Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/7f1a3a1b61108860e6623e05b5be70/fi_workdir/tih_rna_sample_00414_23H5VFLT4_s40.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/bd26b4fd532ef6cf85873ff2ef7e4b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/bd26b4fd532ef6cf85873ff2ef7e4b/.command.run
==> STAGING COMPLETE (3 inputs)
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: 9421
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 9421
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:9421
=> 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:
AC009055.1--ASIC2 HAVANA gene 12504 25985 . + . FI_gene_label "ASIC2^ENSG00000108684.15" ; ID "AC009055.1--ASIC2^ASIC2^ENSG00000108684.15" ; ccdsid "CCDS11276.1" ; exon_id "ENSE00001248823.4" ; exon_number 1 ; gene_id "AC009055.1--ASIC2^ASIC2^ENSG00000108684.15" ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4" ; havana_transcript "OTTHUMT00000256378.1" ; hgnc_id "HGNC:99" ; level 2 ; orig_coord_info "chr17,33291408,33292115,-" ; protein_id "ENSP00000225823.2" ; tag basic MANE_Select CCDS ; transcript_id "AC009055.1--ASIC2^ENST00000225823.7" ; transcript_name "ASIC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC009055.1--ASIC2 HAVANA mRNA 12504 25985 . + . FI_gene_label "ASIC2^ENSG00000108684.15" ; ID "AC009055.1--ASIC2^ENST00000225823.7" ; Parent "AC009055.1--ASIC2^ASIC2^ENSG00000108684.15" ; ccdsid "CCDS11276.1" ; exon_id "ENSE00001248823.4" ; exon_number 1 ; gene_id "AC009055.1--ASIC2^ASIC2^ENSG00000108684.15" ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4" ; havana_transcript "OTTHUMT00000256378.1" ; hgnc_id "HGNC:99" ; level 2 ; orig_coord_info "chr17,33291408,33292115,-" ; protein_id "ENSP00000225823.2" ; tag basic MANE_Select CCDS ; transcript_id "AC009055.1--ASIC2^ENST00000225823.7" ; transcript_name "ASIC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
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:
APBB2--KCTD8 HAVANA gene 2210 37225 . + . FI_gene_label "APBB2^ENSG00000163697.17" ; ID "APBB2--KCTD8^APBB2^ENSG00000163697.17" ; ccdsid "CCDS54761.1" ; exon_id "ENSE00001308464.1" ; exon_number 5 ; gene_id "APBB2--KCTD8^APBB2^ENSG00000163697.17" ; gene_name APBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160416.12" ; havana_transcript "OTTHUMT00000360523.3" ; hgnc_id "HGNC:582" ; level 2 ; orig_coord_info "chr4,41033236,41033254,-" ; protein_id "ENSP00000295974.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "APBB2--KCTD8^ENST00000295974.12" ; transcript_name "APBB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
APBB2--KCTD8 HAVANA mRNA 2210 37225 . + . FI_gene_label "APBB2^ENSG00000163697.17" ; ID "APBB2--KCTD8^ENST00000295974.12" ; Parent "APBB2--KCTD8^APBB2^ENSG00000163697.17" ; ccdsid "CCDS54761.1" ; exon_id "ENSE00001308464.1" ; exon_number 5 ; gene_id "APBB2--KCTD8^APBB2^ENSG00000163697.17" ; gene_name APBB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160416.12" ; havana_transcript "OTTHUMT00000360523.3" ; hgnc_id "HGNC:582" ; level 2 ; orig_coord_info "chr4,41033236,41033254,-" ; protein_id "ENSP00000295974.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "APBB2--KCTD8^ENST00000295974.12" ; transcript_name "APBB2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
APBB2--KCTD8 HAVANA gene 40226 45248 . + . FI_gene_label "KCTD8^ENSG00000183783.7" ; ID "APBB2--KCTD8^KCTD8^ENSG00000183783.7" ; ccdsid "CCDS3467.1" ; exon_id "ENSE00001400795.4" ; exon_number 1 ; gene_id "APBB2--KCTD8^KCTD8^ENSG00000183783.7" ; gene_name KCTD8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099409.4" ; havana_transcript "OTTHUMT00000216868.2" ; hgnc_id "HGNC:22394" ; level 2 ; orig_coord_info "chr4,44447563,44448523,-" ; protein_id "ENSP00000353129.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "APBB2--KCTD8^ENST00000360029.4" ; transcript_name "KCTD8-201" ; transcript_support_level 1 ; transcript_type protein_coding
APBB2--KCTD8 HAVANA mRNA 40226 45248 . + . FI_gene_label "KCTD8^ENSG00000183783.7" ; ID "APBB2--KCTD8^ENST00000360029.4" ; Parent "APBB2--KCTD8^KCTD8^ENSG00000183783.7" ; ccdsid "CCDS3467.1" ; exon_id "ENSE00001400795.4" ; exon_number 1 ; gene_id "APBB2--KCTD8^KCTD8^ENSG00000183783.7" ; gene_name KCTD8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000099409.4" ; havana_transcript "OTTHUMT00000216868.2" ; hgnc_id "HGNC:22394" ; level 2 ; orig_coord_info "chr4,44447563,44448523,-" ; protein_id "ENSP00000353129.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "APBB2--KCTD8^ENST00000360029.4" ; transcript_name "KCTD8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CIITA--NEDD4L HAVANA gene 40981 112212 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "CIITA--NEDD4L^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "CIITA--NEDD4L^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "CIITA--NEDD4L^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
CIITA--NEDD4L HAVANA mRNA 40981 112212 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "CIITA--NEDD4L^ENST00000256830.13" ; Parent "CIITA--NEDD4L^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "CIITA--NEDD4L^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "CIITA--NEDD4L^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CIITA--NEDD4L HAVANA gene 2356 34242 . + . FI_gene_label "CIITA^ENSG00000179583.20" ; ID "CIITA--NEDD4L^CIITA^ENSG00000179583.20" ; ccdsid "CCDS10544.1" ; exon_id "ENSE00003915466.1" ; exon_number 1 ; gene_id "CIITA--NEDD4L^CIITA^ENSG00000179583.20" ; gene_name CIITA ; gene_type protein_coding ; havana_gene "OTTHUMG00000129753.7" ; havana_transcript "OTTHUMT00000251966.5" ; hgnc_id "HGNC:7067" ; level 2 ; orig_coord_info "chr16,10877331,10877382,+" ; protein_id "ENSP00000316328.8" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "CIITA--NEDD4L^ENST00000324288.14" ; transcript_name "CIITA-201" ; transcript_support_level 1 ; transcript_type protein_coding
CIITA--NEDD4L HAVANA mRNA 2356 34242 . + . FI_gene_label "CIITA^ENSG00000179583.20" ; ID "CIITA--NEDD4L^ENST00000324288.14" ; Parent "CIITA--NEDD4L^CIITA^ENSG00000179583.20" ; ccdsid "CCDS10544.1" ; exon_id "ENSE00003915466.1" ; exon_number 1 ; gene_id "CIITA--NEDD4L^CIITA^ENSG00000179583.20" ; gene_name CIITA ; gene_type protein_coding ; havana_gene "OTTHUMG00000129753.7" ; havana_transcript "OTTHUMT00000251966.5" ; hgnc_id "HGNC:7067" ; level 2 ; orig_coord_info "chr16,10877331,10877382,+" ; protein_id "ENSP00000316328.8" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "CIITA--NEDD4L^ENST00000324288.14" ; transcript_name "CIITA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EIF2B3--NEDD4L HAVANA gene 25377 96608 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "EIF2B3--NEDD4L^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "EIF2B3--NEDD4L^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "EIF2B3--NEDD4L^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
EIF2B3--NEDD4L HAVANA mRNA 25377 96608 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "EIF2B3--NEDD4L^ENST00000256830.13" ; Parent "EIF2B3--NEDD4L^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "EIF2B3--NEDD4L^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "EIF2B3--NEDD4L^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
EIF2B3--NEDD4L HAVANA gene 1128 21941 . + . FI_gene_label "EIF2B3^ENSG00000070785.17" ; ID "EIF2B3--NEDD4L^EIF2B3^ENSG00000070785.17" ; ccdsid "CCDS517.1" ; exon_id "ENSE00003470577.1" ; exon_number 2 ; gene_id "EIF2B3--NEDD4L^EIF2B3^ENSG00000070785.17" ; gene_name EIF2B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008585.5" ; havana_transcript "OTTHUMT00000023724.2" ; hgnc_id "HGNC:3259" ; level 2 ; orig_coord_info "chr1,44981021,44981168,-" ; protein_id "ENSP00000353575.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2B3--NEDD4L^ENST00000360403.7" ; transcript_name "EIF2B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
EIF2B3--NEDD4L HAVANA mRNA 1128 21941 . + . FI_gene_label "EIF2B3^ENSG00000070785.17" ; ID "EIF2B3--NEDD4L^ENST00000360403.7" ; Parent "EIF2B3--NEDD4L^EIF2B3^ENSG00000070785.17" ; ccdsid "CCDS517.1" ; exon_id "ENSE00003470577.1" ; exon_number 2 ; gene_id "EIF2B3--NEDD4L^EIF2B3^ENSG00000070785.17" ; gene_name EIF2B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008585.5" ; havana_transcript "OTTHUMT00000023724.2" ; hgnc_id "HGNC:3259" ; level 2 ; orig_coord_info "chr1,44981021,44981168,-" ; protein_id "ENSP00000353575.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2B3--NEDD4L^ENST00000360403.7" ; transcript_name "EIF2B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NEDD4L--AC005670.3 HAVANA gene 1436 72667 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "NEDD4L--AC005670.3^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "NEDD4L--AC005670.3^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "NEDD4L--AC005670.3^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
NEDD4L--AC005670.3 HAVANA mRNA 1436 72667 . + . FI_gene_label "NEDD4L^ENSG00000049759.20" ; ID "NEDD4L--AC005670.3^ENST00000256830.13" ; Parent "NEDD4L--AC005670.3^NEDD4L^ENSG00000049759.20" ; exon_id "ENSE00002934128.1" ; exon_number 1 ; gene_id "NEDD4L--AC005670.3^NEDD4L^ENSG00000049759.20" ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12" ; havana_transcript "OTTHUMT00000449050.2" ; hgnc_id "HGNC:7728" ; level 1 ; orig_coord_info "chr18,58044661,58044708,+" ; protein_id "ENSP00000256830.8" ; tag basic exp_conf ; transcript_id "NEDD4L--AC005670.3^ENST00000256830.13" ; transcript_name "NEDD4L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
NPM1--MT-RNR2 HAVANA gene 1734 14723 . + . FI_gene_label "NPM1^ENSG00000181163.14" ; ID "NPM1--MT-RNR2^NPM1^ENSG00000181163.14" ; ccdsid "CCDS4376.1" ; exon_id "ENSE00003906984.1" ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14" ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4" ; havana_transcript "OTTHUMT00000252858.2" ; hgnc_id "HGNC:7910" ; level 2 ; orig_coord_info "chr5,171387949,171388006,+" ; protein_id "ENSP00000296930.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10" ; transcript_name "NPM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NPM1--MT-RNR2 HAVANA mRNA 1734 14723 . + . FI_gene_label "NPM1^ENSG00000181163.14" ; ID "NPM1--MT-RNR2^ENST00000296930.10" ; Parent "NPM1--MT-RNR2^NPM1^ENSG00000181163.14" ; ccdsid "CCDS4376.1" ; exon_id "ENSE00003906984.1" ; exon_number 1 ; gene_id "NPM1--MT-RNR2^NPM1^ENSG00000181163.14" ; gene_name NPM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130465.4" ; havana_transcript "OTTHUMT00000252858.2" ; hgnc_id "HGNC:7910" ; level 2 ; orig_coord_info "chr5,171387949,171388006,+" ; protein_id "ENSP00000296930.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPM1--MT-RNR2^ENST00000296930.10" ; transcript_name "NPM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PHLPP1--USPL1 HAVANA gene 33902 46319 . + . FI_gene_label "USPL1^ENSG00000132952.12" ; ID "PHLPP1--USPL1^USPL1^ENSG00000132952.12" ; ccdsid "CCDS9336.1" ; exon_id "ENSE00000906658.1" ; exon_number 2 ; gene_id "PHLPP1--USPL1^USPL1^ENSG00000132952.12" ; gene_name USPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016675.4" ; havana_transcript "OTTHUMT00000044369.2" ; hgnc_id "HGNC:20294" ; level 2 ; orig_coord_info "chr13,30621141,30621239,+" ; protein_id "ENSP00000255304.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHLPP1--USPL1^ENST00000255304.9" ; transcript_name "USPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PHLPP1--USPL1 HAVANA mRNA 33902 46319 . + . FI_gene_label "USPL1^ENSG00000132952.12" ; ID "PHLPP1--USPL1^ENST00000255304.9" ; Parent "PHLPP1--USPL1^USPL1^ENSG00000132952.12" ; ccdsid "CCDS9336.1" ; exon_id "ENSE00000906658.1" ; exon_number 2 ; gene_id "PHLPP1--USPL1^USPL1^ENSG00000132952.12" ; gene_name USPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016675.4" ; havana_transcript "OTTHUMT00000044369.2" ; hgnc_id "HGNC:20294" ; level 2 ; orig_coord_info "chr13,30621141,30621239,+" ; protein_id "ENSP00000255304.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHLPP1--USPL1^ENST00000255304.9" ; transcript_name "USPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PHLPP1--USPL1 HAVANA gene 1001 30674 . + . FI_gene_label "PHLPP1^ENSG00000081913.14" ; ID "PHLPP1--USPL1^PHLPP1^ENSG00000081913.14" ; ccdsid "CCDS45881.2" ; exon_id "ENSE00001234525.5" ; exon_number 1 ; gene_id "PHLPP1--USPL1^PHLPP1^ENSG00000081913.14" ; gene_name PHLPP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150629.4" ; havana_transcript "OTTHUMT00000319249.3" ; hgnc_id "HGNC:20610" ; level 2 ; orig_coord_info "chr18,62715684,62717259,+" ; protein_id "ENSP00000262719.4" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHLPP1--USPL1^ENST00000262719.10" ; transcript_name "PHLPP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PHLPP1--USPL1 HAVANA mRNA 1001 30674 . + . FI_gene_label "PHLPP1^ENSG00000081913.14" ; ID "PHLPP1--USPL1^ENST00000262719.10" ; Parent "PHLPP1--USPL1^PHLPP1^ENSG00000081913.14" ; ccdsid "CCDS45881.2" ; exon_id "ENSE00001234525.5" ; exon_number 1 ; gene_id "PHLPP1--USPL1^PHLPP1^ENSG00000081913.14" ; gene_name PHLPP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150629.4" ; havana_transcript "OTTHUMT00000319249.3" ; hgnc_id "HGNC:20610" ; level 2 ; orig_coord_info "chr18,62715684,62717259,+" ; protein_id "ENSP00000262719.4" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHLPP1--USPL1^ENST00000262719.10" ; transcript_name "PHLPP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PMS2P6--CCDC146 HAVANA gene 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146 HAVANA mRNA 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^ENST00000285871.5" ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RNF126--CORO7 HAVANA gene 14382 37132 . + . FI_gene_label "CORO7^ENSG00000262246.6" ; ID "RNF126--CORO7^CORO7^ENSG00000262246.6" ; ccdsid "CCDS10513.1" ; exon_id "ENSE00002209549.1" ; exon_number 1 ; gene_id "RNF126--CORO7^CORO7^ENSG00000262246.6" ; gene_name CORO7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129465.6" ; havana_transcript "OTTHUMT00000251628.3" ; hgnc_id "HGNC:26161" ; level 2 ; orig_coord_info "chr16,4416459,4416518,-" ; protein_id "ENSP00000251166.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF126--CORO7^ENST00000251166.9" ; transcript_name "CORO7-201" ; transcript_support_level 1 ; transcript_type protein_coding
RNF126--CORO7 HAVANA mRNA 14382 37132 . + . FI_gene_label "CORO7^ENSG00000262246.6" ; ID "RNF126--CORO7^ENST00000251166.9" ; Parent "RNF126--CORO7^CORO7^ENSG00000262246.6" ; ccdsid "CCDS10513.1" ; exon_id "ENSE00002209549.1" ; exon_number 1 ; gene_id "RNF126--CORO7^CORO7^ENSG00000262246.6" ; gene_name CORO7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129465.6" ; havana_transcript "OTTHUMT00000251628.3" ; hgnc_id "HGNC:26161" ; level 2 ; orig_coord_info "chr16,4416459,4416518,-" ; protein_id "ENSP00000251166.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF126--CORO7^ENST00000251166.9" ; transcript_name "CORO7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RNF126--CORO7 HAVANA gene 1020 8593 . + . FI_gene_label "RNF126^ENSG00000070423.18" ; ID "RNF126--CORO7^RNF126^ENSG00000070423.18" ; ccdsid "CCDS12039.1" ; exon_id "ENSE00003702081.2" ; exon_number 1 ; gene_id "RNF126--CORO7^RNF126^ENSG00000070423.18" ; gene_name RNF126 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180592.10" ; havana_transcript "OTTHUMT00000452104.7" ; hgnc_id "HGNC:21151" ; level 2 ; orig_coord_info "chr19,663047,663121,-" ; protein_id "ENSP00000292363.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF126--CORO7^ENST00000292363.10" ; transcript_name "RNF126-201" ; transcript_support_level 1 ; transcript_type protein_coding
RNF126--CORO7 HAVANA mRNA 1020 8593 . + . FI_gene_label "RNF126^ENSG00000070423.18" ; ID "RNF126--CORO7^ENST00000292363.10" ; Parent "RNF126--CORO7^RNF126^ENSG00000070423.18" ; ccdsid "CCDS12039.1" ; exon_id "ENSE00003702081.2" ; exon_number 1 ; gene_id "RNF126--CORO7^RNF126^ENSG00000070423.18" ; gene_name RNF126 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180592.10" ; havana_transcript "OTTHUMT00000452104.7" ; hgnc_id "HGNC:21151" ; level 2 ; orig_coord_info "chr19,663047,663121,-" ; protein_id "ENSP00000292363.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF126--CORO7^ENST00000292363.10" ; transcript_name "RNF126-201" ; 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:
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:
VCP--FP236383.6 HAVANA gene 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP236383.6^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP236383.6^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP236383.6^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
VCP--FP236383.6 HAVANA mRNA 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP236383.6^ENST00000358901.11" ; Parent "VCP--FP236383.6^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP236383.6^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP236383.6^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VCP--FP671120.11 HAVANA gene 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP671120.11^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP671120.11^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP671120.11^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
VCP--FP671120.11 HAVANA mRNA 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP671120.11^ENST00000358901.11" ; Parent "VCP--FP671120.11^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP671120.11^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP671120.11^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VCP--FP671120.9 HAVANA gene 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP671120.9^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP671120.9^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP671120.9^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
VCP--FP671120.9 HAVANA mRNA 1044 15600 . + . FI_gene_label "VCP^ENSG00000165280.18" ; ID "VCP--FP671120.9^ENST00000358901.11" ; Parent "VCP--FP671120.9^VCP^ENSG00000165280.18" ; ccdsid "CCDS6573.1" ; exon_id "ENSE00001885505.2" ; exon_number 1 ; gene_id "VCP--FP671120.9^VCP^ENSG00000165280.18" ; gene_name VCP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019855.5" ; havana_transcript "OTTHUMT00000052290.2" ; hgnc_id "HGNC:12666" ; level 2 ; orig_coord_info "chr9,35072337,35072353,-" ; protein_id "ENSP00000351777.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "VCP--FP671120.9^ENST00000358901.11" ; transcript_name "VCP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF629--PTOV1 HAVANA gene 1001 8238 . + . FI_gene_label "ZNF629^ENSG00000102870.6" ; ID "ZNF629--PTOV1^ZNF629^ENSG00000102870.6" ; ccdsid "CCDS45463.1" ; exon_id "ENSE00000682598.1" ; exon_number 2 ; gene_id "ZNF629--PTOV1^ZNF629^ENSG00000102870.6" ; gene_name ZNF629 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176905.3" ; havana_transcript "OTTHUMT00000434291.3" ; hgnc_id "HGNC:29008" ; level 2 ; orig_coord_info "chr16,30784410,30784482,-" ; protein_id "ENSP00000262525.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF629--PTOV1^ENST00000262525.6" ; transcript_name "ZNF629-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF629--PTOV1 HAVANA mRNA 1001 8238 . + . FI_gene_label "ZNF629^ENSG00000102870.6" ; ID "ZNF629--PTOV1^ENST00000262525.6" ; Parent "ZNF629--PTOV1^ZNF629^ENSG00000102870.6" ; ccdsid "CCDS45463.1" ; exon_id "ENSE00000682598.1" ; exon_number 2 ; gene_id "ZNF629--PTOV1^ZNF629^ENSG00000102870.6" ; gene_name ZNF629 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176905.3" ; havana_transcript "OTTHUMT00000434291.3" ; hgnc_id "HGNC:29008" ; level 2 ; orig_coord_info "chr16,30784410,30784482,-" ; protein_id "ENSP00000262525.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF629--PTOV1^ENST00000262525.6" ; transcript_name "ZNF629-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF629--PTOV1 ENSEMBL gene 11663 20406 . + . FI_gene_label "PTOV1^ENSG00000104960.15" ; ID "ZNF629--PTOV1^PTOV1^ENSG00000104960.15" ; ccdsid "CCDS12782.1" ; exon_id "ENSE00001509862.1" ; exon_number 1 ; gene_id "ZNF629--PTOV1^PTOV1^ENSG00000104960.15" ; gene_name PTOV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183162.3" ; hgnc_id "HGNC:9632" ; level 3 ; orig_coord_info "chr19,49851329,49851499,+" ; protein_id "ENSP00000375717.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF629--PTOV1^ENST00000391842.5" ; transcript_name "PTOV1-201" ; transcript_support_level 5 ; transcript_type protein_coding
ZNF629--PTOV1 ENSEMBL mRNA 11663 20406 . + . FI_gene_label "PTOV1^ENSG00000104960.15" ; ID "ZNF629--PTOV1^ENST00000391842.5" ; Parent "ZNF629--PTOV1^PTOV1^ENSG00000104960.15" ; ccdsid "CCDS12782.1" ; exon_id "ENSE00001509862.1" ; exon_number 1 ; gene_id "ZNF629--PTOV1^PTOV1^ENSG00000104960.15" ; gene_name PTOV1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183162.3" ; hgnc_id "HGNC:9632" ; level 3 ; orig_coord_info "chr19,49851329,49851499,+" ; protein_id "ENSP00000375717.1" ; tag basic appris_principal_1 CCDS ; transcript_id "ZNF629--PTOV1^ENST00000391842.5" ; transcript_name "PTOV1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AC009055.1--ASIC2 HAVANA gene 1001 5781 . + . FI_gene_label "AC009055.1^ENSG00000260364.1" ; ID "AC009055.1--ASIC2^AC009055.1^ENSG00000260364.1" ; exon_id "ENSE00002627183.1" ; exon_number 1 ; gene_id "AC009055.1--ASIC2^AC009055.1^ENSG00000260364.1" ; gene_name "AC009055.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172811.2" ; havana_transcript "OTTHUMT00000420600.2" ; level 2 ; orig_coord_info "chr16,65233056,65233180,+" ; tag basic ; transcript_id "AC009055.1--ASIC2^ENST00000562656.1" ; transcript_name "AC009055.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC009055.1--ASIC2 HAVANA RNA 1001 5781 . + . FI_gene_label "AC009055.1^ENSG00000260364.1" ; ID "AC009055.1--ASIC2^ENST00000562656.1" ; Parent "AC009055.1--ASIC2^AC009055.1^ENSG00000260364.1" ; exon_id "ENSE00002627183.1" ; exon_number 1 ; gene_id "AC009055.1--ASIC2^AC009055.1^ENSG00000260364.1" ; gene_name "AC009055.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172811.2" ; havana_transcript "OTTHUMT00000420600.2" ; level 2 ; orig_coord_info "chr16,65233056,65233180,+" ; tag basic ; transcript_id "AC009055.1--ASIC2^ENST00000562656.1" ; transcript_name "AC009055.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
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:
NEDD4L--AC005670.3 HAVANA gene 85693 107712 . + . FI_gene_label "AC005670.3^ENSG00000262879.6" ; ID "NEDD4L--AC005670.3^AC005670.3^ENSG00000262879.6" ; exon_id "ENSE00003857049.1" ; exon_number 1 ; gene_id "NEDD4L--AC005670.3^AC005670.3^ENSG00000262879.6" ; gene_name "AC005670.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000178188.23" ; havana_transcript "OTTHUMT00000440922.2" ; level 2 ; orig_coord_info "chr17,47067414,47067513,-" ; tag TAGENE ; transcript_id "NEDD4L--AC005670.3^ENST00000570314.2" ; transcript_name "AC005670.3-210" ; transcript_support_level 3 ; transcript_type lncRNA
NEDD4L--AC005670.3 HAVANA RNA 85693 107712 . + . FI_gene_label "AC005670.3^ENSG00000262879.6" ; ID "NEDD4L--AC005670.3^ENST00000570314.2" ; Parent "NEDD4L--AC005670.3^AC005670.3^ENSG00000262879.6" ; exon_id "ENSE00003857049.1" ; exon_number 1 ; gene_id "NEDD4L--AC005670.3^AC005670.3^ENSG00000262879.6" ; gene_name "AC005670.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000178188.23" ; havana_transcript "OTTHUMT00000440922.2" ; level 2 ; orig_coord_info "chr17,47067414,47067513,-" ; tag TAGENE ; transcript_id "NEDD4L--AC005670.3^ENST00000570314.2" ; transcript_name "AC005670.3-210" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
NPM1--MT-RNR2 ENSEMBL gene 18634 20192 . + . FI_gene_label "MT-RNR2^ENSG00000210082.2" ; ID "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2" ; exon_id "ENSE00001544497.2" ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2" ; gene_name "MT-RNR2" ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471" ; level 3 ; orig_coord_info "chrM,1671,3229,+" ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2" ; transcript_name "MT-RNR2-201" ; transcript_support_level NA ; transcript_type Mt_rRNA
NPM1--MT-RNR2 ENSEMBL RNA 18634 20192 . + . FI_gene_label "MT-RNR2^ENSG00000210082.2" ; ID "NPM1--MT-RNR2^ENST00000387347.2" ; Parent "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2" ; exon_id "ENSE00001544497.2" ; exon_number 1 ; gene_id "NPM1--MT-RNR2^MT-RNR2^ENSG00000210082.2" ; gene_name "MT-RNR2" ; gene_type Mt_rRNA ; hgnc_id "HGNC:7471" ; level 3 ; orig_coord_info "chrM,1671,3229,+" ; tag basic ; transcript_id "NPM1--MT-RNR2^ENST00000387347.2" ; transcript_name "MT-RNR2-201" ; transcript_support_level NA ; transcript_type Mt_rRNA
L1 and L2 created:
PMS2P6--CCDC146 HAVANA gene 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146 HAVANA RNA 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^ENST00000333674.5" ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; 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:
VCP--FP236383.6 HAVANA gene 20737 21069 . + . FI_gene_label "FP236383.6^ENSG00000286032.1" ; ID "VCP--FP236383.6^FP236383.6^ENSG00000286032.1" ; exon_id "ENSE00003846747.1" ; exon_number 1 ; gene_id "VCP--FP236383.6^FP236383.6^ENSG00000286032.1" ; gene_name "FP236383.6" ; gene_type TEC ; havana_gene "OTTHUMG00000193762.1" ; havana_transcript "OTTHUMT00000504496.1" ; level 2 ; orig_coord_info "chr21,8465254,8465586,+" ; tag basic ; transcript_id "VCP--FP236383.6^ENST00000651130.1" ; transcript_name "FP236383.6-201" ; transcript_type TEC
VCP--FP236383.6 HAVANA RNA 20737 21069 . + . FI_gene_label "FP236383.6^ENSG00000286032.1" ; ID "VCP--FP236383.6^ENST00000651130.1" ; Parent "VCP--FP236383.6^FP236383.6^ENSG00000286032.1" ; exon_id "ENSE00003846747.1" ; exon_number 1 ; gene_id "VCP--FP236383.6^FP236383.6^ENSG00000286032.1" ; gene_name "FP236383.6" ; gene_type TEC ; havana_gene "OTTHUMG00000193762.1" ; havana_transcript "OTTHUMT00000504496.1" ; level 2 ; orig_coord_info "chr21,8465254,8465586,+" ; tag basic ; transcript_id "VCP--FP236383.6^ENST00000651130.1" ; transcript_name "FP236383.6-201" ; transcript_type TEC
L1 and L2 created:
VCP--FP671120.11 HAVANA gene 20737 21067 . + . FI_gene_label "FP671120.11^ENSG00000286252.1" ; ID "VCP--FP671120.11^FP671120.11^ENSG00000286252.1" ; exon_id "ENSE00003841268.1" ; exon_number 1 ; gene_id "VCP--FP671120.11^FP671120.11^ENSG00000286252.1" ; gene_name "FP671120.11" ; gene_type TEC ; havana_gene "OTTHUMG00000193754.1" ; havana_transcript "OTTHUMT00000504488.1" ; level 2 ; orig_coord_info "chr21,8237649,8237979,+" ; tag basic ; transcript_id "VCP--FP671120.11^ENST00000651797.1" ; transcript_name "FP671120.11-201" ; transcript_type TEC
VCP--FP671120.11 HAVANA RNA 20737 21067 . + . FI_gene_label "FP671120.11^ENSG00000286252.1" ; ID "VCP--FP671120.11^ENST00000651797.1" ; Parent "VCP--FP671120.11^FP671120.11^ENSG00000286252.1" ; exon_id "ENSE00003841268.1" ; exon_number 1 ; gene_id "VCP--FP671120.11^FP671120.11^ENSG00000286252.1" ; gene_name "FP671120.11" ; gene_type TEC ; havana_gene "OTTHUMG00000193754.1" ; havana_transcript "OTTHUMT00000504488.1" ; level 2 ; orig_coord_info "chr21,8237649,8237979,+" ; tag basic ; transcript_id "VCP--FP671120.11^ENST00000651797.1" ; transcript_name "FP671120.11-201" ; transcript_type TEC
L1 and L2 created:
VCP--FP671120.9 HAVANA gene 20737 20970 . + . FI_gene_label "FP671120.9^ENSG00000286057.1" ; ID "VCP--FP671120.9^FP671120.9^ENSG00000286057.1" ; exon_id "ENSE00003846470.1" ; exon_number 1 ; gene_id "VCP--FP671120.9^FP671120.9^ENSG00000286057.1" ; gene_name "FP671120.9" ; gene_type TEC ; havana_gene "OTTHUMG00000193755.1" ; havana_transcript "OTTHUMT00000504489.1" ; level 2 ; orig_coord_info "chr21,8238859,8239092,+" ; tag basic ; transcript_id "VCP--FP671120.9^ENST00000652328.1" ; transcript_name "FP671120.9-201" ; transcript_type TEC
VCP--FP671120.9 HAVANA RNA 20737 20970 . + . FI_gene_label "FP671120.9^ENSG00000286057.1" ; ID "VCP--FP671120.9^ENST00000652328.1" ; Parent "VCP--FP671120.9^FP671120.9^ENSG00000286057.1" ; exon_id "ENSE00003846470.1" ; exon_number 1 ; gene_id "VCP--FP671120.9^FP671120.9^ENSG00000286057.1" ; gene_name "FP671120.9" ; gene_type TEC ; havana_gene "OTTHUMG00000193755.1" ; havana_transcript "OTTHUMT00000504489.1" ; level 2 ; orig_coord_info "chr21,8238859,8239092,+" ; tag basic ; transcript_id "VCP--FP671120.9^ENST00000652328.1" ; transcript_name "FP671120.9-201" ; transcript_type TEC
580 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 ------------------------------
1185 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 23 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