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: 2120
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2120
=> 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:2120
=> 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:
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:
CCDC169--SOHLH2 HAVANA gene 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 1027 13795 . + . FI_gene_label "CCDC169^ENSG00000242715.8" ; ID "CCDC169--SOHLH2^ENST00000239859.8" ; Parent "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; ccdsid "CCDS45028.1" ; exon_id "ENSE00003461130.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^CCDC169^ENSG00000242715.8" ; gene_name CCDC169 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016731.4" ; havana_transcript "OTTHUMT00000368255.2" ; hgnc_id "HGNC:34361" ; level 2 ; orig_coord_info "chr13,36297637,36297719,-" ; protein_id "ENSP00000239859.7" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000239859.8" ; transcript_name "CCDC169-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CCDC169--SOHLH2 HAVANA gene 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC169--SOHLH2 HAVANA mRNA 23170 30158 . + . FI_gene_label "SOHLH2^ENSG00000120669.16" ; ID "CCDC169--SOHLH2^ENST00000317764.6" ; Parent "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; ccdsid "CCDS61309.1" ; exon_id "ENSE00001482819.2" ; exon_number 1 ; gene_id "CCDC169--SOHLH2^SOHLH2^ENSG00000120669.16" ; gene_name SOHLH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016728.4" ; havana_transcript "OTTHUMT00000368257.1" ; hgnc_id "HGNC:26026" ; level 1 ; orig_coord_info "chr13,36214479,36214526,-" ; protein_id "ENSP00000326838.6" ; tag basic exp_conf CCDS ; transcript_id "CCDC169--SOHLH2^ENST00000317764.6" ; transcript_name "SOHLH2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GTF2A1L--STON1-GTF2A1L HAVANA gene 1059 10137 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17" ; havana_transcript "OTTHUMT00000323852.5" ; hgnc_id "HGNC:30727" ; level 2 ; orig_coord_info "chr2,48617875,48617895,+" ; protein_id "ENSP00000384597.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
GTF2A1L--STON1-GTF2A1L HAVANA mRNA 1059 10137 . + . FI_gene_label "GTF2A1L^ENSG00000242441.8" ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; Parent "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; ccdsid "CCDS46281.1" ; exon_id "ENSE00001939761.2" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^GTF2A1L^ENSG00000242441.8" ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17" ; havana_transcript "OTTHUMT00000323852.5" ; hgnc_id "HGNC:30727" ; level 2 ; orig_coord_info "chr2,48617875,48617895,+" ; protein_id "ENSP00000384597.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000403751.8" ; transcript_name "GTF2A1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUSBP13--NAIP ENSEMBL gene 10656 31835 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8" ; transcript_name "NAIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUSBP13--NAIP ENSEMBL mRNA 10656 31835 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSBP13--NAIP^ENST00000194097.8" ; Parent "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSBP13--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSBP13--NAIP^ENST00000194097.8" ; transcript_name "NAIP-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:
NHSL2--SLC43A2 HAVANA gene 31516 55929 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "NHSL2--SLC43A2^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "NHSL2--SLC43A2^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NHSL2--SLC43A2^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NHSL2--SLC43A2 HAVANA mRNA 31516 55929 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "NHSL2--SLC43A2^ENST00000301335.10" ; Parent "NHSL2--SLC43A2^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "NHSL2--SLC43A2^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NHSL2--SLC43A2^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NHSL2--SLC43A2 ENSEMBL gene 8017 13520 . + . FI_gene_label "NHSL2^ENSG00000204131.9" ; ID "NHSL2--SLC43A2^NHSL2^ENSG00000204131.9" ; exon_id "ENSE00003461107.1" ; exon_number 3 ; gene_id "NHSL2--SLC43A2^NHSL2^ENSG00000204131.9" ; gene_name NHSL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021807.4" ; hgnc_id "HGNC:33737" ; level 3 ; orig_coord_info "chrX,72138647,72140773,+" ; protein_id "ENSP00000424079.2" ; tag basic appris_alternative_2 ; transcript_id "NHSL2--SLC43A2^ENST00000510661.2" ; transcript_name "NHSL2-202" ; transcript_support_level 1 ; transcript_type protein_coding
NHSL2--SLC43A2 ENSEMBL mRNA 8017 13520 . + . FI_gene_label "NHSL2^ENSG00000204131.9" ; ID "NHSL2--SLC43A2^ENST00000510661.2" ; Parent "NHSL2--SLC43A2^NHSL2^ENSG00000204131.9" ; exon_id "ENSE00003461107.1" ; exon_number 3 ; gene_id "NHSL2--SLC43A2^NHSL2^ENSG00000204131.9" ; gene_name NHSL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021807.4" ; hgnc_id "HGNC:33737" ; level 3 ; orig_coord_info "chrX,72138647,72140773,+" ; protein_id "ENSP00000424079.2" ; tag basic appris_alternative_2 ; transcript_id "NHSL2--SLC43A2^ENST00000510661.2" ; transcript_name "NHSL2-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PIN4--SLC43A2 HAVANA gene 1324 5427 . + . FI_gene_label "PIN4^ENSG00000102309.15" ; ID "PIN4--SLC43A2^PIN4^ENSG00000102309.15" ; exon_id "ENSE00001306206.2" ; exon_number 1 ; gene_id "PIN4--SLC43A2^PIN4^ENSG00000102309.15" ; gene_name PIN4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021811.6" ; havana_transcript "OTTHUMT00000057176.3" ; hgnc_id "HGNC:8992" ; level 2 ; orig_coord_info "chrX,72181786,72181828,+" ; protein_id "ENSP00000218432.6" ; tag upstream_ATG basic ; transcript_id "PIN4--SLC43A2^ENST00000218432.10" ; transcript_name "PIN4-201" ; transcript_support_level 2 ; transcript_type protein_coding
PIN4--SLC43A2 HAVANA mRNA 1324 5427 . + . FI_gene_label "PIN4^ENSG00000102309.15" ; ID "PIN4--SLC43A2^ENST00000218432.10" ; Parent "PIN4--SLC43A2^PIN4^ENSG00000102309.15" ; exon_id "ENSE00001306206.2" ; exon_number 1 ; gene_id "PIN4--SLC43A2^PIN4^ENSG00000102309.15" ; gene_name PIN4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021811.6" ; havana_transcript "OTTHUMT00000057176.3" ; hgnc_id "HGNC:8992" ; level 2 ; orig_coord_info "chrX,72181786,72181828,+" ; protein_id "ENSP00000218432.6" ; tag upstream_ATG basic ; transcript_id "PIN4--SLC43A2^ENST00000218432.10" ; transcript_name "PIN4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PIN4--SLC43A2 HAVANA gene 14410 38823 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "PIN4--SLC43A2^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "PIN4--SLC43A2^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PIN4--SLC43A2^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PIN4--SLC43A2 HAVANA mRNA 14410 38823 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "PIN4--SLC43A2^ENST00000301335.10" ; Parent "PIN4--SLC43A2^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "PIN4--SLC43A2^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PIN4--SLC43A2^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC43A2--SEPTIN11 HAVANA gene 28468 52215 . + . FI_gene_label "SEPTIN11^ENSG00000138758.12" ; ID "SLC43A2--SEPTIN11^SEPTIN11^ENSG00000138758.12" ; ccdsid "CCDS34018.1" ; exon_id "ENSE00002079778.2" ; exon_number 1 ; gene_id "SLC43A2--SEPTIN11^SEPTIN11^ENSG00000138758.12" ; gene_name SEPTIN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160854.2" ; havana_transcript "OTTHUMT00000362676.1" ; hgnc_id "HGNC:25589" ; level 2 ; orig_coord_info "chr4,76949904,76949930,+" ; protein_id "ENSP00000264893.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SEPTIN11^ENST00000264893.11" ; transcript_name "SEPTIN11-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC43A2--SEPTIN11 HAVANA mRNA 28468 52215 . + . FI_gene_label "SEPTIN11^ENSG00000138758.12" ; ID "SLC43A2--SEPTIN11^ENST00000264893.11" ; Parent "SLC43A2--SEPTIN11^SEPTIN11^ENSG00000138758.12" ; ccdsid "CCDS34018.1" ; exon_id "ENSE00002079778.2" ; exon_number 1 ; gene_id "SLC43A2--SEPTIN11^SEPTIN11^ENSG00000138758.12" ; gene_name SEPTIN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160854.2" ; havana_transcript "OTTHUMT00000362676.1" ; hgnc_id "HGNC:25589" ; level 2 ; orig_coord_info "chr4,76949904,76949930,+" ; protein_id "ENSP00000264893.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SEPTIN11^ENST00000264893.11" ; transcript_name "SEPTIN11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC43A2--SEPTIN11 HAVANA gene 1053 25466 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "SLC43A2--SEPTIN11^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "SLC43A2--SEPTIN11^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SEPTIN11^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC43A2--SEPTIN11 HAVANA mRNA 1053 25466 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "SLC43A2--SEPTIN11^ENST00000301335.10" ; Parent "SLC43A2--SEPTIN11^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "SLC43A2--SEPTIN11^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SEPTIN11^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC43A2--SOWAHB HAVANA gene 1053 25466 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "SLC43A2--SOWAHB^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "SLC43A2--SOWAHB^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SOWAHB^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC43A2--SOWAHB HAVANA mRNA 1053 25466 . + . FI_gene_label "SLC43A2^ENSG00000167703.15" ; ID "SLC43A2--SOWAHB^ENST00000301335.10" ; Parent "SLC43A2--SOWAHB^SLC43A2^ENSG00000167703.15" ; ccdsid "CCDS11006.1" ; exon_id "ENSE00003570444.1" ; exon_number 2 ; gene_id "SLC43A2--SOWAHB^SLC43A2^ENSG00000167703.15" ; gene_name SLC43A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090345.7" ; havana_transcript "OTTHUMT00000206717.4" ; hgnc_id "HGNC:23087" ; level 2 ; orig_coord_info "chr17,1627715,1627874,-" ; protein_id "ENSP00000301335.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SLC43A2--SOWAHB^ENST00000301335.10" ; transcript_name "SLC43A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC43A2--SOWAHB HAVANA gene 28467 32459 . + . FI_gene_label "SOWAHB^ENSG00000186212.4" ; ID "SLC43A2--SOWAHB^SOWAHB^ENSG00000186212.4" ; ccdsid "CCDS34017.1" ; exon_id "ENSE00001331297.4" ; exon_number 1 ; gene_id "SLC43A2--SOWAHB^SOWAHB^ENSG00000186212.4" ; gene_name SOWAHB ; gene_type protein_coding ; havana_gene "OTTHUMG00000160876.2" ; havana_transcript "OTTHUMT00000362762.2" ; hgnc_id "HGNC:32958" ; level 2 ; orig_coord_info "chr4,76895471,76897849,-" ; protein_id "ENSP00000334879.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC43A2--SOWAHB^ENST00000334306.4" ; transcript_name "SOWAHB-201" ; transcript_support_level NA ; transcript_type protein_coding
SLC43A2--SOWAHB HAVANA mRNA 28467 32459 . + . FI_gene_label "SOWAHB^ENSG00000186212.4" ; ID "SLC43A2--SOWAHB^ENST00000334306.4" ; Parent "SLC43A2--SOWAHB^SOWAHB^ENSG00000186212.4" ; ccdsid "CCDS34017.1" ; exon_id "ENSE00001331297.4" ; exon_number 1 ; gene_id "SLC43A2--SOWAHB^SOWAHB^ENSG00000186212.4" ; gene_name SOWAHB ; gene_type protein_coding ; havana_gene "OTTHUMG00000160876.2" ; havana_transcript "OTTHUMT00000362762.2" ; hgnc_id "HGNC:32958" ; level 2 ; orig_coord_info "chr4,76895471,76897849,-" ; protein_id "ENSP00000334879.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC43A2--SOWAHB^ENST00000334306.4" ; transcript_name "SOWAHB-201" ; transcript_support_level NA ; 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--AL669831.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AL669831.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AL669831.1^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--AL669831.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AL669831.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AL669831.1^ENST00000326270.13" ; Parent "TLK2--AL669831.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AL669831.1^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--AL669831.1^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:
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:
GTF2A1L--STON1-GTF2A1L HAVANA gene 14395 15764 . + . FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21" ; ID "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; exon_id "ENSE00001916353.1" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; gene_name "STON1-GTF2A1L" ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6" ; havana_transcript "OTTHUMT00000325207.1" ; hgnc_id "HGNC:30651" ; level 1 ; orig_coord_info "chr2,48768954,48769121,+" ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; transcript_name "STON1-GTF2A1L-205" ; transcript_support_level 5 ; transcript_type processed_transcript
GTF2A1L--STON1-GTF2A1L HAVANA RNA 14395 15764 . + . FI_gene_label "STON1-GTF2A1L^ENSG00000068781.21" ; ID "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; Parent "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; exon_id "ENSE00001916353.1" ; exon_number 1 ; gene_id "GTF2A1L--STON1-GTF2A1L^STON1-GTF2A1L^ENSG00000068781.21" ; gene_name "STON1-GTF2A1L" ; gene_type protein_coding ; havana_gene "OTTHUMG00000152037.6" ; havana_transcript "OTTHUMT00000325207.1" ; hgnc_id "HGNC:30651" ; level 1 ; orig_coord_info "chr2,48768954,48769121,+" ; tag exp_conf ; transcript_id "GTF2A1L--STON1-GTF2A1L^ENST00000463040.5" ; transcript_name "STON1-GTF2A1L-205" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
GUSBP13--NAIP HAVANA gene 1001 5633 . + . FI_gene_label "GUSBP13^ENSG00000198237.8" ; ID "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; exon_id "ENSE00002091111.1" ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1" ; havana_transcript "OTTHUMT00000379319.1" ; hgnc_id "HGNC:54495" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr5,69875271,69875319,+" ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2" ; transcript_name "GUSBP13-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GUSBP13--NAIP HAVANA RNA 1001 5633 . + . FI_gene_label "GUSBP13^ENSG00000198237.8" ; ID "GUSBP13--NAIP^ENST00000506490.2" ; Parent "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; exon_id "ENSE00002091111.1" ; exon_number 1 ; gene_id "GUSBP13--NAIP^GUSBP13^ENSG00000198237.8" ; gene_name GUSBP13 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000164581.1" ; havana_transcript "OTTHUMT00000379319.1" ; hgnc_id "HGNC:54495" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr5,69875271,69875319,+" ; tag basic ; transcript_id "GUSBP13--NAIP^ENST00000506490.2" ; transcript_name "GUSBP13-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
TLK2--AL669831.1 HAVANA gene 41389 47379 . + . FI_gene_label "AL669831.1^ENSG00000228327.3" ; ID "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3" ; exon_id "ENSE00001630466.1" ; exon_number 1 ; gene_id "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3" ; gene_name "AL669831.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2" ; havana_transcript "OTTHUMT00000488438.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,774171,774280,-" ; tag basic ; transcript_id "TLK2--AL669831.1^ENST00000428504.2" ; transcript_name "AL669831.1-202" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--AL669831.1 HAVANA RNA 41389 47379 . + . FI_gene_label "AL669831.1^ENSG00000228327.3" ; ID "TLK2--AL669831.1^ENST00000428504.2" ; Parent "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3" ; exon_id "ENSE00001630466.1" ; exon_number 1 ; gene_id "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3" ; gene_name "AL669831.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2" ; havana_transcript "OTTHUMT00000488438.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,774171,774280,-" ; tag basic ; transcript_id "TLK2--AL669831.1^ENST00000428504.2" ; transcript_name "AL669831.1-202" ; 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
195 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
385 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 19 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed