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: 1911
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1911
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:1911
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 1 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
BCAR3--GLMN HAVANA gene 11472 31098 . + . FI_gene_label "BCAR3^ENSG00000137936.18" ; ID "BCAR3--GLMN^BCAR3^ENSG00000137936.18" ; ccdsid "CCDS745.1" ; exon_id "ENSE00001452146.1" ; exon_number 2 ; gene_id "BCAR3--GLMN^BCAR3^ENSG00000137936.18" ; gene_name BCAR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010301.5" ; havana_transcript "OTTHUMT00000028418.2" ; hgnc_id "HGNC:973" ; level 2 ; orig_coord_info "chr1,93674614,93674930,-" ; protein_id "ENSP00000260502.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "BCAR3--GLMN^ENST00000260502.11" ; transcript_name "BCAR3-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAR3--GLMN HAVANA mRNA 11472 31098 . + . FI_gene_label "BCAR3^ENSG00000137936.18" ; ID "BCAR3--GLMN^ENST00000260502.11" ; Parent "BCAR3--GLMN^BCAR3^ENSG00000137936.18" ; ccdsid "CCDS745.1" ; exon_id "ENSE00001452146.1" ; exon_number 2 ; gene_id "BCAR3--GLMN^BCAR3^ENSG00000137936.18" ; gene_name BCAR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010301.5" ; havana_transcript "OTTHUMT00000028418.2" ; hgnc_id "HGNC:973" ; level 2 ; orig_coord_info "chr1,93674614,93674930,-" ; protein_id "ENSP00000260502.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "BCAR3--GLMN^ENST00000260502.11" ; transcript_name "BCAR3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BCAR3--GLMN HAVANA gene 34099 50823 . + . FI_gene_label "GLMN^ENSG00000174842.17" ; ID "BCAR3--GLMN^GLMN^ENSG00000174842.17" ; ccdsid "CCDS738.1" ; exon_id "ENSE00002159430.1" ; exon_number 2 ; gene_id "BCAR3--GLMN^GLMN^ENSG00000174842.17" ; gene_name GLMN ; gene_type protein_coding ; havana_gene "OTTHUMG00000010283.9" ; havana_transcript "OTTHUMT00000028358.2" ; hgnc_id "HGNC:14373" ; level 2 ; orig_coord_info "chr1,92297961,92297999,-" ; protein_id "ENSP00000359385.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAR3--GLMN^ENST00000370360.8" ; transcript_name "GLMN-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAR3--GLMN HAVANA mRNA 34099 50823 . + . FI_gene_label "GLMN^ENSG00000174842.17" ; ID "BCAR3--GLMN^ENST00000370360.8" ; Parent "BCAR3--GLMN^GLMN^ENSG00000174842.17" ; ccdsid "CCDS738.1" ; exon_id "ENSE00002159430.1" ; exon_number 2 ; gene_id "BCAR3--GLMN^GLMN^ENSG00000174842.17" ; gene_name GLMN ; gene_type protein_coding ; havana_gene "OTTHUMG00000010283.9" ; havana_transcript "OTTHUMT00000028358.2" ; hgnc_id "HGNC:14373" ; level 2 ; orig_coord_info "chr1,92297961,92297999,-" ; protein_id "ENSP00000359385.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAR3--GLMN^ENST00000370360.8" ; transcript_name "GLMN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DYRK1A--LINC02756 HAVANA gene 2985 36922 . + . FI_gene_label "DYRK1A^ENSG00000157540.22" ; ID "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22" ; ccdsid "CCDS42926.1" ; exon_id "ENSE00003829613.1" ; exon_number 3 ; gene_id "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22" ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9" ; havana_transcript "OTTHUMT00000194799.2" ; hgnc_id "HGNC:3091" ; level 2 ; orig_coord_info "chr21,37420375,37420384,+" ; protein_id "ENSP00000342690.3" ; tag basic CCDS ; transcript_id "DYRK1A--LINC02756^ENST00000338785.8" ; transcript_name "DYRK1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
DYRK1A--LINC02756 HAVANA mRNA 2985 36922 . + . FI_gene_label "DYRK1A^ENSG00000157540.22" ; ID "DYRK1A--LINC02756^ENST00000338785.8" ; Parent "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22" ; ccdsid "CCDS42926.1" ; exon_id "ENSE00003829613.1" ; exon_number 3 ; gene_id "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22" ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9" ; havana_transcript "OTTHUMT00000194799.2" ; hgnc_id "HGNC:3091" ; level 2 ; orig_coord_info "chr21,37420375,37420384,+" ; protein_id "ENSP00000342690.3" ; tag basic CCDS ; transcript_id "DYRK1A--LINC02756^ENST00000338785.8" ; transcript_name "DYRK1A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3 HAVANA mRNA 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^ENST00000260795.8" ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3 HAVANA mRNA 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^ENST00000313288.9" ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MTAP--DMRTA1 HAVANA gene 29696 36281 . + . FI_gene_label "DMRTA1^ENSG00000176399.4" ; ID "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4" ; ccdsid "CCDS6514.1" ; exon_id "ENSE00001268100.3" ; exon_number 1 ; gene_id "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4" ; gene_name DMRTA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019693.3" ; havana_transcript "OTTHUMT00000051935.3" ; hgnc_id "HGNC:13826" ; level 2 ; orig_coord_info "chr9,22447066,22447732,+" ; protein_id "ENSP00000319651.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MTAP--DMRTA1^ENST00000325870.3" ; transcript_name "DMRTA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MTAP--DMRTA1 HAVANA mRNA 29696 36281 . + . FI_gene_label "DMRTA1^ENSG00000176399.4" ; ID "MTAP--DMRTA1^ENST00000325870.3" ; Parent "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4" ; ccdsid "CCDS6514.1" ; exon_id "ENSE00001268100.3" ; exon_number 1 ; gene_id "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4" ; gene_name DMRTA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019693.3" ; havana_transcript "OTTHUMT00000051935.3" ; hgnc_id "HGNC:13826" ; level 2 ; orig_coord_info "chr9,22447066,22447732,+" ; protein_id "ENSP00000319651.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MTAP--DMRTA1^ENST00000325870.3" ; transcript_name "DMRTA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MTAP--DMRTA1 HAVANA gene 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--DMRTA1^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--DMRTA1^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--DMRTA1^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--DMRTA1 HAVANA mRNA 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--DMRTA1^ENST00000419385.5" ; Parent "MTAP--DMRTA1^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--DMRTA1^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--DMRTA1^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
MTAP--LINC01239 HAVANA gene 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--LINC01239^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--LINC01239^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--LINC01239^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--LINC01239 HAVANA mRNA 1022 14638 . + . FI_gene_label "MTAP^ENSG00000099810.21" ; ID "MTAP--LINC01239^ENST00000419385.5" ; Parent "MTAP--LINC01239^MTAP^ENSG00000099810.21" ; exon_id "ENSE00001547793.2" ; exon_number 1 ; gene_id "MTAP--LINC01239^MTAP^ENSG00000099810.21" ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10" ; havana_transcript "OTTHUMT00000334287.1" ; hgnc_id "HGNC:7413" ; level 2 ; orig_coord_info "chr9,21802749,21802781,+" ; protein_id "ENSP00000393507.1" ; tag not_organism_supported ; transcript_id "MTAP--LINC01239^ENST00000419385.5" ; transcript_name "MTAP-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^ENST00000289272.3" ; Parent "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^ENST00000562220.2" ; Parent "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
UBR5--BAALC-AS1 HAVANA gene 1071 53320 . + . FI_gene_label "UBR5^ENSG00000104517.13" ; ID "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13" ; ccdsid "CCDS64946.1" ; exon_id "ENSE00001162016.4" ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13" ; gene_name UBR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164755.5" ; havana_transcript "OTTHUMT00000380196.1" ; hgnc_id "HGNC:16806" ; level 2 ; orig_coord_info "chr8,102412173,102412234,-" ; protein_id "ENSP00000220959.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "UBR5--BAALC-AS1^ENST00000220959.8" ; transcript_name "UBR5-201" ; transcript_support_level 1 ; transcript_type protein_coding
UBR5--BAALC-AS1 HAVANA mRNA 1071 53320 . + . FI_gene_label "UBR5^ENSG00000104517.13" ; ID "UBR5--BAALC-AS1^ENST00000220959.8" ; Parent "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13" ; ccdsid "CCDS64946.1" ; exon_id "ENSE00001162016.4" ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13" ; gene_name UBR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164755.5" ; havana_transcript "OTTHUMT00000380196.1" ; hgnc_id "HGNC:16806" ; level 2 ; orig_coord_info "chr8,102412173,102412234,-" ; protein_id "ENSP00000220959.4" ; tag basic appris_alternative_1 CCDS ; transcript_id "UBR5--BAALC-AS1^ENST00000220959.8" ; transcript_name "UBR5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
DYRK1A--LINC02756 HAVANA gene 50943 56986 . + . FI_gene_label "LINC02756^ENSG00000255332.8" ; ID "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8" ; exon_id "ENSE00002711875.2" ; exon_number 1 ; gene_id "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8" ; gene_name LINC02756 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167330.10" ; havana_transcript "OTTHUMT00000447347.2" ; hgnc_id "HGNC:54276" ; level 1 ; orig_coord_info "chr11,91794358,91794422,+" ; tag basic TAGENE exp_conf ; transcript_id "DYRK1A--LINC02756^ENST00000525832.3" ; transcript_name "LINC02756-201" ; transcript_support_level 3 ; transcript_type lncRNA
DYRK1A--LINC02756 HAVANA RNA 50943 56986 . + . FI_gene_label "LINC02756^ENSG00000255332.8" ; ID "DYRK1A--LINC02756^ENST00000525832.3" ; Parent "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8" ; exon_id "ENSE00002711875.2" ; exon_number 1 ; gene_id "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8" ; gene_name LINC02756 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167330.10" ; havana_transcript "OTTHUMT00000447347.2" ; hgnc_id "HGNC:54276" ; level 1 ; orig_coord_info "chr11,91794358,91794422,+" ; tag basic TAGENE exp_conf ; transcript_id "DYRK1A--LINC02756^ENST00000525832.3" ; transcript_name "LINC02756-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
MTAP--LINC01239 HAVANA gene 32024 33348 . + . FI_gene_label "LINC01239^ENSG00000234840.2" ; ID "MTAP--LINC01239^LINC01239^ENSG00000234840.2" ; exon_id "ENSE00001647776.1" ; exon_number 1 ; gene_id "MTAP--LINC01239^LINC01239^ENSG00000234840.2" ; gene_name LINC01239 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019696.2" ; havana_transcript "OTTHUMT00000051939.1" ; hgnc_id "HGNC:49796" ; level 2 ; orig_coord_info "chr9,22682470,22682713,+" ; transcript_id "MTAP--LINC01239^ENST00000433645.1" ; transcript_name "LINC01239-201" ; transcript_support_level 3 ; transcript_type retained_intron
MTAP--LINC01239 HAVANA RNA 32024 33348 . + . FI_gene_label "LINC01239^ENSG00000234840.2" ; ID "MTAP--LINC01239^ENST00000433645.1" ; Parent "MTAP--LINC01239^LINC01239^ENSG00000234840.2" ; exon_id "ENSE00001647776.1" ; exon_number 1 ; gene_id "MTAP--LINC01239^LINC01239^ENSG00000234840.2" ; gene_name LINC01239 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019696.2" ; havana_transcript "OTTHUMT00000051939.1" ; hgnc_id "HGNC:49796" ; level 2 ; orig_coord_info "chr9,22682470,22682713,+" ; transcript_id "MTAP--LINC01239^ENST00000433645.1" ; transcript_name "LINC01239-201" ; transcript_support_level 3 ; transcript_type retained_intron
L1 and L2 created:
NUS1P1--AC114501.3 HAVANA gene 1001 1882 . + . FI_gene_label "NUS1P1^ENSG00000235636.1" ; ID "NUS1P1--AC114501.3^NUS1P1^ENSG00000235636.1" ; exon_id "ENSE00001722346.1" ; exon_number 1 ; gene_id "NUS1P1--AC114501.3^NUS1P1^ENSG00000235636.1" ; gene_name NUS1P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021444.1" ; havana_transcript "OTTHUMT00000056416.1" ; hgnc_id "HGNC:38472" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chrX,47512602,47513483,-" ; tag basic ; transcript_id "NUS1P1--AC114501.3^ENST00000446295.1" ; transcript_name "NUS1P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
NUS1P1--AC114501.3 HAVANA RNA 1001 1882 . + . FI_gene_label "NUS1P1^ENSG00000235636.1" ; ID "NUS1P1--AC114501.3^ENST00000446295.1" ; Parent "NUS1P1--AC114501.3^NUS1P1^ENSG00000235636.1" ; exon_id "ENSE00001722346.1" ; exon_number 1 ; gene_id "NUS1P1--AC114501.3^NUS1P1^ENSG00000235636.1" ; gene_name NUS1P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000021444.1" ; havana_transcript "OTTHUMT00000056416.1" ; hgnc_id "HGNC:38472" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chrX,47512602,47513483,-" ; tag basic ; transcript_id "NUS1P1--AC114501.3^ENST00000446295.1" ; transcript_name "NUS1P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
NUS1P1--AC114501.3 HAVANA gene 4883 5250 . + . FI_gene_label "AC114501.3^ENSG00000238124.1" ; ID "NUS1P1--AC114501.3^AC114501.3^ENSG00000238124.1" ; exon_id "ENSE00001603093.1" ; exon_number 1 ; gene_id "NUS1P1--AC114501.3^AC114501.3^ENSG00000238124.1" ; gene_name "AC114501.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000156731.1" ; havana_transcript "OTTHUMT00000345494.1" ; level 2 ; orig_coord_info "chr7,65463071,65463168,+" ; tag basic ; transcript_id "NUS1P1--AC114501.3^ENST00000453648.1" ; transcript_name "AC114501.3-201" ; transcript_support_level 5 ; transcript_type lncRNA
NUS1P1--AC114501.3 HAVANA RNA 4883 5250 . + . FI_gene_label "AC114501.3^ENSG00000238124.1" ; ID "NUS1P1--AC114501.3^ENST00000453648.1" ; Parent "NUS1P1--AC114501.3^AC114501.3^ENSG00000238124.1" ; exon_id "ENSE00001603093.1" ; exon_number 1 ; gene_id "NUS1P1--AC114501.3^AC114501.3^ENSG00000238124.1" ; gene_name "AC114501.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000156731.1" ; havana_transcript "OTTHUMT00000345494.1" ; level 2 ; orig_coord_info "chr7,65463071,65463168,+" ; tag basic ; transcript_id "NUS1P1--AC114501.3^ENST00000453648.1" ; transcript_name "AC114501.3-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
UBR5--BAALC-AS1 HAVANA gene 59208 75845 . + . FI_gene_label "BAALC-AS1^ENSG00000247081.8" ; ID "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8" ; exon_id "ENSE00001974416.1" ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8" ; gene_name "BAALC-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164798.6" ; havana_transcript "OTTHUMT00000380348.1" ; hgnc_id "HGNC:50461" ; level 2 ; orig_coord_info "chr8,103285838,103285907,-" ; tag basic ; transcript_id "UBR5--BAALC-AS1^ENST00000499522.6" ; transcript_name "BAALC-AS1-201" ; transcript_support_level 5 ; transcript_type lncRNA
UBR5--BAALC-AS1 HAVANA RNA 59208 75845 . + . FI_gene_label "BAALC-AS1^ENSG00000247081.8" ; ID "UBR5--BAALC-AS1^ENST00000499522.6" ; Parent "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8" ; exon_id "ENSE00001974416.1" ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8" ; gene_name "BAALC-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164798.6" ; havana_transcript "OTTHUMT00000380348.1" ; hgnc_id "HGNC:50461" ; level 2 ; orig_coord_info "chr8,103285838,103285907,-" ; tag basic ; transcript_id "UBR5--BAALC-AS1^ENST00000499522.6" ; transcript_name "BAALC-AS1-201" ; transcript_support_level 5 ; transcript_type lncRNA
173 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 -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
235 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 16 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed