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: 4219
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4219
=> 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:4219
=> 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:
DNM2--SMARCA4 HAVANA gene 40944 86415 . + . FI_gene_label "SMARCA4^ENSG00000127616.19" ; ID "DNM2--SMARCA4^SMARCA4^ENSG00000127616.19" ; ccdsid "CCDS12253.1" ; exon_id "ENSE00000874191.1" ; exon_number 2 ; gene_id "DNM2--SMARCA4^SMARCA4^ENSG00000127616.19" ; gene_name SMARCA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169272.16" ; havana_transcript "OTTHUMT00000403235.3" ; hgnc_id "HGNC:11100" ; level 2 ; orig_coord_info "chr19,10984152,10984373,+" ; protein_id "ENSP00000343896.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNM2--SMARCA4^ENST00000344626.10" ; transcript_name "SMARCA4-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNM2--SMARCA4 HAVANA mRNA 40944 86415 . + . FI_gene_label "SMARCA4^ENSG00000127616.19" ; ID "DNM2--SMARCA4^ENST00000344626.10" ; Parent "DNM2--SMARCA4^SMARCA4^ENSG00000127616.19" ; ccdsid "CCDS12253.1" ; exon_id "ENSE00000874191.1" ; exon_number 2 ; gene_id "DNM2--SMARCA4^SMARCA4^ENSG00000127616.19" ; gene_name SMARCA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169272.16" ; havana_transcript "OTTHUMT00000403235.3" ; hgnc_id "HGNC:11100" ; level 2 ; orig_coord_info "chr19,10984152,10984373,+" ; protein_id "ENSP00000343896.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNM2--SMARCA4^ENST00000344626.10" ; transcript_name "SMARCA4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNM2--SMARCA4 HAVANA gene 1001 36260 . + . FI_gene_label "DNM2^ENSG00000079805.18" ; ID "DNM2--SMARCA4^DNM2^ENSG00000079805.18" ; ccdsid "CCDS45968.1" ; exon_id "ENSE00003902790.1" ; exon_number 1 ; gene_id "DNM2--SMARCA4^DNM2^ENSG00000079805.18" ; gene_name DNM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180694.3" ; havana_transcript "OTTHUMT00000452592.1" ; hgnc_id "HGNC:2974" ; level 2 ; orig_coord_info "chr19,10718243,10718403,+" ; protein_id "ENSP00000347890.6" ; tag basic appris_principal_3 CCDS ; transcript_id "DNM2--SMARCA4^ENST00000355667.11" ; transcript_name "DNM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DNM2--SMARCA4 HAVANA mRNA 1001 36260 . + . FI_gene_label "DNM2^ENSG00000079805.18" ; ID "DNM2--SMARCA4^ENST00000355667.11" ; Parent "DNM2--SMARCA4^DNM2^ENSG00000079805.18" ; ccdsid "CCDS45968.1" ; exon_id "ENSE00003902790.1" ; exon_number 1 ; gene_id "DNM2--SMARCA4^DNM2^ENSG00000079805.18" ; gene_name DNM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180694.3" ; havana_transcript "OTTHUMT00000452592.1" ; hgnc_id "HGNC:2974" ; level 2 ; orig_coord_info "chr19,10718243,10718403,+" ; protein_id "ENSP00000347890.6" ; tag basic appris_principal_3 CCDS ; transcript_id "DNM2--SMARCA4^ENST00000355667.11" ; transcript_name "DNM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EFL1--GOLGA6L11P HAVANA gene 1001 25062 . + . FI_gene_label "EFL1^ENSG00000140598.15" ; ID "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; ccdsid "CCDS42071.1" ; exon_id "ENSE00003786417.1" ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5" ; havana_transcript "OTTHUMT00000419252.2" ; hgnc_id "HGNC:25789" ; level 2 ; orig_coord_info "chr15,82261688,82261778,-" ; protein_id "ENSP00000268206.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12" ; transcript_name "EFL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFL1--GOLGA6L11P HAVANA mRNA 1001 25062 . + . FI_gene_label "EFL1^ENSG00000140598.15" ; ID "EFL1--GOLGA6L11P^ENST00000268206.12" ; Parent "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; ccdsid "CCDS42071.1" ; exon_id "ENSE00003786417.1" ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5" ; havana_transcript "OTTHUMT00000419252.2" ; hgnc_id "HGNC:25789" ; level 2 ; orig_coord_info "chr15,82261688,82261778,-" ; protein_id "ENSP00000268206.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12" ; transcript_name "EFL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--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:
TMED7--TICAM2 HAVANA gene 11056 15867 . + . FI_gene_label "TICAM2^ENSG00000243414.6" ; ID "TMED7--TICAM2^TICAM2^ENSG00000243414.6" ; ccdsid "CCDS4119.1" ; exon_id "ENSE00001741902.2" ; exon_number 2 ; gene_id "TMED7--TICAM2^TICAM2^ENSG00000243414.6" ; gene_name TICAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162905.2" ; havana_transcript "OTTHUMT00000338755.1" ; hgnc_id "HGNC:21354" ; level 2 ; orig_coord_info "chr5,115580552,115581256,-" ; protein_id "ENSP00000415139.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000427199.3" ; transcript_name "TICAM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMED7--TICAM2 HAVANA mRNA 11056 15867 . + . FI_gene_label "TICAM2^ENSG00000243414.6" ; ID "TMED7--TICAM2^ENST00000427199.3" ; Parent "TMED7--TICAM2^TICAM2^ENSG00000243414.6" ; ccdsid "CCDS4119.1" ; exon_id "ENSE00001741902.2" ; exon_number 2 ; gene_id "TMED7--TICAM2^TICAM2^ENSG00000243414.6" ; gene_name TICAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162905.2" ; havana_transcript "OTTHUMT00000338755.1" ; hgnc_id "HGNC:21354" ; level 2 ; orig_coord_info "chr5,115580552,115581256,-" ; protein_id "ENSP00000415139.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000427199.3" ; transcript_name "TICAM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMED7--TICAM2 HAVANA gene 2138 8055 . + . FI_gene_label "TMED7^ENSG00000134970.14" ; ID "TMED7--TICAM2^TMED7^ENSG00000134970.14" ; ccdsid "CCDS4120.1" ; exon_id "ENSE00002252373.2" ; exon_number 1 ; gene_id "TMED7--TICAM2^TMED7^ENSG00000134970.14" ; gene_name TMED7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132013.8" ; havana_transcript "OTTHUMT00000254990.5" ; hgnc_id "HGNC:24253" ; level 2 ; orig_coord_info "chr5,115625601,115625792,-" ; protein_id "ENSP00000405926.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000456936.4" ; transcript_name "TMED7-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMED7--TICAM2 HAVANA mRNA 2138 8055 . + . FI_gene_label "TMED7^ENSG00000134970.14" ; ID "TMED7--TICAM2^ENST00000456936.4" ; Parent "TMED7--TICAM2^TMED7^ENSG00000134970.14" ; ccdsid "CCDS4120.1" ; exon_id "ENSE00002252373.2" ; exon_number 1 ; gene_id "TMED7--TICAM2^TMED7^ENSG00000134970.14" ; gene_name TMED7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132013.8" ; havana_transcript "OTTHUMT00000254990.5" ; hgnc_id "HGNC:24253" ; level 2 ; orig_coord_info "chr5,115625601,115625792,-" ; protein_id "ENSP00000405926.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMED7--TICAM2^ENST00000456936.4" ; transcript_name "TMED7-201" ; 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:
UBA1--ZFX HAVANA gene 22787 42629 . + . FI_gene_label "ZFX^ENSG00000005889.16" ; ID "UBA1--ZFX^ZFX^ENSG00000005889.16" ; ccdsid "CCDS14211.1" ; exon_id "ENSE00002688681.1" ; exon_number 4 ; gene_id "UBA1--ZFX^ZFX^ENSG00000005889.16" ; gene_name ZFX ; gene_type protein_coding ; havana_gene "OTTHUMG00000021264.2" ; havana_transcript "OTTHUMT00000056085.1" ; hgnc_id "HGNC:12869" ; level 2 ; orig_coord_info "chrX,24172743,24172800,+" ; protein_id "ENSP00000304985.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UBA1--ZFX^ENST00000304543.10" ; transcript_name "ZFX-201" ; transcript_support_level 5 ; transcript_type protein_coding
UBA1--ZFX HAVANA mRNA 22787 42629 . + . FI_gene_label "ZFX^ENSG00000005889.16" ; ID "UBA1--ZFX^ENST00000304543.10" ; Parent "UBA1--ZFX^ZFX^ENSG00000005889.16" ; ccdsid "CCDS14211.1" ; exon_id "ENSE00002688681.1" ; exon_number 4 ; gene_id "UBA1--ZFX^ZFX^ENSG00000005889.16" ; gene_name ZFX ; gene_type protein_coding ; havana_gene "OTTHUMG00000021264.2" ; havana_transcript "OTTHUMT00000056085.1" ; hgnc_id "HGNC:12869" ; level 2 ; orig_coord_info "chrX,24172743,24172800,+" ; protein_id "ENSP00000304985.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UBA1--ZFX^ENST00000304543.10" ; transcript_name "ZFX-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
UBA1--ZFX HAVANA gene 2875 19230 . + . FI_gene_label "UBA1^ENSG00000130985.17" ; ID "UBA1--ZFX^UBA1^ENSG00000130985.17" ; ccdsid "CCDS14275.1" ; exon_id "ENSE00003758789.1" ; exon_number 2 ; gene_id "UBA1--ZFX^UBA1^ENSG00000130985.17" ; gene_name UBA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021436.4" ; havana_transcript "OTTHUMT00000056389.1" ; hgnc_id "HGNC:12469" ; level 2 ; orig_coord_info "chrX,47198803,47198919,+" ; protein_id "ENSP00000338413.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBA1--ZFX^ENST00000335972.11" ; transcript_name "UBA1-201" ; transcript_support_level 1 ; transcript_type protein_coding
UBA1--ZFX HAVANA mRNA 2875 19230 . + . FI_gene_label "UBA1^ENSG00000130985.17" ; ID "UBA1--ZFX^ENST00000335972.11" ; Parent "UBA1--ZFX^UBA1^ENSG00000130985.17" ; ccdsid "CCDS14275.1" ; exon_id "ENSE00003758789.1" ; exon_number 2 ; gene_id "UBA1--ZFX^UBA1^ENSG00000130985.17" ; gene_name UBA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021436.4" ; havana_transcript "OTTHUMT00000056389.1" ; hgnc_id "HGNC:12469" ; level 2 ; orig_coord_info "chrX,47198803,47198919,+" ; protein_id "ENSP00000338413.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBA1--ZFX^ENST00000335972.11" ; transcript_name "UBA1-201" ; 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:
AP001347.1--ANKRD20A11P HAVANA gene 8798 22852 . + . FI_gene_label "ANKRD20A11P^ENSG00000215559.8" ; ID "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8" ; exon_id "ENSE00002284794.1" ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8" ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2" ; havana_transcript "OTTHUMT00000157750.1" ; hgnc_id "HGNC:42024" ; level 2 ; orig_coord_info "chr21,13979702,13980437,-" ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5" ; transcript_name "ANKRD20A11P-201" ; transcript_support_level 1 ; transcript_type processed_transcript
AP001347.1--ANKRD20A11P HAVANA RNA 8798 22852 . + . FI_gene_label "ANKRD20A11P^ENSG00000215559.8" ; ID "AP001347.1--ANKRD20A11P^ENST00000344693.5" ; Parent "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8" ; exon_id "ENSE00002284794.1" ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8" ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2" ; havana_transcript "OTTHUMT00000157750.1" ; hgnc_id "HGNC:42024" ; level 2 ; orig_coord_info "chr21,13979702,13980437,-" ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5" ; transcript_name "ANKRD20A11P-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
AP001347.1--ANKRD20A11P HAVANA gene 1003 5797 . + . FI_gene_label "AP001347.1^ENSG00000224905.7" ; ID "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7" ; exon_id "ENSE00001608016.1" ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7" ; gene_name "AP001347.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3" ; havana_transcript "OTTHUMT00000157812.1" ; level 2 ; orig_coord_info "chr21,14027421,14027597,+" ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5" ; transcript_name "AP001347.1-202" ; transcript_support_level 1 ; transcript_type lncRNA
AP001347.1--ANKRD20A11P HAVANA RNA 1003 5797 . + . FI_gene_label "AP001347.1^ENSG00000224905.7" ; ID "AP001347.1--ANKRD20A11P^ENST00000428809.5" ; Parent "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7" ; exon_id "ENSE00001608016.1" ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7" ; gene_name "AP001347.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3" ; havana_transcript "OTTHUMT00000157812.1" ; level 2 ; orig_coord_info "chr21,14027421,14027597,+" ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5" ; transcript_name "AP001347.1-202" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
EFL1--GOLGA6L11P HAVANA gene 28063 33687 . + . FI_gene_label "GOLGA6L11P^ENSG00000223698.3" ; ID "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; exon_id "ENSE00001742768.1" ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2" ; havana_transcript "OTTHUMT00000104689.2" ; hgnc_id "HGNC:23958" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chrY,24168187,24168270,+" ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2" ; transcript_name "GOLGA6L11P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EFL1--GOLGA6L11P HAVANA RNA 28063 33687 . + . FI_gene_label "GOLGA6L11P^ENSG00000223698.3" ; ID "EFL1--GOLGA6L11P^ENST00000417252.2" ; Parent "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; exon_id "ENSE00001742768.1" ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2" ; havana_transcript "OTTHUMT00000104689.2" ; hgnc_id "HGNC:23958" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chrY,24168187,24168270,+" ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2" ; transcript_name "GOLGA6L11P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2--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
219 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 ------------------------------
428 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