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: 4260
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4260
=> 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:4260
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 2 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
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:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BLACE--STON2 HAVANA gene 23606 27563 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "BLACE--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "BLACE--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "BLACE--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding
BLACE--STON2 HAVANA mRNA 23606 27563 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "BLACE--STON2^ENST00000553821.2" ; Parent "BLACE--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "BLACE--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "BLACE--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
EPHA5--RYR3 HAVANA gene 1153 27562 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EPHA5--RYR3^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EPHA5--RYR3^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPHA5--RYR3^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPHA5--RYR3 HAVANA mRNA 1153 27562 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EPHA5--RYR3^ENST00000273854.7" ; Parent "EPHA5--RYR3^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EPHA5--RYR3^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EPHA5--RYR3^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPHA5--RYR3 HAVANA gene 30577 147967 . + . FI_gene_label "RYR3^ENSG00000198838.14" ; ID "EPHA5--RYR3^RYR3^ENSG00000198838.14" ; exon_id "ENSE00001540954.1" ; exon_number 1 ; gene_id "EPHA5--RYR3^RYR3^ENSG00000198838.14" ; gene_name RYR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172253.8" ; havana_transcript "OTTHUMT00000488324.1" ; hgnc_id "HGNC:10485" ; level 2 ; orig_coord_info "chr15,33311046,33311096,+" ; protein_id "ENSP00000373884.5" ; tag NAGNAG_splice_site not_organism_supported basic appris_alternative_2 ; transcript_id "EPHA5--RYR3^ENST00000389232.9" ; transcript_name "RYR3-201" ; transcript_support_level 5 ; transcript_type protein_coding
EPHA5--RYR3 HAVANA mRNA 30577 147967 . + . FI_gene_label "RYR3^ENSG00000198838.14" ; ID "EPHA5--RYR3^ENST00000389232.9" ; Parent "EPHA5--RYR3^RYR3^ENSG00000198838.14" ; exon_id "ENSE00001540954.1" ; exon_number 1 ; gene_id "EPHA5--RYR3^RYR3^ENSG00000198838.14" ; gene_name RYR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172253.8" ; havana_transcript "OTTHUMT00000488324.1" ; hgnc_id "HGNC:10485" ; level 2 ; orig_coord_info "chr15,33311046,33311096,+" ; protein_id "ENSP00000373884.5" ; tag NAGNAG_splice_site not_organism_supported basic appris_alternative_2 ; transcript_id "EPHA5--RYR3^ENST00000389232.9" ; transcript_name "RYR3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
EWSR1--ATF1 HAVANA gene 25489 35522 . + . FI_gene_label "ATF1^ENSG00000123268.9" ; ID "EWSR1--ATF1^ATF1^ENSG00000123268.9" ; ccdsid "CCDS8803.1" ; exon_id "ENSE00003503033.1" ; exon_number 2 ; gene_id "EWSR1--ATF1^ATF1^ENSG00000123268.9" ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3" ; havana_transcript "OTTHUMT00000404285.2" ; hgnc_id "HGNC:783" ; level 2 ; orig_coord_info "chr12,50780146,50780238,+" ; protein_id "ENSP00000262053.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EWSR1--ATF1^ENST00000262053.8" ; transcript_name "ATF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
EWSR1--ATF1 HAVANA mRNA 25489 35522 . + . FI_gene_label "ATF1^ENSG00000123268.9" ; ID "EWSR1--ATF1^ENST00000262053.8" ; Parent "EWSR1--ATF1^ATF1^ENSG00000123268.9" ; ccdsid "CCDS8803.1" ; exon_id "ENSE00003503033.1" ; exon_number 2 ; gene_id "EWSR1--ATF1^ATF1^ENSG00000123268.9" ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3" ; havana_transcript "OTTHUMT00000404285.2" ; hgnc_id "HGNC:783" ; level 2 ; orig_coord_info "chr12,50780146,50780238,+" ; protein_id "ENSP00000262053.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EWSR1--ATF1^ENST00000262053.8" ; transcript_name "ATF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EWSR1--ATF1 HAVANA gene 1283 22097 . + . FI_gene_label "EWSR1^ENSG00000182944.18" ; ID "EWSR1--ATF1^EWSR1^ENSG00000182944.18" ; exon_id "ENSE00001930494.1" ; exon_number 1 ; gene_id "EWSR1--ATF1^EWSR1^ENSG00000182944.18" ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9" ; havana_transcript "OTTHUMT00000321351.1" ; hgnc_id "HGNC:3508" ; level 2 ; orig_coord_info "chr22,29268337,29268349,+" ; protein_id "ENSP00000330516.7" ; tag not_organism_supported basic ; transcript_id "EWSR1--ATF1^ENST00000331029.11" ; transcript_name "EWSR1-201" ; transcript_support_level 5 ; transcript_type protein_coding
EWSR1--ATF1 HAVANA mRNA 1283 22097 . + . FI_gene_label "EWSR1^ENSG00000182944.18" ; ID "EWSR1--ATF1^ENST00000331029.11" ; Parent "EWSR1--ATF1^EWSR1^ENSG00000182944.18" ; exon_id "ENSE00001930494.1" ; exon_number 1 ; gene_id "EWSR1--ATF1^EWSR1^ENSG00000182944.18" ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9" ; havana_transcript "OTTHUMT00000321351.1" ; hgnc_id "HGNC:3508" ; level 2 ; orig_coord_info "chr22,29268337,29268349,+" ; protein_id "ENSP00000330516.7" ; tag not_organism_supported basic ; transcript_id "EWSR1--ATF1^ENST00000331029.11" ; transcript_name "EWSR1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
LINC02835--RYR3 HAVANA gene 6873 124263 . + . FI_gene_label "RYR3^ENSG00000198838.14" ; ID "LINC02835--RYR3^RYR3^ENSG00000198838.14" ; exon_id "ENSE00001540954.1" ; exon_number 1 ; gene_id "LINC02835--RYR3^RYR3^ENSG00000198838.14" ; gene_name RYR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172253.8" ; havana_transcript "OTTHUMT00000488324.1" ; hgnc_id "HGNC:10485" ; level 2 ; orig_coord_info "chr15,33311046,33311096,+" ; protein_id "ENSP00000373884.5" ; tag NAGNAG_splice_site not_organism_supported basic appris_alternative_2 ; transcript_id "LINC02835--RYR3^ENST00000389232.9" ; transcript_name "RYR3-201" ; transcript_support_level 5 ; transcript_type protein_coding
LINC02835--RYR3 HAVANA mRNA 6873 124263 . + . FI_gene_label "RYR3^ENSG00000198838.14" ; ID "LINC02835--RYR3^ENST00000389232.9" ; Parent "LINC02835--RYR3^RYR3^ENSG00000198838.14" ; exon_id "ENSE00001540954.1" ; exon_number 1 ; gene_id "LINC02835--RYR3^RYR3^ENSG00000198838.14" ; gene_name RYR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172253.8" ; havana_transcript "OTTHUMT00000488324.1" ; hgnc_id "HGNC:10485" ; level 2 ; orig_coord_info "chr15,33311046,33311096,+" ; protein_id "ENSP00000373884.5" ; tag NAGNAG_splice_site not_organism_supported basic appris_alternative_2 ; transcript_id "LINC02835--RYR3^ENST00000389232.9" ; transcript_name "RYR3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
MAST2--AC104041.1 HAVANA gene 2147 31461 . + . FI_gene_label "MAST2^ENSG00000086015.22" ; ID "MAST2--AC104041.1^MAST2^ENSG00000086015.22" ; ccdsid "CCDS41326.1" ; exon_id "ENSE00002687770.2" ; exon_number 1 ; gene_id "MAST2--AC104041.1^MAST2^ENSG00000086015.22" ; gene_name MAST2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008007.7" ; havana_transcript "OTTHUMT00000021977.2" ; hgnc_id "HGNC:19035" ; level 2 ; orig_coord_info "chr1,45803896,45804072,+" ; protein_id "ENSP00000354671.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MAST2--AC104041.1^ENST00000361297.7" ; transcript_name "MAST2-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAST2--AC104041.1 HAVANA mRNA 2147 31461 . + . FI_gene_label "MAST2^ENSG00000086015.22" ; ID "MAST2--AC104041.1^ENST00000361297.7" ; Parent "MAST2--AC104041.1^MAST2^ENSG00000086015.22" ; ccdsid "CCDS41326.1" ; exon_id "ENSE00002687770.2" ; exon_number 1 ; gene_id "MAST2--AC104041.1^MAST2^ENSG00000086015.22" ; gene_name MAST2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008007.7" ; havana_transcript "OTTHUMT00000021977.2" ; hgnc_id "HGNC:19035" ; level 2 ; orig_coord_info "chr1,45803896,45804072,+" ; protein_id "ENSP00000354671.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "MAST2--AC104041.1^ENST00000361297.7" ; transcript_name "MAST2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4B HAVANA gene 15007 22557 . + . FI_gene_label "RBM4B^ENSG00000173914.12" ; ID "RBM14--RBM4B^RBM4B^ENSG00000173914.12" ; ccdsid "CCDS8149.1" ; exon_id "ENSE00002463386.1" ; exon_number 2 ; gene_id "RBM14--RBM4B^RBM4B^ENSG00000173914.12" ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4" ; havana_transcript "OTTHUMT00000393852.2" ; hgnc_id "HGNC:28842" ; level 2 ; orig_coord_info "chr11,66676668,66677079,-" ; protein_id "ENSP00000310471.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310046.9" ; transcript_name "RBM4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4B HAVANA mRNA 15007 22557 . + . FI_gene_label "RBM4B^ENSG00000173914.12" ; ID "RBM14--RBM4B^ENST00000310046.9" ; Parent "RBM14--RBM4B^RBM4B^ENSG00000173914.12" ; ccdsid "CCDS8149.1" ; exon_id "ENSE00002463386.1" ; exon_number 2 ; gene_id "RBM14--RBM4B^RBM4B^ENSG00000173914.12" ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4" ; havana_transcript "OTTHUMT00000393852.2" ; hgnc_id "HGNC:28842" ; level 2 ; orig_coord_info "chr11,66676668,66677079,-" ; protein_id "ENSP00000310471.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310046.9" ; transcript_name "RBM4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4B HAVANA gene 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4B^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4B^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4B HAVANA mRNA 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4B^ENST00000310137.5" ; Parent "RBM14--RBM4B^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4B^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RNASE10--STON2 HAVANA gene 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--STON2^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding
RNASE10--STON2 HAVANA mRNA 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--STON2^ENST00000328444.5" ; Parent "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--STON2^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
RNASE10--STON2 HAVANA gene 19313 23270 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "RNASE10--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "RNASE10--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "RNASE10--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding
RNASE10--STON2 HAVANA mRNA 19313 23270 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "RNASE10--STON2^ENST00000553821.2" ; Parent "RNASE10--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "RNASE10--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "RNASE10--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--LINC01347 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^ENST00000326270.13" ; Parent "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
BLACE--STON2 HAVANA gene 1001 7493 . + . FI_gene_label "BLACE^ENSG00000204960.7" ; ID "BLACE--STON2^BLACE^ENSG00000204960.7" ; exon_id "ENSE00001552014.3" ; exon_number 1 ; gene_id "BLACE--STON2^BLACE^ENSG00000204960.7" ; gene_name BLACE ; gene_type lncRNA ; havana_gene "OTTHUMG00000151351.1" ; havana_transcript "OTTHUMT00000322333.1" ; hgnc_id "HGNC:20484" ; level 1 ; orig_coord_info "chr7,155367809,155367934,-" ; tag basic exp_conf ; transcript_id "BLACE--STON2^ENST00000378120.5" ; transcript_name "BLACE-201" ; transcript_support_level 1 ; transcript_type lncRNA
BLACE--STON2 HAVANA RNA 1001 7493 . + . FI_gene_label "BLACE^ENSG00000204960.7" ; ID "BLACE--STON2^ENST00000378120.5" ; Parent "BLACE--STON2^BLACE^ENSG00000204960.7" ; exon_id "ENSE00001552014.3" ; exon_number 1 ; gene_id "BLACE--STON2^BLACE^ENSG00000204960.7" ; gene_name BLACE ; gene_type lncRNA ; havana_gene "OTTHUMG00000151351.1" ; havana_transcript "OTTHUMT00000322333.1" ; hgnc_id "HGNC:20484" ; level 1 ; orig_coord_info "chr7,155367809,155367934,-" ; tag basic exp_conf ; transcript_id "BLACE--STON2^ENST00000378120.5" ; transcript_name "BLACE-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
LINC02835--RYR3 HAVANA gene 1001 3858 . + . FI_gene_label "LINC02835^ENSG00000285711.1" ; ID "LINC02835--RYR3^LINC02835^ENSG00000285711.1" ; exon_id "ENSE00003831505.1" ; exon_number 1 ; gene_id "LINC02835--RYR3^LINC02835^ENSG00000285711.1" ; gene_name LINC02835 ; gene_type lncRNA ; havana_gene "OTTHUMG00000193080.1" ; havana_transcript "OTTHUMT00000500087.1" ; hgnc_id "HGNC:54369" ; level 2 ; orig_coord_info "chr4,65241182,65241814,-" ; tag basic ; transcript_id "LINC02835--RYR3^ENST00000649562.1" ; transcript_name "LINC02835-201" ; transcript_type lncRNA
LINC02835--RYR3 HAVANA RNA 1001 3858 . + . FI_gene_label "LINC02835^ENSG00000285711.1" ; ID "LINC02835--RYR3^ENST00000649562.1" ; Parent "LINC02835--RYR3^LINC02835^ENSG00000285711.1" ; exon_id "ENSE00003831505.1" ; exon_number 1 ; gene_id "LINC02835--RYR3^LINC02835^ENSG00000285711.1" ; gene_name LINC02835 ; gene_type lncRNA ; havana_gene "OTTHUMG00000193080.1" ; havana_transcript "OTTHUMT00000500087.1" ; hgnc_id "HGNC:54369" ; level 2 ; orig_coord_info "chr4,65241182,65241814,-" ; tag basic ; transcript_id "LINC02835--RYR3^ENST00000649562.1" ; transcript_name "LINC02835-201" ; transcript_type lncRNA
L1 and L2 created:
MAST2--AC104041.1 HAVANA gene 37101 50513 . + . FI_gene_label "AC104041.1^ENSG00000259692.6" ; ID "MAST2--AC104041.1^AC104041.1^ENSG00000259692.6" ; exon_id "ENSE00002541371.1" ; exon_number 1 ; gene_id "MAST2--AC104041.1^AC104041.1^ENSG00000259692.6" ; gene_name "AC104041.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172170.6" ; havana_transcript "OTTHUMT00000417173.2" ; level 2 ; orig_coord_info "chr15,81995427,81995666,-" ; tag basic ; transcript_id "MAST2--AC104041.1^ENST00000559299.2" ; transcript_name "AC104041.1-204" ; transcript_support_level 4 ; transcript_type lncRNA
MAST2--AC104041.1 HAVANA RNA 37101 50513 . + . FI_gene_label "AC104041.1^ENSG00000259692.6" ; ID "MAST2--AC104041.1^ENST00000559299.2" ; Parent "MAST2--AC104041.1^AC104041.1^ENSG00000259692.6" ; exon_id "ENSE00002541371.1" ; exon_number 1 ; gene_id "MAST2--AC104041.1^AC104041.1^ENSG00000259692.6" ; gene_name "AC104041.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172170.6" ; havana_transcript "OTTHUMT00000417173.2" ; level 2 ; orig_coord_info "chr15,81995427,81995666,-" ; tag basic ; transcript_id "MAST2--AC104041.1^ENST00000559299.2" ; transcript_name "AC104041.1-204" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--LINC01347 HAVANA RNA 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^ENST00000417964.2" ; Parent "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
211 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
338 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 17 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