HAVANA mRNA 3257 23940 . + . FI_gene_label "GGA2^ENSG00000103365.15" ; ID "GGA2--WARS2-AS1^ENST00000309859.8" ; Parent "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15" ; ccdsid "CCDS10611.1" ; exon_id "ENSE00003495136.1" ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^GGA2^ENSG00000103365.15" ; gene_name GGA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000096957.5" ; havana_transcript "OTTHUMT00000214019.1" ; hgnc_id "HGNC:16064" ; level 2 ; orig_coord_info "chr16,23510321,23510411,-" ; protein_id "ENSP00000311962.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA2--WARS2-AS1^ENST00000309859.8" ; transcript_name "GGA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP3K1--LMNB1 HAVANA gene 25964 39721 . + . FI_gene_label "LMNB1^ENSG00000113368.12" ; ID "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12" ; ccdsid "CCDS4140.1" ; exon_id "ENSE00001294154.7" ; exon_number 1 ; gene_id "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12" ; gene_name LMNB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128969.8" ; havana_transcript "OTTHUMT00000250956.3" ; hgnc_id "HGNC:6637" ; level 2 ; orig_coord_info "chr5,126777509,126777867,+" ; protein_id "ENSP00000261366.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000261366.10" ; transcript_name "LMNB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--LMNB1 HAVANA mRNA 25964 39721 . + . FI_gene_label "LMNB1^ENSG00000113368.12" ; ID "MAP3K1--LMNB1^ENST00000261366.10" ; Parent "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12" ; ccdsid "CCDS4140.1" ; exon_id "ENSE00001294154.7" ; exon_number 1 ; gene_id "MAP3K1--LMNB1^LMNB1^ENSG00000113368.12" ; gene_name LMNB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128969.8" ; havana_transcript "OTTHUMT00000250956.3" ; hgnc_id "HGNC:6637" ; level 2 ; orig_coord_info "chr5,126777509,126777867,+" ; protein_id "ENSP00000261366.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000261366.10" ; transcript_name "LMNB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP3K1--LMNB1 HAVANA gene 1001 22450 . + . FI_gene_label "MAP3K1^ENSG00000095015.6" ; ID "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6" ; ccdsid "CCDS43318.1" ; exon_id "ENSE00001538799.4" ; exon_number 1 ; gene_id "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6" ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3" ; havana_transcript "OTTHUMT00000132309.3" ; hgnc_id "HGNC:6848" ; level 1 ; orig_coord_info "chr5,56815574,56816055,+" ; protein_id "ENSP00000382423.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000399503.4" ; transcript_name "MAP3K1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--LMNB1 HAVANA mRNA 1001 22450 . + . FI_gene_label "MAP3K1^ENSG00000095015.6" ; ID "MAP3K1--LMNB1^ENST00000399503.4" ; Parent "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6" ; ccdsid "CCDS43318.1" ; exon_id "ENSE00001538799.4" ; exon_number 1 ; gene_id "MAP3K1--LMNB1^MAP3K1^ENSG00000095015.6" ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3" ; havana_transcript "OTTHUMT00000132309.3" ; hgnc_id "HGNC:6848" ; level 1 ; orig_coord_info "chr5,56815574,56816055,+" ; protein_id "ENSP00000382423.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--LMNB1^ENST00000399503.4" ; transcript_name "MAP3K1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP3K1--MARCHF3 HAVANA gene 25451 36559 . + . FI_gene_label "MARCHF3^ENSG00000173926.6" ; ID "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6" ; ccdsid "CCDS4141.1" ; exon_id "ENSE00003676575.1" ; exon_number 2 ; gene_id "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6" ; gene_name MARCHF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128968.4" ; havana_transcript "OTTHUMT00000250955.3" ; hgnc_id "HGNC:28728" ; level 2 ; orig_coord_info "chr5,126917984,126918171,-" ; protein_id "ENSP00000309141.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000308660.6" ; transcript_name "MARCHF3-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--MARCHF3 HAVANA mRNA 25451 36559 . + . FI_gene_label "MARCHF3^ENSG00000173926.6" ; ID "MAP3K1--MARCHF3^ENST00000308660.6" ; Parent "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6" ; ccdsid "CCDS4141.1" ; exon_id "ENSE00003676575.1" ; exon_number 2 ; gene_id "MAP3K1--MARCHF3^MARCHF3^ENSG00000173926.6" ; gene_name MARCHF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128968.4" ; havana_transcript "OTTHUMT00000250955.3" ; hgnc_id "HGNC:28728" ; level 2 ; orig_coord_info "chr5,126917984,126918171,-" ; protein_id "ENSP00000309141.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000308660.6" ; transcript_name "MARCHF3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP3K1--MARCHF3 HAVANA gene 1001 22450 . + . FI_gene_label "MAP3K1^ENSG00000095015.6" ; ID "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6" ; ccdsid "CCDS43318.1" ; exon_id "ENSE00001538799.4" ; exon_number 1 ; gene_id "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6" ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3" ; havana_transcript "OTTHUMT00000132309.3" ; hgnc_id "HGNC:6848" ; level 1 ; orig_coord_info "chr5,56815574,56816055,+" ; protein_id "ENSP00000382423.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000399503.4" ; transcript_name "MAP3K1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP3K1--MARCHF3 HAVANA mRNA 1001 22450 . + . FI_gene_label "MAP3K1^ENSG00000095015.6" ; ID "MAP3K1--MARCHF3^ENST00000399503.4" ; Parent "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6" ; ccdsid "CCDS43318.1" ; exon_id "ENSE00001538799.4" ; exon_number 1 ; gene_id "MAP3K1--MARCHF3^MAP3K1^ENSG00000095015.6" ; gene_name MAP3K1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059486.3" ; havana_transcript "OTTHUMT00000132309.3" ; hgnc_id "HGNC:6848" ; level 1 ; orig_coord_info "chr5,56815574,56816055,+" ; protein_id "ENSP00000382423.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "MAP3K1--MARCHF3^ENST00000399503.4" ; transcript_name "MAP3K1-201" ; transcript_support_level 1 ; 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:
PDE7A--CLVS1 HAVANA gene 32042 48239 . + . FI_gene_label "CLVS1^ENSG00000177182.11" ; ID "PDE7A--CLVS1^CLVS1^ENSG00000177182.11" ; ccdsid "CCDS6176.1" ; exon_id "ENSE00001087276.4" ; exon_number 2 ; gene_id "PDE7A--CLVS1^CLVS1^ENSG00000177182.11" ; gene_name CLVS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164334.8" ; havana_transcript "OTTHUMT00000378326.2" ; hgnc_id "HGNC:23139" ; level 2 ; orig_coord_info "chr8,61299828,61300282,+" ; protein_id "ENSP00000325506.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000325897.5" ; transcript_name "CLVS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PDE7A--CLVS1 HAVANA mRNA 32042 48239 . + . FI_gene_label "CLVS1^ENSG00000177182.11" ; ID "PDE7A--CLVS1^ENST00000325897.5" ; Parent "PDE7A--CLVS1^CLVS1^ENSG00000177182.11" ; ccdsid "CCDS6176.1" ; exon_id "ENSE00001087276.4" ; exon_number 2 ; gene_id "PDE7A--CLVS1^CLVS1^ENSG00000177182.11" ; gene_name CLVS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164334.8" ; havana_transcript "OTTHUMT00000378326.2" ; hgnc_id "HGNC:23139" ; level 2 ; orig_coord_info "chr8,61299828,61300282,+" ; protein_id "ENSP00000325506.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000325897.5" ; transcript_name "CLVS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PDE7A--CLVS1 HAVANA gene 4228 22817 . + . FI_gene_label "PDE7A^ENSG00000205268.11" ; ID "PDE7A--CLVS1^PDE7A^ENSG00000205268.11" ; ccdsid "CCDS34901.1" ; exon_id "ENSE00001480936.4" ; exon_number 1 ; gene_id "PDE7A--CLVS1^PDE7A^ENSG00000205268.11" ; gene_name PDE7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000164469.3" ; havana_transcript "OTTHUMT00000378906.1" ; hgnc_id "HGNC:8791" ; level 2 ; orig_coord_info "chr8,65788882,65788941,-" ; protein_id "ENSP00000368730.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000379419.8" ; transcript_name "PDE7A-201" ; transcript_support_level 2 ; transcript_type protein_coding
PDE7A--CLVS1 HAVANA mRNA 4228 22817 . + . FI_gene_label "PDE7A^ENSG00000205268.11" ; ID "PDE7A--CLVS1^ENST00000379419.8" ; Parent "PDE7A--CLVS1^PDE7A^ENSG00000205268.11" ; ccdsid "CCDS34901.1" ; exon_id "ENSE00001480936.4" ; exon_number 1 ; gene_id "PDE7A--CLVS1^PDE7A^ENSG00000205268.11" ; gene_name PDE7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000164469.3" ; havana_transcript "OTTHUMT00000378906.1" ; hgnc_id "HGNC:8791" ; level 2 ; orig_coord_info "chr8,65788882,65788941,-" ; protein_id "ENSP00000368730.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "PDE7A--CLVS1^ENST00000379419.8" ; transcript_name "PDE7A-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
RAB11FIP3--DCTN5 HAVANA gene 1001 19602 . + . FI_gene_label "RAB11FIP3^ENSG00000090565.17" ; ID "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17" ; ccdsid "CCDS32351.1" ; exon_id "ENSE00002222336.2" ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17" ; gene_name RAB11FIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047843.9" ; havana_transcript "OTTHUMT00000109066.5" ; hgnc_id "HGNC:17224" ; level 2 ; orig_coord_info "chr16,426007,426720,+" ; protein_id "ENSP00000262305.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000262305.9" ; transcript_name "RAB11FIP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
RAB11FIP3--DCTN5 HAVANA mRNA 1001 19602 . + . FI_gene_label "RAB11FIP3^ENSG00000090565.17" ; ID "RAB11FIP3--DCTN5^ENST00000262305.9" ; Parent "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17" ; ccdsid "CCDS32351.1" ; exon_id "ENSE00002222336.2" ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^RAB11FIP3^ENSG00000090565.17" ; gene_name RAB11FIP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047843.9" ; havana_transcript "OTTHUMT00000109066.5" ; hgnc_id "HGNC:17224" ; level 2 ; orig_coord_info "chr16,426007,426720,+" ; protein_id "ENSP00000262305.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000262305.9" ; transcript_name "RAB11FIP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RAB11FIP3--DCTN5 HAVANA gene 22603 41651 . + . FI_gene_label "DCTN5^ENSG00000166847.10" ; ID "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10" ; ccdsid "CCDS10615.1" ; exon_id "ENSE00001830153.2" ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10" ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7" ; havana_transcript "OTTHUMT00000254497.3" ; hgnc_id "HGNC:24594" ; level 2 ; orig_coord_info "chr16,23641543,23641590,+" ; protein_id "ENSP00000300087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000300087.7" ; transcript_name "DCTN5-201" ; transcript_support_level 1 ; transcript_type protein_coding
RAB11FIP3--DCTN5 HAVANA mRNA 22603 41651 . + . FI_gene_label "DCTN5^ENSG00000166847.10" ; ID "RAB11FIP3--DCTN5^ENST00000300087.7" ; Parent "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10" ; ccdsid "CCDS10615.1" ; exon_id "ENSE00001830153.2" ; exon_number 1 ; gene_id "RAB11FIP3--DCTN5^DCTN5^ENSG00000166847.10" ; gene_name DCTN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131610.7" ; havana_transcript "OTTHUMT00000254497.3" ; hgnc_id "HGNC:24594" ; level 2 ; orig_coord_info "chr16,23641543,23641590,+" ; protein_id "ENSP00000300087.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB11FIP3--DCTN5^ENST00000300087.7" ; transcript_name "DCTN5-201" ; transcript_support_level 1 ; 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:
SCML2--AC095353.1 HAVANA gene 1001 20080 . + . FI_gene_label "SCML2^ENSG00000102098.19" ; ID "SCML2--AC095353.1^SCML2^ENSG00000102098.19" ; ccdsid "CCDS14185.1" ; exon_id "ENSE00002285630.1" ; exon_number 2 ; gene_id "SCML2--AC095353.1^SCML2^ENSG00000102098.19" ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4" ; havana_transcript "OTTHUMT00000055941.2" ; hgnc_id "HGNC:10581" ; level 2 ; orig_coord_info "chrX,18334050,18334071,-" ; protein_id "ENSP00000251900.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC095353.1^ENST00000251900.9" ; transcript_name "SCML2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SCML2--AC095353.1 HAVANA mRNA 1001 20080 . + . FI_gene_label "SCML2^ENSG00000102098.19" ; ID "SCML2--AC095353.1^ENST00000251900.9" ; Parent "SCML2--AC095353.1^SCML2^ENSG00000102098.19" ; ccdsid "CCDS14185.1" ; exon_id "ENSE00002285630.1" ; exon_number 2 ; gene_id "SCML2--AC095353.1^SCML2^ENSG00000102098.19" ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4" ; havana_transcript "OTTHUMT00000055941.2" ; hgnc_id "HGNC:10581" ; level 2 ; orig_coord_info "chrX,18334050,18334071,-" ; protein_id "ENSP00000251900.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC095353.1^ENST00000251900.9" ; transcript_name "SCML2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SCML2--AC110995.1 HAVANA gene 1001 20080 . + . FI_gene_label "SCML2^ENSG00000102098.19" ; ID "SCML2--AC110995.1^SCML2^ENSG00000102098.19" ; ccdsid "CCDS14185.1" ; exon_id "ENSE00002285630.1" ; exon_number 2 ; gene_id "SCML2--AC110995.1^SCML2^ENSG00000102098.19" ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4" ; havana_transcript "OTTHUMT00000055941.2" ; hgnc_id "HGNC:10581" ; level 2 ; orig_coord_info "chrX,18334050,18334071,-" ; protein_id "ENSP00000251900.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC110995.1^ENST00000251900.9" ; transcript_name "SCML2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SCML2--AC110995.1 HAVANA mRNA 1001 20080 . + . FI_gene_label "SCML2^ENSG00000102098.19" ; ID "SCML2--AC110995.1^ENST00000251900.9" ; Parent "SCML2--AC110995.1^SCML2^ENSG00000102098.19" ; ccdsid "CCDS14185.1" ; exon_id "ENSE00002285630.1" ; exon_number 2 ; gene_id "SCML2--AC110995.1^SCML2^ENSG00000102098.19" ; gene_name SCML2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021212.4" ; havana_transcript "OTTHUMT00000055941.2" ; hgnc_id "HGNC:10581" ; level 2 ; orig_coord_info "chrX,18334050,18334071,-" ; protein_id "ENSP00000251900.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCML2--AC110995.1^ENST00000251900.9" ; transcript_name "SCML2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLCO1B3--SLCO1B7 ENSEMBL gene 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLCO1B3--SLCO1B7 ENSEMBL mRNA 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6" ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNX29--MRTFB ENSEMBL gene 42313 78553 . + . FI_gene_label "MRTFB^ENSG00000186260.17" ; ID "SNX29--MRTFB^MRTFB^ENSG00000186260.17" ; ccdsid "CCDS32391.1" ; exon_id "ENSE00003525727.1" ; exon_number 2 ; gene_id "SNX29--MRTFB^MRTFB^ENSG00000186260.17" ; gene_name MRTFB ; gene_type protein_coding ; havana_gene "OTTHUMG00000177379.3" ; hgnc_id "HGNC:29819" ; level 3 ; orig_coord_info "chr16,14140607,14140760,+" ; protein_id "ENSP00000339086.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "SNX29--MRTFB^ENST00000318282.9" ; transcript_name "MRTFB-201" ; transcript_support_level 5 ; transcript_type protein_coding
SNX29--MRTFB ENSEMBL mRNA 42313 78553 . + . FI_gene_label "MRTFB^ENSG00000186260.17" ; ID "SNX29--MRTFB^ENST00000318282.9" ; Parent "SNX29--MRTFB^MRTFB^ENSG00000186260.17" ; ccdsid "CCDS32391.1" ; exon_id "ENSE00003525727.1" ; exon_number 2 ; gene_id "SNX29--MRTFB^MRTFB^ENSG00000186260.17" ; gene_name MRTFB ; gene_type protein_coding ; havana_gene "OTTHUMG00000177379.3" ; hgnc_id "HGNC:29819" ; level 3 ; orig_coord_info "chr16,14140607,14140760,+" ; protein_id "ENSP00000339086.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "SNX29--MRTFB^ENST00000318282.9" ; transcript_name "MRTFB-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SNX29--MRTFB HAVANA gene 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--MRTFB^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--MRTFB^SNX29^ENSG00000048471.14" ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4" ; havana_transcript "OTTHUMT00000422625.1" ; hgnc_id "HGNC:30542" ; level 2 ; orig_coord_info "chr16,12356253,12356279,+" ; protein_id "ENSP00000455327.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--MRTFB^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--MRTFB HAVANA mRNA 23819 27354 . + . FI_gene_label "SNX29^ENSG00000048471.14" ; ID "SNX29--MRTFB^ENST00000562510.1" ; Parent "SNX29--MRTFB^SNX29^ENSG00000048471.14" ; exon_id "ENSE00002616399.1" ; exon_number 1 ; gene_id "SNX29--MRTFB^SNX29^ENSG00000048471.14" ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4" ; havana_transcript "OTTHUMT00000422625.1" ; hgnc_id "HGNC:30542" ; level 2 ; orig_coord_info "chr16,12356253,12356279,+" ; protein_id "ENSP00000455327.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--MRTFB^ENST00000562510.1" ; transcript_name "SNX29-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STARD13--MTUS2 HAVANA gene 7683 28646 . + . FI_gene_label "STARD13^ENSG00000133121.21" ; ID "STARD13--MTUS2^STARD13^ENSG00000133121.21" ; ccdsid "CCDS9349.1" ; exon_id "ENSE00001333091.2" ; exon_number 1 ; gene_id "STARD13--MTUS2^STARD13^ENSG00000133121.21" ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8" ; havana_transcript "OTTHUMT00000044439.3" ; hgnc_id "HGNC:19164" ; level 2 ; orig_coord_info "chr13,33185878,33186022,-" ; protein_id "ENSP00000255486.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--MTUS2^ENST00000255486.8" ; transcript_name "STARD13-201" ; transcript_support_level 1 ; transcript_type protein_coding
STARD13--MTUS2 HAVANA mRNA 7683 28646 . + . FI_gene_label "STARD13^ENSG00000133121.21" ; ID "STARD13--MTUS2^ENST00000255486.8" ; Parent "STARD13--MTUS2^STARD13^ENSG00000133121.21" ; ccdsid "CCDS9349.1" ; exon_id "ENSE00001333091.2" ; exon_number 1 ; gene_id "STARD13--MTUS2^STARD13^ENSG00000133121.21" ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8" ; havana_transcript "OTTHUMT00000044439.3" ; hgnc_id "HGNC:19164" ; level 2 ; orig_coord_info "chr13,33185878,33186022,-" ; protein_id "ENSP00000255486.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--MTUS2^ENST00000255486.8" ; transcript_name "STARD13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STARD13--MTUS2 HAVANA gene 44573 55337 . + . FI_gene_label "MTUS2^ENSG00000132938.22" ; ID "STARD13--MTUS2^MTUS2^ENSG00000132938.22" ; ccdsid "CCDS41874.1" ; exon_id "ENSE00001486334.1" ; exon_number 1 ; gene_id "STARD13--MTUS2^MTUS2^ENSG00000132938.22" ; gene_name MTUS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016657.6" ; havana_transcript "OTTHUMT00000044335.2" ; hgnc_id "HGNC:20595" ; level 2 ; orig_coord_info "chr13,29428843,29428896,+" ; protein_id "ENSP00000370186.2" ; tag basic appris_principal_1 CCDS ; transcript_id "STARD13--MTUS2^ENST00000380808.6" ; transcript_name "MTUS2-202" ; transcript_support_level 1 ; transcript_type protein_coding
STARD13--MTUS2 HAVANA mRNA 44573 55337 . + . FI_gene_label "MTUS2^ENSG00000132938.22" ; ID "STARD13--MTUS2^ENST00000380808.6" ; Parent "STARD13--MTUS2^MTUS2^ENSG00000132938.22" ; ccdsid "CCDS41874.1" ; exon_id "ENSE00001486334.1" ; exon_number 1 ; gene_id "STARD13--MTUS2^MTUS2^ENSG00000132938.22" ; gene_name MTUS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016657.6" ; havana_transcript "OTTHUMT00000044335.2" ; hgnc_id "HGNC:20595" ; level 2 ; orig_coord_info "chr13,29428843,29428896,+" ; protein_id "ENSP00000370186.2" ; tag basic appris_principal_1 CCDS ; transcript_id "STARD13--MTUS2^ENST00000380808.6" ; transcript_name "MTUS2-202" ; transcript_support_level 1 ; 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:
TARS3--TM2D3 HAVANA gene 29125 36112 . + . FI_gene_label "TM2D3^ENSG00000184277.13" ; ID "TARS3--TM2D3^TM2D3^ENSG00000184277.13" ; ccdsid "CCDS10393.1" ; exon_id "ENSE00001838012.2" ; exon_number 1 ; gene_id "TARS3--TM2D3^TM2D3^ENSG00000184277.13" ; gene_name TM2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149872.5" ; havana_transcript "OTTHUMT00000313623.2" ; hgnc_id "HGNC:24128" ; level 2 ; orig_coord_info "chr15,101652271,101652361,-" ; protein_id "ENSP00000330433.3" ; tag basic MANE_Select CCDS ; transcript_id "TARS3--TM2D3^ENST00000333202.8" ; transcript_name "TM2D3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TARS3--TM2D3 HAVANA mRNA 29125 36112 . + . FI_gene_label "TM2D3^ENSG00000184277.13" ; ID "TARS3--TM2D3^ENST00000333202.8" ; Parent "TARS3--TM2D3^TM2D3^ENSG00000184277.13" ; ccdsid "CCDS10393.1" ; exon_id "ENSE00001838012.2" ; exon_number 1 ; gene_id "TARS3--TM2D3^TM2D3^ENSG00000184277.13" ; gene_name TM2D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149872.5" ; havana_transcript "OTTHUMT00000313623.2" ; hgnc_id "HGNC:24128" ; level 2 ; orig_coord_info "chr15,101652271,101652361,-" ; protein_id "ENSP00000330433.3" ; tag basic MANE_Select CCDS ; transcript_id "TARS3--TM2D3^ENST00000333202.8" ; transcript_name "TM2D3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TARS3--TM2D3 HAVANA gene 1001 26114 . + . FI_gene_label "TARS3^ENSG00000185418.16" ; ID "TARS3--TM2D3^TARS3^ENSG00000185418.16" ; ccdsid "CCDS10394.1" ; exon_id "ENSE00001876578.2" ; exon_number 1 ; gene_id "TARS3--TM2D3^TARS3^ENSG00000185418.16" ; gene_name TARS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149869.6" ; havana_transcript "OTTHUMT00000313619.4" ; hgnc_id "HGNC:24728" ; level 2 ; orig_coord_info "chr15,101724091,101724387,-" ; protein_id "ENSP00000338093.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TARS3--TM2D3^ENST00000335968.8" ; transcript_name "TARS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TARS3--TM2D3 HAVANA mRNA 1001 26114 . + . FI_gene_label "TARS3^ENSG00000185418.16" ; ID "TARS3--TM2D3^ENST00000335968.8" ; Parent "TARS3--TM2D3^TARS3^ENSG00000185418.16" ; ccdsid "CCDS10394.1" ; exon_id "ENSE00001876578.2" ; exon_number 1 ; gene_id "TARS3--TM2D3^TARS3^ENSG00000185418.16" ; gene_name TARS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149869.6" ; havana_transcript "OTTHUMT00000313619.4" ; hgnc_id "HGNC:24728" ; level 2 ; orig_coord_info "chr15,101724091,101724387,-" ; protein_id "ENSP00000338093.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TARS3--TM2D3^ENST00000335968.8" ; transcript_name "TARS3-201" ; 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:
TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
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:
COX6CP1--COX6C HAVANA gene 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
COX6CP1--COX6C HAVANA RNA 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^ENST00000564972.1" ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
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:
GGA2--WARS2-AS1 HAVANA gene 27280 41999 . + . FI_gene_label "WARS2-AS1^ENSG00000231365.6" ; ID "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6" ; exon_id "ENSE00001758700.1" ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6" ; gene_name "WARS2-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000012342.2" ; havana_transcript "OTTHUMT00000034378.1" ; hgnc_id "HGNC:40612" ; level 2 ; orig_coord_info "chr1,119140730,119140793,+" ; transcript_id "GGA2--WARS2-AS1^ENST00000413531.5" ; transcript_name "WARS2-AS1-201" ; transcript_support_level 1 ; transcript_type lncRNA
GGA2--WARS2-AS1 HAVANA RNA 27280 41999 . + . FI_gene_label "WARS2-AS1^ENSG00000231365.6" ; ID "GGA2--WARS2-AS1^ENST00000413531.5" ; Parent "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6" ; exon_id "ENSE00001758700.1" ; exon_number 1 ; gene_id "GGA2--WARS2-AS1^WARS2-AS1^ENSG00000231365.6" ; gene_name "WARS2-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000012342.2" ; havana_transcript "OTTHUMT00000034378.1" ; hgnc_id "HGNC:40612" ; level 2 ; orig_coord_info "chr1,119140730,119140793,+" ; transcript_id "GGA2--WARS2-AS1^ENST00000413531.5" ; transcript_name "WARS2-AS1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
SCML2--AC095353.1 ENSEMBL gene 23081 23210 . + . FI_gene_label "AC095353.1^ENSG00000201660.1" ; ID "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1" ; exon_id "ENSE00001439553.1" ; exon_number 1 ; gene_id "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1" ; gene_name "AC095353.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chrX,5410122,5410251,+" ; tag basic ; transcript_id "SCML2--AC095353.1^ENST00000364790.1" ; transcript_name "AC095353.1-201" ; transcript_support_level NA ; transcript_type snoRNA
SCML2--AC095353.1 ENSEMBL RNA 23081 23210 . + . FI_gene_label "AC095353.1^ENSG00000201660.1" ; ID "SCML2--AC095353.1^ENST00000364790.1" ; Parent "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1" ; exon_id "ENSE00001439553.1" ; exon_number 1 ; gene_id "SCML2--AC095353.1^AC095353.1^ENSG00000201660.1" ; gene_name "AC095353.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chrX,5410122,5410251,+" ; tag basic ; transcript_id "SCML2--AC095353.1^ENST00000364790.1" ; transcript_name "AC095353.1-201" ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created:
SCML2--AC110995.1 HAVANA gene 23081 30004 . + . FI_gene_label "AC110995.1^ENSG00000236120.7" ; ID "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7" ; exon_id "ENSE00001766557.2" ; exon_number 1 ; gene_id "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7" ; gene_name "AC110995.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000021092.4" ; havana_transcript "OTTHUMT00000055667.2" ; level 2 ; orig_coord_info "chrX,5725930,5726326,-" ; tag TAGENE ; transcript_id "SCML2--AC110995.1^ENST00000422914.2" ; transcript_name "AC110995.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
SCML2--AC110995.1 HAVANA RNA 23081 30004 . + . FI_gene_label "AC110995.1^ENSG00000236120.7" ; ID "SCML2--AC110995.1^ENST00000422914.2" ; Parent "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7" ; exon_id "ENSE00001766557.2" ; exon_number 1 ; gene_id "SCML2--AC110995.1^AC110995.1^ENSG00000236120.7" ; gene_name "AC110995.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000021092.4" ; havana_transcript "OTTHUMT00000055667.2" ; level 2 ; orig_coord_info "chrX,5725930,5726326,-" ; tag TAGENE ; transcript_id "SCML2--AC110995.1^ENST00000422914.2" ; transcript_name "AC110995.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
SLCO1B3--SLCO1B7 HAVANA gene 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript
SLCO1B3--SLCO1B7 HAVANA RNA 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1" ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript
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:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
397 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 ------------------------------
815 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 33 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed