Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c9f0b10f518872bb3ce736508fbaed/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/5c77c4710dbdf6f66879257f05f592/fi_workdir/tih_rna_sample_00115_23H5VFLT4_s35.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c9f0b10f518872bb3ce736508fbaed/.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: 2236
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2236
=> 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:2236
=> 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 0 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:
COL1A1--SLC45A4 HAVANA gene 25435 34927 . + . FI_gene_label "SLC45A4^ENSG00000022567.10" ; ID "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10" ; ccdsid "CCDS34948.1" ; exon_id "ENSE00001475008.1" ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10" ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4" ; havana_transcript "OTTHUMT00000378571.3" ; hgnc_id "HGNC:29196" ; level 2 ; orig_coord_info "chr8,141228179,141228266,-" ; protein_id "ENSP00000024061.3" ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7" ; transcript_name "SLC45A4-201" ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4 HAVANA mRNA 25435 34927 . + . FI_gene_label "SLC45A4^ENSG00000022567.10" ; ID "COL1A1--SLC45A4^ENST00000024061.7" ; Parent "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10" ; ccdsid "CCDS34948.1" ; exon_id "ENSE00001475008.1" ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10" ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4" ; havana_transcript "OTTHUMT00000378571.3" ; hgnc_id "HGNC:29196" ; level 2 ; orig_coord_info "chr8,141228179,141228266,-" ; protein_id "ENSP00000024061.3" ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7" ; transcript_name "SLC45A4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COL1A1--SLC45A4 HAVANA gene 1002 18313 . + . FI_gene_label "COL1A1^ENSG00000108821.14" ; ID "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14" ; ccdsid "CCDS11561.1" ; exon_id "ENSE00003500023.2" ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14" ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9" ; havana_transcript "OTTHUMT00000309036.3" ; hgnc_id "HGNC:2197" ; level 2 ; orig_coord_info "chr17,50201411,50201513,-" ; protein_id "ENSP00000225964.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10" ; transcript_name "COL1A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4 HAVANA mRNA 1002 18313 . + . FI_gene_label "COL1A1^ENSG00000108821.14" ; ID "COL1A1--SLC45A4^ENST00000225964.10" ; Parent "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14" ; ccdsid "CCDS11561.1" ; exon_id "ENSE00003500023.2" ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14" ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9" ; havana_transcript "OTTHUMT00000309036.3" ; hgnc_id "HGNC:2197" ; level 2 ; orig_coord_info "chr17,50201411,50201513,-" ; protein_id "ENSP00000225964.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10" ; transcript_name "COL1A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EFNA2--GPX4 HAVANA gene 1001 6424 . + . FI_gene_label "EFNA2^ENSG00000099617.4" ; ID "EFNA2--GPX4^EFNA2^ENSG00000099617.4" ; ccdsid "CCDS12061.1" ; exon_id "ENSE00000795141.5" ; exon_number 1 ; gene_id "EFNA2--GPX4^EFNA2^ENSG00000099617.4" ; gene_name EFNA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180148.4" ; havana_transcript "OTTHUMT00000450016.4" ; hgnc_id "HGNC:3222" ; level 2 ; orig_coord_info "chr19,1286169,1286308,+" ; protein_id "ENSP00000215368.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFNA2--GPX4^ENST00000215368.4" ; transcript_name "EFNA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFNA2--GPX4 HAVANA mRNA 1001 6424 . + . FI_gene_label "EFNA2^ENSG00000099617.4" ; ID "EFNA2--GPX4^ENST00000215368.4" ; Parent "EFNA2--GPX4^EFNA2^ENSG00000099617.4" ; ccdsid "CCDS12061.1" ; exon_id "ENSE00000795141.5" ; exon_number 1 ; gene_id "EFNA2--GPX4^EFNA2^ENSG00000099617.4" ; gene_name EFNA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180148.4" ; havana_transcript "OTTHUMT00000450016.4" ; hgnc_id "HGNC:3222" ; level 2 ; orig_coord_info "chr19,1286169,1286308,+" ; protein_id "ENSP00000215368.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFNA2--GPX4^ENST00000215368.4" ; transcript_name "EFNA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EFNA2--GPX4 HAVANA gene 9493 12278 . + . FI_gene_label "GPX4^ENSG00000167468.18" ; ID "EFNA2--GPX4^GPX4^ENSG00000167468.18" ; ccdsid "CCDS42457.1" ; exon_id "ENSE00001399156.7" ; exon_number 1 ; gene_id "EFNA2--GPX4^GPX4^ENSG00000167468.18" ; gene_name GPX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181874.11" ; havana_transcript "OTTHUMT00000458052.4" ; hgnc_id "HGNC:4556" ; level 2 ; orig_coord_info "chr19,1104044,1104127,+" ; protein_id "ENSP00000346103.7" ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "EFNA2--GPX4^ENST00000354171.13" ; transcript_name "GPX4-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFNA2--GPX4 HAVANA mRNA 9493 12278 . + . FI_gene_label "GPX4^ENSG00000167468.18" ; ID "EFNA2--GPX4^ENST00000354171.13" ; Parent "EFNA2--GPX4^GPX4^ENSG00000167468.18" ; ccdsid "CCDS42457.1" ; exon_id "ENSE00001399156.7" ; exon_number 1 ; gene_id "EFNA2--GPX4^GPX4^ENSG00000167468.18" ; gene_name GPX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181874.11" ; havana_transcript "OTTHUMT00000458052.4" ; hgnc_id "HGNC:4556" ; level 2 ; orig_coord_info "chr19,1104044,1104127,+" ; protein_id "ENSP00000346103.7" ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "EFNA2--GPX4^ENST00000354171.13" ; transcript_name "GPX4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPHX2--PTK2B HAVANA gene 30387 59569 . + . FI_gene_label "PTK2B^ENSG00000120899.18" ; ID "EPHX2--PTK2B^PTK2B^ENSG00000120899.18" ; ccdsid "CCDS6057.1" ; exon_id "ENSE00000818684.3" ; exon_number 2 ; gene_id "EPHX2--PTK2B^PTK2B^ENSG00000120899.18" ; gene_name PTK2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000102082.9" ; havana_transcript "OTTHUMT00000376116.3" ; hgnc_id "HGNC:9612" ; level 2 ; orig_coord_info "chr8,27397585,27397788,+" ; protein_id "ENSP00000332816.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPHX2--PTK2B^ENST00000346049.10" ; transcript_name "PTK2B-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPHX2--PTK2B HAVANA mRNA 30387 59569 . + . FI_gene_label "PTK2B^ENSG00000120899.18" ; ID "EPHX2--PTK2B^ENST00000346049.10" ; Parent "EPHX2--PTK2B^PTK2B^ENSG00000120899.18" ; ccdsid "CCDS6057.1" ; exon_id "ENSE00000818684.3" ; exon_number 2 ; gene_id "EPHX2--PTK2B^PTK2B^ENSG00000120899.18" ; gene_name PTK2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000102082.9" ; havana_transcript "OTTHUMT00000376116.3" ; hgnc_id "HGNC:9612" ; level 2 ; orig_coord_info "chr8,27397585,27397788,+" ; protein_id "ENSP00000332816.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "EPHX2--PTK2B^ENST00000346049.10" ; transcript_name "PTK2B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPHX2--PTK2B HAVANA gene 1386 21697 . + . FI_gene_label "EPHX2^ENSG00000120915.14" ; ID "EPHX2--PTK2B^EPHX2^ENSG00000120915.14" ; ccdsid "CCDS59097.1" ; exon_id "ENSE00002129396.1" ; exon_number 2 ; gene_id "EPHX2--PTK2B^EPHX2^ENSG00000120915.14" ; gene_name EPHX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000102115.7" ; havana_transcript "OTTHUMT00000376138.1" ; hgnc_id "HGNC:3402" ; level 2 ; orig_coord_info "chr8,27500984,27501010,+" ; protein_id "ENSP00000369843.3" ; tag alternative_5_UTR basic CCDS ; transcript_id "EPHX2--PTK2B^ENST00000380476.7" ; transcript_name "EPHX2-201" ; transcript_support_level 2 ; transcript_type protein_coding
EPHX2--PTK2B HAVANA mRNA 1386 21697 . + . FI_gene_label "EPHX2^ENSG00000120915.14" ; ID "EPHX2--PTK2B^ENST00000380476.7" ; Parent "EPHX2--PTK2B^EPHX2^ENSG00000120915.14" ; ccdsid "CCDS59097.1" ; exon_id "ENSE00002129396.1" ; exon_number 2 ; gene_id "EPHX2--PTK2B^EPHX2^ENSG00000120915.14" ; gene_name EPHX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000102115.7" ; havana_transcript "OTTHUMT00000376138.1" ; hgnc_id "HGNC:3402" ; level 2 ; orig_coord_info "chr8,27500984,27501010,+" ; protein_id "ENSP00000369843.3" ; tag alternative_5_UTR basic CCDS ; transcript_id "EPHX2--PTK2B^ENST00000380476.7" ; transcript_name "EPHX2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
FBXO27--AC005392.2 HAVANA gene 1237 6427 . + . FI_gene_label "FBXO27^ENSG00000161243.9" ; ID "FBXO27--AC005392.2^FBXO27^ENSG00000161243.9" ; ccdsid "CCDS12527.1" ; exon_id "ENSE00001057108.3" ; exon_number 2 ; gene_id "FBXO27--AC005392.2^FBXO27^ENSG00000161243.9" ; gene_name FBXO27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182719.3" ; havana_transcript "OTTHUMT00000463281.2" ; hgnc_id "HGNC:18753" ; level 2 ; orig_coord_info "chr19,39031864,39032227,-" ; protein_id "ENSP00000292853.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "FBXO27--AC005392.2^ENST00000292853.9" ; transcript_name "FBXO27-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO27--AC005392.2 HAVANA mRNA 1237 6427 . + . FI_gene_label "FBXO27^ENSG00000161243.9" ; ID "FBXO27--AC005392.2^ENST00000292853.9" ; Parent "FBXO27--AC005392.2^FBXO27^ENSG00000161243.9" ; ccdsid "CCDS12527.1" ; exon_id "ENSE00001057108.3" ; exon_number 2 ; gene_id "FBXO27--AC005392.2^FBXO27^ENSG00000161243.9" ; gene_name FBXO27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182719.3" ; havana_transcript "OTTHUMT00000463281.2" ; hgnc_id "HGNC:18753" ; level 2 ; orig_coord_info "chr19,39031864,39032227,-" ; protein_id "ENSP00000292853.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "FBXO27--AC005392.2^ENST00000292853.9" ; transcript_name "FBXO27-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO27--CD177 HAVANA gene 1237 6427 . + . FI_gene_label "FBXO27^ENSG00000161243.9" ; ID "FBXO27--CD177^FBXO27^ENSG00000161243.9" ; ccdsid "CCDS12527.1" ; exon_id "ENSE00001057108.3" ; exon_number 2 ; gene_id "FBXO27--CD177^FBXO27^ENSG00000161243.9" ; gene_name FBXO27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182719.3" ; havana_transcript "OTTHUMT00000463281.2" ; hgnc_id "HGNC:18753" ; level 2 ; orig_coord_info "chr19,39031864,39032227,-" ; protein_id "ENSP00000292853.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "FBXO27--CD177^ENST00000292853.9" ; transcript_name "FBXO27-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO27--CD177 HAVANA mRNA 1237 6427 . + . FI_gene_label "FBXO27^ENSG00000161243.9" ; ID "FBXO27--CD177^ENST00000292853.9" ; Parent "FBXO27--CD177^FBXO27^ENSG00000161243.9" ; ccdsid "CCDS12527.1" ; exon_id "ENSE00001057108.3" ; exon_number 2 ; gene_id "FBXO27--CD177^FBXO27^ENSG00000161243.9" ; gene_name FBXO27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182719.3" ; havana_transcript "OTTHUMT00000463281.2" ; hgnc_id "HGNC:18753" ; level 2 ; orig_coord_info "chr19,39031864,39032227,-" ; protein_id "ENSP00000292853.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "FBXO27--CD177^ENST00000292853.9" ; transcript_name "FBXO27-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO27--CD177 HAVANA gene 11666 17167 . + . FI_gene_label "CD177^ENSG00000204936.10" ; ID "FBXO27--CD177^CD177^ENSG00000204936.10" ; exon_id "ENSE00003739430.1" ; exon_number 1 ; gene_id "FBXO27--CD177^CD177^ENSG00000204936.10" ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4" ; havana_transcript "OTTHUMT00000470164.2" ; hgnc_id "HGNC:30072" ; level 2 ; orig_coord_info "chr19,43353715,43353766,+" ; protein_id "ENSP00000367251.2" ; transcript_id "FBXO27--CD177^ENST00000378012.3" ; transcript_name "CD177-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
FBXO27--CD177 HAVANA mRNA 11666 17167 . + . FI_gene_label "CD177^ENSG00000204936.10" ; ID "FBXO27--CD177^ENST00000378012.3" ; Parent "FBXO27--CD177^CD177^ENSG00000204936.10" ; exon_id "ENSE00003739430.1" ; exon_number 1 ; gene_id "FBXO27--CD177^CD177^ENSG00000204936.10" ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4" ; havana_transcript "OTTHUMT00000470164.2" ; hgnc_id "HGNC:30072" ; level 2 ; orig_coord_info "chr19,43353715,43353766,+" ; protein_id "ENSP00000367251.2" ; transcript_id "FBXO27--CD177^ENST00000378012.3" ; transcript_name "CD177-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
IL32--FLYWCH1 HAVANA gene 1335 4973 . + . FI_gene_label "IL32^ENSG00000008517.18" ; ID "IL32--FLYWCH1^IL32^ENSG00000008517.18" ; ccdsid "CCDS45394.1" ; exon_id "ENSE00003602260.1" ; exon_number 2 ; gene_id "IL32--FLYWCH1^IL32^ENSG00000008517.18" ; gene_name IL32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167498.6" ; havana_transcript "OTTHUMT00000394827.2" ; hgnc_id "HGNC:16830" ; level 2 ; orig_coord_info "chr16,3065812,3065826,+" ; protein_id "ENSP00000008180.9" ; tag basic appris_alternative_2 CCDS ; transcript_id "IL32--FLYWCH1^ENST00000008180.13" ; transcript_name "IL32-201" ; transcript_support_level 2 ; transcript_type protein_coding
IL32--FLYWCH1 HAVANA mRNA 1335 4973 . + . FI_gene_label "IL32^ENSG00000008517.18" ; ID "IL32--FLYWCH1^ENST00000008180.13" ; Parent "IL32--FLYWCH1^IL32^ENSG00000008517.18" ; ccdsid "CCDS45394.1" ; exon_id "ENSE00003602260.1" ; exon_number 2 ; gene_id "IL32--FLYWCH1^IL32^ENSG00000008517.18" ; gene_name IL32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167498.6" ; havana_transcript "OTTHUMT00000394827.2" ; hgnc_id "HGNC:16830" ; level 2 ; orig_coord_info "chr16,3065812,3065826,+" ; protein_id "ENSP00000008180.9" ; tag basic appris_alternative_2 CCDS ; transcript_id "IL32--FLYWCH1^ENST00000008180.13" ; transcript_name "IL32-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
IL32--FLYWCH1 HAVANA gene 9534 29620 . + . FI_gene_label "FLYWCH1^ENSG00000059122.17" ; ID "IL32--FLYWCH1^FLYWCH1^ENSG00000059122.17" ; ccdsid "CCDS76809.1" ; exon_id "ENSE00001693676.1" ; exon_number 3 ; gene_id "IL32--FLYWCH1^FLYWCH1^ENSG00000059122.17" ; gene_name FLYWCH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177364.3" ; havana_transcript "OTTHUMT00000436479.1" ; hgnc_id "HGNC:25404" ; level 2 ; orig_coord_info "chr16,2929686,2930010,+" ; protein_id "ENSP00000253928.9" ; tag basic MANE_Select appris_principal_5 CCDS ; transcript_id "IL32--FLYWCH1^ENST00000253928.14" ; transcript_name "FLYWCH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
IL32--FLYWCH1 HAVANA mRNA 9534 29620 . + . FI_gene_label "FLYWCH1^ENSG00000059122.17" ; ID "IL32--FLYWCH1^ENST00000253928.14" ; Parent "IL32--FLYWCH1^FLYWCH1^ENSG00000059122.17" ; ccdsid "CCDS76809.1" ; exon_id "ENSE00001693676.1" ; exon_number 3 ; gene_id "IL32--FLYWCH1^FLYWCH1^ENSG00000059122.17" ; gene_name FLYWCH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177364.3" ; havana_transcript "OTTHUMT00000436479.1" ; hgnc_id "HGNC:25404" ; level 2 ; orig_coord_info "chr16,2929686,2930010,+" ; protein_id "ENSP00000253928.9" ; tag basic MANE_Select appris_principal_5 CCDS ; transcript_id "IL32--FLYWCH1^ENST00000253928.14" ; transcript_name "FLYWCH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^ENST00000289272.3" ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^ENST00000616325.1" ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PTPRVP--ELF3 HAVANA gene 21396 29276 . + . FI_gene_label "ELF3^ENSG00000163435.16" ; ID "PTPRVP--ELF3^ELF3^ENSG00000163435.16" ; ccdsid "CCDS1419.1" ; exon_id "ENSE00001346715.1" ; exon_number 1 ; gene_id "PTPRVP--ELF3^ELF3^ENSG00000163435.16" ; gene_name ELF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035867.5" ; havana_transcript "OTTHUMT00000087360.1" ; hgnc_id "HGNC:3318" ; level 2 ; orig_coord_info "chr1,202011137,202011299,+" ; protein_id "ENSP00000352673.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "PTPRVP--ELF3^ENST00000359651.7" ; transcript_name "ELF3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRVP--ELF3 HAVANA mRNA 21396 29276 . + . FI_gene_label "ELF3^ENSG00000163435.16" ; ID "PTPRVP--ELF3^ENST00000359651.7" ; Parent "PTPRVP--ELF3^ELF3^ENSG00000163435.16" ; ccdsid "CCDS1419.1" ; exon_id "ENSE00001346715.1" ; exon_number 1 ; gene_id "PTPRVP--ELF3^ELF3^ENSG00000163435.16" ; gene_name ELF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035867.5" ; havana_transcript "OTTHUMT00000087360.1" ; hgnc_id "HGNC:3318" ; level 2 ; orig_coord_info "chr1,202011137,202011299,+" ; protein_id "ENSP00000352673.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "PTPRVP--ELF3^ENST00000359651.7" ; transcript_name "ELF3-201" ; 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:
ZFP36--CAPNS1 HAVANA gene 6680 13458 . + . FI_gene_label "CAPNS1^ENSG00000126247.11" ; ID "ZFP36--CAPNS1^CAPNS1^ENSG00000126247.11" ; ccdsid "CCDS12489.1" ; exon_id "ENSE00001057386.1" ; exon_number 2 ; gene_id "ZFP36--CAPNS1^CAPNS1^ENSG00000126247.11" ; gene_name CAPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160811.10" ; havana_transcript "OTTHUMT00000457411.3" ; hgnc_id "HGNC:1481" ; level 2 ; orig_coord_info "chr19,36141012,36141220,+" ; protein_id "ENSP00000246533.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ZFP36--CAPNS1^ENST00000246533.8" ; transcript_name "CAPNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZFP36--CAPNS1 HAVANA mRNA 6680 13458 . + . FI_gene_label "CAPNS1^ENSG00000126247.11" ; ID "ZFP36--CAPNS1^ENST00000246533.8" ; Parent "ZFP36--CAPNS1^CAPNS1^ENSG00000126247.11" ; ccdsid "CCDS12489.1" ; exon_id "ENSE00001057386.1" ; exon_number 2 ; gene_id "ZFP36--CAPNS1^CAPNS1^ENSG00000126247.11" ; gene_name CAPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000160811.10" ; havana_transcript "OTTHUMT00000457411.3" ; hgnc_id "HGNC:1481" ; level 2 ; orig_coord_info "chr19,36141012,36141220,+" ; protein_id "ENSP00000246533.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ZFP36--CAPNS1^ENST00000246533.8" ; transcript_name "CAPNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZFP36--CAPNS1 HAVANA gene 1011 2333 . + . FI_gene_label "ZFP36^ENSG00000128016.7" ; ID "ZFP36--CAPNS1^ZFP36^ENSG00000128016.7" ; exon_id "ENSE00003092704.1" ; exon_number 1 ; gene_id "ZFP36--CAPNS1^ZFP36^ENSG00000128016.7" ; gene_name ZFP36 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182970.4" ; havana_transcript "OTTHUMT00000464496.2" ; hgnc_id "HGNC:12862" ; level 1 ; orig_coord_info "chr19,39406905,39407099,+" ; protein_id "ENSP00000472329.2" ; tag upstream_ATG basic exp_conf ; transcript_id "ZFP36--CAPNS1^ENST00000594045.2" ; transcript_name "ZFP36-201" ; transcript_support_level 3 ; transcript_type protein_coding
ZFP36--CAPNS1 HAVANA mRNA 1011 2333 . + . FI_gene_label "ZFP36^ENSG00000128016.7" ; ID "ZFP36--CAPNS1^ENST00000594045.2" ; Parent "ZFP36--CAPNS1^ZFP36^ENSG00000128016.7" ; exon_id "ENSE00003092704.1" ; exon_number 1 ; gene_id "ZFP36--CAPNS1^ZFP36^ENSG00000128016.7" ; gene_name ZFP36 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182970.4" ; havana_transcript "OTTHUMT00000464496.2" ; hgnc_id "HGNC:12862" ; level 1 ; orig_coord_info "chr19,39406905,39407099,+" ; protein_id "ENSP00000472329.2" ; tag upstream_ATG basic exp_conf ; transcript_id "ZFP36--CAPNS1^ENST00000594045.2" ; transcript_name "ZFP36-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
FBXO27--AC005392.2 HAVANA gene 11637 12937 . + . FI_gene_label "AC005392.2^ENSG00000231412.2" ; ID "FBXO27--AC005392.2^AC005392.2^ENSG00000231412.2" ; exon_id "ENSE00002978565.1" ; exon_number 1 ; gene_id "FBXO27--AC005392.2^AC005392.2^ENSG00000231412.2" ; gene_name "AC005392.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182827.1" ; havana_transcript "OTTHUMT00000463917.1" ; level 2 ; orig_coord_info "chr19,43331344,43331430,-" ; tag basic ; transcript_id "FBXO27--AC005392.2^ENST00000595748.1" ; transcript_name "AC005392.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
FBXO27--AC005392.2 HAVANA RNA 11637 12937 . + . FI_gene_label "AC005392.2^ENSG00000231412.2" ; ID "FBXO27--AC005392.2^ENST00000595748.1" ; Parent "FBXO27--AC005392.2^AC005392.2^ENSG00000231412.2" ; exon_id "ENSE00002978565.1" ; exon_number 1 ; gene_id "FBXO27--AC005392.2^AC005392.2^ENSG00000231412.2" ; gene_name "AC005392.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000182827.1" ; havana_transcript "OTTHUMT00000463917.1" ; level 2 ; orig_coord_info "chr19,43331344,43331430,-" ; tag basic ; transcript_id "FBXO27--AC005392.2^ENST00000595748.1" ; transcript_name "AC005392.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
PTPRVP--AL691482.3 HAVANA gene 1001 18293 . + . FI_gene_label "PTPRVP^ENSG00000243323.7" ; ID "PTPRVP--AL691482.3^PTPRVP^ENSG00000243323.7" ; exon_id "ENSE00001917095.1" ; exon_number 1 ; gene_id "PTPRVP--AL691482.3^PTPRVP^ENSG00000243323.7" ; gene_name PTPRVP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000040524.3" ; havana_transcript "OTTHUMT00000334021.1" ; hgnc_id "HGNC:13421" ; level 2 ; orig_coord_info "chr1,202168051,202168511,+" ; tag basic ; transcript_id "PTPRVP--AL691482.3^ENST00000482597.5" ; transcript_name "PTPRVP-201" ; transcript_support_level 1 ; transcript_type processed_transcript
PTPRVP--AL691482.3 HAVANA RNA 1001 18293 . + . FI_gene_label "PTPRVP^ENSG00000243323.7" ; ID "PTPRVP--AL691482.3^ENST00000482597.5" ; Parent "PTPRVP--AL691482.3^PTPRVP^ENSG00000243323.7" ; exon_id "ENSE00001917095.1" ; exon_number 1 ; gene_id "PTPRVP--AL691482.3^PTPRVP^ENSG00000243323.7" ; gene_name PTPRVP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000040524.3" ; havana_transcript "OTTHUMT00000334021.1" ; hgnc_id "HGNC:13421" ; level 2 ; orig_coord_info "chr1,202168051,202168511,+" ; tag basic ; transcript_id "PTPRVP--AL691482.3^ENST00000482597.5" ; transcript_name "PTPRVP-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
PTPRVP--AL691482.3 HAVANA gene 21396 23382 . + . FI_gene_label "AL691482.3^ENSG00000249007.1" ; ID "PTPRVP--AL691482.3^AL691482.3^ENSG00000249007.1" ; exon_id "ENSE00002073989.1" ; exon_number 1 ; gene_id "PTPRVP--AL691482.3^AL691482.3^ENSG00000249007.1" ; gene_name "AL691482.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000040657.1" ; havana_transcript "OTTHUMT00000097761.1" ; level 1 ; orig_coord_info "chr1,202011370,202011584,+" ; tag basic exp_conf ; transcript_id "PTPRVP--AL691482.3^ENST00000504773.1" ; transcript_name "AL691482.3-201" ; transcript_support_level 2 ; transcript_type lncRNA
PTPRVP--AL691482.3 HAVANA RNA 21396 23382 . + . FI_gene_label "AL691482.3^ENSG00000249007.1" ; ID "PTPRVP--AL691482.3^ENST00000504773.1" ; Parent "PTPRVP--AL691482.3^AL691482.3^ENSG00000249007.1" ; exon_id "ENSE00002073989.1" ; exon_number 1 ; gene_id "PTPRVP--AL691482.3^AL691482.3^ENSG00000249007.1" ; gene_name "AL691482.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000040657.1" ; havana_transcript "OTTHUMT00000097761.1" ; level 1 ; orig_coord_info "chr1,202011370,202011584,+" ; tag basic exp_conf ; transcript_id "PTPRVP--AL691482.3^ENST00000504773.1" ; transcript_name "AL691482.3-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
PTPRVP--ELF3 HAVANA gene 1001 18293 . + . FI_gene_label "PTPRVP^ENSG00000243323.7" ; ID "PTPRVP--ELF3^PTPRVP^ENSG00000243323.7" ; exon_id "ENSE00001917095.1" ; exon_number 1 ; gene_id "PTPRVP--ELF3^PTPRVP^ENSG00000243323.7" ; gene_name PTPRVP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000040524.3" ; havana_transcript "OTTHUMT00000334021.1" ; hgnc_id "HGNC:13421" ; level 2 ; orig_coord_info "chr1,202168051,202168511,+" ; tag basic ; transcript_id "PTPRVP--ELF3^ENST00000482597.5" ; transcript_name "PTPRVP-201" ; transcript_support_level 1 ; transcript_type processed_transcript
PTPRVP--ELF3 HAVANA RNA 1001 18293 . + . FI_gene_label "PTPRVP^ENSG00000243323.7" ; ID "PTPRVP--ELF3^ENST00000482597.5" ; Parent "PTPRVP--ELF3^PTPRVP^ENSG00000243323.7" ; exon_id "ENSE00001917095.1" ; exon_number 1 ; gene_id "PTPRVP--ELF3^PTPRVP^ENSG00000243323.7" ; gene_name PTPRVP ; gene_type unitary_pseudogene ; havana_gene "OTTHUMG00000040524.3" ; havana_transcript "OTTHUMT00000334021.1" ; hgnc_id "HGNC:13421" ; level 2 ; orig_coord_info "chr1,202168051,202168511,+" ; tag basic ; transcript_id "PTPRVP--ELF3^ENST00000482597.5" ; transcript_name "PTPRVP-201" ; transcript_support_level 1 ; transcript_type processed_transcript
199 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 ------------------------------
317 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 17 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
Lets remove isoform IL32--FLYWCH1^ENST00000675975.1
1 identical isoforms removed
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------ End checks (done in 1 second) ------
GFF3 file parsed