Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/bacb5ddad45aa89e83a2f8717ba1a2/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/371adfee8611fd1b051a6741e4cdf9/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/371adfee8611fd1b051a6741e4cdf9/.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: 6153
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6153
=> 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:6153
=> 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:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CPSF7--AP005139.1 HAVANA gene 1121 13344 . + . FI_gene_label "CPSF7^ENSG00000149532.16" ; ID "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16" ; ccdsid "CCDS8006.2" ; exon_id "ENSE00001745275.1" ; exon_number 1 ; gene_id "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16" ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5" ; havana_transcript "OTTHUMT00000347830.2" ; hgnc_id "HGNC:30098" ; level 2 ; orig_coord_info "chr11,61429757,61429830,-" ; protein_id "ENSP00000345412.4" ; tag basic CCDS ; transcript_id "CPSF7--AP005139.1^ENST00000340437.8" ; transcript_name "CPSF7-201" ; transcript_support_level 1 ; transcript_type protein_coding
CPSF7--AP005139.1 HAVANA mRNA 1121 13344 . + . FI_gene_label "CPSF7^ENSG00000149532.16" ; ID "CPSF7--AP005139.1^ENST00000340437.8" ; Parent "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16" ; ccdsid "CCDS8006.2" ; exon_id "ENSE00001745275.1" ; exon_number 1 ; gene_id "CPSF7--AP005139.1^CPSF7^ENSG00000149532.16" ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5" ; havana_transcript "OTTHUMT00000347830.2" ; hgnc_id "HGNC:30098" ; level 2 ; orig_coord_info "chr11,61429757,61429830,-" ; protein_id "ENSP00000345412.4" ; tag basic CCDS ; transcript_id "CPSF7--AP005139.1^ENST00000340437.8" ; transcript_name "CPSF7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CPSF7--PIEZO2 HAVANA gene 17326 83462 . + . FI_gene_label "PIEZO2^ENSG00000154864.13" ; ID "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13" ; exon_id "ENSE00002236501.2" ; exon_number 1 ; gene_id "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13" ; gene_name PIEZO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178507.14" ; havana_transcript "OTTHUMT00000254528.5" ; hgnc_id "HGNC:26270" ; level 2 ; orig_coord_info "chr18,11148525,11148588,-" ; protein_id "ENSP00000303316.6" ; tag basic ; transcript_id "CPSF7--PIEZO2^ENST00000302079.10" ; transcript_name "PIEZO2-201" ; transcript_support_level 5 ; transcript_type protein_coding
CPSF7--PIEZO2 HAVANA mRNA 17326 83462 . + . FI_gene_label "PIEZO2^ENSG00000154864.13" ; ID "CPSF7--PIEZO2^ENST00000302079.10" ; Parent "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13" ; exon_id "ENSE00002236501.2" ; exon_number 1 ; gene_id "CPSF7--PIEZO2^PIEZO2^ENSG00000154864.13" ; gene_name PIEZO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178507.14" ; havana_transcript "OTTHUMT00000254528.5" ; hgnc_id "HGNC:26270" ; level 2 ; orig_coord_info "chr18,11148525,11148588,-" ; protein_id "ENSP00000303316.6" ; tag basic ; transcript_id "CPSF7--PIEZO2^ENST00000302079.10" ; transcript_name "PIEZO2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CPSF7--PIEZO2 HAVANA gene 1121 13344 . + . FI_gene_label "CPSF7^ENSG00000149532.16" ; ID "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16" ; ccdsid "CCDS8006.2" ; exon_id "ENSE00001745275.1" ; exon_number 1 ; gene_id "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16" ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5" ; havana_transcript "OTTHUMT00000347830.2" ; hgnc_id "HGNC:30098" ; level 2 ; orig_coord_info "chr11,61429757,61429830,-" ; protein_id "ENSP00000345412.4" ; tag basic CCDS ; transcript_id "CPSF7--PIEZO2^ENST00000340437.8" ; transcript_name "CPSF7-201" ; transcript_support_level 1 ; transcript_type protein_coding
CPSF7--PIEZO2 HAVANA mRNA 1121 13344 . + . FI_gene_label "CPSF7^ENSG00000149532.16" ; ID "CPSF7--PIEZO2^ENST00000340437.8" ; Parent "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16" ; ccdsid "CCDS8006.2" ; exon_id "ENSE00001745275.1" ; exon_number 1 ; gene_id "CPSF7--PIEZO2^CPSF7^ENSG00000149532.16" ; gene_name CPSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168198.5" ; havana_transcript "OTTHUMT00000347830.2" ; hgnc_id "HGNC:30098" ; level 2 ; orig_coord_info "chr11,61429757,61429830,-" ; protein_id "ENSP00000345412.4" ; tag basic CCDS ; transcript_id "CPSF7--PIEZO2^ENST00000340437.8" ; transcript_name "CPSF7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DDX5--SMURF2 HAVANA gene 2911 10946 . + . FI_gene_label "DDX5^ENSG00000108654.16" ; ID "DDX5--SMURF2^DDX5^ENSG00000108654.16" ; ccdsid "CCDS11659.1" ; exon_id "ENSE00003466024.1" ; exon_number 1 ; gene_id "DDX5--SMURF2^DDX5^ENSG00000108654.16" ; gene_name DDX5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178936.11" ; havana_transcript "OTTHUMT00000444030.2" ; hgnc_id "HGNC:2746" ; level 2 ; orig_coord_info "chr17,64506076,64506119,-" ; protein_id "ENSP00000225792.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000225792.10" ; transcript_name "DDX5-201" ; transcript_support_level 1 ; transcript_type protein_coding
DDX5--SMURF2 HAVANA mRNA 2911 10946 . + . FI_gene_label "DDX5^ENSG00000108654.16" ; ID "DDX5--SMURF2^ENST00000225792.10" ; Parent "DDX5--SMURF2^DDX5^ENSG00000108654.16" ; ccdsid "CCDS11659.1" ; exon_id "ENSE00003466024.1" ; exon_number 1 ; gene_id "DDX5--SMURF2^DDX5^ENSG00000108654.16" ; gene_name DDX5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178936.11" ; havana_transcript "OTTHUMT00000444030.2" ; hgnc_id "HGNC:2746" ; level 2 ; orig_coord_info "chr17,64506076,64506119,-" ; protein_id "ENSP00000225792.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000225792.10" ; transcript_name "DDX5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DDX5--SMURF2 HAVANA gene 13947 40224 . + . FI_gene_label "SMURF2^ENSG00000108854.16" ; ID "DDX5--SMURF2^SMURF2^ENSG00000108854.16" ; ccdsid "CCDS32707.1" ; exon_id "ENSE00001331843.8" ; exon_number 1 ; gene_id "DDX5--SMURF2^SMURF2^ENSG00000108854.16" ; gene_name SMURF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179189.3" ; havana_transcript "OTTHUMT00000445227.2" ; hgnc_id "HGNC:16809" ; level 2 ; orig_coord_info "chr17,64661829,64661880,-" ; protein_id "ENSP00000262435.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000262435.14" ; transcript_name "SMURF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DDX5--SMURF2 HAVANA mRNA 13947 40224 . + . FI_gene_label "SMURF2^ENSG00000108854.16" ; ID "DDX5--SMURF2^ENST00000262435.14" ; Parent "DDX5--SMURF2^SMURF2^ENSG00000108854.16" ; ccdsid "CCDS32707.1" ; exon_id "ENSE00001331843.8" ; exon_number 1 ; gene_id "DDX5--SMURF2^SMURF2^ENSG00000108854.16" ; gene_name SMURF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179189.3" ; havana_transcript "OTTHUMT00000445227.2" ; hgnc_id "HGNC:16809" ; level 2 ; orig_coord_info "chr17,64661829,64661880,-" ; protein_id "ENSP00000262435.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDX5--SMURF2^ENST00000262435.14" ; transcript_name "SMURF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DHX38--WWOX HAVANA gene 1235 18399 . + . FI_gene_label "DHX38^ENSG00000140829.12" ; ID "DHX38--WWOX^DHX38^ENSG00000140829.12" ; ccdsid "CCDS10907.1" ; exon_id "ENSE00000945215.1" ; exon_number 2 ; gene_id "DHX38--WWOX^DHX38^ENSG00000140829.12" ; gene_name DHX38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137596.7" ; havana_transcript "OTTHUMT00000269004.4" ; hgnc_id "HGNC:17211" ; level 2 ; orig_coord_info "chr16,72096158,72096480,+" ; protein_id "ENSP00000268482.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX38--WWOX^ENST00000268482.8" ; transcript_name "DHX38-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHX38--WWOX HAVANA mRNA 1235 18399 . + . FI_gene_label "DHX38^ENSG00000140829.12" ; ID "DHX38--WWOX^ENST00000268482.8" ; Parent "DHX38--WWOX^DHX38^ENSG00000140829.12" ; ccdsid "CCDS10907.1" ; exon_id "ENSE00000945215.1" ; exon_number 2 ; gene_id "DHX38--WWOX^DHX38^ENSG00000140829.12" ; gene_name DHX38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137596.7" ; havana_transcript "OTTHUMT00000269004.4" ; hgnc_id "HGNC:17211" ; level 2 ; orig_coord_info "chr16,72096158,72096480,+" ; protein_id "ENSP00000268482.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX38--WWOX^ENST00000268482.8" ; transcript_name "DHX38-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DHX38--WWOX HAVANA gene 21649 39167 . + . FI_gene_label "WWOX^ENSG00000186153.17" ; ID "DHX38--WWOX^WWOX^ENSG00000186153.17" ; ccdsid "CCDS42197.1" ; exon_id "ENSE00002598693.1" ; exon_number 1 ; gene_id "DHX38--WWOX^WWOX^ENSG00000186153.17" ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3" ; havana_transcript "OTTHUMT00000434020.1" ; hgnc_id "HGNC:12799" ; level 2 ; orig_coord_info "chr16,78099779,78099885,+" ; protein_id "ENSP00000348119.3" ; tag basic CCDS ; transcript_id "DHX38--WWOX^ENST00000355860.7" ; transcript_name "WWOX-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHX38--WWOX HAVANA mRNA 21649 39167 . + . FI_gene_label "WWOX^ENSG00000186153.17" ; ID "DHX38--WWOX^ENST00000355860.7" ; Parent "DHX38--WWOX^WWOX^ENSG00000186153.17" ; ccdsid "CCDS42197.1" ; exon_id "ENSE00002598693.1" ; exon_number 1 ; gene_id "DHX38--WWOX^WWOX^ENSG00000186153.17" ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3" ; havana_transcript "OTTHUMT00000434020.1" ; hgnc_id "HGNC:12799" ; level 2 ; orig_coord_info "chr16,78099779,78099885,+" ; protein_id "ENSP00000348119.3" ; tag basic CCDS ; transcript_id "DHX38--WWOX^ENST00000355860.7" ; transcript_name "WWOX-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERC1--RASSF7 HAVANA gene 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--RASSF7^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--RASSF7^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--RASSF7^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ERC1--RASSF7 HAVANA mRNA 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--RASSF7^ENST00000347735.10" ; Parent "ERC1--RASSF7^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--RASSF7^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--RASSF7^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ERC1--RASSF7 HAVANA gene 45360 48416 . + . FI_gene_label "RASSF7^ENSG00000099849.15" ; ID "ERC1--RASSF7^RASSF7^ENSG00000099849.15" ; ccdsid "CCDS44506.1" ; exon_id "ENSE00001694199.1" ; exon_number 2 ; gene_id "ERC1--RASSF7^RASSF7^ENSG00000099849.15" ; gene_name RASSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132004.5" ; havana_transcript "OTTHUMT00000254970.2" ; hgnc_id "HGNC:1166" ; level 2 ; orig_coord_info "chr11,561769,561892,+" ; protein_id "ENSP00000380712.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ERC1--RASSF7^ENST00000397582.7" ; transcript_name "RASSF7-201" ; transcript_support_level 2 ; transcript_type protein_coding
ERC1--RASSF7 HAVANA mRNA 45360 48416 . + . FI_gene_label "RASSF7^ENSG00000099849.15" ; ID "ERC1--RASSF7^ENST00000397582.7" ; Parent "ERC1--RASSF7^RASSF7^ENSG00000099849.15" ; ccdsid "CCDS44506.1" ; exon_id "ENSE00001694199.1" ; exon_number 2 ; gene_id "ERC1--RASSF7^RASSF7^ENSG00000099849.15" ; gene_name RASSF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132004.5" ; havana_transcript "OTTHUMT00000254970.2" ; hgnc_id "HGNC:1166" ; level 2 ; orig_coord_info "chr11,561769,561892,+" ; protein_id "ENSP00000380712.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "ERC1--RASSF7^ENST00000397582.7" ; transcript_name "RASSF7-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KIAA1958--NTRK2 HAVANA gene 22318 60261 . + . FI_gene_label "NTRK2^ENSG00000148053.17" ; ID "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17" ; ccdsid "CCDS6671.1" ; exon_id "ENSE00001343633.1" ; exon_number 2 ; gene_id "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17" ; gene_name NTRK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020120.3" ; havana_transcript "OTTHUMT00000052885.2" ; hgnc_id "HGNC:8032" ; level 2 ; orig_coord_info "chr9,84670749,84670960,+" ; protein_id "ENSP00000277120.3" ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_1 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000277120.8" ; transcript_name "NTRK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
KIAA1958--NTRK2 HAVANA mRNA 22318 60261 . + . FI_gene_label "NTRK2^ENSG00000148053.17" ; ID "KIAA1958--NTRK2^ENST00000277120.8" ; Parent "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17" ; ccdsid "CCDS6671.1" ; exon_id "ENSE00001343633.1" ; exon_number 2 ; gene_id "KIAA1958--NTRK2^NTRK2^ENSG00000148053.17" ; gene_name NTRK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020120.3" ; havana_transcript "OTTHUMT00000052885.2" ; hgnc_id "HGNC:8032" ; level 2 ; orig_coord_info "chr9,84670749,84670960,+" ; protein_id "ENSP00000277120.3" ; tag CAGE_supported_TSS basic MANE_Select appris_alternative_1 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000277120.8" ; transcript_name "NTRK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KIAA1958--NTRK2 HAVANA gene 1001 18139 . + . FI_gene_label "KIAA1958^ENSG00000165185.15" ; ID "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15" ; ccdsid "CCDS35108.1" ; exon_id "ENSE00001410398.2" ; exon_number 2 ; gene_id "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15" ; gene_name KIAA1958 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020508.1" ; havana_transcript "OTTHUMT00000053690.1" ; hgnc_id "HGNC:23427" ; level 2 ; orig_coord_info "chr9,112574081,112575251,+" ; protein_id "ENSP00000336940.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000337530.11" ; transcript_name "KIAA1958-201" ; transcript_support_level 1 ; transcript_type protein_coding
KIAA1958--NTRK2 HAVANA mRNA 1001 18139 . + . FI_gene_label "KIAA1958^ENSG00000165185.15" ; ID "KIAA1958--NTRK2^ENST00000337530.11" ; Parent "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15" ; ccdsid "CCDS35108.1" ; exon_id "ENSE00001410398.2" ; exon_number 2 ; gene_id "KIAA1958--NTRK2^KIAA1958^ENSG00000165185.15" ; gene_name KIAA1958 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020508.1" ; havana_transcript "OTTHUMT00000053690.1" ; hgnc_id "HGNC:23427" ; level 2 ; orig_coord_info "chr9,112574081,112575251,+" ; protein_id "ENSP00000336940.6" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "KIAA1958--NTRK2^ENST00000337530.11" ; transcript_name "KIAA1958-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LMNTD2--ERC1 HAVANA gene 1001 6889 . + . FI_gene_label "LMNTD2^ENSG00000185522.9" ; ID "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9" ; ccdsid "CCDS7701.1" ; exon_id "ENSE00001296983.2" ; exon_number 1 ; gene_id "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9" ; gene_name LMNTD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132005.5" ; havana_transcript "OTTHUMT00000254973.3" ; hgnc_id "HGNC:28561" ; level 2 ; orig_coord_info "chr11,560683,560716,-" ; protein_id "ENSP00000331167.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LMNTD2--ERC1^ENST00000329451.8" ; transcript_name "LMNTD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
LMNTD2--ERC1 HAVANA mRNA 1001 6889 . + . FI_gene_label "LMNTD2^ENSG00000185522.9" ; ID "LMNTD2--ERC1^ENST00000329451.8" ; Parent "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9" ; ccdsid "CCDS7701.1" ; exon_id "ENSE00001296983.2" ; exon_number 1 ; gene_id "LMNTD2--ERC1^LMNTD2^ENSG00000185522.9" ; gene_name LMNTD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132005.5" ; havana_transcript "OTTHUMT00000254973.3" ; hgnc_id "HGNC:28561" ; level 2 ; orig_coord_info "chr11,560683,560716,-" ; protein_id "ENSP00000331167.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LMNTD2--ERC1^ENST00000329451.8" ; transcript_name "LMNTD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LMNTD2--ERC1 HAVANA gene 10619 46330 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "LMNTD2--ERC1^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "LMNTD2--ERC1^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "LMNTD2--ERC1^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
LMNTD2--ERC1 HAVANA mRNA 10619 46330 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "LMNTD2--ERC1^ENST00000347735.10" ; Parent "LMNTD2--ERC1^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "LMNTD2--ERC1^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "LMNTD2--ERC1^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
NAE1--CAPNS2 HAVANA gene 2144 19536 . + . FI_gene_label "NAE1^ENSG00000159593.15" ; ID "NAE1--CAPNS2^NAE1^ENSG00000159593.15" ; ccdsid "CCDS10820.1" ; exon_id "ENSE00003672944.1" ; exon_number 1 ; gene_id "NAE1--CAPNS2^NAE1^ENSG00000159593.15" ; gene_name NAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137513.8" ; havana_transcript "OTTHUMT00000268832.2" ; hgnc_id "HGNC:621" ; level 2 ; orig_coord_info "chr16,66830847,66830899,-" ; protein_id "ENSP00000290810.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000290810.8" ; transcript_name "NAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAE1--CAPNS2 HAVANA mRNA 2144 19536 . + . FI_gene_label "NAE1^ENSG00000159593.15" ; ID "NAE1--CAPNS2^ENST00000290810.8" ; Parent "NAE1--CAPNS2^NAE1^ENSG00000159593.15" ; ccdsid "CCDS10820.1" ; exon_id "ENSE00003672944.1" ; exon_number 1 ; gene_id "NAE1--CAPNS2^NAE1^ENSG00000159593.15" ; gene_name NAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137513.8" ; havana_transcript "OTTHUMT00000268832.2" ; hgnc_id "HGNC:621" ; level 2 ; orig_coord_info "chr16,66830847,66830899,-" ; protein_id "ENSP00000290810.3" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000290810.8" ; transcript_name "NAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NAE1--CAPNS2 HAVANA gene 22540 23543 . + . FI_gene_label "CAPNS2^ENSG00000256812.2" ; ID "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2" ; ccdsid "CCDS54010.1" ; exon_id "ENSE00002251412.2" ; exon_number 1 ; gene_id "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2" ; gene_name CAPNS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167812.2" ; havana_transcript "OTTHUMT00000396391.2" ; hgnc_id "HGNC:16371" ; level 2 ; orig_coord_info "chr16,55566757,55567500,+" ; protein_id "ENSP00000400882.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000457326.3" ; transcript_name "CAPNS2-201" ; transcript_support_level NA ; transcript_type protein_coding
NAE1--CAPNS2 HAVANA mRNA 22540 23543 . + . FI_gene_label "CAPNS2^ENSG00000256812.2" ; ID "NAE1--CAPNS2^ENST00000457326.3" ; Parent "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2" ; ccdsid "CCDS54010.1" ; exon_id "ENSE00002251412.2" ; exon_number 1 ; gene_id "NAE1--CAPNS2^CAPNS2^ENSG00000256812.2" ; gene_name CAPNS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167812.2" ; havana_transcript "OTTHUMT00000396391.2" ; hgnc_id "HGNC:16371" ; level 2 ; orig_coord_info "chr16,55566757,55567500,+" ; protein_id "ENSP00000400882.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAE1--CAPNS2^ENST00000457326.3" ; transcript_name "CAPNS2-201" ; transcript_support_level NA ; 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:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^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:
TXNL4B--CARMIL2 HAVANA gene 1812 7811 . + . FI_gene_label "TXNL4B^ENSG00000140830.9" ; ID "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9" ; ccdsid "CCDS10906.1" ; exon_id "ENSE00000945241.1" ; exon_number 2 ; gene_id "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9" ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3" ; havana_transcript "OTTHUMT00000269007.3" ; hgnc_id "HGNC:26041" ; level 2 ; orig_coord_info "chr16,72090618,72090749,-" ; protein_id "ENSP00000268483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000268483.8" ; transcript_name "TXNL4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CARMIL2 HAVANA mRNA 1812 7811 . + . FI_gene_label "TXNL4B^ENSG00000140830.9" ; ID "TXNL4B--CARMIL2^ENST00000268483.8" ; Parent "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9" ; ccdsid "CCDS10906.1" ; exon_id "ENSE00000945241.1" ; exon_number 2 ; gene_id "TXNL4B--CARMIL2^TXNL4B^ENSG00000140830.9" ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3" ; havana_transcript "OTTHUMT00000269007.3" ; hgnc_id "HGNC:26041" ; level 2 ; orig_coord_info "chr16,72090618,72090749,-" ; protein_id "ENSP00000268483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000268483.8" ; transcript_name "TXNL4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TXNL4B--CARMIL2 HAVANA gene 12037 24332 . + . FI_gene_label "CARMIL2^ENSG00000159753.14" ; ID "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14" ; ccdsid "CCDS45513.1" ; exon_id "ENSE00003304989.2" ; exon_number 1 ; gene_id "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14" ; gene_name CARMIL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184043.3" ; havana_transcript "OTTHUMT00000467858.2" ; hgnc_id "HGNC:27089" ; level 2 ; orig_coord_info "chr16,67645247,67645286,+" ; protein_id "ENSP00000334958.5" ; tag basic MANE_Select CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000334583.11" ; transcript_name "CARMIL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CARMIL2 HAVANA mRNA 12037 24332 . + . FI_gene_label "CARMIL2^ENSG00000159753.14" ; ID "TXNL4B--CARMIL2^ENST00000334583.11" ; Parent "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14" ; ccdsid "CCDS45513.1" ; exon_id "ENSE00003304989.2" ; exon_number 1 ; gene_id "TXNL4B--CARMIL2^CARMIL2^ENSG00000159753.14" ; gene_name CARMIL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184043.3" ; havana_transcript "OTTHUMT00000467858.2" ; hgnc_id "HGNC:27089" ; level 2 ; orig_coord_info "chr16,67645247,67645286,+" ; protein_id "ENSP00000334958.5" ; tag basic MANE_Select CCDS ; transcript_id "TXNL4B--CARMIL2^ENST00000334583.11" ; transcript_name "CARMIL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TXNL4B--CTCF HAVANA gene 11940 34463 . + . FI_gene_label "CTCF^ENSG00000102974.16" ; ID "TXNL4B--CTCF^CTCF^ENSG00000102974.16" ; ccdsid "CCDS10841.1" ; exon_id "ENSE00002242686.1" ; exon_number 3 ; gene_id "TXNL4B--CTCF^CTCF^ENSG00000102974.16" ; gene_name CTCF ; gene_type protein_coding ; havana_gene "OTTHUMG00000137539.7" ; havana_transcript "OTTHUMT00000268870.4" ; hgnc_id "HGNC:13723" ; level 2 ; orig_coord_info "chr16,67610833,67611613,+" ; protein_id "ENSP00000264010.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000264010.10" ; transcript_name "CTCF-201" ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CTCF HAVANA mRNA 11940 34463 . + . FI_gene_label "CTCF^ENSG00000102974.16" ; ID "TXNL4B--CTCF^ENST00000264010.10" ; Parent "TXNL4B--CTCF^CTCF^ENSG00000102974.16" ; ccdsid "CCDS10841.1" ; exon_id "ENSE00002242686.1" ; exon_number 3 ; gene_id "TXNL4B--CTCF^CTCF^ENSG00000102974.16" ; gene_name CTCF ; gene_type protein_coding ; havana_gene "OTTHUMG00000137539.7" ; havana_transcript "OTTHUMT00000268870.4" ; hgnc_id "HGNC:13723" ; level 2 ; orig_coord_info "chr16,67610833,67611613,+" ; protein_id "ENSP00000264010.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000264010.10" ; transcript_name "CTCF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TXNL4B--CTCF HAVANA gene 1812 7811 . + . FI_gene_label "TXNL4B^ENSG00000140830.9" ; ID "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9" ; ccdsid "CCDS10906.1" ; exon_id "ENSE00000945241.1" ; exon_number 2 ; gene_id "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9" ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3" ; havana_transcript "OTTHUMT00000269007.3" ; hgnc_id "HGNC:26041" ; level 2 ; orig_coord_info "chr16,72090618,72090749,-" ; protein_id "ENSP00000268483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000268483.8" ; transcript_name "TXNL4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
TXNL4B--CTCF HAVANA mRNA 1812 7811 . + . FI_gene_label "TXNL4B^ENSG00000140830.9" ; ID "TXNL4B--CTCF^ENST00000268483.8" ; Parent "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9" ; ccdsid "CCDS10906.1" ; exon_id "ENSE00000945241.1" ; exon_number 2 ; gene_id "TXNL4B--CTCF^TXNL4B^ENSG00000140830.9" ; gene_name TXNL4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000173453.3" ; havana_transcript "OTTHUMT00000269007.3" ; hgnc_id "HGNC:26041" ; level 2 ; orig_coord_info "chr16,72090618,72090749,-" ; protein_id "ENSP00000268483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNL4B--CTCF^ENST00000268483.8" ; transcript_name "TXNL4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWP2--MPHOSPH6 HAVANA gene 37937 45966 . + . FI_gene_label "MPHOSPH6^ENSG00000135698.10" ; ID "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10" ; ccdsid "CCDS10937.1" ; exon_id "ENSE00000920946.5" ; exon_number 1 ; gene_id "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10" ; gene_name MPHOSPH6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137632.3" ; havana_transcript "OTTHUMT00000269058.2" ; hgnc_id "HGNC:7214" ; level 2 ; orig_coord_info "chr16,82170125,82170175,-" ; protein_id "ENSP00000258169.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000258169.9" ; transcript_name "MPHOSPH6-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWP2--MPHOSPH6 HAVANA mRNA 37937 45966 . + . FI_gene_label "MPHOSPH6^ENSG00000135698.10" ; ID "WWP2--MPHOSPH6^ENST00000258169.9" ; Parent "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10" ; ccdsid "CCDS10937.1" ; exon_id "ENSE00000920946.5" ; exon_number 1 ; gene_id "WWP2--MPHOSPH6^MPHOSPH6^ENSG00000135698.10" ; gene_name MPHOSPH6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137632.3" ; havana_transcript "OTTHUMT00000269058.2" ; hgnc_id "HGNC:7214" ; level 2 ; orig_coord_info "chr16,82170125,82170175,-" ; protein_id "ENSP00000258169.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000258169.9" ; transcript_name "MPHOSPH6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWP2--MPHOSPH6 ENSEMBL gene 10833 34936 . + . FI_gene_label "WWP2^ENSG00000198373.13" ; ID "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13" ; ccdsid "CCDS58476.1" ; exon_id "ENSE00003538515.1" ; exon_number 2 ; gene_id "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13" ; gene_name WWP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137573.3" ; hgnc_id "HGNC:16804" ; level 3 ; orig_coord_info "chr16,69840134,69840263,+" ; protein_id "ENSP00000348283.3" ; tag basic CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000356003.6" ; transcript_name "WWP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
WWP2--MPHOSPH6 ENSEMBL mRNA 10833 34936 . + . FI_gene_label "WWP2^ENSG00000198373.13" ; ID "WWP2--MPHOSPH6^ENST00000356003.6" ; Parent "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13" ; ccdsid "CCDS58476.1" ; exon_id "ENSE00003538515.1" ; exon_number 2 ; gene_id "WWP2--MPHOSPH6^WWP2^ENSG00000198373.13" ; gene_name WWP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137573.3" ; hgnc_id "HGNC:16804" ; level 3 ; orig_coord_info "chr16,69840134,69840263,+" ; protein_id "ENSP00000348283.3" ; tag basic CCDS ; transcript_id "WWP2--MPHOSPH6^ENST00000356003.6" ; transcript_name "WWP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ZFHX3--CNTNAP4 HAVANA gene 21649 45862 . + . FI_gene_label "ZFHX3^ENSG00000140836.17" ; ID "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17" ; ccdsid "CCDS10908.1" ; exon_id "ENSE00001171638.5" ; exon_number 2 ; gene_id "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17" ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7" ; havana_transcript "OTTHUMT00000269008.2" ; hgnc_id "HGNC:777" ; level 2 ; orig_coord_info "chr16,72957427,72960145,-" ; protein_id "ENSP00000268489.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--CNTNAP4^ENST00000268489.10" ; transcript_name "ZFHX3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZFHX3--CNTNAP4 HAVANA mRNA 21649 45862 . + . FI_gene_label "ZFHX3^ENSG00000140836.17" ; ID "ZFHX3--CNTNAP4^ENST00000268489.10" ; Parent "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17" ; ccdsid "CCDS10908.1" ; exon_id "ENSE00001171638.5" ; exon_number 2 ; gene_id "ZFHX3--CNTNAP4^ZFHX3^ENSG00000140836.17" ; gene_name ZFHX3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137599.7" ; havana_transcript "OTTHUMT00000269008.2" ; hgnc_id "HGNC:777" ; level 2 ; orig_coord_info "chr16,72957427,72960145,-" ; protein_id "ENSP00000268489.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZFHX3--CNTNAP4^ENST00000268489.10" ; transcript_name "ZFHX3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZFHX3--CNTNAP4 ENSEMBL gene 48863 78570 . + . FI_gene_label "CNTNAP4^ENSG00000152910.19" ; ID "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19" ; exon_id "ENSE00001629021.3" ; exon_number 1 ; gene_id "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19" ; gene_name CNTNAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137617.8" ; hgnc_id "HGNC:18747" ; level 3 ; orig_coord_info "chr16,76277663,76277747,+" ; protein_id "ENSP00000306893.9" ; tag basic appris_alternative_1 ; transcript_id "ZFHX3--CNTNAP4^ENST00000307431.12" ; transcript_name "CNTNAP4-201" ; transcript_support_level 5 ; transcript_type protein_coding
ZFHX3--CNTNAP4 ENSEMBL mRNA 48863 78570 . + . FI_gene_label "CNTNAP4^ENSG00000152910.19" ; ID "ZFHX3--CNTNAP4^ENST00000307431.12" ; Parent "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19" ; exon_id "ENSE00001629021.3" ; exon_number 1 ; gene_id "ZFHX3--CNTNAP4^CNTNAP4^ENSG00000152910.19" ; gene_name CNTNAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137617.8" ; hgnc_id "HGNC:18747" ; level 3 ; orig_coord_info "chr16,76277663,76277747,+" ; protein_id "ENSP00000306893.9" ; tag basic appris_alternative_1 ; transcript_id "ZFHX3--CNTNAP4^ENST00000307431.12" ; transcript_name "CNTNAP4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
CPSF7--AP005139.1 HAVANA gene 16345 18907 . + . FI_gene_label "AP005139.1^ENSG00000263682.1" ; ID "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1" ; exon_id "ENSE00002684615.1" ; exon_number 1 ; gene_id "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1" ; gene_name "AP005139.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000178558.2" ; havana_transcript "OTTHUMT00000442454.2" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr18,11326270,11326789,+" ; tag pseudo_consens basic ; transcript_id "CPSF7--AP005139.1^ENST00000580702.1" ; transcript_name "AP005139.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
CPSF7--AP005139.1 HAVANA RNA 16345 18907 . + . FI_gene_label "AP005139.1^ENSG00000263682.1" ; ID "CPSF7--AP005139.1^ENST00000580702.1" ; Parent "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1" ; exon_id "ENSE00002684615.1" ; exon_number 1 ; gene_id "CPSF7--AP005139.1^AP005139.1^ENSG00000263682.1" ; gene_name "AP005139.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000178558.2" ; havana_transcript "OTTHUMT00000442454.2" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr18,11326270,11326789,+" ; tag pseudo_consens basic ; transcript_id "CPSF7--AP005139.1^ENST00000580702.1" ; transcript_name "AP005139.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
451 cases fixed where L3 features have parent feature(s) missing
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--------------------------- 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
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------------------------- 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 ------------------------------
944 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 30 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