Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9025474a5f4a00f4269736cd817c21/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/1c88fd726b3c1f594e55d55eb2a2ee/fi_workdir/tih_rna_sample_00599_B23MVV7LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9025474a5f4a00f4269736cd817c21/.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: 10262
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 10262
=> 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:10262
=> 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 3 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:
AL162726.3--SVEP1 HAVANA gene 29214 45236 . + . FI_gene_label "SVEP1^ENSG00000165124.18" ; ID "AL162726.3--SVEP1^SVEP1^ENSG00000165124.18" ; exon_id "ENSE00001463572.1" ; exon_number 1 ; gene_id "AL162726.3--SVEP1^SVEP1^ENSG00000165124.18" ; gene_name SVEP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020482.3" ; havana_transcript "OTTHUMT00000053620.2" ; hgnc_id "HGNC:15985" ; level 2 ; orig_coord_info "chr9,110579013,110579543,-" ; protein_id "ENSP00000363585.2" ; tag basic ; transcript_id "AL162726.3--SVEP1^ENST00000374461.1" ; transcript_name "SVEP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AL162726.3--SVEP1 HAVANA mRNA 29214 45236 . + . FI_gene_label "SVEP1^ENSG00000165124.18" ; ID "AL162726.3--SVEP1^ENST00000374461.1" ; Parent "AL162726.3--SVEP1^SVEP1^ENSG00000165124.18" ; exon_id "ENSE00001463572.1" ; exon_number 1 ; gene_id "AL162726.3--SVEP1^SVEP1^ENSG00000165124.18" ; gene_name SVEP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020482.3" ; havana_transcript "OTTHUMT00000053620.2" ; hgnc_id "HGNC:15985" ; level 2 ; orig_coord_info "chr9,110579013,110579543,-" ; protein_id "ENSP00000363585.2" ; tag basic ; transcript_id "AL162726.3--SVEP1^ENST00000374461.1" ; transcript_name "SVEP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATP5F1C--DENND5A HAVANA gene 13071 49794 . + . FI_gene_label "DENND5A^ENSG00000184014.9" ; ID "ATP5F1C--DENND5A^DENND5A^ENSG00000184014.9" ; ccdsid "CCDS31423.1" ; exon_id "ENSE00001302149.6" ; exon_number 1 ; gene_id "ATP5F1C--DENND5A^DENND5A^ENSG00000184014.9" ; gene_name DENND5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000165716.5" ; havana_transcript "OTTHUMT00000385910.3" ; hgnc_id "HGNC:19344" ; level 2 ; orig_coord_info "chr11,9264961,9265069,-" ; protein_id "ENSP00000328524.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATP5F1C--DENND5A^ENST00000328194.8" ; transcript_name "DENND5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATP5F1C--DENND5A HAVANA mRNA 13071 49794 . + . FI_gene_label "DENND5A^ENSG00000184014.9" ; ID "ATP5F1C--DENND5A^ENST00000328194.8" ; Parent "ATP5F1C--DENND5A^DENND5A^ENSG00000184014.9" ; ccdsid "CCDS31423.1" ; exon_id "ENSE00001302149.6" ; exon_number 1 ; gene_id "ATP5F1C--DENND5A^DENND5A^ENSG00000184014.9" ; gene_name DENND5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000165716.5" ; havana_transcript "OTTHUMT00000385910.3" ; hgnc_id "HGNC:19344" ; level 2 ; orig_coord_info "chr11,9264961,9265069,-" ; protein_id "ENSP00000328524.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATP5F1C--DENND5A^ENST00000328194.8" ; transcript_name "DENND5A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATP5F1C--DENND5A HAVANA gene 1031 9461 . + . FI_gene_label "ATP5F1C^ENSG00000165629.20" ; ID "ATP5F1C--DENND5A^ATP5F1C^ENSG00000165629.20" ; ccdsid "CCDS7081.1" ; exon_id "ENSE00003600827.1" ; exon_number 1 ; gene_id "ATP5F1C--DENND5A^ATP5F1C^ENSG00000165629.20" ; gene_name ATP5F1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000017639.3" ; havana_transcript "OTTHUMT00000046709.1" ; hgnc_id "HGNC:833" ; level 2 ; orig_coord_info "chr10,7788208,7788263,+" ; protein_id "ENSP00000338568.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "ATP5F1C--DENND5A^ENST00000335698.4" ; transcript_name "ATP5F1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATP5F1C--DENND5A HAVANA mRNA 1031 9461 . + . FI_gene_label "ATP5F1C^ENSG00000165629.20" ; ID "ATP5F1C--DENND5A^ENST00000335698.4" ; Parent "ATP5F1C--DENND5A^ATP5F1C^ENSG00000165629.20" ; ccdsid "CCDS7081.1" ; exon_id "ENSE00003600827.1" ; exon_number 1 ; gene_id "ATP5F1C--DENND5A^ATP5F1C^ENSG00000165629.20" ; gene_name ATP5F1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000017639.3" ; havana_transcript "OTTHUMT00000046709.1" ; hgnc_id "HGNC:833" ; level 2 ; orig_coord_info "chr10,7788208,7788263,+" ; protein_id "ENSP00000338568.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "ATP5F1C--DENND5A^ENST00000335698.4" ; transcript_name "ATP5F1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDC123--MPP7 HAVANA gene 1224 13786 . + . FI_gene_label "CDC123^ENSG00000151465.14" ; ID "CDC123--MPP7^CDC123^ENSG00000151465.14" ; ccdsid "CCDS7090.1" ; exon_id "ENSE00000999748.4" ; exon_number 1 ; gene_id "CDC123--MPP7^CDC123^ENSG00000151465.14" ; gene_name CDC123 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017680.7" ; havana_transcript "OTTHUMT00000046801.2" ; hgnc_id "HGNC:16827" ; level 2 ; orig_coord_info "chr10,12196246,12196319,+" ; protein_id "ENSP00000281141.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDC123--MPP7^ENST00000281141.9" ; transcript_name "CDC123-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDC123--MPP7 HAVANA mRNA 1224 13786 . + . FI_gene_label "CDC123^ENSG00000151465.14" ; ID "CDC123--MPP7^ENST00000281141.9" ; Parent "CDC123--MPP7^CDC123^ENSG00000151465.14" ; ccdsid "CCDS7090.1" ; exon_id "ENSE00000999748.4" ; exon_number 1 ; gene_id "CDC123--MPP7^CDC123^ENSG00000151465.14" ; gene_name CDC123 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017680.7" ; havana_transcript "OTTHUMT00000046801.2" ; hgnc_id "HGNC:16827" ; level 2 ; orig_coord_info "chr10,12196246,12196319,+" ; protein_id "ENSP00000281141.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDC123--MPP7^ENST00000281141.9" ; transcript_name "CDC123-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDC123--MPP7 ENSEMBL gene 20059 43060 . + . FI_gene_label "MPP7^ENSG00000150054.18" ; ID "CDC123--MPP7^MPP7^ENSG00000150054.18" ; ccdsid "CCDS7158.1" ; exon_id "ENSE00003581254.1" ; exon_number 3 ; gene_id "CDC123--MPP7^MPP7^ENSG00000150054.18" ; gene_name MPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017868.4" ; hgnc_id "HGNC:26542" ; level 3 ; orig_coord_info "chr10,28238568,28238604,-" ; protein_id "ENSP00000337907.5" ; tag basic appris_principal_1 CCDS ; transcript_id "CDC123--MPP7^ENST00000337532.9" ; transcript_name "MPP7-201" ; transcript_support_level 5 ; transcript_type protein_coding
CDC123--MPP7 ENSEMBL mRNA 20059 43060 . + . FI_gene_label "MPP7^ENSG00000150054.18" ; ID "CDC123--MPP7^ENST00000337532.9" ; Parent "CDC123--MPP7^MPP7^ENSG00000150054.18" ; ccdsid "CCDS7158.1" ; exon_id "ENSE00003581254.1" ; exon_number 3 ; gene_id "CDC123--MPP7^MPP7^ENSG00000150054.18" ; gene_name MPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017868.4" ; hgnc_id "HGNC:26542" ; level 3 ; orig_coord_info "chr10,28238568,28238604,-" ; protein_id "ENSP00000337907.5" ; tag basic appris_principal_1 CCDS ; transcript_id "CDC123--MPP7^ENST00000337532.9" ; transcript_name "MPP7-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CERCAM--SEMA4D HAVANA gene 19071 52349 . + . FI_gene_label "SEMA4D^ENSG00000187764.12" ; ID "CERCAM--SEMA4D^SEMA4D^ENSG00000187764.12" ; ccdsid "CCDS47991.1" ; exon_id "ENSE00001416368.1" ; exon_number 3 ; gene_id "CERCAM--SEMA4D^SEMA4D^ENSG00000187764.12" ; gene_name SEMA4D ; gene_type protein_coding ; havana_gene "OTTHUMG00000020185.10" ; havana_transcript "OTTHUMT00000342403.3" ; hgnc_id "HGNC:10732" ; level 2 ; orig_coord_info "chr9,89405351,89405456,-" ; protein_id "ENSP00000344923.4" ; tag alternative_5_UTR not_organism_supported basic CCDS ; transcript_id "CERCAM--SEMA4D^ENST00000339861.8" ; transcript_name "SEMA4D-201" ; transcript_support_level 5 ; transcript_type protein_coding
CERCAM--SEMA4D HAVANA mRNA 19071 52349 . + . FI_gene_label "SEMA4D^ENSG00000187764.12" ; ID "CERCAM--SEMA4D^ENST00000339861.8" ; Parent "CERCAM--SEMA4D^SEMA4D^ENSG00000187764.12" ; ccdsid "CCDS47991.1" ; exon_id "ENSE00001416368.1" ; exon_number 3 ; gene_id "CERCAM--SEMA4D^SEMA4D^ENSG00000187764.12" ; gene_name SEMA4D ; gene_type protein_coding ; havana_gene "OTTHUMG00000020185.10" ; havana_transcript "OTTHUMT00000342403.3" ; hgnc_id "HGNC:10732" ; level 2 ; orig_coord_info "chr9,89405351,89405456,-" ; protein_id "ENSP00000344923.4" ; tag alternative_5_UTR not_organism_supported basic CCDS ; transcript_id "CERCAM--SEMA4D^ENST00000339861.8" ; transcript_name "SEMA4D-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CERCAM--SEMA4D HAVANA gene 4066 15974 . + . FI_gene_label "CERCAM^ENSG00000167123.19" ; ID "CERCAM--SEMA4D^CERCAM^ENSG00000167123.19" ; ccdsid "CCDS6901.2" ; exon_id "ENSE00001720937.2" ; exon_number 1 ; gene_id "CERCAM--SEMA4D^CERCAM^ENSG00000167123.19" ; gene_name CERCAM ; gene_type protein_coding ; havana_gene "OTTHUMG00000020747.6" ; havana_transcript "OTTHUMT00000054435.4" ; hgnc_id "HGNC:23723" ; level 2 ; orig_coord_info "chr9,128420878,128421074,+" ; protein_id "ENSP00000361929.4" ; tag basic MANE_Select CCDS ; transcript_id "CERCAM--SEMA4D^ENST00000372838.9" ; transcript_name "CERCAM-201" ; transcript_support_level 1 ; transcript_type protein_coding
CERCAM--SEMA4D HAVANA mRNA 4066 15974 . + . FI_gene_label "CERCAM^ENSG00000167123.19" ; ID "CERCAM--SEMA4D^ENST00000372838.9" ; Parent "CERCAM--SEMA4D^CERCAM^ENSG00000167123.19" ; ccdsid "CCDS6901.2" ; exon_id "ENSE00001720937.2" ; exon_number 1 ; gene_id "CERCAM--SEMA4D^CERCAM^ENSG00000167123.19" ; gene_name CERCAM ; gene_type protein_coding ; havana_gene "OTTHUMG00000020747.6" ; havana_transcript "OTTHUMT00000054435.4" ; hgnc_id "HGNC:23723" ; level 2 ; orig_coord_info "chr9,128420878,128421074,+" ; protein_id "ENSP00000361929.4" ; tag basic MANE_Select CCDS ; transcript_id "CERCAM--SEMA4D^ENST00000372838.9" ; transcript_name "CERCAM-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CNTNAP2--GABRA5 HAVANA gene 64985 77957 . + . FI_gene_label "GABRA5^ENSG00000186297.12" ; ID "CNTNAP2--GABRA5^GABRA5^ENSG00000186297.12" ; ccdsid "CCDS45194.1" ; exon_id "ENSE00003566900.1" ; exon_number 3 ; gene_id "CNTNAP2--GABRA5^GABRA5^ENSG00000186297.12" ; gene_name GABRA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171824.6" ; havana_transcript "OTTHUMT00000415234.2" ; hgnc_id "HGNC:4079" ; level 2 ; orig_coord_info "chr15,26869249,26869334,+" ; protein_id "ENSP00000335592.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNTNAP2--GABRA5^ENST00000335625.10" ; transcript_name "GABRA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
CNTNAP2--GABRA5 HAVANA mRNA 64985 77957 . + . FI_gene_label "GABRA5^ENSG00000186297.12" ; ID "CNTNAP2--GABRA5^ENST00000335625.10" ; Parent "CNTNAP2--GABRA5^GABRA5^ENSG00000186297.12" ; ccdsid "CCDS45194.1" ; exon_id "ENSE00003566900.1" ; exon_number 3 ; gene_id "CNTNAP2--GABRA5^GABRA5^ENSG00000186297.12" ; gene_name GABRA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171824.6" ; havana_transcript "OTTHUMT00000415234.2" ; hgnc_id "HGNC:4079" ; level 2 ; orig_coord_info "chr15,26869249,26869334,+" ; protein_id "ENSP00000335592.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNTNAP2--GABRA5^ENST00000335625.10" ; transcript_name "GABRA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CNTNAP2--GABRA5 HAVANA gene 1800 61833 . + . FI_gene_label "CNTNAP2^ENSG00000174469.23" ; ID "CNTNAP2--GABRA5^CNTNAP2^ENSG00000174469.23" ; ccdsid "CCDS5889.1" ; exon_id "ENSE00001384688.4" ; exon_number 1 ; gene_id "CNTNAP2--GABRA5^CNTNAP2^ENSG00000174469.23" ; gene_name CNTNAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152743.11" ; havana_transcript "OTTHUMT00000327668.3" ; hgnc_id "HGNC:13830" ; level 2 ; orig_coord_info "chr7,146116877,146116973,+" ; protein_id "ENSP00000354778.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNTNAP2--GABRA5^ENST00000361727.8" ; transcript_name "CNTNAP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CNTNAP2--GABRA5 HAVANA mRNA 1800 61833 . + . FI_gene_label "CNTNAP2^ENSG00000174469.23" ; ID "CNTNAP2--GABRA5^ENST00000361727.8" ; Parent "CNTNAP2--GABRA5^CNTNAP2^ENSG00000174469.23" ; ccdsid "CCDS5889.1" ; exon_id "ENSE00001384688.4" ; exon_number 1 ; gene_id "CNTNAP2--GABRA5^CNTNAP2^ENSG00000174469.23" ; gene_name CNTNAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152743.11" ; havana_transcript "OTTHUMT00000327668.3" ; hgnc_id "HGNC:13830" ; level 2 ; orig_coord_info "chr7,146116877,146116973,+" ; protein_id "ENSP00000354778.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "CNTNAP2--GABRA5^ENST00000361727.8" ; transcript_name "CNTNAP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTNNBL1--BPIFA2 HAVANA gene 28912 38483 . + . FI_gene_label "BPIFA2^ENSG00000131050.11" ; ID "CTNNBL1--BPIFA2^BPIFA2^ENSG00000131050.11" ; ccdsid "CCDS13214.1" ; exon_id "ENSE00000898449.3" ; exon_number 2 ; gene_id "CTNNBL1--BPIFA2^BPIFA2^ENSG00000131050.11" ; gene_name BPIFA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032244.3" ; havana_transcript "OTTHUMT00000257117.1" ; hgnc_id "HGNC:16203" ; level 2 ; orig_coord_info "chr20,33169146,33169302,+" ; protein_id "ENSP00000253362.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFA2^ENST00000253362.6" ; transcript_name "BPIFA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTNNBL1--BPIFA2 HAVANA mRNA 28912 38483 . + . FI_gene_label "BPIFA2^ENSG00000131050.11" ; ID "CTNNBL1--BPIFA2^ENST00000253362.6" ; Parent "CTNNBL1--BPIFA2^BPIFA2^ENSG00000131050.11" ; ccdsid "CCDS13214.1" ; exon_id "ENSE00000898449.3" ; exon_number 2 ; gene_id "CTNNBL1--BPIFA2^BPIFA2^ENSG00000131050.11" ; gene_name BPIFA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032244.3" ; havana_transcript "OTTHUMT00000257117.1" ; hgnc_id "HGNC:16203" ; level 2 ; orig_coord_info "chr20,33169146,33169302,+" ; protein_id "ENSP00000253362.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFA2^ENST00000253362.6" ; transcript_name "BPIFA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTNNBL1--BPIFA2 HAVANA gene 1076 25900 . + . FI_gene_label "CTNNBL1^ENSG00000132792.19" ; ID "CTNNBL1--BPIFA2^CTNNBL1^ENSG00000132792.19" ; ccdsid "CCDS13298.1" ; exon_id "ENSE00001827583.2" ; exon_number 1 ; gene_id "CTNNBL1--BPIFA2^CTNNBL1^ENSG00000132792.19" ; gene_name CTNNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032428.6" ; havana_transcript "OTTHUMT00000079125.2" ; hgnc_id "HGNC:15879" ; level 2 ; orig_coord_info "chr20,37694123,37694152,+" ; protein_id "ENSP00000355050.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFA2^ENST00000361383.11" ; transcript_name "CTNNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTNNBL1--BPIFA2 HAVANA mRNA 1076 25900 . + . FI_gene_label "CTNNBL1^ENSG00000132792.19" ; ID "CTNNBL1--BPIFA2^ENST00000361383.11" ; Parent "CTNNBL1--BPIFA2^CTNNBL1^ENSG00000132792.19" ; ccdsid "CCDS13298.1" ; exon_id "ENSE00001827583.2" ; exon_number 1 ; gene_id "CTNNBL1--BPIFA2^CTNNBL1^ENSG00000132792.19" ; gene_name CTNNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032428.6" ; havana_transcript "OTTHUMT00000079125.2" ; hgnc_id "HGNC:15879" ; level 2 ; orig_coord_info "chr20,37694123,37694152,+" ; protein_id "ENSP00000355050.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFA2^ENST00000361383.11" ; transcript_name "CTNNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTNNBL1--BPIFB4 HAVANA gene 1076 25900 . + . FI_gene_label "CTNNBL1^ENSG00000132792.19" ; ID "CTNNBL1--BPIFB4^CTNNBL1^ENSG00000132792.19" ; ccdsid "CCDS13298.1" ; exon_id "ENSE00001827583.2" ; exon_number 1 ; gene_id "CTNNBL1--BPIFB4^CTNNBL1^ENSG00000132792.19" ; gene_name CTNNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032428.6" ; havana_transcript "OTTHUMT00000079125.2" ; hgnc_id "HGNC:15879" ; level 2 ; orig_coord_info "chr20,37694123,37694152,+" ; protein_id "ENSP00000355050.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFB4^ENST00000361383.11" ; transcript_name "CTNNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTNNBL1--BPIFB4 HAVANA mRNA 1076 25900 . + . FI_gene_label "CTNNBL1^ENSG00000132792.19" ; ID "CTNNBL1--BPIFB4^ENST00000361383.11" ; Parent "CTNNBL1--BPIFB4^CTNNBL1^ENSG00000132792.19" ; ccdsid "CCDS13298.1" ; exon_id "ENSE00001827583.2" ; exon_number 1 ; gene_id "CTNNBL1--BPIFB4^CTNNBL1^ENSG00000132792.19" ; gene_name CTNNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032428.6" ; havana_transcript "OTTHUMT00000079125.2" ; hgnc_id "HGNC:15879" ; level 2 ; orig_coord_info "chr20,37694123,37694152,+" ; protein_id "ENSP00000355050.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "CTNNBL1--BPIFB4^ENST00000361383.11" ; transcript_name "CTNNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTNNBL1--BPIFB4 HAVANA gene 30795 46893 . + . FI_gene_label "BPIFB4^ENSG00000186191.8" ; ID "CTNNBL1--BPIFB4^BPIFB4^ENSG00000186191.8" ; ccdsid "CCDS13213.2" ; exon_id "ENSE00001844165.1" ; exon_number 1 ; gene_id "CTNNBL1--BPIFB4^BPIFB4^ENSG00000186191.8" ; gene_name BPIFB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032235.6" ; havana_transcript "OTTHUMT00000078655.6" ; hgnc_id "HGNC:16179" ; level 2 ; orig_coord_info "chr20,33081527,33081632,+" ; protein_id "ENSP00000364632.3" ; tag basic appris_principal_4 CCDS ; transcript_id "CTNNBL1--BPIFB4^ENST00000375483.3" ; transcript_name "BPIFB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
CTNNBL1--BPIFB4 HAVANA mRNA 30795 46893 . + . FI_gene_label "BPIFB4^ENSG00000186191.8" ; ID "CTNNBL1--BPIFB4^ENST00000375483.3" ; Parent "CTNNBL1--BPIFB4^BPIFB4^ENSG00000186191.8" ; ccdsid "CCDS13213.2" ; exon_id "ENSE00001844165.1" ; exon_number 1 ; gene_id "CTNNBL1--BPIFB4^BPIFB4^ENSG00000186191.8" ; gene_name BPIFB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032235.6" ; havana_transcript "OTTHUMT00000078655.6" ; hgnc_id "HGNC:16179" ; level 2 ; orig_coord_info "chr20,33081527,33081632,+" ; protein_id "ENSP00000364632.3" ; tag basic appris_principal_4 CCDS ; transcript_id "CTNNBL1--BPIFB4^ENST00000375483.3" ; transcript_name "BPIFB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
GRHPR--ZBTB34 HAVANA gene 1031 13460 . + . FI_gene_label "GRHPR^ENSG00000137106.18" ; ID "GRHPR--ZBTB34^GRHPR^ENSG00000137106.18" ; ccdsid "CCDS6609.1" ; exon_id "ENSE00001934486.2" ; exon_number 1 ; gene_id "GRHPR--ZBTB34^GRHPR^ENSG00000137106.18" ; gene_name GRHPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000019914.6" ; havana_transcript "OTTHUMT00000052442.2" ; hgnc_id "HGNC:4570" ; level 2 ; orig_coord_info "chr9,37422751,37422833,+" ; protein_id "ENSP00000313432.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRHPR--ZBTB34^ENST00000318158.11" ; transcript_name "GRHPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
GRHPR--ZBTB34 HAVANA mRNA 1031 13460 . + . FI_gene_label "GRHPR^ENSG00000137106.18" ; ID "GRHPR--ZBTB34^ENST00000318158.11" ; Parent "GRHPR--ZBTB34^GRHPR^ENSG00000137106.18" ; ccdsid "CCDS6609.1" ; exon_id "ENSE00001934486.2" ; exon_number 1 ; gene_id "GRHPR--ZBTB34^GRHPR^ENSG00000137106.18" ; gene_name GRHPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000019914.6" ; havana_transcript "OTTHUMT00000052442.2" ; hgnc_id "HGNC:4570" ; level 2 ; orig_coord_info "chr9,37422751,37422833,+" ; protein_id "ENSP00000313432.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GRHPR--ZBTB34^ENST00000318158.11" ; transcript_name "GRHPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GRHPR--ZBTB34 HAVANA gene 16461 24066 . + . FI_gene_label "ZBTB34^ENSG00000177125.5" ; ID "GRHPR--ZBTB34^ZBTB34^ENSG00000177125.5" ; exon_id "ENSE00001259345.4" ; exon_number 2 ; gene_id "GRHPR--ZBTB34^ZBTB34^ENSG00000177125.5" ; gene_name ZBTB34 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020694.1" ; havana_transcript "OTTHUMT00000054128.1" ; hgnc_id "HGNC:31446" ; level 2 ; orig_coord_info "chr9,126879400,126880911,+" ; protein_id "ENSP00000317534.4" ; tag basic appris_alternative_1 ; transcript_id "GRHPR--ZBTB34^ENST00000319119.4" ; transcript_name "ZBTB34-201" ; transcript_support_level 1 ; transcript_type protein_coding
GRHPR--ZBTB34 HAVANA mRNA 16461 24066 . + . FI_gene_label "ZBTB34^ENSG00000177125.5" ; ID "GRHPR--ZBTB34^ENST00000319119.4" ; Parent "GRHPR--ZBTB34^ZBTB34^ENSG00000177125.5" ; exon_id "ENSE00001259345.4" ; exon_number 2 ; gene_id "GRHPR--ZBTB34^ZBTB34^ENSG00000177125.5" ; gene_name ZBTB34 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020694.1" ; havana_transcript "OTTHUMT00000054128.1" ; hgnc_id "HGNC:31446" ; level 2 ; orig_coord_info "chr9,126879400,126880911,+" ; protein_id "ENSP00000317534.4" ; tag basic appris_alternative_1 ; transcript_id "GRHPR--ZBTB34^ENST00000319119.4" ; transcript_name "ZBTB34-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GSE1--CMIP HAVANA gene 10503 31660 . + . FI_gene_label "GSE1^ENSG00000131149.19" ; ID "GSE1--CMIP^GSE1^ENSG00000131149.19" ; ccdsid "CCDS10952.1" ; exon_id "ENSE00001399788.3" ; exon_number 1 ; gene_id "GSE1--CMIP^GSE1^ENSG00000131149.19" ; gene_name GSE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137650.8" ; havana_transcript "OTTHUMT00000325527.3" ; hgnc_id "HGNC:28979" ; level 2 ; orig_coord_info "chr16,85613392,85613398,+" ; protein_id "ENSP00000253458.6" ; tag not_organism_supported basic MANE_Select appris_principal_4 CCDS ; transcript_id "GSE1--CMIP^ENST00000253458.12" ; transcript_name "GSE1-201" ; transcript_support_level 5 ; transcript_type protein_coding
GSE1--CMIP HAVANA mRNA 10503 31660 . + . FI_gene_label "GSE1^ENSG00000131149.19" ; ID "GSE1--CMIP^ENST00000253458.12" ; Parent "GSE1--CMIP^GSE1^ENSG00000131149.19" ; ccdsid "CCDS10952.1" ; exon_id "ENSE00001399788.3" ; exon_number 1 ; gene_id "GSE1--CMIP^GSE1^ENSG00000131149.19" ; gene_name GSE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137650.8" ; havana_transcript "OTTHUMT00000325527.3" ; hgnc_id "HGNC:28979" ; level 2 ; orig_coord_info "chr16,85613392,85613398,+" ; protein_id "ENSP00000253458.6" ; tag not_organism_supported basic MANE_Select appris_principal_4 CCDS ; transcript_id "GSE1--CMIP^ENST00000253458.12" ; transcript_name "GSE1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
GSE1--CMIP HAVANA gene 42849 70427 . + . FI_gene_label "CMIP^ENSG00000153815.17" ; ID "GSE1--CMIP^CMIP^ENSG00000153815.17" ; exon_id "ENSE00002595737.1" ; exon_number 1 ; gene_id "GSE1--CMIP^CMIP^ENSG00000153815.17" ; gene_name CMIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000176520.4" ; havana_transcript "OTTHUMT00000432404.1" ; hgnc_id "HGNC:24319" ; level 2 ; orig_coord_info "chr16,81645581,81645598,+" ; protein_id "ENSP00000381120.4" ; tag upstream_ATG basic ; transcript_id "GSE1--CMIP^ENST00000398040.8" ; transcript_name "CMIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
GSE1--CMIP HAVANA mRNA 42849 70427 . + . FI_gene_label "CMIP^ENSG00000153815.17" ; ID "GSE1--CMIP^ENST00000398040.8" ; Parent "GSE1--CMIP^CMIP^ENSG00000153815.17" ; exon_id "ENSE00002595737.1" ; exon_number 1 ; gene_id "GSE1--CMIP^CMIP^ENSG00000153815.17" ; gene_name CMIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000176520.4" ; havana_transcript "OTTHUMT00000432404.1" ; hgnc_id "HGNC:24319" ; level 2 ; orig_coord_info "chr16,81645581,81645598,+" ; protein_id "ENSP00000381120.4" ; tag upstream_ATG basic ; transcript_id "GSE1--CMIP^ENST00000398040.8" ; transcript_name "CMIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HTRA1--ABLIM1 HAVANA gene 16870 50135 . + . FI_gene_label "ABLIM1^ENSG00000099204.20" ; ID "HTRA1--ABLIM1^ABLIM1^ENSG00000099204.20" ; ccdsid "CCDS7590.1" ; exon_id "ENSE00001647651.2" ; exon_number 1 ; gene_id "HTRA1--ABLIM1^ABLIM1^ENSG00000099204.20" ; gene_name ABLIM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019088.9" ; havana_transcript "OTTHUMT00000050469.3" ; hgnc_id "HGNC:78" ; level 2 ; orig_coord_info "chr10,114657957,114658200,-" ; protein_id "ENSP00000277895.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "HTRA1--ABLIM1^ENST00000277895.9" ; transcript_name "ABLIM1-201" ; transcript_support_level 5 ; transcript_type protein_coding
HTRA1--ABLIM1 HAVANA mRNA 16870 50135 . + . FI_gene_label "ABLIM1^ENSG00000099204.20" ; ID "HTRA1--ABLIM1^ENST00000277895.9" ; Parent "HTRA1--ABLIM1^ABLIM1^ENSG00000099204.20" ; ccdsid "CCDS7590.1" ; exon_id "ENSE00001647651.2" ; exon_number 1 ; gene_id "HTRA1--ABLIM1^ABLIM1^ENSG00000099204.20" ; gene_name ABLIM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019088.9" ; havana_transcript "OTTHUMT00000050469.3" ; hgnc_id "HGNC:78" ; level 2 ; orig_coord_info "chr10,114657957,114658200,-" ; protein_id "ENSP00000277895.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "HTRA1--ABLIM1^ENST00000277895.9" ; transcript_name "ABLIM1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
HTRA1--ABLIM1 HAVANA gene 2160 11154 . + . FI_gene_label "HTRA1^ENSG00000166033.13" ; ID "HTRA1--ABLIM1^HTRA1^ENSG00000166033.13" ; ccdsid "CCDS7630.1" ; exon_id "ENSE00001448527.4" ; exon_number 1 ; gene_id "HTRA1--ABLIM1^HTRA1^ENSG00000166033.13" ; gene_name HTRA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019186.4" ; havana_transcript "OTTHUMT00000128327.3" ; hgnc_id "HGNC:9476" ; level 2 ; orig_coord_info "chr10,122461653,122462124,+" ; protein_id "ENSP00000357980.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HTRA1--ABLIM1^ENST00000368984.8" ; transcript_name "HTRA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
HTRA1--ABLIM1 HAVANA mRNA 2160 11154 . + . FI_gene_label "HTRA1^ENSG00000166033.13" ; ID "HTRA1--ABLIM1^ENST00000368984.8" ; Parent "HTRA1--ABLIM1^HTRA1^ENSG00000166033.13" ; ccdsid "CCDS7630.1" ; exon_id "ENSE00001448527.4" ; exon_number 1 ; gene_id "HTRA1--ABLIM1^HTRA1^ENSG00000166033.13" ; gene_name HTRA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019186.4" ; havana_transcript "OTTHUMT00000128327.3" ; hgnc_id "HGNC:9476" ; level 2 ; orig_coord_info "chr10,122461653,122462124,+" ; protein_id "ENSP00000357980.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HTRA1--ABLIM1^ENST00000368984.8" ; transcript_name "HTRA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
IARS1--GRHPR HAVANA gene 38170 50599 . + . FI_gene_label "GRHPR^ENSG00000137106.18" ; ID "IARS1--GRHPR^GRHPR^ENSG00000137106.18" ; ccdsid "CCDS6609.1" ; exon_id "ENSE00001934486.2" ; exon_number 1 ; gene_id "IARS1--GRHPR^GRHPR^ENSG00000137106.18" ; gene_name GRHPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000019914.6" ; havana_transcript "OTTHUMT00000052442.2" ; hgnc_id "HGNC:4570" ; level 2 ; orig_coord_info "chr9,37422751,37422833,+" ; protein_id "ENSP00000313432.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IARS1--GRHPR^ENST00000318158.11" ; transcript_name "GRHPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
IARS1--GRHPR HAVANA mRNA 38170 50599 . + . FI_gene_label "GRHPR^ENSG00000137106.18" ; ID "IARS1--GRHPR^ENST00000318158.11" ; Parent "IARS1--GRHPR^GRHPR^ENSG00000137106.18" ; ccdsid "CCDS6609.1" ; exon_id "ENSE00001934486.2" ; exon_number 1 ; gene_id "IARS1--GRHPR^GRHPR^ENSG00000137106.18" ; gene_name GRHPR ; gene_type protein_coding ; havana_gene "OTTHUMG00000019914.6" ; havana_transcript "OTTHUMT00000052442.2" ; hgnc_id "HGNC:4570" ; level 2 ; orig_coord_info "chr9,37422751,37422833,+" ; protein_id "ENSP00000313432.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IARS1--GRHPR^ENST00000318158.11" ; transcript_name "GRHPR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
IARS1--GRHPR HAVANA gene 1057 35139 . + . FI_gene_label "IARS1^ENSG00000196305.18" ; ID "IARS1--GRHPR^IARS1^ENSG00000196305.18" ; ccdsid "CCDS6694.1" ; exon_id "ENSE00003562910.1" ; exon_number 2 ; gene_id "IARS1--GRHPR^IARS1^ENSG00000196305.18" ; gene_name IARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020219.3" ; havana_transcript "OTTHUMT00000053059.2" ; hgnc_id "HGNC:5330" ; level 2 ; orig_coord_info "chr9,92289301,92289419,-" ; protein_id "ENSP00000364794.3" ; tag basic appris_principal_1 CCDS ; transcript_id "IARS1--GRHPR^ENST00000375643.7" ; transcript_name "IARS1-202" ; transcript_support_level 1 ; transcript_type protein_coding
IARS1--GRHPR HAVANA mRNA 1057 35139 . + . FI_gene_label "IARS1^ENSG00000196305.18" ; ID "IARS1--GRHPR^ENST00000375643.7" ; Parent "IARS1--GRHPR^IARS1^ENSG00000196305.18" ; ccdsid "CCDS6694.1" ; exon_id "ENSE00003562910.1" ; exon_number 2 ; gene_id "IARS1--GRHPR^IARS1^ENSG00000196305.18" ; gene_name IARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020219.3" ; havana_transcript "OTTHUMT00000053059.2" ; hgnc_id "HGNC:5330" ; level 2 ; orig_coord_info "chr9,92289301,92289419,-" ; protein_id "ENSP00000364794.3" ; tag basic appris_principal_1 CCDS ; transcript_id "IARS1--GRHPR^ENST00000375643.7" ; transcript_name "IARS1-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MRGPRX12P--CKAP5 ENSEMBL gene 4980 46249 . + . FI_gene_label "CKAP5^ENSG00000175216.15" ; ID "MRGPRX12P--CKAP5^CKAP5^ENSG00000175216.15" ; ccdsid "CCDS7924.1" ; exon_id "ENSE00001423871.2" ; exon_number 2 ; gene_id "MRGPRX12P--CKAP5^CKAP5^ENSG00000175216.15" ; gene_name CKAP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166599.5" ; hgnc_id "HGNC:28959" ; level 3 ; orig_coord_info "chr11,46821175,46821231,-" ; protein_id "ENSP00000310227.5" ; tag basic CCDS ; transcript_id "MRGPRX12P--CKAP5^ENST00000312055.9" ; transcript_name "CKAP5-201" ; transcript_support_level 5 ; transcript_type protein_coding
MRGPRX12P--CKAP5 ENSEMBL mRNA 4980 46249 . + . FI_gene_label "CKAP5^ENSG00000175216.15" ; ID "MRGPRX12P--CKAP5^ENST00000312055.9" ; Parent "MRGPRX12P--CKAP5^CKAP5^ENSG00000175216.15" ; ccdsid "CCDS7924.1" ; exon_id "ENSE00001423871.2" ; exon_number 2 ; gene_id "MRGPRX12P--CKAP5^CKAP5^ENSG00000175216.15" ; gene_name CKAP5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166599.5" ; hgnc_id "HGNC:28959" ; level 3 ; orig_coord_info "chr11,46821175,46821231,-" ; protein_id "ENSP00000310227.5" ; tag basic CCDS ; transcript_id "MRGPRX12P--CKAP5^ENST00000312055.9" ; transcript_name "CKAP5-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
NAA35--TMEM139 HAVANA gene 32289 35379 . + . FI_gene_label "TMEM139^ENSG00000178826.11" ; ID "NAA35--TMEM139^TMEM139^ENSG00000178826.11" ; ccdsid "CCDS5878.1" ; exon_id "ENSE00001249174.3" ; exon_number 2 ; gene_id "NAA35--TMEM139^TMEM139^ENSG00000178826.11" ; gene_name TMEM139 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152652.3" ; havana_transcript "OTTHUMT00000327145.2" ; hgnc_id "HGNC:22058" ; level 2 ; orig_coord_info "chr7,143285958,143286202,+" ; protein_id "ENSP00000352284.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAA35--TMEM139^ENST00000359333.8" ; transcript_name "TMEM139-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAA35--TMEM139 HAVANA mRNA 32289 35379 . + . FI_gene_label "TMEM139^ENSG00000178826.11" ; ID "NAA35--TMEM139^ENST00000359333.8" ; Parent "NAA35--TMEM139^TMEM139^ENSG00000178826.11" ; ccdsid "CCDS5878.1" ; exon_id "ENSE00001249174.3" ; exon_number 2 ; gene_id "NAA35--TMEM139^TMEM139^ENSG00000178826.11" ; gene_name TMEM139 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152652.3" ; havana_transcript "OTTHUMT00000327145.2" ; hgnc_id "HGNC:22058" ; level 2 ; orig_coord_info "chr7,143285958,143286202,+" ; protein_id "ENSP00000352284.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAA35--TMEM139^ENST00000359333.8" ; transcript_name "TMEM139-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NAA35--TMEM139 HAVANA gene 1001 28186 . + . FI_gene_label "NAA35^ENSG00000135040.16" ; ID "NAA35--TMEM139^NAA35^ENSG00000135040.16" ; ccdsid "CCDS6673.1" ; exon_id "ENSE00003769847.1" ; exon_number 2 ; gene_id "NAA35--TMEM139^NAA35^ENSG00000135040.16" ; gene_name NAA35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020131.3" ; havana_transcript "OTTHUMT00000052906.2" ; hgnc_id "HGNC:24340" ; level 2 ; orig_coord_info "chr9,85942160,85942283,+" ; protein_id "ENSP00000354972.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAA35--TMEM139^ENST00000361671.10" ; transcript_name "NAA35-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAA35--TMEM139 HAVANA mRNA 1001 28186 . + . FI_gene_label "NAA35^ENSG00000135040.16" ; ID "NAA35--TMEM139^ENST00000361671.10" ; Parent "NAA35--TMEM139^NAA35^ENSG00000135040.16" ; ccdsid "CCDS6673.1" ; exon_id "ENSE00003769847.1" ; exon_number 2 ; gene_id "NAA35--TMEM139^NAA35^ENSG00000135040.16" ; gene_name NAA35 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020131.3" ; havana_transcript "OTTHUMT00000052906.2" ; hgnc_id "HGNC:24340" ; level 2 ; orig_coord_info "chr9,85942160,85942283,+" ; protein_id "ENSP00000354972.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAA35--TMEM139^ENST00000361671.10" ; transcript_name "NAA35-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NTM--AC142086.6 HAVANA gene 7859 19676 . + . FI_gene_label "NTM^ENSG00000182667.14" ; ID "NTM--AC142086.6^NTM^ENSG00000182667.14" ; ccdsid "CCDS44778.1" ; exon_id "ENSE00001381126.3" ; exon_number 1 ; gene_id "NTM--AC142086.6^NTM^ENSG00000182667.14" ; gene_name NTM ; gene_type protein_coding ; havana_gene "OTTHUMG00000066364.16" ; havana_transcript "OTTHUMT00000141938.3" ; hgnc_id "HGNC:17941" ; level 2 ; orig_coord_info "chr11,131911482,131911648,+" ; protein_id "ENSP00000363916.1" ; tag basic CCDS ; transcript_id "NTM--AC142086.6^ENST00000374784.5" ; transcript_name "NTM-201" ; transcript_support_level 1 ; transcript_type protein_coding
NTM--AC142086.6 HAVANA mRNA 7859 19676 . + . FI_gene_label "NTM^ENSG00000182667.14" ; ID "NTM--AC142086.6^ENST00000374784.5" ; Parent "NTM--AC142086.6^NTM^ENSG00000182667.14" ; ccdsid "CCDS44778.1" ; exon_id "ENSE00001381126.3" ; exon_number 1 ; gene_id "NTM--AC142086.6^NTM^ENSG00000182667.14" ; gene_name NTM ; gene_type protein_coding ; havana_gene "OTTHUMG00000066364.16" ; havana_transcript "OTTHUMT00000141938.3" ; hgnc_id "HGNC:17941" ; level 2 ; orig_coord_info "chr11,131911482,131911648,+" ; protein_id "ENSP00000363916.1" ; tag basic CCDS ; transcript_id "NTM--AC142086.6^ENST00000374784.5" ; transcript_name "NTM-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PARVA--BTNL8 HAVANA gene 29100 38216 . + . FI_gene_label "BTNL8^ENSG00000113303.12" ; ID "PARVA--BTNL8^BTNL8^ENSG00000113303.12" ; ccdsid "CCDS4459.1" ; exon_id "ENSE00002065219.1" ; exon_number 1 ; gene_id "PARVA--BTNL8^BTNL8^ENSG00000113303.12" ; gene_name BTNL8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130932.3" ; havana_transcript "OTTHUMT00000253528.2" ; hgnc_id "HGNC:26131" ; level 2 ; orig_coord_info "chr5,180899311,180899359,+" ; protein_id "ENSP00000231229.4" ; tag basic CCDS ; transcript_id "PARVA--BTNL8^ENST00000231229.8" ; transcript_name "BTNL8-201" ; transcript_support_level 1 ; transcript_type protein_coding
PARVA--BTNL8 HAVANA mRNA 29100 38216 . + . FI_gene_label "BTNL8^ENSG00000113303.12" ; ID "PARVA--BTNL8^ENST00000231229.8" ; Parent "PARVA--BTNL8^BTNL8^ENSG00000113303.12" ; ccdsid "CCDS4459.1" ; exon_id "ENSE00002065219.1" ; exon_number 1 ; gene_id "PARVA--BTNL8^BTNL8^ENSG00000113303.12" ; gene_name BTNL8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130932.3" ; havana_transcript "OTTHUMT00000253528.2" ; hgnc_id "HGNC:26131" ; level 2 ; orig_coord_info "chr5,180899311,180899359,+" ; protein_id "ENSP00000231229.4" ; tag basic CCDS ; transcript_id "PARVA--BTNL8^ENST00000231229.8" ; transcript_name "BTNL8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PARVA--BTNL8 HAVANA gene 1009 26099 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PARVA--BTNL8^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PARVA--BTNL8^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PARVA--BTNL8^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding
PARVA--BTNL8 HAVANA mRNA 1009 26099 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PARVA--BTNL8^ENST00000334956.15" ; Parent "PARVA--BTNL8^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PARVA--BTNL8^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PARVA--BTNL8^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PDCD6IP--ARPP21 HAVANA gene 34394 67250 . + . FI_gene_label "ARPP21^ENSG00000172995.16" ; ID "PDCD6IP--ARPP21^ARPP21^ENSG00000172995.16" ; ccdsid "CCDS2661.1" ; exon_id "ENSE00003794213.1" ; exon_number 3 ; gene_id "PDCD6IP--ARPP21^ARPP21^ENSG00000172995.16" ; gene_name ARPP21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130795.16" ; havana_transcript "OTTHUMT00000253334.2" ; hgnc_id "HGNC:16968" ; level 2 ; orig_coord_info "chr3,35681752,35681880,+" ; protein_id "ENSP00000187397.4" ; tag basic appris_principal_1 CCDS ; transcript_id "PDCD6IP--ARPP21^ENST00000187397.8" ; transcript_name "ARPP21-201" ; transcript_support_level 1 ; transcript_type protein_coding
PDCD6IP--ARPP21 HAVANA mRNA 34394 67250 . + . FI_gene_label "ARPP21^ENSG00000172995.16" ; ID "PDCD6IP--ARPP21^ENST00000187397.8" ; Parent "PDCD6IP--ARPP21^ARPP21^ENSG00000172995.16" ; ccdsid "CCDS2661.1" ; exon_id "ENSE00003794213.1" ; exon_number 3 ; gene_id "PDCD6IP--ARPP21^ARPP21^ENSG00000172995.16" ; gene_name ARPP21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130795.16" ; havana_transcript "OTTHUMT00000253334.2" ; hgnc_id "HGNC:16968" ; level 2 ; orig_coord_info "chr3,35681752,35681880,+" ; protein_id "ENSP00000187397.4" ; tag basic appris_principal_1 CCDS ; transcript_id "PDCD6IP--ARPP21^ENST00000187397.8" ; transcript_name "ARPP21-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PDCD6IP--ARPP21 HAVANA gene 1060 28169 . + . FI_gene_label "PDCD6IP^ENSG00000170248.15" ; ID "PDCD6IP--ARPP21^PDCD6IP^ENSG00000170248.15" ; ccdsid "CCDS2660.1" ; exon_id "ENSE00001884181.2" ; exon_number 1 ; gene_id "PDCD6IP--ARPP21^PDCD6IP^ENSG00000170248.15" ; gene_name PDCD6IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000130751.10" ; havana_transcript "OTTHUMT00000253251.3" ; hgnc_id "HGNC:8766" ; level 2 ; orig_coord_info "chr3,33798729,33798937,+" ; protein_id "ENSP00000307387.3" ; tag basic MANE_Select CCDS ; transcript_id "PDCD6IP--ARPP21^ENST00000307296.8" ; transcript_name "PDCD6IP-201" ; transcript_support_level 1 ; transcript_type protein_coding
PDCD6IP--ARPP21 HAVANA mRNA 1060 28169 . + . FI_gene_label "PDCD6IP^ENSG00000170248.15" ; ID "PDCD6IP--ARPP21^ENST00000307296.8" ; Parent "PDCD6IP--ARPP21^PDCD6IP^ENSG00000170248.15" ; ccdsid "CCDS2660.1" ; exon_id "ENSE00001884181.2" ; exon_number 1 ; gene_id "PDCD6IP--ARPP21^PDCD6IP^ENSG00000170248.15" ; gene_name PDCD6IP ; gene_type protein_coding ; havana_gene "OTTHUMG00000130751.10" ; havana_transcript "OTTHUMT00000253251.3" ; hgnc_id "HGNC:8766" ; level 2 ; orig_coord_info "chr3,33798729,33798937,+" ; protein_id "ENSP00000307387.3" ; tag basic MANE_Select CCDS ; transcript_id "PDCD6IP--ARPP21^ENST00000307296.8" ; transcript_name "PDCD6IP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PHKB--MOSMO HAVANA gene 1204 44448 . + . FI_gene_label "PHKB^ENSG00000102893.16" ; ID "PHKB--MOSMO^PHKB^ENSG00000102893.16" ; exon_id "ENSE00002601441.1" ; exon_number 1 ; gene_id "PHKB--MOSMO^PHKB^ENSG00000102893.16" ; gene_name PHKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000133102.6" ; havana_transcript "OTTHUMT00000256767.3" ; hgnc_id "HGNC:8927" ; level 2 ; orig_coord_info "chr16,47461351,47461426,+" ; protein_id "ENSP00000299167.8" ; tag alternative_5_UTR basic ; transcript_id "PHKB--MOSMO^ENST00000299167.12" ; transcript_name "PHKB-201" ; transcript_support_level 5 ; transcript_type protein_coding
PHKB--MOSMO HAVANA mRNA 1204 44448 . + . FI_gene_label "PHKB^ENSG00000102893.16" ; ID "PHKB--MOSMO^ENST00000299167.12" ; Parent "PHKB--MOSMO^PHKB^ENSG00000102893.16" ; exon_id "ENSE00002601441.1" ; exon_number 1 ; gene_id "PHKB--MOSMO^PHKB^ENSG00000102893.16" ; gene_name PHKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000133102.6" ; havana_transcript "OTTHUMT00000256767.3" ; hgnc_id "HGNC:8927" ; level 2 ; orig_coord_info "chr16,47461351,47461426,+" ; protein_id "ENSP00000299167.8" ; tag alternative_5_UTR basic ; transcript_id "PHKB--MOSMO^ENST00000299167.12" ; transcript_name "PHKB-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PHKB--MOSMO HAVANA gene 48020 58937 . + . FI_gene_label "MOSMO^ENSG00000185716.12" ; ID "PHKB--MOSMO^MOSMO^ENSG00000185716.12" ; exon_id "ENSE00003737250.1" ; exon_number 1 ; gene_id "PHKB--MOSMO^MOSMO^ENSG00000185716.12" ; gene_name MOSMO ; gene_type protein_coding ; havana_gene "OTTHUMG00000131587.4" ; havana_transcript "OTTHUMT00000254468.2" ; hgnc_id "HGNC:27087" ; level 2 ; orig_coord_info "chr16,22008302,22008407,+" ; protein_id "ENSP00000454543.1" ; transcript_id "PHKB--MOSMO^ENST00000331057.8" ; transcript_name "MOSMO-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
PHKB--MOSMO HAVANA mRNA 48020 58937 . + . FI_gene_label "MOSMO^ENSG00000185716.12" ; ID "PHKB--MOSMO^ENST00000331057.8" ; Parent "PHKB--MOSMO^MOSMO^ENSG00000185716.12" ; exon_id "ENSE00003737250.1" ; exon_number 1 ; gene_id "PHKB--MOSMO^MOSMO^ENSG00000185716.12" ; gene_name MOSMO ; gene_type protein_coding ; havana_gene "OTTHUMG00000131587.4" ; havana_transcript "OTTHUMT00000254468.2" ; hgnc_id "HGNC:27087" ; level 2 ; orig_coord_info "chr16,22008302,22008407,+" ; protein_id "ENSP00000454543.1" ; transcript_id "PHKB--MOSMO^ENST00000331057.8" ; transcript_name "MOSMO-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
PTK2--LINC01270 HAVANA gene 2059 60797 . + . FI_gene_label "PTK2^ENSG00000169398.19" ; ID "PTK2--LINC01270^PTK2^ENSG00000169398.19" ; ccdsid "CCDS56557.1" ; exon_id "ENSE00003798215.1" ; exon_number 3 ; gene_id "PTK2--LINC01270^PTK2^ENSG00000169398.19" ; gene_name PTK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067438.25" ; havana_transcript "OTTHUMT00000378103.1" ; hgnc_id "HGNC:9611" ; level 2 ; orig_coord_info "chr8,140890543,140890737,-" ; protein_id "ENSP00000341189.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "PTK2--LINC01270^ENST00000340930.7" ; transcript_name "PTK2-201" ; transcript_support_level 2 ; transcript_type protein_coding
PTK2--LINC01270 HAVANA mRNA 2059 60797 . + . FI_gene_label "PTK2^ENSG00000169398.19" ; ID "PTK2--LINC01270^ENST00000340930.7" ; Parent "PTK2--LINC01270^PTK2^ENSG00000169398.19" ; ccdsid "CCDS56557.1" ; exon_id "ENSE00003798215.1" ; exon_number 3 ; gene_id "PTK2--LINC01270^PTK2^ENSG00000169398.19" ; gene_name PTK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000067438.25" ; havana_transcript "OTTHUMT00000378103.1" ; hgnc_id "HGNC:9611" ; level 2 ; orig_coord_info "chr8,140890543,140890737,-" ; protein_id "ENSP00000341189.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "PTK2--LINC01270^ENST00000340930.7" ; transcript_name "PTK2-201" ; transcript_support_level 2 ; 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:
RBM4B--BICC1 HAVANA gene 21751 30892 . + . FI_gene_label "BICC1^ENSG00000122870.12" ; ID "RBM4B--BICC1^BICC1^ENSG00000122870.12" ; exon_id "ENSE00001173664.3" ; exon_number 1 ; gene_id "RBM4B--BICC1^BICC1^ENSG00000122870.12" ; gene_name BICC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018271.4" ; havana_transcript "OTTHUMT00000048149.1" ; hgnc_id "HGNC:19351" ; level 2 ; orig_coord_info "chr10,58793559,58793615,+" ; protein_id "ENSP00000263103.1" ; tag basic ; transcript_id "RBM4B--BICC1^ENST00000263103.1" ; transcript_name "BICC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM4B--BICC1 HAVANA mRNA 21751 30892 . + . FI_gene_label "BICC1^ENSG00000122870.12" ; ID "RBM4B--BICC1^ENST00000263103.1" ; Parent "RBM4B--BICC1^BICC1^ENSG00000122870.12" ; exon_id "ENSE00001173664.3" ; exon_number 1 ; gene_id "RBM4B--BICC1^BICC1^ENSG00000122870.12" ; gene_name BICC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018271.4" ; havana_transcript "OTTHUMT00000048149.1" ; hgnc_id "HGNC:19351" ; level 2 ; orig_coord_info "chr10,58793559,58793615,+" ; protein_id "ENSP00000263103.1" ; tag basic ; transcript_id "RBM4B--BICC1^ENST00000263103.1" ; transcript_name "BICC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM4B--BICC1 HAVANA gene 1001 8551 . + . FI_gene_label "RBM4B^ENSG00000173914.12" ; ID "RBM4B--BICC1^RBM4B^ENSG00000173914.12" ; ccdsid "CCDS8149.1" ; exon_id "ENSE00002463386.1" ; exon_number 2 ; gene_id "RBM4B--BICC1^RBM4B^ENSG00000173914.12" ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4" ; havana_transcript "OTTHUMT00000393852.2" ; hgnc_id "HGNC:28842" ; level 2 ; orig_coord_info "chr11,66676668,66677079,-" ; protein_id "ENSP00000310471.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM4B--BICC1^ENST00000310046.9" ; transcript_name "RBM4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM4B--BICC1 HAVANA mRNA 1001 8551 . + . FI_gene_label "RBM4B^ENSG00000173914.12" ; ID "RBM4B--BICC1^ENST00000310046.9" ; Parent "RBM4B--BICC1^RBM4B^ENSG00000173914.12" ; ccdsid "CCDS8149.1" ; exon_id "ENSE00002463386.1" ; exon_number 2 ; gene_id "RBM4B--BICC1^RBM4B^ENSG00000173914.12" ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4" ; havana_transcript "OTTHUMT00000393852.2" ; hgnc_id "HGNC:28842" ; level 2 ; orig_coord_info "chr11,66676668,66677079,-" ; protein_id "ENSP00000310471.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM4B--BICC1^ENST00000310046.9" ; transcript_name "RBM4B-201" ; 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:
TBXAS1--LAMC3 HAVANA gene 2350 29382 . + . FI_gene_label "TBXAS1^ENSG00000059377.18" ; ID "TBXAS1--LAMC3^TBXAS1^ENSG00000059377.18" ; exon_id "ENSE00001156245.6" ; exon_number 5 ; gene_id "TBXAS1--LAMC3^TBXAS1^ENSG00000059377.18" ; gene_name TBXAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157302.9" ; havana_transcript "OTTHUMT00000348373.4" ; hgnc_id "HGNC:11609" ; level 2 ; orig_coord_info "chr7,139829391,139829479,+" ; protein_id "ENSP00000338087.7" ; tag upstream_ATG basic appris_alternative_2 ; transcript_id "TBXAS1--LAMC3^ENST00000336425.10" ; transcript_name "TBXAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBXAS1--LAMC3 HAVANA mRNA 2350 29382 . + . FI_gene_label "TBXAS1^ENSG00000059377.18" ; ID "TBXAS1--LAMC3^ENST00000336425.10" ; Parent "TBXAS1--LAMC3^TBXAS1^ENSG00000059377.18" ; exon_id "ENSE00001156245.6" ; exon_number 5 ; gene_id "TBXAS1--LAMC3^TBXAS1^ENSG00000059377.18" ; gene_name TBXAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157302.9" ; havana_transcript "OTTHUMT00000348373.4" ; hgnc_id "HGNC:11609" ; level 2 ; orig_coord_info "chr7,139829391,139829479,+" ; protein_id "ENSP00000338087.7" ; tag upstream_ATG basic appris_alternative_2 ; transcript_id "TBXAS1--LAMC3^ENST00000336425.10" ; transcript_name "TBXAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TBXAS1--LAMC3 HAVANA gene 55963 64835 . + . FI_gene_label "LAMC3^ENSG00000050555.19" ; ID "TBXAS1--LAMC3^LAMC3^ENSG00000050555.19" ; exon_id "ENSE00001750717.1" ; exon_number 1 ; gene_id "TBXAS1--LAMC3^LAMC3^ENSG00000050555.19" ; gene_name LAMC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020819.5" ; havana_transcript "OTTHUMT00000054718.1" ; hgnc_id "HGNC:6494" ; level 2 ; orig_coord_info "chr9,131079243,131079298,+" ; protein_id "ENSP00000347627.5" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TBXAS1--LAMC3^ENST00000355452.5" ; transcript_name "LAMC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBXAS1--LAMC3 HAVANA mRNA 55963 64835 . + . FI_gene_label "LAMC3^ENSG00000050555.19" ; ID "TBXAS1--LAMC3^ENST00000355452.5" ; Parent "TBXAS1--LAMC3^LAMC3^ENSG00000050555.19" ; exon_id "ENSE00001750717.1" ; exon_number 1 ; gene_id "TBXAS1--LAMC3^LAMC3^ENSG00000050555.19" ; gene_name LAMC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020819.5" ; havana_transcript "OTTHUMT00000054718.1" ; hgnc_id "HGNC:6494" ; level 2 ; orig_coord_info "chr9,131079243,131079298,+" ; protein_id "ENSP00000347627.5" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TBXAS1--LAMC3^ENST00000355452.5" ; transcript_name "LAMC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM209--DENND1A HAVANA gene 21884 49199 . + . FI_gene_label "DENND1A^ENSG00000119522.16" ; ID "TMEM209--DENND1A^DENND1A^ENSG00000119522.16" ; ccdsid "CCDS87687.1" ; exon_id "ENSE00003643105.1" ; exon_number 2 ; gene_id "TMEM209--DENND1A^DENND1A^ENSG00000119522.16" ; gene_name DENND1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020643.1" ; havana_transcript "OTTHUMT00000053998.1" ; hgnc_id "HGNC:29324" ; level 2 ; orig_coord_info "chr9,123878951,123878992,-" ; protein_id "ENSP00000362720.1" ; tag basic CCDS ; transcript_id "TMEM209--DENND1A^ENST00000373618.1" ; transcript_name "DENND1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM209--DENND1A HAVANA mRNA 21884 49199 . + . FI_gene_label "DENND1A^ENSG00000119522.16" ; ID "TMEM209--DENND1A^ENST00000373618.1" ; Parent "TMEM209--DENND1A^DENND1A^ENSG00000119522.16" ; ccdsid "CCDS87687.1" ; exon_id "ENSE00003643105.1" ; exon_number 2 ; gene_id "TMEM209--DENND1A^DENND1A^ENSG00000119522.16" ; gene_name DENND1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020643.1" ; havana_transcript "OTTHUMT00000053998.1" ; hgnc_id "HGNC:29324" ; level 2 ; orig_coord_info "chr9,123878951,123878992,-" ; protein_id "ENSP00000362720.1" ; tag basic CCDS ; transcript_id "TMEM209--DENND1A^ENST00000373618.1" ; transcript_name "DENND1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM209--DENND1A HAVANA gene 2895 18883 . + . FI_gene_label "TMEM209^ENSG00000146842.17" ; ID "TMEM209--DENND1A^TMEM209^ENSG00000146842.17" ; ccdsid "CCDS47712.1" ; exon_id "ENSE00002231198.2" ; exon_number 1 ; gene_id "TMEM209--DENND1A^TMEM209^ENSG00000146842.17" ; gene_name TMEM209 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157653.3" ; havana_transcript "OTTHUMT00000349339.2" ; hgnc_id "HGNC:21898" ; level 2 ; orig_coord_info "chr7,130205373,130205375,-" ; protein_id "ENSP00000380747.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TMEM209--DENND1A^ENST00000397622.7" ; transcript_name "TMEM209-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM209--DENND1A HAVANA mRNA 2895 18883 . + . FI_gene_label "TMEM209^ENSG00000146842.17" ; ID "TMEM209--DENND1A^ENST00000397622.7" ; Parent "TMEM209--DENND1A^TMEM209^ENSG00000146842.17" ; ccdsid "CCDS47712.1" ; exon_id "ENSE00002231198.2" ; exon_number 1 ; gene_id "TMEM209--DENND1A^TMEM209^ENSG00000146842.17" ; gene_name TMEM209 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157653.3" ; havana_transcript "OTTHUMT00000349339.2" ; hgnc_id "HGNC:21898" ; level 2 ; orig_coord_info "chr7,130205373,130205375,-" ; protein_id "ENSP00000380747.2" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TMEM209--DENND1A^ENST00000397622.7" ; transcript_name "TMEM209-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM38B--ZNF462 HAVANA gene 16226 41291 . + . FI_gene_label "ZNF462^ENSG00000148143.13" ; ID "TMEM38B--ZNF462^ZNF462^ENSG00000148143.13" ; ccdsid "CCDS35096.1" ; exon_id "ENSE00003701112.1" ; exon_number 2 ; gene_id "TMEM38B--ZNF462^ZNF462^ENSG00000148143.13" ; gene_name ZNF462 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020438.5" ; havana_transcript "OTTHUMT00000053532.3" ; hgnc_id "HGNC:21684" ; level 2 ; orig_coord_info "chr9,106923384,106923603,+" ; protein_id "ENSP00000277225.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM38B--ZNF462^ENST00000277225.10" ; transcript_name "ZNF462-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM38B--ZNF462 HAVANA mRNA 16226 41291 . + . FI_gene_label "ZNF462^ENSG00000148143.13" ; ID "TMEM38B--ZNF462^ENST00000277225.10" ; Parent "TMEM38B--ZNF462^ZNF462^ENSG00000148143.13" ; ccdsid "CCDS35096.1" ; exon_id "ENSE00003701112.1" ; exon_number 2 ; gene_id "TMEM38B--ZNF462^ZNF462^ENSG00000148143.13" ; gene_name ZNF462 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020438.5" ; havana_transcript "OTTHUMT00000053532.3" ; hgnc_id "HGNC:21684" ; level 2 ; orig_coord_info "chr9,106923384,106923603,+" ; protein_id "ENSP00000277225.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM38B--ZNF462^ENST00000277225.10" ; transcript_name "ZNF462-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM38B--ZNF462 HAVANA gene 2233 13208 . + . FI_gene_label "TMEM38B^ENSG00000095209.12" ; ID "TMEM38B--ZNF462^TMEM38B^ENSG00000095209.12" ; exon_id "ENSE00003798742.1" ; exon_number 2 ; gene_id "TMEM38B--ZNF462^TMEM38B^ENSG00000095209.12" ; gene_name TMEM38B ; gene_type protein_coding ; havana_gene "OTTHUMG00000020429.7" ; havana_transcript "OTTHUMT00000053518.1" ; hgnc_id "HGNC:25535" ; level 2 ; orig_coord_info "chr9,105705647,105705753,+" ; protein_id "ENSP00000363820.1" ; tag basic ; transcript_id "TMEM38B--ZNF462^ENST00000374688.5" ; transcript_name "TMEM38B-201" ; transcript_support_level 2 ; transcript_type protein_coding
TMEM38B--ZNF462 HAVANA mRNA 2233 13208 . + . FI_gene_label "TMEM38B^ENSG00000095209.12" ; ID "TMEM38B--ZNF462^ENST00000374688.5" ; Parent "TMEM38B--ZNF462^TMEM38B^ENSG00000095209.12" ; exon_id "ENSE00003798742.1" ; exon_number 2 ; gene_id "TMEM38B--ZNF462^TMEM38B^ENSG00000095209.12" ; gene_name TMEM38B ; gene_type protein_coding ; havana_gene "OTTHUMG00000020429.7" ; havana_transcript "OTTHUMT00000053518.1" ; hgnc_id "HGNC:25535" ; level 2 ; orig_coord_info "chr9,105705647,105705753,+" ; protein_id "ENSP00000363820.1" ; tag basic ; transcript_id "TMEM38B--ZNF462^ENST00000374688.5" ; transcript_name "TMEM38B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TMEM41B--NUCB2 HAVANA gene 1070 10646 . + . FI_gene_label "TMEM41B^ENSG00000166471.11" ; ID "TMEM41B--NUCB2^TMEM41B^ENSG00000166471.11" ; ccdsid "CCDS31424.1" ; exon_id "ENSE00002196659.1" ; exon_number 1 ; gene_id "TMEM41B--NUCB2^TMEM41B^ENSG00000166471.11" ; gene_name TMEM41B ; gene_type protein_coding ; havana_gene "OTTHUMG00000165719.3" ; havana_transcript "OTTHUMT00000386017.1" ; hgnc_id "HGNC:28948" ; level 2 ; orig_coord_info "chr11,9314321,9314441,-" ; protein_id "ENSP00000299596.4" ; tag alternative_3_UTR CCDS ; transcript_id "TMEM41B--NUCB2^ENST00000299596.8" ; transcript_name "TMEM41B-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
TMEM41B--NUCB2 HAVANA mRNA 1070 10646 . + . FI_gene_label "TMEM41B^ENSG00000166471.11" ; ID "TMEM41B--NUCB2^ENST00000299596.8" ; Parent "TMEM41B--NUCB2^TMEM41B^ENSG00000166471.11" ; ccdsid "CCDS31424.1" ; exon_id "ENSE00002196659.1" ; exon_number 1 ; gene_id "TMEM41B--NUCB2^TMEM41B^ENSG00000166471.11" ; gene_name TMEM41B ; gene_type protein_coding ; havana_gene "OTTHUMG00000165719.3" ; havana_transcript "OTTHUMT00000386017.1" ; hgnc_id "HGNC:28948" ; level 2 ; orig_coord_info "chr11,9314321,9314441,-" ; protein_id "ENSP00000299596.4" ; tag alternative_3_UTR CCDS ; transcript_id "TMEM41B--NUCB2^ENST00000299596.8" ; transcript_name "TMEM41B-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
TMEM41B--NUCB2 HAVANA gene 20919 37329 . + . FI_gene_label "NUCB2^ENSG00000070081.17" ; ID "TMEM41B--NUCB2^NUCB2^ENSG00000070081.17" ; exon_id "ENSE00003467633.1" ; exon_number 3 ; gene_id "TMEM41B--NUCB2^NUCB2^ENSG00000070081.17" ; gene_name NUCB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166050.8" ; havana_transcript "OTTHUMT00000387613.3" ; hgnc_id "HGNC:8044" ; level 2 ; orig_coord_info "chr11,17295324,17295467,+" ; protein_id "ENSP00000320168.6" ; tag basic appris_alternative_1 ; transcript_id "TMEM41B--NUCB2^ENST00000323688.10" ; transcript_name "NUCB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
TMEM41B--NUCB2 HAVANA mRNA 20919 37329 . + . FI_gene_label "NUCB2^ENSG00000070081.17" ; ID "TMEM41B--NUCB2^ENST00000323688.10" ; Parent "TMEM41B--NUCB2^NUCB2^ENSG00000070081.17" ; exon_id "ENSE00003467633.1" ; exon_number 3 ; gene_id "TMEM41B--NUCB2^NUCB2^ENSG00000070081.17" ; gene_name NUCB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166050.8" ; havana_transcript "OTTHUMT00000387613.3" ; hgnc_id "HGNC:8044" ; level 2 ; orig_coord_info "chr11,17295324,17295467,+" ; protein_id "ENSP00000320168.6" ; tag basic appris_alternative_1 ; transcript_id "TMEM41B--NUCB2^ENST00000323688.10" ; transcript_name "NUCB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TMPO--APAF1 HAVANA gene 1274 9618 . + . FI_gene_label "TMPO^ENSG00000120802.14" ; ID "TMPO--APAF1^TMPO^ENSG00000120802.14" ; exon_id "ENSE00002404211.1" ; exon_number 1 ; gene_id "TMPO--APAF1^TMPO^ENSG00000120802.14" ; gene_name TMPO ; gene_type protein_coding ; havana_gene "OTTHUMG00000170210.4" ; havana_transcript "OTTHUMT00000407980.1" ; hgnc_id "HGNC:11875" ; level 2 ; orig_coord_info "chr12,98515868,98516146,+" ; protein_id "ENSP00000261210.5" ; tag basic ; transcript_id "TMPO--APAF1^ENST00000261210.9" ; transcript_name "TMPO-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMPO--APAF1 HAVANA mRNA 1274 9618 . + . FI_gene_label "TMPO^ENSG00000120802.14" ; ID "TMPO--APAF1^ENST00000261210.9" ; Parent "TMPO--APAF1^TMPO^ENSG00000120802.14" ; exon_id "ENSE00002404211.1" ; exon_number 1 ; gene_id "TMPO--APAF1^TMPO^ENSG00000120802.14" ; gene_name TMPO ; gene_type protein_coding ; havana_gene "OTTHUMG00000170210.4" ; havana_transcript "OTTHUMT00000407980.1" ; hgnc_id "HGNC:11875" ; level 2 ; orig_coord_info "chr12,98515868,98516146,+" ; protein_id "ENSP00000261210.5" ; tag basic ; transcript_id "TMPO--APAF1^ENST00000261210.9" ; transcript_name "TMPO-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMPO--APAF1 ENSEMBL gene 19357 49058 . + . FI_gene_label "APAF1^ENSG00000120868.14" ; ID "TMPO--APAF1^APAF1^ENSG00000120868.14" ; ccdsid "CCDS9071.1" ; exon_id "ENSE00001290131.2" ; exon_number 2 ; gene_id "TMPO--APAF1^APAF1^ENSG00000120868.14" ; gene_name APAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170214.4" ; hgnc_id "HGNC:576" ; level 3 ; orig_coord_info "chr12,98648360,98648497,+" ; protein_id "ENSP00000334558.1" ; tag basic CCDS ; transcript_id "TMPO--APAF1^ENST00000333991.5" ; transcript_name "APAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
TMPO--APAF1 ENSEMBL mRNA 19357 49058 . + . FI_gene_label "APAF1^ENSG00000120868.14" ; ID "TMPO--APAF1^ENST00000333991.5" ; Parent "TMPO--APAF1^APAF1^ENSG00000120868.14" ; ccdsid "CCDS9071.1" ; exon_id "ENSE00001290131.2" ; exon_number 2 ; gene_id "TMPO--APAF1^APAF1^ENSG00000120868.14" ; gene_name APAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170214.4" ; hgnc_id "HGNC:576" ; level 3 ; orig_coord_info "chr12,98648360,98648497,+" ; protein_id "ENSP00000334558.1" ; tag basic CCDS ; transcript_id "TMPO--APAF1^ENST00000333991.5" ; transcript_name "APAF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TRERF1--C6orf132 HAVANA gene 1791 21300 . + . FI_gene_label "TRERF1^ENSG00000124496.12" ; ID "TRERF1--C6orf132^TRERF1^ENSG00000124496.12" ; exon_id "ENSE00001190134.5" ; exon_number 4 ; gene_id "TRERF1--C6orf132^TRERF1^ENSG00000124496.12" ; gene_name TRERF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014698.2" ; havana_transcript "OTTHUMT00000040552.2" ; hgnc_id "HGNC:18273" ; level 2 ; orig_coord_info "chr6,42268154,42269590,-" ; protein_id "ENSP00000339438.2" ; tag basic ; transcript_id "TRERF1--C6orf132^ENST00000340840.6" ; transcript_name "TRERF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
TRERF1--C6orf132 HAVANA mRNA 1791 21300 . + . FI_gene_label "TRERF1^ENSG00000124496.12" ; ID "TRERF1--C6orf132^ENST00000340840.6" ; Parent "TRERF1--C6orf132^TRERF1^ENSG00000124496.12" ; exon_id "ENSE00001190134.5" ; exon_number 4 ; gene_id "TRERF1--C6orf132^TRERF1^ENSG00000124496.12" ; gene_name TRERF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014698.2" ; havana_transcript "OTTHUMT00000040552.2" ; hgnc_id "HGNC:18273" ; level 2 ; orig_coord_info "chr6,42268154,42269590,-" ; protein_id "ENSP00000339438.2" ; tag basic ; transcript_id "TRERF1--C6orf132^ENST00000340840.6" ; transcript_name "TRERF1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TRERF1--C6orf132 HAVANA gene 27519 38954 . + . FI_gene_label "C6orf132^ENSG00000188112.9" ; ID "TRERF1--C6orf132^C6orf132^ENSG00000188112.9" ; ccdsid "CCDS47428.1" ; exon_id "ENSE00001688858.2" ; exon_number 1 ; gene_id "TRERF1--C6orf132^C6orf132^ENSG00000188112.9" ; gene_name C6orf132 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014695.5" ; havana_transcript "OTTHUMT00000040548.4" ; hgnc_id "HGNC:21288" ; level 1 ; orig_coord_info "chr6,42142300,42142444,-" ; protein_id "ENSP00000341368.4" ; tag basic MANE_Select appris_principal_2 exp_conf CCDS ; transcript_id "TRERF1--C6orf132^ENST00000341865.9" ; transcript_name "C6orf132-201" ; transcript_support_level 5 ; transcript_type protein_coding
TRERF1--C6orf132 HAVANA mRNA 27519 38954 . + . FI_gene_label "C6orf132^ENSG00000188112.9" ; ID "TRERF1--C6orf132^ENST00000341865.9" ; Parent "TRERF1--C6orf132^C6orf132^ENSG00000188112.9" ; ccdsid "CCDS47428.1" ; exon_id "ENSE00001688858.2" ; exon_number 1 ; gene_id "TRERF1--C6orf132^C6orf132^ENSG00000188112.9" ; gene_name C6orf132 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014695.5" ; havana_transcript "OTTHUMT00000040548.4" ; hgnc_id "HGNC:21288" ; level 1 ; orig_coord_info "chr6,42142300,42142444,-" ; protein_id "ENSP00000341368.4" ; tag basic MANE_Select appris_principal_2 exp_conf CCDS ; transcript_id "TRERF1--C6orf132^ENST00000341865.9" ; transcript_name "C6orf132-201" ; transcript_support_level 5 ; 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:
WASH5P--DUX4 HAVANA gene 21550 23621 . + . FI_gene_label "DUX4^ENSG00000260596.5" ; ID "WASH5P--DUX4^DUX4^ENSG00000260596.5" ; ccdsid "CCDS77990.1" ; exon_id "ENSE00002596957.1" ; exon_number 1 ; gene_id "WASH5P--DUX4^DUX4^ENSG00000260596.5" ; gene_name DUX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175568.1" ; havana_transcript "OTTHUMT00000430519.1" ; hgnc_id "HGNC:50800" ; level 2 ; orig_coord_info "chr4,190173774,190175045,+" ; protein_id "ENSP00000458065.1" ; tag NMD_exception basic MANE_Select appris_principal_2 CCDS ; transcript_id "WASH5P--DUX4^ENST00000565211.1" ; transcript_name "DUX4-203" ; transcript_support_level 1 ; transcript_type protein_coding
WASH5P--DUX4 HAVANA mRNA 21550 23621 . + . FI_gene_label "DUX4^ENSG00000260596.5" ; ID "WASH5P--DUX4^ENST00000565211.1" ; Parent "WASH5P--DUX4^DUX4^ENSG00000260596.5" ; ccdsid "CCDS77990.1" ; exon_id "ENSE00002596957.1" ; exon_number 1 ; gene_id "WASH5P--DUX4^DUX4^ENSG00000260596.5" ; gene_name DUX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175568.1" ; havana_transcript "OTTHUMT00000430519.1" ; hgnc_id "HGNC:50800" ; level 2 ; orig_coord_info "chr4,190173774,190175045,+" ; protein_id "ENSP00000458065.1" ; tag NMD_exception basic MANE_Select appris_principal_2 CCDS ; transcript_id "WASH5P--DUX4^ENST00000565211.1" ; transcript_name "DUX4-203" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
XYLT1--SLCO3A1 HAVANA gene 1001 26083 . + . FI_gene_label "XYLT1^ENSG00000103489.12" ; ID "XYLT1--SLCO3A1^XYLT1^ENSG00000103489.12" ; ccdsid "CCDS10569.1" ; exon_id "ENSE00001301632.6" ; exon_number 1 ; gene_id "XYLT1--SLCO3A1^XYLT1^ENSG00000103489.12" ; gene_name XYLT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129975.4" ; havana_transcript "OTTHUMT00000252241.3" ; hgnc_id "HGNC:15516" ; level 2 ; orig_coord_info "chr16,17470434,17470796,-" ; protein_id "ENSP00000261381.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "XYLT1--SLCO3A1^ENST00000261381.7" ; transcript_name "XYLT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
XYLT1--SLCO3A1 HAVANA mRNA 1001 26083 . + . FI_gene_label "XYLT1^ENSG00000103489.12" ; ID "XYLT1--SLCO3A1^ENST00000261381.7" ; Parent "XYLT1--SLCO3A1^XYLT1^ENSG00000103489.12" ; ccdsid "CCDS10569.1" ; exon_id "ENSE00001301632.6" ; exon_number 1 ; gene_id "XYLT1--SLCO3A1^XYLT1^ENSG00000103489.12" ; gene_name XYLT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129975.4" ; havana_transcript "OTTHUMT00000252241.3" ; hgnc_id "HGNC:15516" ; level 2 ; orig_coord_info "chr16,17470434,17470796,-" ; protein_id "ENSP00000261381.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "XYLT1--SLCO3A1^ENST00000261381.7" ; transcript_name "XYLT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
XYLT1--SLCO3A1 HAVANA gene 29084 52007 . + . FI_gene_label "SLCO3A1^ENSG00000176463.14" ; ID "XYLT1--SLCO3A1^SLCO3A1^ENSG00000176463.14" ; ccdsid "CCDS10371.1" ; exon_id "ENSE00001931253.2" ; exon_number 1 ; gene_id "XYLT1--SLCO3A1^SLCO3A1^ENSG00000176463.14" ; gene_name SLCO3A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149846.6" ; havana_transcript "OTTHUMT00000313529.2" ; hgnc_id "HGNC:10952" ; level 2 ; orig_coord_info "chr15,91853909,91854088,+" ; protein_id "ENSP00000320634.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "XYLT1--SLCO3A1^ENST00000318445.11" ; transcript_name "SLCO3A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
XYLT1--SLCO3A1 HAVANA mRNA 29084 52007 . + . FI_gene_label "SLCO3A1^ENSG00000176463.14" ; ID "XYLT1--SLCO3A1^ENST00000318445.11" ; Parent "XYLT1--SLCO3A1^SLCO3A1^ENSG00000176463.14" ; ccdsid "CCDS10371.1" ; exon_id "ENSE00001931253.2" ; exon_number 1 ; gene_id "XYLT1--SLCO3A1^SLCO3A1^ENSG00000176463.14" ; gene_name SLCO3A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149846.6" ; havana_transcript "OTTHUMT00000313529.2" ; hgnc_id "HGNC:10952" ; level 2 ; orig_coord_info "chr15,91853909,91854088,+" ; protein_id "ENSP00000320634.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "XYLT1--SLCO3A1^ENST00000318445.11" ; transcript_name "SLCO3A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZC3H3--MAPRE3 HAVANA gene 17473 27467 . + . FI_gene_label "MAPRE3^ENSG00000084764.12" ; ID "ZC3H3--MAPRE3^MAPRE3^ENSG00000084764.12" ; ccdsid "CCDS1731.1" ; exon_id "ENSE00003677955.1" ; exon_number 2 ; gene_id "ZC3H3--MAPRE3^MAPRE3^ENSG00000084764.12" ; gene_name MAPRE3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097067.6" ; havana_transcript "OTTHUMT00000214183.2" ; hgnc_id "HGNC:6892" ; level 2 ; orig_coord_info "chr2,27022219,27022339,+" ; protein_id "ENSP00000233121.2" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "ZC3H3--MAPRE3^ENST00000233121.7" ; transcript_name "MAPRE3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZC3H3--MAPRE3 HAVANA mRNA 17473 27467 . + . FI_gene_label "MAPRE3^ENSG00000084764.12" ; ID "ZC3H3--MAPRE3^ENST00000233121.7" ; Parent "ZC3H3--MAPRE3^MAPRE3^ENSG00000084764.12" ; ccdsid "CCDS1731.1" ; exon_id "ENSE00003677955.1" ; exon_number 2 ; gene_id "ZC3H3--MAPRE3^MAPRE3^ENSG00000084764.12" ; gene_name MAPRE3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097067.6" ; havana_transcript "OTTHUMT00000214183.2" ; hgnc_id "HGNC:6892" ; level 2 ; orig_coord_info "chr2,27022219,27022339,+" ; protein_id "ENSP00000233121.2" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "ZC3H3--MAPRE3^ENST00000233121.7" ; transcript_name "MAPRE3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZC3H3--MAPRE3 HAVANA gene 1001 14472 . + . FI_gene_label "ZC3H3^ENSG00000014164.7" ; ID "ZC3H3--MAPRE3^ZC3H3^ENSG00000014164.7" ; ccdsid "CCDS6402.1" ; exon_id "ENSE00000876572.6" ; exon_number 1 ; gene_id "ZC3H3--MAPRE3^ZC3H3^ENSG00000014164.7" ; gene_name ZC3H3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165127.3" ; havana_transcript "OTTHUMT00000382011.3" ; hgnc_id "HGNC:28972" ; level 2 ; orig_coord_info "chr8,143541376,143541421,-" ; protein_id "ENSP00000262577.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H3--MAPRE3^ENST00000262577.6" ; transcript_name "ZC3H3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZC3H3--MAPRE3 HAVANA mRNA 1001 14472 . + . FI_gene_label "ZC3H3^ENSG00000014164.7" ; ID "ZC3H3--MAPRE3^ENST00000262577.6" ; Parent "ZC3H3--MAPRE3^ZC3H3^ENSG00000014164.7" ; ccdsid "CCDS6402.1" ; exon_id "ENSE00000876572.6" ; exon_number 1 ; gene_id "ZC3H3--MAPRE3^ZC3H3^ENSG00000014164.7" ; gene_name ZC3H3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165127.3" ; havana_transcript "OTTHUMT00000382011.3" ; hgnc_id "HGNC:28972" ; level 2 ; orig_coord_info "chr8,143541376,143541421,-" ; protein_id "ENSP00000262577.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZC3H3--MAPRE3^ENST00000262577.6" ; transcript_name "ZC3H3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF419--ZNF772 HAVANA gene 1040 9388 . + . FI_gene_label "ZNF419^ENSG00000105136.21" ; ID "ZNF419--ZNF772^ZNF419^ENSG00000105136.21" ; ccdsid "CCDS54326.1" ; exon_id "ENSE00002119234.1" ; exon_number 1 ; gene_id "ZNF419--ZNF772^ZNF419^ENSG00000105136.21" ; gene_name ZNF419 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037073.10" ; havana_transcript "OTTHUMT00000378506.1" ; hgnc_id "HGNC:20648" ; level 2 ; orig_coord_info "chr19,57487951,57487983,+" ; protein_id "ENSP00000221735.7" ; tag NAGNAG_splice_site basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZNF419--ZNF772^ENST00000221735.12" ; transcript_name "ZNF419-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF419--ZNF772 HAVANA mRNA 1040 9388 . + . FI_gene_label "ZNF419^ENSG00000105136.21" ; ID "ZNF419--ZNF772^ENST00000221735.12" ; Parent "ZNF419--ZNF772^ZNF419^ENSG00000105136.21" ; ccdsid "CCDS54326.1" ; exon_id "ENSE00002119234.1" ; exon_number 1 ; gene_id "ZNF419--ZNF772^ZNF419^ENSG00000105136.21" ; gene_name ZNF419 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037073.10" ; havana_transcript "OTTHUMT00000378506.1" ; hgnc_id "HGNC:20648" ; level 2 ; orig_coord_info "chr19,57487951,57487983,+" ; protein_id "ENSP00000221735.7" ; tag NAGNAG_splice_site basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ZNF419--ZNF772^ENST00000221735.12" ; transcript_name "ZNF419-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF419--ZNF772 HAVANA gene 12389 20373 . + . FI_gene_label "ZNF772^ENSG00000197128.12" ; ID "ZNF419--ZNF772^ZNF772^ENSG00000197128.12" ; ccdsid "CCDS33133.1" ; exon_id "ENSE00003691113.1" ; exon_number 1 ; gene_id "ZNF419--ZNF772^ZNF772^ENSG00000197128.12" ; gene_name ZNF772 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168007.3" ; havana_transcript "OTTHUMT00000397447.1" ; hgnc_id "HGNC:33106" ; level 2 ; orig_coord_info "chr19,57477277,57477309,-" ; protein_id "ENSP00000341165.4" ; tag basic appris_principal_4 CCDS ; transcript_id "ZNF419--ZNF772^ENST00000343280.8" ; transcript_name "ZNF772-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF419--ZNF772 HAVANA mRNA 12389 20373 . + . FI_gene_label "ZNF772^ENSG00000197128.12" ; ID "ZNF419--ZNF772^ENST00000343280.8" ; Parent "ZNF419--ZNF772^ZNF772^ENSG00000197128.12" ; ccdsid "CCDS33133.1" ; exon_id "ENSE00003691113.1" ; exon_number 1 ; gene_id "ZNF419--ZNF772^ZNF772^ENSG00000197128.12" ; gene_name ZNF772 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168007.3" ; havana_transcript "OTTHUMT00000397447.1" ; hgnc_id "HGNC:33106" ; level 2 ; orig_coord_info "chr19,57477277,57477309,-" ; protein_id "ENSP00000341165.4" ; tag basic appris_principal_4 CCDS ; transcript_id "ZNF419--ZNF772^ENST00000343280.8" ; transcript_name "ZNF772-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF462--FAM120A HAVANA gene 29067 51802 . + . FI_gene_label "FAM120A^ENSG00000048828.17" ; ID "ZNF462--FAM120A^FAM120A^ENSG00000048828.17" ; ccdsid "CCDS6706.1" ; exon_id "ENSE00003559000.2" ; exon_number 1 ; gene_id "ZNF462--FAM120A^FAM120A^ENSG00000048828.17" ; gene_name FAM120A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020252.4" ; havana_transcript "OTTHUMT00000053160.3" ; hgnc_id "HGNC:13247" ; level 2 ; orig_coord_info "chr9,93451916,93452389,+" ; protein_id "ENSP00000277165.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF462--FAM120A^ENST00000277165.11" ; transcript_name "FAM120A-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF462--FAM120A HAVANA mRNA 29067 51802 . + . FI_gene_label "FAM120A^ENSG00000048828.17" ; ID "ZNF462--FAM120A^ENST00000277165.11" ; Parent "ZNF462--FAM120A^FAM120A^ENSG00000048828.17" ; ccdsid "CCDS6706.1" ; exon_id "ENSE00003559000.2" ; exon_number 1 ; gene_id "ZNF462--FAM120A^FAM120A^ENSG00000048828.17" ; gene_name FAM120A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020252.4" ; havana_transcript "OTTHUMT00000053160.3" ; hgnc_id "HGNC:13247" ; level 2 ; orig_coord_info "chr9,93451916,93452389,+" ; protein_id "ENSP00000277165.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF462--FAM120A^ENST00000277165.11" ; transcript_name "FAM120A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF462--FAM120A HAVANA gene 1001 26066 . + . FI_gene_label "ZNF462^ENSG00000148143.13" ; ID "ZNF462--FAM120A^ZNF462^ENSG00000148143.13" ; ccdsid "CCDS35096.1" ; exon_id "ENSE00003701112.1" ; exon_number 2 ; gene_id "ZNF462--FAM120A^ZNF462^ENSG00000148143.13" ; gene_name ZNF462 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020438.5" ; havana_transcript "OTTHUMT00000053532.3" ; hgnc_id "HGNC:21684" ; level 2 ; orig_coord_info "chr9,106923384,106923603,+" ; protein_id "ENSP00000277225.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF462--FAM120A^ENST00000277225.10" ; transcript_name "ZNF462-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF462--FAM120A HAVANA mRNA 1001 26066 . + . FI_gene_label "ZNF462^ENSG00000148143.13" ; ID "ZNF462--FAM120A^ENST00000277225.10" ; Parent "ZNF462--FAM120A^ZNF462^ENSG00000148143.13" ; ccdsid "CCDS35096.1" ; exon_id "ENSE00003701112.1" ; exon_number 2 ; gene_id "ZNF462--FAM120A^ZNF462^ENSG00000148143.13" ; gene_name ZNF462 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020438.5" ; havana_transcript "OTTHUMT00000053532.3" ; hgnc_id "HGNC:21684" ; level 2 ; orig_coord_info "chr9,106923384,106923603,+" ; protein_id "ENSP00000277225.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF462--FAM120A^ENST00000277225.10" ; transcript_name "ZNF462-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF783--ABBA01045074.1 HAVANA gene 1001 18041 . + . FI_gene_label "ZNF783^ENSG00000204946.10" ; ID "ZNF783--ABBA01045074.1^ZNF783^ENSG00000204946.10" ; exon_id "ENSE00001476049.1" ; exon_number 1 ; gene_id "ZNF783--ABBA01045074.1^ZNF783^ENSG00000204946.10" ; gene_name ZNF783 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158969.3" ; havana_transcript "OTTHUMT00000352718.1" ; hgnc_id "HGNC:27222" ; level 2 ; orig_coord_info "chr7,149262334,149262357,+" ; protein_id "ENSP00000367291.1" ; transcript_id "ZNF783--ABBA01045074.1^ENST00000378052.5" ; transcript_name "ZNF783-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ZNF783--ABBA01045074.1 HAVANA mRNA 1001 18041 . + . FI_gene_label "ZNF783^ENSG00000204946.10" ; ID "ZNF783--ABBA01045074.1^ENST00000378052.5" ; Parent "ZNF783--ABBA01045074.1^ZNF783^ENSG00000204946.10" ; exon_id "ENSE00001476049.1" ; exon_number 1 ; gene_id "ZNF783--ABBA01045074.1^ZNF783^ENSG00000204946.10" ; gene_name ZNF783 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158969.3" ; havana_transcript "OTTHUMT00000352718.1" ; hgnc_id "HGNC:27222" ; level 2 ; orig_coord_info "chr7,149262334,149262357,+" ; protein_id "ENSP00000367291.1" ; transcript_id "ZNF783--ABBA01045074.1^ENST00000378052.5" ; transcript_name "ZNF783-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ZNF783--BX088702.1 HAVANA gene 1001 18041 . + . FI_gene_label "ZNF783^ENSG00000204946.10" ; ID "ZNF783--BX088702.1^ZNF783^ENSG00000204946.10" ; exon_id "ENSE00001476049.1" ; exon_number 1 ; gene_id "ZNF783--BX088702.1^ZNF783^ENSG00000204946.10" ; gene_name ZNF783 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158969.3" ; havana_transcript "OTTHUMT00000352718.1" ; hgnc_id "HGNC:27222" ; level 2 ; orig_coord_info "chr7,149262334,149262357,+" ; protein_id "ENSP00000367291.1" ; transcript_id "ZNF783--BX088702.1^ENST00000378052.5" ; transcript_name "ZNF783-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ZNF783--BX088702.1 HAVANA mRNA 1001 18041 . + . FI_gene_label "ZNF783^ENSG00000204946.10" ; ID "ZNF783--BX088702.1^ENST00000378052.5" ; Parent "ZNF783--BX088702.1^ZNF783^ENSG00000204946.10" ; exon_id "ENSE00001476049.1" ; exon_number 1 ; gene_id "ZNF783--BX088702.1^ZNF783^ENSG00000204946.10" ; gene_name ZNF783 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158969.3" ; havana_transcript "OTTHUMT00000352718.1" ; hgnc_id "HGNC:27222" ; level 2 ; orig_coord_info "chr7,149262334,149262357,+" ; protein_id "ENSP00000367291.1" ; transcript_id "ZNF783--BX088702.1^ENST00000378052.5" ; transcript_name "ZNF783-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
AC142086.6--AC090099.1 HAVANA gene 15551 17577 . + . FI_gene_label "AC090099.1^ENSG00000255470.1" ; ID "AC142086.6--AC090099.1^AC090099.1^ENSG00000255470.1" ; exon_id "ENSE00002169041.1" ; exon_number 1 ; gene_id "AC142086.6--AC090099.1^AC090099.1^ENSG00000255470.1" ; gene_name "AC090099.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166434.2" ; havana_transcript "OTTHUMT00000389787.1" ; level 2 ; orig_coord_info "chr11,18188895,18189495,-" ; tag dotter_confirmed basic ; transcript_id "AC142086.6--AC090099.1^ENST00000527671.1" ; transcript_name "AC090099.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
AC142086.6--AC090099.1 HAVANA RNA 15551 17577 . + . FI_gene_label "AC090099.1^ENSG00000255470.1" ; ID "AC142086.6--AC090099.1^ENST00000527671.1" ; Parent "AC142086.6--AC090099.1^AC090099.1^ENSG00000255470.1" ; exon_id "ENSE00002169041.1" ; exon_number 1 ; gene_id "AC142086.6--AC090099.1^AC090099.1^ENSG00000255470.1" ; gene_name "AC090099.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166434.2" ; havana_transcript "OTTHUMT00000389787.1" ; level 2 ; orig_coord_info "chr11,18188895,18189495,-" ; tag dotter_confirmed basic ; transcript_id "AC142086.6--AC090099.1^ENST00000527671.1" ; transcript_name "AC090099.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
AC142086.6--AC090099.1 HAVANA gene 1001 12550 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "AC142086.6--AC090099.1^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "AC142086.6--AC090099.1^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "AC142086.6--AC090099.1^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC142086.6--AC090099.1 HAVANA RNA 1001 12550 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "AC142086.6--AC090099.1^ENST00000621154.1" ; Parent "AC142086.6--AC090099.1^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "AC142086.6--AC090099.1^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "AC142086.6--AC090099.1^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC142086.6--MRGPRX12P HAVANA gene 15551 16529 . + . FI_gene_label "MRGPRX12P^ENSG00000254857.1" ; ID "AC142086.6--MRGPRX12P^MRGPRX12P^ENSG00000254857.1" ; exon_id "ENSE00002179645.1" ; exon_number 1 ; gene_id "AC142086.6--MRGPRX12P^MRGPRX12P^ENSG00000254857.1" ; gene_name MRGPRX12P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166436.1" ; havana_transcript "OTTHUMT00000389769.1" ; hgnc_id "HGNC:54336" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr11,18153277,18154255,+" ; tag basic ; transcript_id "AC142086.6--MRGPRX12P^ENST00000524640.1" ; transcript_name "MRGPRX12P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
AC142086.6--MRGPRX12P HAVANA RNA 15551 16529 . + . FI_gene_label "MRGPRX12P^ENSG00000254857.1" ; ID "AC142086.6--MRGPRX12P^ENST00000524640.1" ; Parent "AC142086.6--MRGPRX12P^MRGPRX12P^ENSG00000254857.1" ; exon_id "ENSE00002179645.1" ; exon_number 1 ; gene_id "AC142086.6--MRGPRX12P^MRGPRX12P^ENSG00000254857.1" ; gene_name MRGPRX12P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166436.1" ; havana_transcript "OTTHUMT00000389769.1" ; hgnc_id "HGNC:54336" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr11,18153277,18154255,+" ; tag basic ; transcript_id "AC142086.6--MRGPRX12P^ENST00000524640.1" ; transcript_name "MRGPRX12P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
AC142086.6--MRGPRX12P HAVANA gene 1001 12550 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "AC142086.6--MRGPRX12P^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "AC142086.6--MRGPRX12P^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "AC142086.6--MRGPRX12P^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC142086.6--MRGPRX12P HAVANA RNA 1001 12550 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "AC142086.6--MRGPRX12P^ENST00000621154.1" ; Parent "AC142086.6--MRGPRX12P^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "AC142086.6--MRGPRX12P^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "AC142086.6--MRGPRX12P^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AL162726.3--SVEP1 HAVANA gene 2907 13543 . + . FI_gene_label "AL162726.3^ENSG00000228430.9" ; ID "AL162726.3--SVEP1^AL162726.3^ENSG00000228430.9" ; exon_id "ENSE00001768989.2" ; exon_number 1 ; gene_id "AL162726.3--SVEP1^AL162726.3^ENSG00000228430.9" ; gene_name "AL162726.3" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000020098.5" ; havana_transcript "OTTHUMT00000052823.2" ; level 2 ; orig_coord_info "chr9,82273407,82273481,+" ; transcript_id "AL162726.3--SVEP1^ENST00000457558.7" ; transcript_name "AL162726.3-203" ; transcript_support_level 5 ; transcript_type processed_transcript
AL162726.3--SVEP1 HAVANA RNA 2907 13543 . + . FI_gene_label "AL162726.3^ENSG00000228430.9" ; ID "AL162726.3--SVEP1^ENST00000457558.7" ; Parent "AL162726.3--SVEP1^AL162726.3^ENSG00000228430.9" ; exon_id "ENSE00001768989.2" ; exon_number 1 ; gene_id "AL162726.3--SVEP1^AL162726.3^ENSG00000228430.9" ; gene_name "AL162726.3" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000020098.5" ; havana_transcript "OTTHUMT00000052823.2" ; level 2 ; orig_coord_info "chr9,82273407,82273481,+" ; transcript_id "AL162726.3--SVEP1^ENST00000457558.7" ; transcript_name "AL162726.3-203" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
MRGPRX12P--CKAP5 HAVANA gene 1001 1979 . + . FI_gene_label "MRGPRX12P^ENSG00000254857.1" ; ID "MRGPRX12P--CKAP5^MRGPRX12P^ENSG00000254857.1" ; exon_id "ENSE00002179645.1" ; exon_number 1 ; gene_id "MRGPRX12P--CKAP5^MRGPRX12P^ENSG00000254857.1" ; gene_name MRGPRX12P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166436.1" ; havana_transcript "OTTHUMT00000389769.1" ; hgnc_id "HGNC:54336" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr11,18153277,18154255,+" ; tag basic ; transcript_id "MRGPRX12P--CKAP5^ENST00000524640.1" ; transcript_name "MRGPRX12P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
MRGPRX12P--CKAP5 HAVANA RNA 1001 1979 . + . FI_gene_label "MRGPRX12P^ENSG00000254857.1" ; ID "MRGPRX12P--CKAP5^ENST00000524640.1" ; Parent "MRGPRX12P--CKAP5^MRGPRX12P^ENSG00000254857.1" ; exon_id "ENSE00002179645.1" ; exon_number 1 ; gene_id "MRGPRX12P--CKAP5^MRGPRX12P^ENSG00000254857.1" ; gene_name MRGPRX12P ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166436.1" ; havana_transcript "OTTHUMT00000389769.1" ; hgnc_id "HGNC:54336" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr11,18153277,18154255,+" ; tag basic ; transcript_id "MRGPRX12P--CKAP5^ENST00000524640.1" ; transcript_name "MRGPRX12P-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
NTM--AC142086.6 HAVANA gene 29043 40592 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "NTM--AC142086.6^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "NTM--AC142086.6^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "NTM--AC142086.6^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
NTM--AC142086.6 HAVANA RNA 29043 40592 . + . FI_gene_label "AC142086.6^ENSG00000277304.1" ; ID "NTM--AC142086.6^ENST00000621154.1" ; Parent "NTM--AC142086.6^AC142086.6^ENSG00000277304.1" ; exon_id "ENSE00003748863.1" ; exon_number 1 ; gene_id "NTM--AC142086.6^AC142086.6^ENSG00000277304.1" ; gene_name "AC142086.6" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187973.1" ; havana_transcript "OTTHUMT00000475750.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,32916974,32917129,+" ; tag basic ; transcript_id "NTM--AC142086.6^ENST00000621154.1" ; transcript_name "AC142086.6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
PTK2--LINC01270 HAVANA gene 64314 72656 . + . FI_gene_label "LINC01270^ENSG00000203999.9" ; ID "PTK2--LINC01270^LINC01270^ENSG00000203999.9" ; exon_id "ENSE00001455727.2" ; exon_number 1 ; gene_id "PTK2--LINC01270^LINC01270^ENSG00000203999.9" ; gene_name LINC01270 ; gene_type lncRNA ; havana_gene "OTTHUMG00000032719.15" ; havana_transcript "OTTHUMT00000079678.2" ; hgnc_id "HGNC:27658" ; level 2 ; orig_coord_info "chr20,50292720,50292830,+" ; tag TAGENE ; transcript_id "PTK2--LINC01270^ENST00000371639.8" ; transcript_name "LINC01270-201" ; transcript_support_level 2 ; transcript_type lncRNA
PTK2--LINC01270 HAVANA RNA 64314 72656 . + . FI_gene_label "LINC01270^ENSG00000203999.9" ; ID "PTK2--LINC01270^ENST00000371639.8" ; Parent "PTK2--LINC01270^LINC01270^ENSG00000203999.9" ; exon_id "ENSE00001455727.2" ; exon_number 1 ; gene_id "PTK2--LINC01270^LINC01270^ENSG00000203999.9" ; gene_name LINC01270 ; gene_type lncRNA ; havana_gene "OTTHUMG00000032719.15" ; havana_transcript "OTTHUMT00000079678.2" ; hgnc_id "HGNC:27658" ; level 2 ; orig_coord_info "chr20,50292720,50292830,+" ; tag TAGENE ; transcript_id "PTK2--LINC01270^ENST00000371639.8" ; transcript_name "LINC01270-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
WASH5P--DUX4 HAVANA gene 1664 3678 . + . FI_gene_label "WASH5P^ENSG00000282458.1" ; ID "WASH5P--DUX4^WASH5P^ENSG00000282458.1" ; exon_id "ENSE00003775509.1" ; exon_number 1 ; gene_id "WASH5P--DUX4^WASH5P^ENSG00000282458.1" ; gene_name WASH5P ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000180466.8" ; havana_transcript "OTTHUMT00000475089.2" ; hgnc_id "HGNC:33884" ; level 2 ; orig_coord_info "chr19,70928,70963,-" ; transcript_id "WASH5P--DUX4^ENST00000631796.1" ; transcript_name "WASH5P-201" ; transcript_support_level 2 ; transcript_type processed_transcript
WASH5P--DUX4 HAVANA RNA 1664 3678 . + . FI_gene_label "WASH5P^ENSG00000282458.1" ; ID "WASH5P--DUX4^ENST00000631796.1" ; Parent "WASH5P--DUX4^WASH5P^ENSG00000282458.1" ; exon_id "ENSE00003775509.1" ; exon_number 1 ; gene_id "WASH5P--DUX4^WASH5P^ENSG00000282458.1" ; gene_name WASH5P ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000180466.8" ; havana_transcript "OTTHUMT00000475089.2" ; hgnc_id "HGNC:33884" ; level 2 ; orig_coord_info "chr19,70928,70963,-" ; transcript_id "WASH5P--DUX4^ENST00000631796.1" ; transcript_name "WASH5P-201" ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created:
WASH5P--DUX4L2 HAVANA gene 11550 12824 . + . FI_gene_label "DUX4L2^ENSG00000280457.1" ; ID "WASH5P--DUX4L2^DUX4L2^ENSG00000280457.1" ; exon_id "ENSE00002591235.3" ; exon_number 1 ; gene_id "WASH5P--DUX4L2^DUX4L2^ENSG00000280457.1" ; gene_name DUX4L2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000161316.4" ; havana_transcript "OTTHUMT00000364515.3" ; hgnc_id "HGNC:37267" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr4,190091005,190092279,+" ; tag basic ; transcript_id "WASH5P--DUX4L2^ENST00000561772.3" ; transcript_name "DUX4L2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
WASH5P--DUX4L2 HAVANA RNA 11550 12824 . + . FI_gene_label "DUX4L2^ENSG00000280457.1" ; ID "WASH5P--DUX4L2^ENST00000561772.3" ; Parent "WASH5P--DUX4L2^DUX4L2^ENSG00000280457.1" ; exon_id "ENSE00002591235.3" ; exon_number 1 ; gene_id "WASH5P--DUX4L2^DUX4L2^ENSG00000280457.1" ; gene_name DUX4L2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000161316.4" ; havana_transcript "OTTHUMT00000364515.3" ; hgnc_id "HGNC:37267" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr4,190091005,190092279,+" ; tag basic ; transcript_id "WASH5P--DUX4L2^ENST00000561772.3" ; transcript_name "DUX4L2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
WASH5P--DUX4L2 HAVANA gene 1664 3678 . + . FI_gene_label "WASH5P^ENSG00000282458.1" ; ID "WASH5P--DUX4L2^WASH5P^ENSG00000282458.1" ; exon_id "ENSE00003775509.1" ; exon_number 1 ; gene_id "WASH5P--DUX4L2^WASH5P^ENSG00000282458.1" ; gene_name WASH5P ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000180466.8" ; havana_transcript "OTTHUMT00000475089.2" ; hgnc_id "HGNC:33884" ; level 2 ; orig_coord_info "chr19,70928,70963,-" ; transcript_id "WASH5P--DUX4L2^ENST00000631796.1" ; transcript_name "WASH5P-201" ; transcript_support_level 2 ; transcript_type processed_transcript
WASH5P--DUX4L2 HAVANA RNA 1664 3678 . + . FI_gene_label "WASH5P^ENSG00000282458.1" ; ID "WASH5P--DUX4L2^ENST00000631796.1" ; Parent "WASH5P--DUX4L2^WASH5P^ENSG00000282458.1" ; exon_id "ENSE00003775509.1" ; exon_number 1 ; gene_id "WASH5P--DUX4L2^WASH5P^ENSG00000282458.1" ; gene_name WASH5P ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000180466.8" ; havana_transcript "OTTHUMT00000475089.2" ; hgnc_id "HGNC:33884" ; level 2 ; orig_coord_info "chr19,70928,70963,-" ; transcript_id "WASH5P--DUX4L2^ENST00000631796.1" ; transcript_name "WASH5P-201" ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created:
ZNF783--ABBA01045074.1 HAVANA gene 21043 21399 . + . FI_gene_label "ABBA01045074.1^ENSG00000286916.1" ; ID "ZNF783--ABBA01045074.1^ABBA01045074.1^ENSG00000286916.1" ; exon_id "ENSE00003853769.1" ; exon_number 1 ; gene_id "ZNF783--ABBA01045074.1^ABBA01045074.1^ENSG00000286916.1" ; gene_name "ABBA01045074.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000193802.1" ; havana_transcript "OTTHUMT00000504834.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,43244631,43244987,-" ; tag basic ; transcript_id "ZNF783--ABBA01045074.1^ENST00000654042.1" ; transcript_name "ABBA01045074.1-201" ; transcript_type processed_pseudogene
ZNF783--ABBA01045074.1 HAVANA RNA 21043 21399 . + . FI_gene_label "ABBA01045074.1^ENSG00000286916.1" ; ID "ZNF783--ABBA01045074.1^ENST00000654042.1" ; Parent "ZNF783--ABBA01045074.1^ABBA01045074.1^ENSG00000286916.1" ; exon_id "ENSE00003853769.1" ; exon_number 1 ; gene_id "ZNF783--ABBA01045074.1^ABBA01045074.1^ENSG00000286916.1" ; gene_name "ABBA01045074.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000193802.1" ; havana_transcript "OTTHUMT00000504834.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,43244631,43244987,-" ; tag basic ; transcript_id "ZNF783--ABBA01045074.1^ENST00000654042.1" ; transcript_name "ABBA01045074.1-201" ; transcript_type processed_pseudogene
L1 and L2 created:
ZNF783--BX088702.1 HAVANA gene 21043 21277 . + . FI_gene_label "BX088702.1^ENSG00000277598.1" ; ID "ZNF783--BX088702.1^BX088702.1^ENSG00000277598.1" ; exon_id "ENSE00003720630.1" ; exon_number 1 ; gene_id "ZNF783--BX088702.1^BX088702.1^ENSG00000277598.1" ; gene_name "BX088702.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000188282.1" ; havana_transcript "OTTHUMT00000476814.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,60546920,60547154,-" ; tag basic ; transcript_id "ZNF783--BX088702.1^ENST00000610784.1" ; transcript_name "BX088702.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
ZNF783--BX088702.1 HAVANA RNA 21043 21277 . + . FI_gene_label "BX088702.1^ENSG00000277598.1" ; ID "ZNF783--BX088702.1^ENST00000610784.1" ; Parent "ZNF783--BX088702.1^BX088702.1^ENSG00000277598.1" ; exon_id "ENSE00003720630.1" ; exon_number 1 ; gene_id "ZNF783--BX088702.1^BX088702.1^ENSG00000277598.1" ; gene_name "BX088702.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000188282.1" ; havana_transcript "OTTHUMT00000476814.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr9,60546920,60547154,-" ; tag basic ; transcript_id "ZNF783--BX088702.1^ENST00000610784.1" ; transcript_name "BX088702.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
809 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
1377 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 55 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed