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: 9981
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 9981
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:9981
=> 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:
AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ATXN7L1--NAMPT HAVANA gene 30520 59548 . + . FI_gene_label "NAMPT^ENSG00000105835.13" ; ID "ATXN7L1--NAMPT^NAMPT^ENSG00000105835.13" ; ccdsid "CCDS5737.1" ; exon_id "ENSE00001516080.2" ; exon_number 1 ; gene_id "ATXN7L1--NAMPT^NAMPT^ENSG00000105835.13" ; gene_name NAMPT ; gene_type protein_coding ; havana_gene "OTTHUMG00000140388.5" ; havana_transcript "OTTHUMT00000277146.2" ; hgnc_id "HGNC:30092" ; level 2 ; orig_coord_info "chr7,106284828,106284884,-" ; protein_id "ENSP00000222553.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATXN7L1--NAMPT^ENST00000222553.8" ; transcript_name "NAMPT-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATXN7L1--NAMPT HAVANA mRNA 30520 59548 . + . FI_gene_label "NAMPT^ENSG00000105835.13" ; ID "ATXN7L1--NAMPT^ENST00000222553.8" ; Parent "ATXN7L1--NAMPT^NAMPT^ENSG00000105835.13" ; ccdsid "CCDS5737.1" ; exon_id "ENSE00001516080.2" ; exon_number 1 ; gene_id "ATXN7L1--NAMPT^NAMPT^ENSG00000105835.13" ; gene_name NAMPT ; gene_type protein_coding ; havana_gene "OTTHUMG00000140388.5" ; havana_transcript "OTTHUMT00000277146.2" ; hgnc_id "HGNC:30092" ; level 2 ; orig_coord_info "chr7,106284828,106284884,-" ; protein_id "ENSP00000222553.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATXN7L1--NAMPT^ENST00000222553.8" ; transcript_name "NAMPT-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATXN7L1--NAMPT HAVANA gene 1018 6186 . + . FI_gene_label "ATXN7L1^ENSG00000146776.15" ; ID "ATXN7L1--NAMPT^ATXN7L1^ENSG00000146776.15" ; ccdsid "CCDS34727.1" ; exon_id "ENSE00001954928.1" ; exon_number 1 ; gene_id "ATXN7L1--NAMPT^ATXN7L1^ENSG00000146776.15" ; gene_name ATXN7L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157521.3" ; havana_transcript "OTTHUMT00000349036.1" ; hgnc_id "HGNC:22210" ; level 2 ; orig_coord_info "chr7,105876378,105876558,-" ; protein_id "ENSP00000326344.4" ; tag basic CCDS ; transcript_id "ATXN7L1--NAMPT^ENST00000318724.8" ; transcript_name "ATXN7L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATXN7L1--NAMPT HAVANA mRNA 1018 6186 . + . FI_gene_label "ATXN7L1^ENSG00000146776.15" ; ID "ATXN7L1--NAMPT^ENST00000318724.8" ; Parent "ATXN7L1--NAMPT^ATXN7L1^ENSG00000146776.15" ; ccdsid "CCDS34727.1" ; exon_id "ENSE00001954928.1" ; exon_number 1 ; gene_id "ATXN7L1--NAMPT^ATXN7L1^ENSG00000146776.15" ; gene_name ATXN7L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157521.3" ; havana_transcript "OTTHUMT00000349036.1" ; hgnc_id "HGNC:22210" ; level 2 ; orig_coord_info "chr7,105876378,105876558,-" ; protein_id "ENSP00000326344.4" ; tag basic CCDS ; transcript_id "ATXN7L1--NAMPT^ENST00000318724.8" ; transcript_name "ATXN7L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CAMK2G--C10orf55 HAVANA gene 1131 23253 . + . FI_gene_label "CAMK2G^ENSG00000148660.21" ; ID "CAMK2G--C10orf55^CAMK2G^ENSG00000148660.21" ; exon_id "ENSE00002521481.1" ; exon_number 1 ; gene_id "CAMK2G--C10orf55^CAMK2G^ENSG00000148660.21" ; gene_name CAMK2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000018492.4" ; havana_transcript "OTTHUMT00000048718.1" ; hgnc_id "HGNC:1463" ; level 2 ; orig_coord_info "chr10,73874397,73874461,-" ; protein_id "ENSP00000307082.7" ; tag basic appris_alternative_1 ; transcript_id "CAMK2G--C10orf55^ENST00000305762.11" ; transcript_name "CAMK2G-201" ; transcript_support_level 5 ; transcript_type protein_coding
CAMK2G--C10orf55 HAVANA mRNA 1131 23253 . + . FI_gene_label "CAMK2G^ENSG00000148660.21" ; ID "CAMK2G--C10orf55^ENST00000305762.11" ; Parent "CAMK2G--C10orf55^CAMK2G^ENSG00000148660.21" ; exon_id "ENSE00002521481.1" ; exon_number 1 ; gene_id "CAMK2G--C10orf55^CAMK2G^ENSG00000148660.21" ; gene_name CAMK2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000018492.4" ; havana_transcript "OTTHUMT00000048718.1" ; hgnc_id "HGNC:1463" ; level 2 ; orig_coord_info "chr10,73874397,73874461,-" ; protein_id "ENSP00000307082.7" ; tag basic appris_alternative_1 ; transcript_id "CAMK2G--C10orf55^ENST00000305762.11" ; transcript_name "CAMK2G-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CAMK2G--VCL HAVANA gene 30014 59784 . + . FI_gene_label "VCL^ENSG00000035403.18" ; ID "CAMK2G--VCL^VCL^ENSG00000035403.18" ; ccdsid "CCDS7341.1" ; exon_id "ENSE00000000338.2" ; exon_number 1 ; gene_id "CAMK2G--VCL^VCL^ENSG00000035403.18" ; gene_name VCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000018498.4" ; havana_transcript "OTTHUMT00000048752.3" ; hgnc_id "HGNC:12665" ; level 2 ; orig_coord_info "chr10,73998208,73998375,+" ; protein_id "ENSP00000211998.5" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CAMK2G--VCL^ENST00000211998.10" ; transcript_name "VCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
CAMK2G--VCL HAVANA mRNA 30014 59784 . + . FI_gene_label "VCL^ENSG00000035403.18" ; ID "CAMK2G--VCL^ENST00000211998.10" ; Parent "CAMK2G--VCL^VCL^ENSG00000035403.18" ; ccdsid "CCDS7341.1" ; exon_id "ENSE00000000338.2" ; exon_number 1 ; gene_id "CAMK2G--VCL^VCL^ENSG00000035403.18" ; gene_name VCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000018498.4" ; havana_transcript "OTTHUMT00000048752.3" ; hgnc_id "HGNC:12665" ; level 2 ; orig_coord_info "chr10,73998208,73998375,+" ; protein_id "ENSP00000211998.5" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "CAMK2G--VCL^ENST00000211998.10" ; transcript_name "VCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CAMK2G--VCL HAVANA gene 1131 23253 . + . FI_gene_label "CAMK2G^ENSG00000148660.21" ; ID "CAMK2G--VCL^CAMK2G^ENSG00000148660.21" ; exon_id "ENSE00002521481.1" ; exon_number 1 ; gene_id "CAMK2G--VCL^CAMK2G^ENSG00000148660.21" ; gene_name CAMK2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000018492.4" ; havana_transcript "OTTHUMT00000048718.1" ; hgnc_id "HGNC:1463" ; level 2 ; orig_coord_info "chr10,73874397,73874461,-" ; protein_id "ENSP00000307082.7" ; tag basic appris_alternative_1 ; transcript_id "CAMK2G--VCL^ENST00000305762.11" ; transcript_name "CAMK2G-201" ; transcript_support_level 5 ; transcript_type protein_coding
CAMK2G--VCL HAVANA mRNA 1131 23253 . + . FI_gene_label "CAMK2G^ENSG00000148660.21" ; ID "CAMK2G--VCL^ENST00000305762.11" ; Parent "CAMK2G--VCL^CAMK2G^ENSG00000148660.21" ; exon_id "ENSE00002521481.1" ; exon_number 1 ; gene_id "CAMK2G--VCL^CAMK2G^ENSG00000148660.21" ; gene_name CAMK2G ; gene_type protein_coding ; havana_gene "OTTHUMG00000018492.4" ; havana_transcript "OTTHUMT00000048718.1" ; hgnc_id "HGNC:1463" ; level 2 ; orig_coord_info "chr10,73874397,73874461,-" ; protein_id "ENSP00000307082.7" ; tag basic appris_alternative_1 ; transcript_id "CAMK2G--VCL^ENST00000305762.11" ; transcript_name "CAMK2G-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CRTC1--IFI30 HAVANA gene 1003 22034 . + . FI_gene_label "CRTC1^ENSG00000105662.16" ; ID "CRTC1--IFI30^CRTC1^ENSG00000105662.16" ; ccdsid "CCDS32963.1" ; exon_id "ENSE00003001563.2" ; exon_number 1 ; gene_id "CRTC1--IFI30^CRTC1^ENSG00000105662.16" ; gene_name CRTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183115.5" ; havana_transcript "OTTHUMT00000465151.4" ; hgnc_id "HGNC:16062" ; level 2 ; orig_coord_info "chr19,18683703,18683828,+" ; protein_id "ENSP00000323332.7" ; tag non_canonical_U12 basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRTC1--IFI30^ENST00000321949.13" ; transcript_name "CRTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRTC1--IFI30 HAVANA mRNA 1003 22034 . + . FI_gene_label "CRTC1^ENSG00000105662.16" ; ID "CRTC1--IFI30^ENST00000321949.13" ; Parent "CRTC1--IFI30^CRTC1^ENSG00000105662.16" ; ccdsid "CCDS32963.1" ; exon_id "ENSE00003001563.2" ; exon_number 1 ; gene_id "CRTC1--IFI30^CRTC1^ENSG00000105662.16" ; gene_name CRTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183115.5" ; havana_transcript "OTTHUMT00000465151.4" ; hgnc_id "HGNC:16062" ; level 2 ; orig_coord_info "chr19,18683703,18683828,+" ; protein_id "ENSP00000323332.7" ; tag non_canonical_U12 basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRTC1--IFI30^ENST00000321949.13" ; transcript_name "CRTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CRTC1--IFI30 HAVANA gene 25686 29548 . + . FI_gene_label "IFI30^ENSG00000216490.4" ; ID "CRTC1--IFI30^IFI30^ENSG00000216490.4" ; ccdsid "CCDS46015.1" ; exon_id "ENSE00000871115.7" ; exon_number 1 ; gene_id "CRTC1--IFI30^IFI30^ENSG00000216490.4" ; gene_name IFI30 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183373.6" ; havana_transcript "OTTHUMT00000466396.4" ; hgnc_id "HGNC:5398" ; level 2 ; orig_coord_info "chr19,18173842,18173973,+" ; protein_id "ENSP00000384886.1" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRTC1--IFI30^ENST00000407280.4" ; transcript_name "IFI30-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRTC1--IFI30 HAVANA mRNA 25686 29548 . + . FI_gene_label "IFI30^ENSG00000216490.4" ; ID "CRTC1--IFI30^ENST00000407280.4" ; Parent "CRTC1--IFI30^IFI30^ENSG00000216490.4" ; ccdsid "CCDS46015.1" ; exon_id "ENSE00000871115.7" ; exon_number 1 ; gene_id "CRTC1--IFI30^IFI30^ENSG00000216490.4" ; gene_name IFI30 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183373.6" ; havana_transcript "OTTHUMT00000466396.4" ; hgnc_id "HGNC:5398" ; level 2 ; orig_coord_info "chr19,18173842,18173973,+" ; protein_id "ENSP00000384886.1" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRTC1--IFI30^ENST00000407280.4" ; transcript_name "IFI30-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DYNC2I2--SH3GLB2 HAVANA gene 9985 21269 . + . FI_gene_label "SH3GLB2^ENSG00000148341.18" ; ID "DYNC2I2--SH3GLB2^SH3GLB2^ENSG00000148341.18" ; ccdsid "CCDS69680.1" ; exon_id "ENSE00001954305.1" ; exon_number 1 ; gene_id "DYNC2I2--SH3GLB2^SH3GLB2^ENSG00000148341.18" ; gene_name SH3GLB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020769.8" ; havana_transcript "OTTHUMT00000106248.1" ; hgnc_id "HGNC:10834" ; level 2 ; orig_coord_info "chr9,129028092,129028154,-" ; protein_id "ENSP00000361634.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "DYNC2I2--SH3GLB2^ENST00000372554.8" ; transcript_name "SH3GLB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DYNC2I2--SH3GLB2 HAVANA mRNA 9985 21269 . + . FI_gene_label "SH3GLB2^ENSG00000148341.18" ; ID "DYNC2I2--SH3GLB2^ENST00000372554.8" ; Parent "DYNC2I2--SH3GLB2^SH3GLB2^ENSG00000148341.18" ; ccdsid "CCDS69680.1" ; exon_id "ENSE00001954305.1" ; exon_number 1 ; gene_id "DYNC2I2--SH3GLB2^SH3GLB2^ENSG00000148341.18" ; gene_name SH3GLB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020769.8" ; havana_transcript "OTTHUMT00000106248.1" ; hgnc_id "HGNC:10834" ; level 2 ; orig_coord_info "chr9,129028092,129028154,-" ; protein_id "ENSP00000361634.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "DYNC2I2--SH3GLB2^ENST00000372554.8" ; transcript_name "SH3GLB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DYNC2I2--SH3GLB2 HAVANA gene 1001 6932 . + . FI_gene_label "DYNC2I2^ENSG00000119333.12" ; ID "DYNC2I2--SH3GLB2^DYNC2I2^ENSG00000119333.12" ; ccdsid "CCDS6906.2" ; exon_id "ENSE00001458450.3" ; exon_number 1 ; gene_id "DYNC2I2--SH3GLB2^DYNC2I2^ENSG00000119333.12" ; gene_name DYNC2I2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020750.2" ; havana_transcript "OTTHUMT00000054463.1" ; hgnc_id "HGNC:28296" ; level 2 ; orig_coord_info "chr9,128656541,128656726,-" ; protein_id "ENSP00000361800.2" ; tag basic appris_principal_1 CCDS ; transcript_id "DYNC2I2--SH3GLB2^ENST00000372715.7" ; transcript_name "DYNC2I2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DYNC2I2--SH3GLB2 HAVANA mRNA 1001 6932 . + . FI_gene_label "DYNC2I2^ENSG00000119333.12" ; ID "DYNC2I2--SH3GLB2^ENST00000372715.7" ; Parent "DYNC2I2--SH3GLB2^DYNC2I2^ENSG00000119333.12" ; ccdsid "CCDS6906.2" ; exon_id "ENSE00001458450.3" ; exon_number 1 ; gene_id "DYNC2I2--SH3GLB2^DYNC2I2^ENSG00000119333.12" ; gene_name DYNC2I2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020750.2" ; havana_transcript "OTTHUMT00000054463.1" ; hgnc_id "HGNC:28296" ; level 2 ; orig_coord_info "chr9,128656541,128656726,-" ; protein_id "ENSP00000361800.2" ; tag basic appris_principal_1 CCDS ; transcript_id "DYNC2I2--SH3GLB2^ENST00000372715.7" ; transcript_name "DYNC2I2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EEF1G--AHNAK HAVANA gene 11790 37132 . + . FI_gene_label "AHNAK^ENSG00000124942.14" ; ID "EEF1G--AHNAK^AHNAK^ENSG00000124942.14" ; ccdsid "CCDS44625.1" ; exon_id "ENSE00001286844.4" ; exon_number 3 ; gene_id "EEF1G--AHNAK^AHNAK^ENSG00000124942.14" ; gene_name AHNAK ; gene_type protein_coding ; havana_gene "OTTHUMG00000167558.7" ; havana_transcript "OTTHUMT00000395014.1" ; hgnc_id "HGNC:347" ; level 2 ; orig_coord_info "chr11,62535945,62536098,-" ; protein_id "ENSP00000257247.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "EEF1G--AHNAK^ENST00000257247.11" ; transcript_name "AHNAK-201" ; transcript_support_level 1 ; transcript_type protein_coding
EEF1G--AHNAK HAVANA mRNA 11790 37132 . + . FI_gene_label "AHNAK^ENSG00000124942.14" ; ID "EEF1G--AHNAK^ENST00000257247.11" ; Parent "EEF1G--AHNAK^AHNAK^ENSG00000124942.14" ; ccdsid "CCDS44625.1" ; exon_id "ENSE00001286844.4" ; exon_number 3 ; gene_id "EEF1G--AHNAK^AHNAK^ENSG00000124942.14" ; gene_name AHNAK ; gene_type protein_coding ; havana_gene "OTTHUMG00000167558.7" ; havana_transcript "OTTHUMT00000395014.1" ; hgnc_id "HGNC:347" ; level 2 ; orig_coord_info "chr11,62535945,62536098,-" ; protein_id "ENSP00000257247.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "EEF1G--AHNAK^ENST00000257247.11" ; transcript_name "AHNAK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EEF1G--AHNAK HAVANA gene 1196 7704 . + . FI_gene_label "EEF1G^ENSG00000254772.10" ; ID "EEF1G--AHNAK^EEF1G^ENSG00000254772.10" ; ccdsid "CCDS44626.1" ; exon_id "ENSE00001715491.3" ; exon_number 1 ; gene_id "EEF1G--AHNAK^EEF1G^ENSG00000254772.10" ; gene_name EEF1G ; gene_type protein_coding ; havana_gene "OTTHUMG00000167567.2" ; havana_transcript "OTTHUMT00000395047.2" ; hgnc_id "HGNC:3213" ; level 2 ; orig_coord_info "chr11,62573831,62573842,-" ; protein_id "ENSP00000331901.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1G--AHNAK^ENST00000329251.5" ; transcript_name "EEF1G-201" ; transcript_support_level 1 ; transcript_type protein_coding
EEF1G--AHNAK HAVANA mRNA 1196 7704 . + . FI_gene_label "EEF1G^ENSG00000254772.10" ; ID "EEF1G--AHNAK^ENST00000329251.5" ; Parent "EEF1G--AHNAK^EEF1G^ENSG00000254772.10" ; ccdsid "CCDS44626.1" ; exon_id "ENSE00001715491.3" ; exon_number 1 ; gene_id "EEF1G--AHNAK^EEF1G^ENSG00000254772.10" ; gene_name EEF1G ; gene_type protein_coding ; havana_gene "OTTHUMG00000167567.2" ; havana_transcript "OTTHUMT00000395047.2" ; hgnc_id "HGNC:3213" ; level 2 ; orig_coord_info "chr11,62573831,62573842,-" ; protein_id "ENSP00000331901.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EEF1G--AHNAK^ENST00000329251.5" ; transcript_name "EEF1G-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EFCAB14--CYP4A11 HAVANA gene 28051 38027 . + . FI_gene_label "CYP4A11^ENSG00000187048.13" ; ID "EFCAB14--CYP4A11^CYP4A11^ENSG00000187048.13" ; ccdsid "CCDS543.1" ; exon_id "ENSE00001823232.1" ; exon_number 1 ; gene_id "EFCAB14--CYP4A11^CYP4A11^ENSG00000187048.13" ; gene_name CYP4A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008020.4" ; havana_transcript "OTTHUMT00000022022.2" ; hgnc_id "HGNC:2642" ; level 2 ; orig_coord_info "chr1,46941239,46941433,-" ; protein_id "ENSP00000311095.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EFCAB14--CYP4A11^ENST00000310638.9" ; transcript_name "CYP4A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFCAB14--CYP4A11 HAVANA mRNA 28051 38027 . + . FI_gene_label "CYP4A11^ENSG00000187048.13" ; ID "EFCAB14--CYP4A11^ENST00000310638.9" ; Parent "EFCAB14--CYP4A11^CYP4A11^ENSG00000187048.13" ; ccdsid "CCDS543.1" ; exon_id "ENSE00001823232.1" ; exon_number 1 ; gene_id "EFCAB14--CYP4A11^CYP4A11^ENSG00000187048.13" ; gene_name CYP4A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008020.4" ; havana_transcript "OTTHUMT00000022022.2" ; hgnc_id "HGNC:2642" ; level 2 ; orig_coord_info "chr1,46941239,46941433,-" ; protein_id "ENSP00000311095.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EFCAB14--CYP4A11^ENST00000310638.9" ; transcript_name "CYP4A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EFCAB14--CYP4A11 HAVANA gene 1033 24542 . + . FI_gene_label "EFCAB14^ENSG00000159658.15" ; ID "EFCAB14--CYP4A11^EFCAB14^ENSG00000159658.15" ; ccdsid "CCDS30706.1" ; exon_id "ENSE00001456489.2" ; exon_number 1 ; gene_id "EFCAB14--CYP4A11^EFCAB14^ENSG00000159658.15" ; gene_name EFCAB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007992.10" ; havana_transcript "OTTHUMT00000021931.2" ; hgnc_id "HGNC:29051" ; level 2 ; orig_coord_info "chr1,46717903,46718087,-" ; protein_id "ENSP00000361001.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EFCAB14--CYP4A11^ENST00000371933.8" ; transcript_name "EFCAB14-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFCAB14--CYP4A11 HAVANA mRNA 1033 24542 . + . FI_gene_label "EFCAB14^ENSG00000159658.15" ; ID "EFCAB14--CYP4A11^ENST00000371933.8" ; Parent "EFCAB14--CYP4A11^EFCAB14^ENSG00000159658.15" ; ccdsid "CCDS30706.1" ; exon_id "ENSE00001456489.2" ; exon_number 1 ; gene_id "EFCAB14--CYP4A11^EFCAB14^ENSG00000159658.15" ; gene_name EFCAB14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007992.10" ; havana_transcript "OTTHUMT00000021931.2" ; hgnc_id "HGNC:29051" ; level 2 ; orig_coord_info "chr1,46717903,46718087,-" ; protein_id "ENSP00000361001.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EFCAB14--CYP4A11^ENST00000371933.8" ; transcript_name "EFCAB14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EIF4B--KRT3 HAVANA gene 1175 17793 . + . FI_gene_label "EIF4B^ENSG00000063046.18" ; ID "EIF4B--KRT3^EIF4B^ENSG00000063046.18" ; ccdsid "CCDS41788.1" ; exon_id "ENSE00002278277.1" ; exon_number 1 ; gene_id "EIF4B--KRT3^EIF4B^ENSG00000063046.18" ; gene_name EIF4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169570.7" ; havana_transcript "OTTHUMT00000404852.2" ; hgnc_id "HGNC:3285" ; level 2 ; orig_coord_info "chr12,53006484,53006496,+" ; protein_id "ENSP00000262056.9" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EIF4B--KRT3^ENST00000262056.14" ; transcript_name "EIF4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
EIF4B--KRT3 HAVANA mRNA 1175 17793 . + . FI_gene_label "EIF4B^ENSG00000063046.18" ; ID "EIF4B--KRT3^ENST00000262056.14" ; Parent "EIF4B--KRT3^EIF4B^ENSG00000063046.18" ; ccdsid "CCDS41788.1" ; exon_id "ENSE00002278277.1" ; exon_number 1 ; gene_id "EIF4B--KRT3^EIF4B^ENSG00000063046.18" ; gene_name EIF4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000169570.7" ; havana_transcript "OTTHUMT00000404852.2" ; hgnc_id "HGNC:3285" ; level 2 ; orig_coord_info "chr12,53006484,53006496,+" ; protein_id "ENSP00000262056.9" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EIF4B--KRT3^ENST00000262056.14" ; transcript_name "EIF4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EIF4B--KRT3 HAVANA gene 20794 27160 . + . FI_gene_label "KRT3^ENSG00000186442.7" ; ID "EIF4B--KRT3^KRT3^ENSG00000186442.7" ; ccdsid "CCDS44895.1" ; exon_id "ENSE00002337704.1" ; exon_number 1 ; gene_id "EIF4B--KRT3^KRT3^ENSG00000186442.7" ; gene_name KRT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169799.1" ; havana_transcript "OTTHUMT00000405930.1" ; hgnc_id "HGNC:6440" ; level 2 ; orig_coord_info "chr12,52795398,52796042,-" ; protein_id "ENSP00000413479.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF4B--KRT3^ENST00000417996.2" ; transcript_name "KRT3-201" ; transcript_support_level 1 ; transcript_type protein_coding
EIF4B--KRT3 HAVANA mRNA 20794 27160 . + . FI_gene_label "KRT3^ENSG00000186442.7" ; ID "EIF4B--KRT3^ENST00000417996.2" ; Parent "EIF4B--KRT3^KRT3^ENSG00000186442.7" ; ccdsid "CCDS44895.1" ; exon_id "ENSE00002337704.1" ; exon_number 1 ; gene_id "EIF4B--KRT3^KRT3^ENSG00000186442.7" ; gene_name KRT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169799.1" ; havana_transcript "OTTHUMT00000405930.1" ; hgnc_id "HGNC:6440" ; level 2 ; orig_coord_info "chr12,52795398,52796042,-" ; protein_id "ENSP00000413479.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF4B--KRT3^ENST00000417996.2" ; transcript_name "KRT3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERBIN--SREK1 HAVANA gene 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--SREK1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--SREK1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--SREK1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERBIN--SREK1 HAVANA mRNA 1020 35474 . + . FI_gene_label "ERBIN^ENSG00000112851.15" ; ID "ERBIN--SREK1^ENST00000284037.10" ; Parent "ERBIN--SREK1^ERBIN^ENSG00000112851.15" ; ccdsid "CCDS58953.1" ; exon_id "ENSE00000912221.1" ; exon_number 3 ; gene_id "ERBIN--SREK1^ERBIN^ENSG00000112851.15" ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3" ; havana_transcript "OTTHUMT00000215070.1" ; hgnc_id "HGNC:15842" ; level 2 ; orig_coord_info "chr5,65992719,65992907,+" ; protein_id "ENSP00000284037.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--SREK1^ENST00000284037.10" ; transcript_name "ERBIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERBIN--SREK1 HAVANA gene 39598 64565 . + . FI_gene_label "SREK1^ENSG00000153914.16" ; ID "ERBIN--SREK1^SREK1^ENSG00000153914.16" ; ccdsid "CCDS43323.1" ; exon_id "ENSE00003843436.1" ; exon_number 1 ; gene_id "ERBIN--SREK1^SREK1^ENSG00000153914.16" ; gene_name SREK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097809.5" ; havana_transcript "OTTHUMT00000215071.2" ; hgnc_id "HGNC:17882" ; level 2 ; orig_coord_info "chr5,66144377,66144537,+" ; protein_id "ENSP00000334538.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERBIN--SREK1^ENST00000334121.11" ; transcript_name "SREK1-202" ; transcript_support_level 2 ; transcript_type protein_coding
ERBIN--SREK1 HAVANA mRNA 39598 64565 . + . FI_gene_label "SREK1^ENSG00000153914.16" ; ID "ERBIN--SREK1^ENST00000334121.11" ; Parent "ERBIN--SREK1^SREK1^ENSG00000153914.16" ; ccdsid "CCDS43323.1" ; exon_id "ENSE00003843436.1" ; exon_number 1 ; gene_id "ERBIN--SREK1^SREK1^ENSG00000153914.16" ; gene_name SREK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097809.5" ; havana_transcript "OTTHUMT00000215071.2" ; hgnc_id "HGNC:17882" ; level 2 ; orig_coord_info "chr5,66144377,66144537,+" ; protein_id "ENSP00000334538.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERBIN--SREK1^ENST00000334121.11" ; transcript_name "SREK1-202" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
FAM222B--RBL1 ENSEMBL gene 6802 14514 . + . FI_gene_label "FAM222B^ENSG00000173065.13" ; ID "FAM222B--RBL1^FAM222B^ENSG00000173065.13" ; ccdsid "CCDS74022.1" ; exon_id "ENSE00001244420.3" ; exon_number 3 ; gene_id "FAM222B--RBL1^FAM222B^ENSG00000173065.13" ; gene_name FAM222B ; gene_type protein_coding ; havana_gene "OTTHUMG00000179495.4" ; hgnc_id "HGNC:25563" ; level 3 ; orig_coord_info "chr17,28758273,28759574,-" ; protein_id "ENSP00000343115.6" ; tag basic CCDS ; transcript_id "FAM222B--RBL1^ENST00000341217.6" ; transcript_name "FAM222B-201" ; transcript_support_level 5 ; transcript_type protein_coding
FAM222B--RBL1 ENSEMBL mRNA 6802 14514 . + . FI_gene_label "FAM222B^ENSG00000173065.13" ; ID "FAM222B--RBL1^ENST00000341217.6" ; Parent "FAM222B--RBL1^FAM222B^ENSG00000173065.13" ; ccdsid "CCDS74022.1" ; exon_id "ENSE00001244420.3" ; exon_number 3 ; gene_id "FAM222B--RBL1^FAM222B^ENSG00000173065.13" ; gene_name FAM222B ; gene_type protein_coding ; havana_gene "OTTHUMG00000179495.4" ; hgnc_id "HGNC:25563" ; level 3 ; orig_coord_info "chr17,28758273,28759574,-" ; protein_id "ENSP00000343115.6" ; tag basic CCDS ; transcript_id "FAM222B--RBL1^ENST00000341217.6" ; transcript_name "FAM222B-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
FAM222B--RBL1 HAVANA gene 17523 39099 . + . FI_gene_label "RBL1^ENSG00000080839.12" ; ID "FAM222B--RBL1^RBL1^ENSG00000080839.12" ; ccdsid "CCDS13290.1" ; exon_id "ENSE00001869508.1" ; exon_number 1 ; gene_id "FAM222B--RBL1^RBL1^ENSG00000080839.12" ; gene_name RBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032406.5" ; havana_transcript "OTTHUMT00000079068.1" ; hgnc_id "HGNC:9893" ; level 2 ; orig_coord_info "chr20,37095773,37095928,-" ; protein_id "ENSP00000343646.3" ; tag basic CCDS ; transcript_id "FAM222B--RBL1^ENST00000344359.7" ; transcript_name "RBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FAM222B--RBL1 HAVANA mRNA 17523 39099 . + . FI_gene_label "RBL1^ENSG00000080839.12" ; ID "FAM222B--RBL1^ENST00000344359.7" ; Parent "FAM222B--RBL1^RBL1^ENSG00000080839.12" ; ccdsid "CCDS13290.1" ; exon_id "ENSE00001869508.1" ; exon_number 1 ; gene_id "FAM222B--RBL1^RBL1^ENSG00000080839.12" ; gene_name RBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032406.5" ; havana_transcript "OTTHUMT00000079068.1" ; hgnc_id "HGNC:9893" ; level 2 ; orig_coord_info "chr20,37095773,37095928,-" ; protein_id "ENSP00000343646.3" ; tag basic CCDS ; transcript_id "FAM222B--RBL1^ENST00000344359.7" ; transcript_name "RBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FXR1--SOX2-OT HAVANA gene 2697 24090 . + . FI_gene_label "FXR1^ENSG00000114416.18" ; ID "FXR1--SOX2-OT^FXR1^ENSG00000114416.18" ; ccdsid "CCDS33894.1" ; exon_id "ENSE00003575231.1" ; exon_number 5 ; gene_id "FXR1--SOX2-OT^FXR1^ENSG00000114416.18" ; gene_name FXR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158138.7" ; havana_transcript "OTTHUMT00000350271.1" ; hgnc_id "HGNC:4023" ; level 2 ; orig_coord_info "chr3,180947922,180947936,+" ; protein_id "ENSP00000307633.7" ; tag basic CCDS ; transcript_id "FXR1--SOX2-OT^ENST00000305586.11" ; transcript_name "FXR1-201" ; transcript_support_level 5 ; transcript_type protein_coding
FXR1--SOX2-OT HAVANA mRNA 2697 24090 . + . FI_gene_label "FXR1^ENSG00000114416.18" ; ID "FXR1--SOX2-OT^ENST00000305586.11" ; Parent "FXR1--SOX2-OT^FXR1^ENSG00000114416.18" ; ccdsid "CCDS33894.1" ; exon_id "ENSE00003575231.1" ; exon_number 5 ; gene_id "FXR1--SOX2-OT^FXR1^ENSG00000114416.18" ; gene_name FXR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158138.7" ; havana_transcript "OTTHUMT00000350271.1" ; hgnc_id "HGNC:4023" ; level 2 ; orig_coord_info "chr3,180947922,180947936,+" ; protein_id "ENSP00000307633.7" ; tag basic CCDS ; transcript_id "FXR1--SOX2-OT^ENST00000305586.11" ; transcript_name "FXR1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
GFPT1--RAB10 HAVANA gene 30018 38326 . + . FI_gene_label "RAB10^ENSG00000084733.11" ; ID "GFPT1--RAB10^RAB10^ENSG00000084733.11" ; ccdsid "CCDS1720.1" ; exon_id "ENSE00001136869.7" ; exon_number 1 ; gene_id "GFPT1--RAB10^RAB10^ENSG00000084733.11" ; gene_name RAB10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094796.4" ; havana_transcript "OTTHUMT00000211610.2" ; hgnc_id "HGNC:9759" ; level 2 ; orig_coord_info "chr2,26034609,26034735,+" ; protein_id "ENSP00000264710.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GFPT1--RAB10^ENST00000264710.5" ; transcript_name "RAB10-201" ; transcript_support_level 1 ; transcript_type protein_coding
GFPT1--RAB10 HAVANA mRNA 30018 38326 . + . FI_gene_label "RAB10^ENSG00000084733.11" ; ID "GFPT1--RAB10^ENST00000264710.5" ; Parent "GFPT1--RAB10^RAB10^ENSG00000084733.11" ; ccdsid "CCDS1720.1" ; exon_id "ENSE00001136869.7" ; exon_number 1 ; gene_id "GFPT1--RAB10^RAB10^ENSG00000084733.11" ; gene_name RAB10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094796.4" ; havana_transcript "OTTHUMT00000211610.2" ; hgnc_id "HGNC:9759" ; level 2 ; orig_coord_info "chr2,26034609,26034735,+" ; protein_id "ENSP00000264710.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GFPT1--RAB10^ENST00000264710.5" ; transcript_name "RAB10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GFPT1--RAB10 HAVANA gene 1024 27017 . + . FI_gene_label "GFPT1^ENSG00000198380.13" ; ID "GFPT1--RAB10^GFPT1^ENSG00000198380.13" ; ccdsid "CCDS58713.1" ; exon_id "ENSE00003470909.3" ; exon_number 1 ; gene_id "GFPT1--RAB10^GFPT1^ENSG00000198380.13" ; gene_name GFPT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152666.5" ; havana_transcript "OTTHUMT00000327277.3" ; hgnc_id "HGNC:4241" ; level 2 ; orig_coord_info "chr2,69387065,69387071,-" ; protein_id "ENSP00000349860.4" ; tag CAGE_supported_TSS RNA_Seq_supported_partial basic MANE_Select CCDS ; transcript_id "GFPT1--RAB10^ENST00000357308.9" ; transcript_name "GFPT1-201" ; transcript_support_level 5 ; transcript_type protein_coding
GFPT1--RAB10 HAVANA mRNA 1024 27017 . + . FI_gene_label "GFPT1^ENSG00000198380.13" ; ID "GFPT1--RAB10^ENST00000357308.9" ; Parent "GFPT1--RAB10^GFPT1^ENSG00000198380.13" ; ccdsid "CCDS58713.1" ; exon_id "ENSE00003470909.3" ; exon_number 1 ; gene_id "GFPT1--RAB10^GFPT1^ENSG00000198380.13" ; gene_name GFPT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152666.5" ; havana_transcript "OTTHUMT00000327277.3" ; hgnc_id "HGNC:4241" ; level 2 ; orig_coord_info "chr2,69387065,69387071,-" ; protein_id "ENSP00000349860.4" ; tag CAGE_supported_TSS RNA_Seq_supported_partial basic MANE_Select CCDS ; transcript_id "GFPT1--RAB10^ENST00000357308.9" ; transcript_name "GFPT1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
HECTD4--CASC11 HAVANA gene 1001 80020 . + . FI_gene_label "HECTD4^ENSG00000173064.13" ; ID "HECTD4--CASC11^HECTD4^ENSG00000173064.13" ; exon_id "ENSE00003748912.1" ; exon_number 1 ; gene_id "HECTD4--CASC11^HECTD4^ENSG00000173064.13" ; gene_name HECTD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150719.10" ; havana_transcript "OTTHUMT00000405222.4" ; hgnc_id "HGNC:26611" ; level 2 ; orig_coord_info "chr12,112381952,112382128,-" ; protein_id "ENSP00000366783.7" ; tag not_organism_supported basic appris_principal_1 ; transcript_id "HECTD4--CASC11^ENST00000377560.9" ; transcript_name "HECTD4-202" ; transcript_support_level 5 ; transcript_type protein_coding
HECTD4--CASC11 HAVANA mRNA 1001 80020 . + . FI_gene_label "HECTD4^ENSG00000173064.13" ; ID "HECTD4--CASC11^ENST00000377560.9" ; Parent "HECTD4--CASC11^HECTD4^ENSG00000173064.13" ; exon_id "ENSE00003748912.1" ; exon_number 1 ; gene_id "HECTD4--CASC11^HECTD4^ENSG00000173064.13" ; gene_name HECTD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150719.10" ; havana_transcript "OTTHUMT00000405222.4" ; hgnc_id "HGNC:26611" ; level 2 ; orig_coord_info "chr12,112381952,112382128,-" ; protein_id "ENSP00000366783.7" ; tag not_organism_supported basic appris_principal_1 ; transcript_id "HECTD4--CASC11^ENST00000377560.9" ; transcript_name "HECTD4-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
HECTD4--VCL HAVANA gene 84996 114766 . + . FI_gene_label "VCL^ENSG00000035403.18" ; ID "HECTD4--VCL^VCL^ENSG00000035403.18" ; ccdsid "CCDS7341.1" ; exon_id "ENSE00000000338.2" ; exon_number 1 ; gene_id "HECTD4--VCL^VCL^ENSG00000035403.18" ; gene_name VCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000018498.4" ; havana_transcript "OTTHUMT00000048752.3" ; hgnc_id "HGNC:12665" ; level 2 ; orig_coord_info "chr10,73998208,73998375,+" ; protein_id "ENSP00000211998.5" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "HECTD4--VCL^ENST00000211998.10" ; transcript_name "VCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
HECTD4--VCL HAVANA mRNA 84996 114766 . + . FI_gene_label "VCL^ENSG00000035403.18" ; ID "HECTD4--VCL^ENST00000211998.10" ; Parent "HECTD4--VCL^VCL^ENSG00000035403.18" ; ccdsid "CCDS7341.1" ; exon_id "ENSE00000000338.2" ; exon_number 1 ; gene_id "HECTD4--VCL^VCL^ENSG00000035403.18" ; gene_name VCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000018498.4" ; havana_transcript "OTTHUMT00000048752.3" ; hgnc_id "HGNC:12665" ; level 2 ; orig_coord_info "chr10,73998208,73998375,+" ; protein_id "ENSP00000211998.5" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "HECTD4--VCL^ENST00000211998.10" ; transcript_name "VCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
HECTD4--VCL HAVANA gene 1001 80020 . + . FI_gene_label "HECTD4^ENSG00000173064.13" ; ID "HECTD4--VCL^HECTD4^ENSG00000173064.13" ; exon_id "ENSE00003748912.1" ; exon_number 1 ; gene_id "HECTD4--VCL^HECTD4^ENSG00000173064.13" ; gene_name HECTD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150719.10" ; havana_transcript "OTTHUMT00000405222.4" ; hgnc_id "HGNC:26611" ; level 2 ; orig_coord_info "chr12,112381952,112382128,-" ; protein_id "ENSP00000366783.7" ; tag not_organism_supported basic appris_principal_1 ; transcript_id "HECTD4--VCL^ENST00000377560.9" ; transcript_name "HECTD4-202" ; transcript_support_level 5 ; transcript_type protein_coding
HECTD4--VCL HAVANA mRNA 1001 80020 . + . FI_gene_label "HECTD4^ENSG00000173064.13" ; ID "HECTD4--VCL^ENST00000377560.9" ; Parent "HECTD4--VCL^HECTD4^ENSG00000173064.13" ; exon_id "ENSE00003748912.1" ; exon_number 1 ; gene_id "HECTD4--VCL^HECTD4^ENSG00000173064.13" ; gene_name HECTD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150719.10" ; havana_transcript "OTTHUMT00000405222.4" ; hgnc_id "HGNC:26611" ; level 2 ; orig_coord_info "chr12,112381952,112382128,-" ; protein_id "ENSP00000366783.7" ; tag not_organism_supported basic appris_principal_1 ; transcript_id "HECTD4--VCL^ENST00000377560.9" ; transcript_name "HECTD4-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
LINC00921--ELOB HAVANA gene 7472 10620 . + . FI_gene_label "ELOB^ENSG00000103363.15" ; ID "LINC00921--ELOB^ELOB^ENSG00000103363.15" ; ccdsid "CCDS32374.1" ; exon_id "ENSE00001491589.2" ; exon_number 1 ; gene_id "LINC00921--ELOB^ELOB^ENSG00000103363.15" ; gene_name ELOB ; gene_type protein_coding ; havana_gene "OTTHUMG00000154125.2" ; havana_transcript "OTTHUMT00000333976.1" ; hgnc_id "HGNC:11619" ; level 2 ; orig_coord_info "chr16,2777237,2777239,-" ; protein_id "ENSP00000262306.7" ; tag basic CCDS ; transcript_id "LINC00921--ELOB^ENST00000262306.11" ; transcript_name "ELOB-201" ; transcript_support_level 2 ; transcript_type protein_coding
LINC00921--ELOB HAVANA mRNA 7472 10620 . + . FI_gene_label "ELOB^ENSG00000103363.15" ; ID "LINC00921--ELOB^ENST00000262306.11" ; Parent "LINC00921--ELOB^ELOB^ENSG00000103363.15" ; ccdsid "CCDS32374.1" ; exon_id "ENSE00001491589.2" ; exon_number 1 ; gene_id "LINC00921--ELOB^ELOB^ENSG00000103363.15" ; gene_name ELOB ; gene_type protein_coding ; havana_gene "OTTHUMG00000154125.2" ; havana_transcript "OTTHUMT00000333976.1" ; hgnc_id "HGNC:11619" ; level 2 ; orig_coord_info "chr16,2777237,2777239,-" ; protein_id "ENSP00000262306.7" ; tag basic CCDS ; transcript_id "LINC00921--ELOB^ENST00000262306.11" ; transcript_name "ELOB-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
LRRC28--VSTM2B HAVANA gene 1120 28115 . + . FI_gene_label "LRRC28^ENSG00000168904.15" ; ID "LRRC28--VSTM2B^LRRC28^ENSG00000168904.15" ; ccdsid "CCDS10380.1" ; exon_id "ENSE00003590874.1" ; exon_number 2 ; gene_id "LRRC28--VSTM2B^LRRC28^ENSG00000168904.15" ; gene_name LRRC28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149854.11" ; havana_transcript "OTTHUMT00000313546.2" ; hgnc_id "HGNC:28355" ; level 2 ; orig_coord_info "chr15,99255958,99256125,+" ; protein_id "ENSP00000304923.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRRC28--VSTM2B^ENST00000301981.8" ; transcript_name "LRRC28-201" ; transcript_support_level 1 ; transcript_type protein_coding
LRRC28--VSTM2B HAVANA mRNA 1120 28115 . + . FI_gene_label "LRRC28^ENSG00000168904.15" ; ID "LRRC28--VSTM2B^ENST00000301981.8" ; Parent "LRRC28--VSTM2B^LRRC28^ENSG00000168904.15" ; ccdsid "CCDS10380.1" ; exon_id "ENSE00003590874.1" ; exon_number 2 ; gene_id "LRRC28--VSTM2B^LRRC28^ENSG00000168904.15" ; gene_name LRRC28 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149854.11" ; havana_transcript "OTTHUMT00000313546.2" ; hgnc_id "HGNC:28355" ; level 2 ; orig_coord_info "chr15,99255958,99256125,+" ; protein_id "ENSP00000304923.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LRRC28--VSTM2B^ENST00000301981.8" ; transcript_name "LRRC28-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LRRC28--VSTM2B HAVANA gene 31116 36148 . + . FI_gene_label "VSTM2B^ENSG00000187135.7" ; ID "LRRC28--VSTM2B^VSTM2B^ENSG00000187135.7" ; ccdsid "CCDS46034.1" ; exon_id "ENSE00001333439.2" ; exon_number 1 ; gene_id "LRRC28--VSTM2B^VSTM2B^ENSG00000187135.7" ; gene_name VSTM2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000182002.1" ; havana_transcript "OTTHUMT00000458601.1" ; hgnc_id "HGNC:33595" ; level 2 ; orig_coord_info "chr19,29526584,29526665,+" ; protein_id "ENSP00000335038.6" ; tag basic appris_principal_1 CCDS ; transcript_id "LRRC28--VSTM2B^ENST00000335523.7" ; transcript_name "VSTM2B-201" ; transcript_support_level 5 ; transcript_type protein_coding
LRRC28--VSTM2B HAVANA mRNA 31116 36148 . + . FI_gene_label "VSTM2B^ENSG00000187135.7" ; ID "LRRC28--VSTM2B^ENST00000335523.7" ; Parent "LRRC28--VSTM2B^VSTM2B^ENSG00000187135.7" ; ccdsid "CCDS46034.1" ; exon_id "ENSE00001333439.2" ; exon_number 1 ; gene_id "LRRC28--VSTM2B^VSTM2B^ENSG00000187135.7" ; gene_name VSTM2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000182002.1" ; havana_transcript "OTTHUMT00000458601.1" ; hgnc_id "HGNC:33595" ; level 2 ; orig_coord_info "chr19,29526584,29526665,+" ; protein_id "ENSP00000335038.6" ; tag basic appris_principal_1 CCDS ; transcript_id "LRRC28--VSTM2B^ENST00000335523.7" ; transcript_name "VSTM2B-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
MAP4--FBXW12 HAVANA gene 40818 49358 . + . FI_gene_label "FBXW12^ENSG00000164049.14" ; ID "MAP4--FBXW12^FBXW12^ENSG00000164049.14" ; ccdsid "CCDS2764.1" ; exon_id "ENSE00001382345.2" ; exon_number 2 ; gene_id "MAP4--FBXW12^FBXW12^ENSG00000164049.14" ; gene_name FBXW12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133530.4" ; havana_transcript "OTTHUMT00000257505.1" ; hgnc_id "HGNC:20729" ; level 2 ; orig_coord_info "chr3,48372768,48372857,+" ; protein_id "ENSP00000296438.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MAP4--FBXW12^ENST00000296438.9" ; transcript_name "FBXW12-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAP4--FBXW12 HAVANA mRNA 40818 49358 . + . FI_gene_label "FBXW12^ENSG00000164049.14" ; ID "MAP4--FBXW12^ENST00000296438.9" ; Parent "MAP4--FBXW12^FBXW12^ENSG00000164049.14" ; ccdsid "CCDS2764.1" ; exon_id "ENSE00001382345.2" ; exon_number 2 ; gene_id "MAP4--FBXW12^FBXW12^ENSG00000164049.14" ; gene_name FBXW12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133530.4" ; havana_transcript "OTTHUMT00000257505.1" ; hgnc_id "HGNC:20729" ; level 2 ; orig_coord_info "chr3,48372768,48372857,+" ; protein_id "ENSP00000296438.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MAP4--FBXW12^ENST00000296438.9" ; transcript_name "FBXW12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAP4--FBXW12 HAVANA gene 23965 35887 . + . FI_gene_label "MAP4^ENSG00000047849.21" ; ID "MAP4--FBXW12^MAP4^ENSG00000047849.21" ; exon_id "ENSE00001649776.1" ; exon_number 1 ; gene_id "MAP4--FBXW12^MAP4^ENSG00000047849.21" ; gene_name MAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156828.7" ; havana_transcript "OTTHUMT00000346096.1" ; hgnc_id "HGNC:6862" ; level 2 ; orig_coord_info "chr3,47891024,47891336,-" ; protein_id "ENSP00000334770.5" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MAP4--FBXW12^ENST00000335271.9" ; transcript_name "MAP4-201" ; transcript_support_level 2 ; transcript_type protein_coding
MAP4--FBXW12 HAVANA mRNA 23965 35887 . + . FI_gene_label "MAP4^ENSG00000047849.21" ; ID "MAP4--FBXW12^ENST00000335271.9" ; Parent "MAP4--FBXW12^MAP4^ENSG00000047849.21" ; exon_id "ENSE00001649776.1" ; exon_number 1 ; gene_id "MAP4--FBXW12^MAP4^ENSG00000047849.21" ; gene_name MAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156828.7" ; havana_transcript "OTTHUMT00000346096.1" ; hgnc_id "HGNC:6862" ; level 2 ; orig_coord_info "chr3,47891024,47891336,-" ; protein_id "ENSP00000334770.5" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MAP4--FBXW12^ENST00000335271.9" ; transcript_name "MAP4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
NTRK3--ABI3BP HAVANA gene 58589 127894 . + . FI_gene_label "ABI3BP^ENSG00000154175.18" ; ID "NTRK3--ABI3BP^ABI3BP^ENSG00000154175.18" ; exon_id "ENSE00001910142.1" ; exon_number 1 ; gene_id "NTRK3--ABI3BP^ABI3BP^ENSG00000154175.18" ; gene_name ABI3BP ; gene_type protein_coding ; havana_gene "OTTHUMG00000159094.7" ; havana_transcript "OTTHUMT00000353260.1" ; hgnc_id "HGNC:17265" ; level 2 ; orig_coord_info "chr3,100993306,100993384,-" ; protein_id "ENSP00000284322.6" ; tag upstream_ATG basic appris_alternative_2 ; transcript_id "NTRK3--ABI3BP^ENST00000284322.10" ; transcript_name "ABI3BP-201" ; transcript_support_level 1 ; transcript_type protein_coding
NTRK3--ABI3BP HAVANA mRNA 58589 127894 . + . FI_gene_label "ABI3BP^ENSG00000154175.18" ; ID "NTRK3--ABI3BP^ENST00000284322.10" ; Parent "NTRK3--ABI3BP^ABI3BP^ENSG00000154175.18" ; exon_id "ENSE00001910142.1" ; exon_number 1 ; gene_id "NTRK3--ABI3BP^ABI3BP^ENSG00000154175.18" ; gene_name ABI3BP ; gene_type protein_coding ; havana_gene "OTTHUMG00000159094.7" ; havana_transcript "OTTHUMT00000353260.1" ; hgnc_id "HGNC:17265" ; level 2 ; orig_coord_info "chr3,100993306,100993384,-" ; protein_id "ENSP00000284322.6" ; tag upstream_ATG basic appris_alternative_2 ; transcript_id "NTRK3--ABI3BP^ENST00000284322.10" ; transcript_name "ABI3BP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NTRK3--ABI3BP HAVANA gene 1610 24319 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "NTRK3--ABI3BP^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "NTRK3--ABI3BP^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "NTRK3--ABI3BP^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
NTRK3--ABI3BP HAVANA mRNA 1610 24319 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "NTRK3--ABI3BP^ENST00000317501.7" ; Parent "NTRK3--ABI3BP^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "NTRK3--ABI3BP^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "NTRK3--ABI3BP^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NTRK3--NEPRO HAVANA gene 58779 71960 . + . FI_gene_label "NEPRO^ENSG00000163608.15" ; ID "NTRK3--NEPRO^NEPRO^ENSG00000163608.15" ; ccdsid "CCDS33824.1" ; exon_id "ENSE00003646667.1" ; exon_number 1 ; gene_id "NTRK3--NEPRO^NEPRO^ENSG00000163608.15" ; gene_name NEPRO ; gene_type protein_coding ; havana_gene "OTTHUMG00000159286.7" ; havana_transcript "OTTHUMT00000354405.4" ; hgnc_id "HGNC:24496" ; level 2 ; orig_coord_info "chr3,113019542,113019647,-" ; protein_id "ENSP00000320251.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NTRK3--NEPRO^ENST00000314400.10" ; transcript_name "NEPRO-201" ; transcript_support_level 1 ; transcript_type protein_coding
NTRK3--NEPRO HAVANA mRNA 58779 71960 . + . FI_gene_label "NEPRO^ENSG00000163608.15" ; ID "NTRK3--NEPRO^ENST00000314400.10" ; Parent "NTRK3--NEPRO^NEPRO^ENSG00000163608.15" ; ccdsid "CCDS33824.1" ; exon_id "ENSE00003646667.1" ; exon_number 1 ; gene_id "NTRK3--NEPRO^NEPRO^ENSG00000163608.15" ; gene_name NEPRO ; gene_type protein_coding ; havana_gene "OTTHUMG00000159286.7" ; havana_transcript "OTTHUMT00000354405.4" ; hgnc_id "HGNC:24496" ; level 2 ; orig_coord_info "chr3,113019542,113019647,-" ; protein_id "ENSP00000320251.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NTRK3--NEPRO^ENST00000314400.10" ; transcript_name "NEPRO-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NTRK3--NEPRO HAVANA gene 1610 24319 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "NTRK3--NEPRO^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "NTRK3--NEPRO^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "NTRK3--NEPRO^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
NTRK3--NEPRO HAVANA mRNA 1610 24319 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "NTRK3--NEPRO^ENST00000317501.7" ; Parent "NTRK3--NEPRO^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "NTRK3--NEPRO^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "NTRK3--NEPRO^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHA13 HAVANA gene 7268 15708 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHA13 HAVANA mRNA 7268 15708 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA6--PCDHA13^ENST00000289272.3" ; Parent "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHA13 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHA13 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHA13^ENST00000378126.4" ; Parent "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC1 HAVANA gene 7268 17283 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC1 HAVANA mRNA 7268 17283 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA6--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC1 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC1 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC1^ENST00000378126.4" ; Parent "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC2 HAVANA gene 7274 18009 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC2 HAVANA mRNA 7274 18009 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA6--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC2 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC2 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC2^ENST00000378126.4" ; Parent "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PLA2G6--FAM227A HAVANA gene 4831 34498 . + . FI_gene_label "PLA2G6^ENSG00000184381.20" ; ID "PLA2G6--FAM227A^PLA2G6^ENSG00000184381.20" ; ccdsid "CCDS13967.1" ; exon_id "ENSE00003503664.1" ; exon_number 2 ; gene_id "PLA2G6--FAM227A^PLA2G6^ENSG00000184381.20" ; gene_name PLA2G6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151246.10" ; havana_transcript "OTTHUMT00000321860.2" ; hgnc_id "HGNC:9039" ; level 2 ; orig_coord_info "chr22,38169218,38169426,-" ; protein_id "ENSP00000333142.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLA2G6--FAM227A^ENST00000332509.8" ; transcript_name "PLA2G6-201" ; transcript_support_level 1 ; transcript_type protein_coding
PLA2G6--FAM227A HAVANA mRNA 4831 34498 . + . FI_gene_label "PLA2G6^ENSG00000184381.20" ; ID "PLA2G6--FAM227A^ENST00000332509.8" ; Parent "PLA2G6--FAM227A^PLA2G6^ENSG00000184381.20" ; ccdsid "CCDS13967.1" ; exon_id "ENSE00003503664.1" ; exon_number 2 ; gene_id "PLA2G6--FAM227A^PLA2G6^ENSG00000184381.20" ; gene_name PLA2G6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151246.10" ; havana_transcript "OTTHUMT00000321860.2" ; hgnc_id "HGNC:9039" ; level 2 ; orig_coord_info "chr22,38169218,38169426,-" ; protein_id "ENSP00000333142.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "PLA2G6--FAM227A^ENST00000332509.8" ; transcript_name "PLA2G6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PLA2G6--FAM227A HAVANA gene 37825 61509 . + . FI_gene_label "FAM227A^ENSG00000184949.17" ; ID "PLA2G6--FAM227A^FAM227A^ENSG00000184949.17" ; exon_id "ENSE00003513808.1" ; exon_number 2 ; gene_id "PLA2G6--FAM227A^FAM227A^ENSG00000184949.17" ; gene_name FAM227A ; gene_type protein_coding ; havana_gene "OTTHUMG00000151133.9" ; havana_transcript "OTTHUMT00000321457.6" ; hgnc_id "HGNC:44197" ; level 1 ; orig_coord_info "chr22,38650027,38650168,-" ; protein_id "ENSP00000348086.7" ; tag inferred_transcript_model non_canonical_U12 basic appris_principal_4 exp_conf ; transcript_id "PLA2G6--FAM227A^ENST00000355830.11" ; transcript_name "FAM227A-201" ; transcript_support_level 5 ; transcript_type protein_coding
PLA2G6--FAM227A HAVANA mRNA 37825 61509 . + . FI_gene_label "FAM227A^ENSG00000184949.17" ; ID "PLA2G6--FAM227A^ENST00000355830.11" ; Parent "PLA2G6--FAM227A^FAM227A^ENSG00000184949.17" ; exon_id "ENSE00003513808.1" ; exon_number 2 ; gene_id "PLA2G6--FAM227A^FAM227A^ENSG00000184949.17" ; gene_name FAM227A ; gene_type protein_coding ; havana_gene "OTTHUMG00000151133.9" ; havana_transcript "OTTHUMT00000321457.6" ; hgnc_id "HGNC:44197" ; level 1 ; orig_coord_info "chr22,38650027,38650168,-" ; protein_id "ENSP00000348086.7" ; tag inferred_transcript_model non_canonical_U12 basic appris_principal_4 exp_conf ; transcript_id "PLA2G6--FAM227A^ENST00000355830.11" ; transcript_name "FAM227A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RAB10--GFPT1 HAVANA gene 1001 9309 . + . FI_gene_label "RAB10^ENSG00000084733.11" ; ID "RAB10--GFPT1^RAB10^ENSG00000084733.11" ; ccdsid "CCDS1720.1" ; exon_id "ENSE00001136869.7" ; exon_number 1 ; gene_id "RAB10--GFPT1^RAB10^ENSG00000084733.11" ; gene_name RAB10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094796.4" ; havana_transcript "OTTHUMT00000211610.2" ; hgnc_id "HGNC:9759" ; level 2 ; orig_coord_info "chr2,26034609,26034735,+" ; protein_id "ENSP00000264710.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB10--GFPT1^ENST00000264710.5" ; transcript_name "RAB10-201" ; transcript_support_level 1 ; transcript_type protein_coding
RAB10--GFPT1 HAVANA mRNA 1001 9309 . + . FI_gene_label "RAB10^ENSG00000084733.11" ; ID "RAB10--GFPT1^ENST00000264710.5" ; Parent "RAB10--GFPT1^RAB10^ENSG00000084733.11" ; ccdsid "CCDS1720.1" ; exon_id "ENSE00001136869.7" ; exon_number 1 ; gene_id "RAB10--GFPT1^RAB10^ENSG00000084733.11" ; gene_name RAB10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000094796.4" ; havana_transcript "OTTHUMT00000211610.2" ; hgnc_id "HGNC:9759" ; level 2 ; orig_coord_info "chr2,26034609,26034735,+" ; protein_id "ENSP00000264710.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB10--GFPT1^ENST00000264710.5" ; transcript_name "RAB10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RAB10--GFPT1 HAVANA gene 12333 38326 . + . FI_gene_label "GFPT1^ENSG00000198380.13" ; ID "RAB10--GFPT1^GFPT1^ENSG00000198380.13" ; ccdsid "CCDS58713.1" ; exon_id "ENSE00003470909.3" ; exon_number 1 ; gene_id "RAB10--GFPT1^GFPT1^ENSG00000198380.13" ; gene_name GFPT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152666.5" ; havana_transcript "OTTHUMT00000327277.3" ; hgnc_id "HGNC:4241" ; level 2 ; orig_coord_info "chr2,69387065,69387071,-" ; protein_id "ENSP00000349860.4" ; tag CAGE_supported_TSS RNA_Seq_supported_partial basic MANE_Select CCDS ; transcript_id "RAB10--GFPT1^ENST00000357308.9" ; transcript_name "GFPT1-201" ; transcript_support_level 5 ; transcript_type protein_coding
RAB10--GFPT1 HAVANA mRNA 12333 38326 . + . FI_gene_label "GFPT1^ENSG00000198380.13" ; ID "RAB10--GFPT1^ENST00000357308.9" ; Parent "RAB10--GFPT1^GFPT1^ENSG00000198380.13" ; ccdsid "CCDS58713.1" ; exon_id "ENSE00003470909.3" ; exon_number 1 ; gene_id "RAB10--GFPT1^GFPT1^ENSG00000198380.13" ; gene_name GFPT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152666.5" ; havana_transcript "OTTHUMT00000327277.3" ; hgnc_id "HGNC:4241" ; level 2 ; orig_coord_info "chr2,69387065,69387071,-" ; protein_id "ENSP00000349860.4" ; tag CAGE_supported_TSS RNA_Seq_supported_partial basic MANE_Select CCDS ; transcript_id "RAB10--GFPT1^ENST00000357308.9" ; transcript_name "GFPT1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SETD2--SMARCC1 HAVANA gene 36520 71141 . + . FI_gene_label "SMARCC1^ENSG00000173473.11" ; ID "SETD2--SMARCC1^SMARCC1^ENSG00000173473.11" ; ccdsid "CCDS2758.1" ; exon_id "ENSE00001294910.6" ; exon_number 1 ; gene_id "SETD2--SMARCC1^SMARCC1^ENSG00000173473.11" ; gene_name SMARCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133519.3" ; havana_transcript "OTTHUMT00000257491.2" ; hgnc_id "HGNC:11104" ; level 2 ; orig_coord_info "chr3,47781603,47781797,-" ; protein_id "ENSP00000254480.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SETD2--SMARCC1^ENST00000254480.10" ; transcript_name "SMARCC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SETD2--SMARCC1 HAVANA mRNA 36520 71141 . + . FI_gene_label "SMARCC1^ENSG00000173473.11" ; ID "SETD2--SMARCC1^ENST00000254480.10" ; Parent "SETD2--SMARCC1^SMARCC1^ENSG00000173473.11" ; ccdsid "CCDS2758.1" ; exon_id "ENSE00001294910.6" ; exon_number 1 ; gene_id "SETD2--SMARCC1^SMARCC1^ENSG00000173473.11" ; gene_name SMARCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133519.3" ; havana_transcript "OTTHUMT00000257491.2" ; hgnc_id "HGNC:11104" ; level 2 ; orig_coord_info "chr3,47781603,47781797,-" ; protein_id "ENSP00000254480.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SETD2--SMARCC1^ENST00000254480.10" ; transcript_name "SMARCC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SETD2--SMARCC1 HAVANA gene 4001 33299 . + . FI_gene_label "SETD2^ENSG00000181555.21" ; ID "SETD2--SMARCC1^SETD2^ENSG00000181555.21" ; exon_id "ENSE00001424129.4" ; exon_number 1 ; gene_id "SETD2--SMARCC1^SETD2^ENSG00000181555.21" ; gene_name SETD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133514.5" ; havana_transcript "OTTHUMT00000277105.2" ; hgnc_id "HGNC:18420" ; level 2 ; orig_coord_info "chr3,47120182,47124250,-" ; protein_id "ENSP00000332415.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SETD2--SMARCC1^ENST00000330022.11" ; transcript_name "SETD2-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
SETD2--SMARCC1 HAVANA mRNA 4001 33299 . + . FI_gene_label "SETD2^ENSG00000181555.21" ; ID "SETD2--SMARCC1^ENST00000330022.11" ; Parent "SETD2--SMARCC1^SETD2^ENSG00000181555.21" ; exon_id "ENSE00001424129.4" ; exon_number 1 ; gene_id "SETD2--SMARCC1^SETD2^ENSG00000181555.21" ; gene_name SETD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133514.5" ; havana_transcript "OTTHUMT00000277105.2" ; hgnc_id "HGNC:18420" ; level 2 ; orig_coord_info "chr3,47120182,47124250,-" ; protein_id "ENSP00000332415.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "SETD2--SMARCC1^ENST00000330022.11" ; transcript_name "SETD2-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
STK4--KCNK15-AS1 HAVANA gene 1044 18317 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "STK4--KCNK15-AS1^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "STK4--KCNK15-AS1^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "STK4--KCNK15-AS1^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
STK4--KCNK15-AS1 HAVANA mRNA 1044 18317 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "STK4--KCNK15-AS1^ENST00000372801.5" ; Parent "STK4--KCNK15-AS1^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "STK4--KCNK15-AS1^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "STK4--KCNK15-AS1^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TRIM59--IFT80 HAVANA gene 2416 9154 . + . FI_gene_label "TRIM59^ENSG00000213186.8" ; ID "TRIM59--IFT80^TRIM59^ENSG00000213186.8" ; ccdsid "CCDS3190.1" ; exon_id "ENSE00001192323.6" ; exon_number 3 ; gene_id "TRIM59--IFT80^TRIM59^ENSG00000213186.8" ; gene_name TRIM59 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159034.4" ; havana_transcript "OTTHUMT00000352963.2" ; hgnc_id "HGNC:30834" ; level 2 ; orig_coord_info "chr3,160437975,160439183,-" ; protein_id "ENSP00000311219.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000309784.9" ; transcript_name "TRIM59-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRIM59--IFT80 HAVANA mRNA 2416 9154 . + . FI_gene_label "TRIM59^ENSG00000213186.8" ; ID "TRIM59--IFT80^ENST00000309784.9" ; Parent "TRIM59--IFT80^TRIM59^ENSG00000213186.8" ; ccdsid "CCDS3190.1" ; exon_id "ENSE00001192323.6" ; exon_number 3 ; gene_id "TRIM59--IFT80^TRIM59^ENSG00000213186.8" ; gene_name TRIM59 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159034.4" ; havana_transcript "OTTHUMT00000352963.2" ; hgnc_id "HGNC:30834" ; level 2 ; orig_coord_info "chr3,160437975,160439183,-" ; protein_id "ENSP00000311219.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000309784.9" ; transcript_name "TRIM59-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRIM59--IFT80 HAVANA gene 15868 46756 . + . FI_gene_label "IFT80^ENSG00000068885.15" ; ID "TRIM59--IFT80^IFT80^ENSG00000068885.15" ; ccdsid "CCDS3188.1" ; exon_id "ENSE00003486065.1" ; exon_number 2 ; gene_id "TRIM59--IFT80^IFT80^ENSG00000068885.15" ; gene_name IFT80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158953.9" ; havana_transcript "OTTHUMT00000352651.3" ; hgnc_id "HGNC:29262" ; level 2 ; orig_coord_info "chr3,160384564,160384600,-" ; protein_id "ENSP00000312778.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000326448.12" ; transcript_name "IFT80-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRIM59--IFT80 HAVANA mRNA 15868 46756 . + . FI_gene_label "IFT80^ENSG00000068885.15" ; ID "TRIM59--IFT80^ENST00000326448.12" ; Parent "TRIM59--IFT80^IFT80^ENSG00000068885.15" ; ccdsid "CCDS3188.1" ; exon_id "ENSE00003486065.1" ; exon_number 2 ; gene_id "TRIM59--IFT80^IFT80^ENSG00000068885.15" ; gene_name IFT80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158953.9" ; havana_transcript "OTTHUMT00000352651.3" ; hgnc_id "HGNC:29262" ; level 2 ; orig_coord_info "chr3,160384564,160384600,-" ; protein_id "ENSP00000312778.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRIM59--IFT80^ENST00000326448.12" ; transcript_name "IFT80-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF251--PIGF HAVANA gene 10455 19903 . + . FI_gene_label "PIGF^ENSG00000151665.13" ; ID "ZNF251--PIGF^PIGF^ENSG00000151665.13" ; ccdsid "CCDS1827.1" ; exon_id "ENSE00001340000.1" ; exon_number 2 ; gene_id "ZNF251--PIGF^PIGF^ENSG00000151665.13" ; gene_name PIGF ; gene_type protein_coding ; havana_gene "OTTHUMG00000128816.6" ; havana_transcript "OTTHUMT00000250749.3" ; hgnc_id "HGNC:8962" ; level 2 ; orig_coord_info "chr2,46614937,46615164,-" ; protein_id "ENSP00000281382.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF251--PIGF^ENST00000281382.11" ; transcript_name "PIGF-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF251--PIGF HAVANA mRNA 10455 19903 . + . FI_gene_label "PIGF^ENSG00000151665.13" ; ID "ZNF251--PIGF^ENST00000281382.11" ; Parent "ZNF251--PIGF^PIGF^ENSG00000151665.13" ; ccdsid "CCDS1827.1" ; exon_id "ENSE00001340000.1" ; exon_number 2 ; gene_id "ZNF251--PIGF^PIGF^ENSG00000151665.13" ; gene_name PIGF ; gene_type protein_coding ; havana_gene "OTTHUMG00000128816.6" ; havana_transcript "OTTHUMT00000250749.3" ; hgnc_id "HGNC:8962" ; level 2 ; orig_coord_info "chr2,46614937,46615164,-" ; protein_id "ENSP00000281382.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF251--PIGF^ENST00000281382.11" ; transcript_name "PIGF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF251--PIGF HAVANA gene 1887 7438 . + . FI_gene_label "ZNF251^ENSG00000198169.9" ; ID "ZNF251--PIGF^ZNF251^ENSG00000198169.9" ; ccdsid "CCDS47944.1" ; exon_id "ENSE00003542789.1" ; exon_number 2 ; gene_id "ZNF251--PIGF^ZNF251^ENSG00000198169.9" ; gene_name ZNF251 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165189.4" ; havana_transcript "OTTHUMT00000382541.2" ; hgnc_id "HGNC:13045" ; level 2 ; orig_coord_info "chr8,144754696,144754728,-" ; protein_id "ENSP00000292562.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF251--PIGF^ENST00000292562.12" ; transcript_name "ZNF251-201" ; transcript_support_level 2 ; transcript_type protein_coding
ZNF251--PIGF HAVANA mRNA 1887 7438 . + . FI_gene_label "ZNF251^ENSG00000198169.9" ; ID "ZNF251--PIGF^ENST00000292562.12" ; Parent "ZNF251--PIGF^ZNF251^ENSG00000198169.9" ; ccdsid "CCDS47944.1" ; exon_id "ENSE00003542789.1" ; exon_number 2 ; gene_id "ZNF251--PIGF^ZNF251^ENSG00000198169.9" ; gene_name ZNF251 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165189.4" ; havana_transcript "OTTHUMT00000382541.2" ; hgnc_id "HGNC:13045" ; level 2 ; orig_coord_info "chr8,144754696,144754728,-" ; protein_id "ENSP00000292562.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF251--PIGF^ENST00000292562.12" ; transcript_name "ZNF251-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ZNF528--ZNF610 HAVANA gene 17953 27667 . + . FI_gene_label "ZNF610^ENSG00000167554.15" ; ID "ZNF528--ZNF610^ZNF610^ENSG00000167554.15" ; ccdsid "CCDS12851.1" ; exon_id "ENSE00002470175.1" ; exon_number 3 ; gene_id "ZNF528--ZNF610^ZNF610^ENSG00000167554.15" ; gene_name ZNF610 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182645.4" ; havana_transcript "OTTHUMT00000462863.1" ; hgnc_id "HGNC:26687" ; level 2 ; orig_coord_info "chr19,52349173,52349235,+" ; protein_id "ENSP00000324441.8" ; tag basic appris_principal_2 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000321287.12" ; transcript_name "ZNF610-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF610 HAVANA mRNA 17953 27667 . + . FI_gene_label "ZNF610^ENSG00000167554.15" ; ID "ZNF528--ZNF610^ENST00000321287.12" ; Parent "ZNF528--ZNF610^ZNF610^ENSG00000167554.15" ; ccdsid "CCDS12851.1" ; exon_id "ENSE00002470175.1" ; exon_number 3 ; gene_id "ZNF528--ZNF610^ZNF610^ENSG00000167554.15" ; gene_name ZNF610 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182645.4" ; havana_transcript "OTTHUMT00000462863.1" ; hgnc_id "HGNC:26687" ; level 2 ; orig_coord_info "chr19,52349173,52349235,+" ; protein_id "ENSP00000324441.8" ; tag basic appris_principal_2 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000321287.12" ; transcript_name "ZNF610-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF528--ZNF610 HAVANA gene 1001 14939 . + . FI_gene_label "ZNF528^ENSG00000167555.14" ; ID "ZNF528--ZNF610^ZNF528^ENSG00000167555.14" ; ccdsid "CCDS33091.1" ; exon_id "ENSE00003647276.1" ; exon_number 4 ; gene_id "ZNF528--ZNF610^ZNF528^ENSG00000167555.14" ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9" ; havana_transcript "OTTHUMT00000344336.2" ; hgnc_id "HGNC:29384" ; level 2 ; orig_coord_info "chr19,52402014,52402028,+" ; protein_id "ENSP00000353652.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000360465.8" ; transcript_name "ZNF528-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF610 HAVANA mRNA 1001 14939 . + . FI_gene_label "ZNF528^ENSG00000167555.14" ; ID "ZNF528--ZNF610^ENST00000360465.8" ; Parent "ZNF528--ZNF610^ZNF528^ENSG00000167555.14" ; ccdsid "CCDS33091.1" ; exon_id "ENSE00003647276.1" ; exon_number 4 ; gene_id "ZNF528--ZNF610^ZNF528^ENSG00000167555.14" ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9" ; havana_transcript "OTTHUMT00000344336.2" ; hgnc_id "HGNC:29384" ; level 2 ; orig_coord_info "chr19,52402014,52402028,+" ; protein_id "ENSP00000353652.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000360465.8" ; transcript_name "ZNF528-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF528--ZNF880 HAVANA gene 17973 21182 . + . FI_gene_label "ZNF880^ENSG00000221923.9" ; ID "ZNF528--ZNF880^ZNF880^ENSG00000221923.9" ; exon_id "ENSE00001665096.1" ; exon_number 1 ; gene_id "ZNF528--ZNF880^ZNF880^ENSG00000221923.9" ; gene_name ZNF880 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167972.3" ; havana_transcript "OTTHUMT00000397373.1" ; hgnc_id "HGNC:37249" ; level 2 ; orig_coord_info "chr19,52369966,52369977,+" ; protein_id "ENSP00000343625.5" ; tag basic ; transcript_id "ZNF528--ZNF880^ENST00000344085.9" ; transcript_name "ZNF880-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF880 HAVANA mRNA 17973 21182 . + . FI_gene_label "ZNF880^ENSG00000221923.9" ; ID "ZNF528--ZNF880^ENST00000344085.9" ; Parent "ZNF528--ZNF880^ZNF880^ENSG00000221923.9" ; exon_id "ENSE00001665096.1" ; exon_number 1 ; gene_id "ZNF528--ZNF880^ZNF880^ENSG00000221923.9" ; gene_name ZNF880 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167972.3" ; havana_transcript "OTTHUMT00000397373.1" ; hgnc_id "HGNC:37249" ; level 2 ; orig_coord_info "chr19,52369966,52369977,+" ; protein_id "ENSP00000343625.5" ; tag basic ; transcript_id "ZNF528--ZNF880^ENST00000344085.9" ; transcript_name "ZNF880-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF528--ZNF880 HAVANA gene 1001 14939 . + . FI_gene_label "ZNF528^ENSG00000167555.14" ; ID "ZNF528--ZNF880^ZNF528^ENSG00000167555.14" ; ccdsid "CCDS33091.1" ; exon_id "ENSE00003647276.1" ; exon_number 4 ; gene_id "ZNF528--ZNF880^ZNF528^ENSG00000167555.14" ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9" ; havana_transcript "OTTHUMT00000344336.2" ; hgnc_id "HGNC:29384" ; level 2 ; orig_coord_info "chr19,52402014,52402028,+" ; protein_id "ENSP00000353652.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF880^ENST00000360465.8" ; transcript_name "ZNF528-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF880 HAVANA mRNA 1001 14939 . + . FI_gene_label "ZNF528^ENSG00000167555.14" ; ID "ZNF528--ZNF880^ENST00000360465.8" ; Parent "ZNF528--ZNF880^ZNF528^ENSG00000167555.14" ; ccdsid "CCDS33091.1" ; exon_id "ENSE00003647276.1" ; exon_number 4 ; gene_id "ZNF528--ZNF880^ZNF528^ENSG00000167555.14" ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9" ; havana_transcript "OTTHUMT00000344336.2" ; hgnc_id "HGNC:29384" ; level 2 ; orig_coord_info "chr19,52402014,52402028,+" ; protein_id "ENSP00000353652.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF880^ENST00000360465.8" ; transcript_name "ZNF528-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF7--EPAS1 HAVANA gene 21863 40574 . + . FI_gene_label "EPAS1^ENSG00000116016.14" ; ID "ZNF7--EPAS1^EPAS1^ENSG00000116016.14" ; ccdsid "CCDS1825.1" ; exon_id "ENSE00001875413.2" ; exon_number 1 ; gene_id "ZNF7--EPAS1^EPAS1^ENSG00000116016.14" ; gene_name EPAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128818.25" ; havana_transcript "OTTHUMT00000250752.4" ; hgnc_id "HGNC:3374" ; level 2 ; orig_coord_info "chr2,46297912,46297937,+" ; protein_id "ENSP00000263734.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF7--EPAS1^ENST00000263734.5" ; transcript_name "EPAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF7--EPAS1 HAVANA mRNA 21863 40574 . + . FI_gene_label "EPAS1^ENSG00000116016.14" ; ID "ZNF7--EPAS1^ENST00000263734.5" ; Parent "ZNF7--EPAS1^EPAS1^ENSG00000116016.14" ; ccdsid "CCDS1825.1" ; exon_id "ENSE00001875413.2" ; exon_number 1 ; gene_id "ZNF7--EPAS1^EPAS1^ENSG00000116016.14" ; gene_name EPAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128818.25" ; havana_transcript "OTTHUMT00000250752.4" ; hgnc_id "HGNC:3374" ; level 2 ; orig_coord_info "chr2,46297912,46297937,+" ; protein_id "ENSP00000263734.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF7--EPAS1^ENST00000263734.5" ; transcript_name "EPAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF7--EPAS1 HAVANA gene 1097 15317 . + . FI_gene_label "ZNF7^ENSG00000147789.15" ; ID "ZNF7--EPAS1^ZNF7^ENSG00000147789.15" ; ccdsid "CCDS83336.1" ; exon_id "ENSE00003497741.1" ; exon_number 2 ; gene_id "ZNF7--EPAS1^ZNF7^ENSG00000147789.15" ; gene_name ZNF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165200.2" ; havana_transcript "OTTHUMT00000382651.1" ; hgnc_id "HGNC:13139" ; level 2 ; orig_coord_info "chr8,144829088,144829090,+" ; protein_id "ENSP00000318848.5" ; tag basic CCDS ; transcript_id "ZNF7--EPAS1^ENST00000325217.9" ; transcript_name "ZNF7-201" ; transcript_support_level 4 ; transcript_type protein_coding
ZNF7--EPAS1 HAVANA mRNA 1097 15317 . + . FI_gene_label "ZNF7^ENSG00000147789.15" ; ID "ZNF7--EPAS1^ENST00000325217.9" ; Parent "ZNF7--EPAS1^ZNF7^ENSG00000147789.15" ; ccdsid "CCDS83336.1" ; exon_id "ENSE00003497741.1" ; exon_number 2 ; gene_id "ZNF7--EPAS1^ZNF7^ENSG00000147789.15" ; gene_name ZNF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165200.2" ; havana_transcript "OTTHUMT00000382651.1" ; hgnc_id "HGNC:13139" ; level 2 ; orig_coord_info "chr8,144829088,144829090,+" ; protein_id "ENSP00000318848.5" ; tag basic CCDS ; transcript_id "ZNF7--EPAS1^ENST00000325217.9" ; transcript_name "ZNF7-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
CAMK2G--C10orf55 HAVANA gene 28041 33415 . + . FI_gene_label "C10orf55^ENSG00000222047.9" ; ID "CAMK2G--C10orf55^C10orf55^ENSG00000222047.9" ; exon_id "ENSE00001579211.1" ; exon_number 1 ; gene_id "CAMK2G--C10orf55^C10orf55^ENSG00000222047.9" ; gene_name C10orf55 ; gene_type lncRNA ; havana_gene "OTTHUMG00000018496.1" ; havana_transcript "OTTHUMT00000048746.1" ; hgnc_id "HGNC:31008" ; level 2 ; orig_coord_info "chr10,73922633,73922777,-" ; tag basic ; transcript_id "CAMK2G--C10orf55^ENST00000409178.5" ; transcript_name "C10orf55-201" ; transcript_support_level 1 ; transcript_type lncRNA
CAMK2G--C10orf55 HAVANA RNA 28041 33415 . + . FI_gene_label "C10orf55^ENSG00000222047.9" ; ID "CAMK2G--C10orf55^ENST00000409178.5" ; Parent "CAMK2G--C10orf55^C10orf55^ENSG00000222047.9" ; exon_id "ENSE00001579211.1" ; exon_number 1 ; gene_id "CAMK2G--C10orf55^C10orf55^ENSG00000222047.9" ; gene_name C10orf55 ; gene_type lncRNA ; havana_gene "OTTHUMG00000018496.1" ; havana_transcript "OTTHUMT00000048746.1" ; hgnc_id "HGNC:31008" ; level 2 ; orig_coord_info "chr10,73922633,73922777,-" ; tag basic ; transcript_id "CAMK2G--C10orf55^ENST00000409178.5" ; transcript_name "C10orf55-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
FXR1--SOX2-OT HAVANA gene 41395 79493 . + . FI_gene_label "SOX2-OT^ENSG00000242808.10" ; ID "FXR1--SOX2-OT^SOX2-OT^ENSG00000242808.10" ; exon_id "ENSE00001840422.1" ; exon_number 1 ; gene_id "FXR1--SOX2-OT^SOX2-OT^ENSG00000242808.10" ; gene_name "SOX2-OT" ; gene_type lncRNA ; havana_gene "OTTHUMG00000158186.13" ; havana_transcript "OTTHUMT00000350422.2" ; hgnc_id "HGNC:20209" ; level 2 ; orig_coord_info "chr3,181056685,181056786,+" ; transcript_id "FXR1--SOX2-OT^ENST00000460739.5" ; transcript_name "SOX2-OT-201" ; transcript_support_level 4 ; transcript_type lncRNA
FXR1--SOX2-OT HAVANA RNA 41395 79493 . + . FI_gene_label "SOX2-OT^ENSG00000242808.10" ; ID "FXR1--SOX2-OT^ENST00000460739.5" ; Parent "FXR1--SOX2-OT^SOX2-OT^ENSG00000242808.10" ; exon_id "ENSE00001840422.1" ; exon_number 1 ; gene_id "FXR1--SOX2-OT^SOX2-OT^ENSG00000242808.10" ; gene_name "SOX2-OT" ; gene_type lncRNA ; havana_gene "OTTHUMG00000158186.13" ; havana_transcript "OTTHUMT00000350422.2" ; hgnc_id "HGNC:20209" ; level 2 ; orig_coord_info "chr3,181056685,181056786,+" ; transcript_id "FXR1--SOX2-OT^ENST00000460739.5" ; transcript_name "SOX2-OT-201" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
HECTD4--CASC11 HAVANA gene 84217 96170 . + . FI_gene_label "CASC11^ENSG00000249375.8" ; ID "HECTD4--CASC11^CASC11^ENSG00000249375.8" ; exon_id "ENSE00002038150.1" ; exon_number 1 ; gene_id "HECTD4--CASC11^CASC11^ENSG00000249375.8" ; gene_name CASC11 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164870.3" ; havana_transcript "OTTHUMT00000380687.2" ; hgnc_id "HGNC:48939" ; level 2 ; orig_coord_info "chr8,127733825,127733967,-" ; tag dotter_confirmed basic ; transcript_id "HECTD4--CASC11^ENST00000502463.7" ; transcript_name "CASC11-201" ; transcript_support_level 2 ; transcript_type lncRNA
HECTD4--CASC11 HAVANA RNA 84217 96170 . + . FI_gene_label "CASC11^ENSG00000249375.8" ; ID "HECTD4--CASC11^ENST00000502463.7" ; Parent "HECTD4--CASC11^CASC11^ENSG00000249375.8" ; exon_id "ENSE00002038150.1" ; exon_number 1 ; gene_id "HECTD4--CASC11^CASC11^ENSG00000249375.8" ; gene_name CASC11 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164870.3" ; havana_transcript "OTTHUMT00000380687.2" ; hgnc_id "HGNC:48939" ; level 2 ; orig_coord_info "chr8,127733825,127733967,-" ; tag dotter_confirmed basic ; transcript_id "HECTD4--CASC11^ENST00000502463.7" ; transcript_name "CASC11-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
LINC00921--ELOB HAVANA gene 1058 4082 . + . FI_gene_label "LINC00921^ENSG00000281005.1" ; ID "LINC00921--ELOB^LINC00921^ENSG00000281005.1" ; exon_id "ENSE00003766422.1" ; exon_number 1 ; gene_id "LINC00921--ELOB^LINC00921^ENSG00000281005.1" ; gene_name LINC00921 ; gene_type lncRNA ; havana_gene "OTTHUMG00000189522.1" ; havana_transcript "OTTHUMT00000479883.1" ; hgnc_id "HGNC:26830" ; level 2 ; orig_coord_info "chr16,3263800,3263883,+" ; tag basic ; transcript_id "LINC00921--ELOB^ENST00000572123.4" ; transcript_name "LINC00921-201" ; transcript_support_level 5 ; transcript_type lncRNA
LINC00921--ELOB HAVANA RNA 1058 4082 . + . FI_gene_label "LINC00921^ENSG00000281005.1" ; ID "LINC00921--ELOB^ENST00000572123.4" ; Parent "LINC00921--ELOB^LINC00921^ENSG00000281005.1" ; exon_id "ENSE00003766422.1" ; exon_number 1 ; gene_id "LINC00921--ELOB^LINC00921^ENSG00000281005.1" ; gene_name LINC00921 ; gene_type lncRNA ; havana_gene "OTTHUMG00000189522.1" ; havana_transcript "OTTHUMT00000479883.1" ; hgnc_id "HGNC:26830" ; level 2 ; orig_coord_info "chr16,3263800,3263883,+" ; tag basic ; transcript_id "LINC00921--ELOB^ENST00000572123.4" ; transcript_name "LINC00921-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
STK4--KCNK15-AS1 HAVANA gene 32534 33542 . + . FI_gene_label "KCNK15-AS1^ENSG00000244558.6" ; ID "STK4--KCNK15-AS1^KCNK15-AS1^ENSG00000244558.6" ; exon_id "ENSE00001685769.1" ; exon_number 1 ; gene_id "STK4--KCNK15-AS1^KCNK15-AS1^ENSG00000244558.6" ; gene_name "KCNK15-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000032545.2" ; havana_transcript "OTTHUMT00000079382.1" ; hgnc_id "HGNC:49901" ; level 2 ; orig_coord_info "chr20,44696003,44696084,-" ; transcript_id "STK4--KCNK15-AS1^ENST00000419931.1" ; transcript_name "KCNK15-AS1-201" ; transcript_support_level 3 ; transcript_type lncRNA
STK4--KCNK15-AS1 HAVANA RNA 32534 33542 . + . FI_gene_label "KCNK15-AS1^ENSG00000244558.6" ; ID "STK4--KCNK15-AS1^ENST00000419931.1" ; Parent "STK4--KCNK15-AS1^KCNK15-AS1^ENSG00000244558.6" ; exon_id "ENSE00001685769.1" ; exon_number 1 ; gene_id "STK4--KCNK15-AS1^KCNK15-AS1^ENSG00000244558.6" ; gene_name "KCNK15-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000032545.2" ; havana_transcript "OTTHUMT00000079382.1" ; hgnc_id "HGNC:49901" ; level 2 ; orig_coord_info "chr20,44696003,44696084,-" ; transcript_id "STK4--KCNK15-AS1^ENST00000419931.1" ; transcript_name "KCNK15-AS1-201" ; transcript_support_level 3 ; transcript_type lncRNA
773 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
1412 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 54 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 1 second) ------
GFF3 file parsed