Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/6ab30b6cd4a195321ccb0923d1700d/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/46dd84845806a170bcc3989b5d8255/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/46dd84845806a170bcc3989b5d8255/.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: 5465
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5465
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:5465
=> 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:
ASS1--SIM2 HAVANA gene 21422 39091 . + . FI_gene_label "SIM2^ENSG00000159263.16" ; ID "ASS1--SIM2^SIM2^ENSG00000159263.16" ; ccdsid "CCDS13646.1" ; exon_id "ENSE00003579996.2" ; exon_number 1 ; gene_id "ASS1--SIM2^SIM2^ENSG00000159263.16" ; gene_name SIM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086637.4" ; havana_transcript "OTTHUMT00000194692.2" ; hgnc_id "HGNC:10883" ; level 2 ; orig_coord_info "chr21,36699747,36699921,+" ; protein_id "ENSP00000290399.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASS1--SIM2^ENST00000290399.11" ; transcript_name "SIM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ASS1--SIM2 HAVANA mRNA 21422 39091 . + . FI_gene_label "SIM2^ENSG00000159263.16" ; ID "ASS1--SIM2^ENST00000290399.11" ; Parent "ASS1--SIM2^SIM2^ENSG00000159263.16" ; ccdsid "CCDS13646.1" ; exon_id "ENSE00003579996.2" ; exon_number 1 ; gene_id "ASS1--SIM2^SIM2^ENSG00000159263.16" ; gene_name SIM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086637.4" ; havana_transcript "OTTHUMT00000194692.2" ; hgnc_id "HGNC:10883" ; level 2 ; orig_coord_info "chr21,36699747,36699921,+" ; protein_id "ENSP00000290399.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASS1--SIM2^ENST00000290399.11" ; transcript_name "SIM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ASS1--SIM2 HAVANA gene 1001 18421 . + . FI_gene_label "ASS1^ENSG00000130707.18" ; ID "ASS1--SIM2^ASS1^ENSG00000130707.18" ; ccdsid "CCDS6933.1" ; exon_id "ENSE00002397383.1" ; exon_number 2 ; gene_id "ASS1--SIM2^ASS1^ENSG00000130707.18" ; gene_name ASS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020806.5" ; havana_transcript "OTTHUMT00000054650.2" ; hgnc_id "HGNC:758" ; level 2 ; orig_coord_info "chr9,130452229,130452333,+" ; protein_id "ENSP00000253004.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASS1--SIM2^ENST00000352480.10" ; transcript_name "ASS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ASS1--SIM2 HAVANA mRNA 1001 18421 . + . FI_gene_label "ASS1^ENSG00000130707.18" ; ID "ASS1--SIM2^ENST00000352480.10" ; Parent "ASS1--SIM2^ASS1^ENSG00000130707.18" ; ccdsid "CCDS6933.1" ; exon_id "ENSE00002397383.1" ; exon_number 2 ; gene_id "ASS1--SIM2^ASS1^ENSG00000130707.18" ; gene_name ASS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020806.5" ; havana_transcript "OTTHUMT00000054650.2" ; hgnc_id "HGNC:758" ; level 2 ; orig_coord_info "chr9,130452229,130452333,+" ; protein_id "ENSP00000253004.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ASS1--SIM2^ENST00000352480.10" ; transcript_name "ASS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATXN2L--MBD3 HAVANA gene 16740 29611 . + . FI_gene_label "MBD3^ENSG00000071655.18" ; ID "ATXN2L--MBD3^MBD3^ENSG00000071655.18" ; ccdsid "CCDS62481.1" ; exon_id "ENSE00002971597.2" ; exon_number 1 ; gene_id "ATXN2L--MBD3^MBD3^ENSG00000071655.18" ; gene_name MBD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180081.9" ; havana_transcript "OTTHUMT00000449657.3" ; hgnc_id "HGNC:6918" ; level 2 ; orig_coord_info "chr19,1592618,1592631,-" ; protein_id "ENSP00000156825.2" ; tag basic CCDS ; transcript_id "ATXN2L--MBD3^ENST00000156825.5" ; transcript_name "MBD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATXN2L--MBD3 HAVANA mRNA 16740 29611 . + . FI_gene_label "MBD3^ENSG00000071655.18" ; ID "ATXN2L--MBD3^ENST00000156825.5" ; Parent "ATXN2L--MBD3^MBD3^ENSG00000071655.18" ; ccdsid "CCDS62481.1" ; exon_id "ENSE00002971597.2" ; exon_number 1 ; gene_id "ATXN2L--MBD3^MBD3^ENSG00000071655.18" ; gene_name MBD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180081.9" ; havana_transcript "OTTHUMT00000449657.3" ; hgnc_id "HGNC:6918" ; level 2 ; orig_coord_info "chr19,1592618,1592631,-" ; protein_id "ENSP00000156825.2" ; tag basic CCDS ; transcript_id "ATXN2L--MBD3^ENST00000156825.5" ; transcript_name "MBD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATXN2L--MBD3 HAVANA gene 1059 13670 . + . FI_gene_label "ATXN2L^ENSG00000168488.18" ; ID "ATXN2L--MBD3^ATXN2L^ENSG00000168488.18" ; ccdsid "CCDS32423.1" ; exon_id "ENSE00001400461.2" ; exon_number 1 ; gene_id "ATXN2L--MBD3^ATXN2L^ENSG00000168488.18" ; gene_name ATXN2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000097038.6" ; havana_transcript "OTTHUMT00000431011.1" ; hgnc_id "HGNC:31326" ; level 2 ; orig_coord_info "chr16,28823260,28823558,+" ; protein_id "ENSP00000315650.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATXN2L--MBD3^ENST00000325215.10" ; transcript_name "ATXN2L-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATXN2L--MBD3 HAVANA mRNA 1059 13670 . + . FI_gene_label "ATXN2L^ENSG00000168488.18" ; ID "ATXN2L--MBD3^ENST00000325215.10" ; Parent "ATXN2L--MBD3^ATXN2L^ENSG00000168488.18" ; ccdsid "CCDS32423.1" ; exon_id "ENSE00001400461.2" ; exon_number 1 ; gene_id "ATXN2L--MBD3^ATXN2L^ENSG00000168488.18" ; gene_name ATXN2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000097038.6" ; havana_transcript "OTTHUMT00000431011.1" ; hgnc_id "HGNC:31326" ; level 2 ; orig_coord_info "chr16,28823260,28823558,+" ; protein_id "ENSP00000315650.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "ATXN2L--MBD3^ENST00000325215.10" ; transcript_name "ATXN2L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CACTIN--PIP5K1C ENSEMBL gene 1001 12882 . + . FI_gene_label "CACTIN^ENSG00000105298.14" ; ID "CACTIN--PIP5K1C^CACTIN^ENSG00000105298.14" ; ccdsid "CCDS45920.1" ; exon_id "ENSE00003712431.1" ; exon_number 1 ; gene_id "CACTIN--PIP5K1C^CACTIN^ENSG00000105298.14" ; gene_name CACTIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000180808.7" ; hgnc_id "HGNC:29938" ; level 3 ; orig_coord_info "chr19,3626596,3626762,-" ; protein_id "ENSP00000221899.4" ; tag basic appris_principal_1 CCDS ; transcript_id "CACTIN--PIP5K1C^ENST00000221899.7" ; transcript_name "CACTIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
CACTIN--PIP5K1C ENSEMBL mRNA 1001 12882 . + . FI_gene_label "CACTIN^ENSG00000105298.14" ; ID "CACTIN--PIP5K1C^ENST00000221899.7" ; Parent "CACTIN--PIP5K1C^CACTIN^ENSG00000105298.14" ; ccdsid "CCDS45920.1" ; exon_id "ENSE00003712431.1" ; exon_number 1 ; gene_id "CACTIN--PIP5K1C^CACTIN^ENSG00000105298.14" ; gene_name CACTIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000180808.7" ; hgnc_id "HGNC:29938" ; level 3 ; orig_coord_info "chr19,3626596,3626762,-" ; protein_id "ENSP00000221899.4" ; tag basic appris_principal_1 CCDS ; transcript_id "CACTIN--PIP5K1C^ENST00000221899.7" ; transcript_name "CACTIN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CACTIN--PIP5K1C HAVANA gene 15898 41895 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "CACTIN--PIP5K1C^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "CACTIN--PIP5K1C^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CACTIN--PIP5K1C^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
CACTIN--PIP5K1C HAVANA mRNA 15898 41895 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "CACTIN--PIP5K1C^ENST00000335312.8" ; Parent "CACTIN--PIP5K1C^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "CACTIN--PIP5K1C^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "CACTIN--PIP5K1C^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GK5--AC063938.1 HAVANA gene 1008 27091 . + . FI_gene_label "GK5^ENSG00000175066.16" ; ID "GK5--AC063938.1^GK5^ENSG00000175066.16" ; ccdsid "CCDS33871.1" ; exon_id "ENSE00001949730.2" ; exon_number 1 ; gene_id "GK5--AC063938.1^GK5^ENSG00000175066.16" ; gene_name GK5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133572.6" ; havana_transcript "OTTHUMT00000353999.3" ; hgnc_id "HGNC:28635" ; level 2 ; orig_coord_info "chr3,142225309,142225455,-" ; protein_id "ENSP00000418001.1" ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "GK5--AC063938.1^ENST00000392993.7" ; transcript_name "GK5-201" ; transcript_support_level 1 ; transcript_type protein_coding
GK5--AC063938.1 HAVANA mRNA 1008 27091 . + . FI_gene_label "GK5^ENSG00000175066.16" ; ID "GK5--AC063938.1^ENST00000392993.7" ; Parent "GK5--AC063938.1^GK5^ENSG00000175066.16" ; ccdsid "CCDS33871.1" ; exon_id "ENSE00001949730.2" ; exon_number 1 ; gene_id "GK5--AC063938.1^GK5^ENSG00000175066.16" ; gene_name GK5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133572.6" ; havana_transcript "OTTHUMT00000353999.3" ; hgnc_id "HGNC:28635" ; level 2 ; orig_coord_info "chr3,142225309,142225455,-" ; protein_id "ENSP00000418001.1" ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "GK5--AC063938.1^ENST00000392993.7" ; transcript_name "GK5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GSK3B--GNG4 HAVANA gene 1548 57727 . + . FI_gene_label "GSK3B^ENSG00000082701.17" ; ID "GSK3B--GNG4^GSK3B^ENSG00000082701.17" ; ccdsid "CCDS54628.1" ; exon_id "ENSE00001206838.5" ; exon_number 1 ; gene_id "GSK3B--GNG4^GSK3B^ENSG00000082701.17" ; gene_name GSK3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133765.7" ; havana_transcript "OTTHUMT00000258240.2" ; hgnc_id "HGNC:4617" ; level 2 ; orig_coord_info "chr3,120093347,120093434,-" ; protein_id "ENSP00000264235.9" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GSK3B--GNG4^ENST00000264235.13" ; transcript_name "GSK3B-201" ; transcript_support_level 1 ; transcript_type protein_coding
GSK3B--GNG4 HAVANA mRNA 1548 57727 . + . FI_gene_label "GSK3B^ENSG00000082701.17" ; ID "GSK3B--GNG4^ENST00000264235.13" ; Parent "GSK3B--GNG4^GSK3B^ENSG00000082701.17" ; ccdsid "CCDS54628.1" ; exon_id "ENSE00001206838.5" ; exon_number 1 ; gene_id "GSK3B--GNG4^GSK3B^ENSG00000082701.17" ; gene_name GSK3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133765.7" ; havana_transcript "OTTHUMT00000258240.2" ; hgnc_id "HGNC:4617" ; level 2 ; orig_coord_info "chr3,120093347,120093434,-" ; protein_id "ENSP00000264235.9" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "GSK3B--GNG4^ENST00000264235.13" ; transcript_name "GSK3B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GSK3B--GNG4 HAVANA gene 62853 67538 . + . FI_gene_label "GNG4^ENSG00000168243.11" ; ID "GSK3B--GNG4^GNG4^ENSG00000168243.11" ; ccdsid "CCDS1607.1" ; exon_id "ENSE00003892798.1" ; exon_number 2 ; gene_id "GSK3B--GNG4^GNG4^ENSG00000168243.11" ; gene_name GNG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040740.4" ; havana_transcript "OTTHUMT00000097907.1" ; hgnc_id "HGNC:4407" ; level 2 ; orig_coord_info "chr1,235583740,235583838,-" ; protein_id "ENSP00000355556.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "GSK3B--GNG4^ENST00000366597.5" ; transcript_name "GNG4-201" ; transcript_support_level 1 ; transcript_type protein_coding
GSK3B--GNG4 HAVANA mRNA 62853 67538 . + . FI_gene_label "GNG4^ENSG00000168243.11" ; ID "GSK3B--GNG4^ENST00000366597.5" ; Parent "GSK3B--GNG4^GNG4^ENSG00000168243.11" ; ccdsid "CCDS1607.1" ; exon_id "ENSE00003892798.1" ; exon_number 2 ; gene_id "GSK3B--GNG4^GNG4^ENSG00000168243.11" ; gene_name GNG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000040740.4" ; havana_transcript "OTTHUMT00000097907.1" ; hgnc_id "HGNC:4407" ; level 2 ; orig_coord_info "chr1,235583740,235583838,-" ; protein_id "ENSP00000355556.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "GSK3B--GNG4^ENST00000366597.5" ; transcript_name "GNG4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLHL22--SMPD4P1 HAVANA gene 1050 16423 . + . FI_gene_label "KLHL22^ENSG00000099910.17" ; ID "KLHL22--SMPD4P1^KLHL22^ENSG00000099910.17" ; ccdsid "CCDS13780.1" ; exon_id "ENSE00003616753.1" ; exon_number 2 ; gene_id "KLHL22--SMPD4P1^KLHL22^ENSG00000099910.17" ; gene_name KLHL22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188269.3" ; havana_transcript "OTTHUMT00000320045.3" ; hgnc_id "HGNC:25888" ; level 2 ; orig_coord_info "chr22,20488985,20489211,-" ; protein_id "ENSP00000331682.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLHL22--SMPD4P1^ENST00000328879.9" ; transcript_name "KLHL22-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLHL22--SMPD4P1 HAVANA mRNA 1050 16423 . + . FI_gene_label "KLHL22^ENSG00000099910.17" ; ID "KLHL22--SMPD4P1^ENST00000328879.9" ; Parent "KLHL22--SMPD4P1^KLHL22^ENSG00000099910.17" ; ccdsid "CCDS13780.1" ; exon_id "ENSE00003616753.1" ; exon_number 2 ; gene_id "KLHL22--SMPD4P1^KLHL22^ENSG00000099910.17" ; gene_name KLHL22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188269.3" ; havana_transcript "OTTHUMT00000320045.3" ; hgnc_id "HGNC:25888" ; level 2 ; orig_coord_info "chr22,20488985,20489211,-" ; protein_id "ENSP00000331682.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLHL22--SMPD4P1^ENST00000328879.9" ; transcript_name "KLHL22-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KRT15--KRT19 HAVANA gene 4640 9785 . + . FI_gene_label "KRT15^ENSG00000171346.16" ; ID "KRT15--KRT19^KRT15^ENSG00000171346.16" ; ccdsid "CCDS11398.1" ; exon_id "ENSE00001849719.2" ; exon_number 1 ; gene_id "KRT15--KRT19^KRT15^ENSG00000171346.16" ; gene_name KRT15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133435.6" ; havana_transcript "OTTHUMT00000257301.2" ; hgnc_id "HGNC:6421" ; level 2 ; orig_coord_info "chr17,41518330,41518827,-" ; protein_id "ENSP00000254043.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KRT15--KRT19^ENST00000254043.8" ; transcript_name "KRT15-201" ; transcript_support_level 1 ; transcript_type protein_coding
KRT15--KRT19 HAVANA mRNA 4640 9785 . + . FI_gene_label "KRT15^ENSG00000171346.16" ; ID "KRT15--KRT19^ENST00000254043.8" ; Parent "KRT15--KRT19^KRT15^ENSG00000171346.16" ; ccdsid "CCDS11398.1" ; exon_id "ENSE00001849719.2" ; exon_number 1 ; gene_id "KRT15--KRT19^KRT15^ENSG00000171346.16" ; gene_name KRT15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133435.6" ; havana_transcript "OTTHUMT00000257301.2" ; hgnc_id "HGNC:6421" ; level 2 ; orig_coord_info "chr17,41518330,41518827,-" ; protein_id "ENSP00000254043.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KRT15--KRT19^ENST00000254043.8" ; transcript_name "KRT15-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KRT15--KRT19 HAVANA gene 12786 16322 . + . FI_gene_label "KRT19^ENSG00000171345.13" ; ID "KRT15--KRT19^KRT19^ENSG00000171345.13" ; ccdsid "CCDS11399.1" ; exon_id "ENSE00000863524.4" ; exon_number 1 ; gene_id "KRT15--KRT19^KRT19^ENSG00000171345.13" ; gene_name KRT19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133422.5" ; havana_transcript "OTTHUMT00000257285.1" ; hgnc_id "HGNC:6436" ; level 2 ; orig_coord_info "chr17,41527828,41528247,-" ; protein_id "ENSP00000355124.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KRT15--KRT19^ENST00000361566.7" ; transcript_name "KRT19-201" ; transcript_support_level 1 ; transcript_type protein_coding
KRT15--KRT19 HAVANA mRNA 12786 16322 . + . FI_gene_label "KRT19^ENSG00000171345.13" ; ID "KRT15--KRT19^ENST00000361566.7" ; Parent "KRT15--KRT19^KRT19^ENSG00000171345.13" ; ccdsid "CCDS11399.1" ; exon_id "ENSE00000863524.4" ; exon_number 1 ; gene_id "KRT15--KRT19^KRT19^ENSG00000171345.13" ; gene_name KRT19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133422.5" ; havana_transcript "OTTHUMT00000257285.1" ; hgnc_id "HGNC:6436" ; level 2 ; orig_coord_info "chr17,41527828,41528247,-" ; protein_id "ENSP00000355124.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KRT15--KRT19^ENST00000361566.7" ; transcript_name "KRT19-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LINC02071--SELENOP HAVANA gene 10678 21161 . + . FI_gene_label "SELENOP^ENSG00000250722.6" ; ID "LINC02071--SELENOP^SELENOP^ENSG00000250722.6" ; ccdsid "CCDS43311.1" ; exon_id "ENSE00003463317.1" ; exon_number 2 ; gene_id "LINC02071--SELENOP^SELENOP^ENSG00000250722.6" ; gene_name SELENOP ; gene_type protein_coding ; havana_gene "OTTHUMG00000162140.5" ; havana_transcript "OTTHUMT00000367486.1" ; hgnc_id "HGNC:10751" ; level 2 ; orig_coord_info "chr5,42808151,42808353,-" ; protein_id "ENSP00000425915.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS seleno ; transcript_id "LINC02071--SELENOP^ENST00000506577.5" ; transcript_name "SELENOP-203" ; transcript_support_level 1 ; transcript_type protein_coding
LINC02071--SELENOP HAVANA mRNA 10678 21161 . + . FI_gene_label "SELENOP^ENSG00000250722.6" ; ID "LINC02071--SELENOP^ENST00000506577.5" ; Parent "LINC02071--SELENOP^SELENOP^ENSG00000250722.6" ; ccdsid "CCDS43311.1" ; exon_id "ENSE00003463317.1" ; exon_number 2 ; gene_id "LINC02071--SELENOP^SELENOP^ENSG00000250722.6" ; gene_name SELENOP ; gene_type protein_coding ; havana_gene "OTTHUMG00000162140.5" ; havana_transcript "OTTHUMT00000367486.1" ; hgnc_id "HGNC:10751" ; level 2 ; orig_coord_info "chr5,42808151,42808353,-" ; protein_id "ENSP00000425915.1" ; tag alternative_5_UTR basic appris_principal_1 CCDS seleno ; transcript_id "LINC02071--SELENOP^ENST00000506577.5" ; transcript_name "SELENOP-203" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 16359 24799 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA10--PCDHA13^ENST00000289272.3" ; Parent "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHA13 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHA13 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHA13^ENST00000562220.2" ; Parent "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 16359 26374 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA10--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC1 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC1 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC1^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 16365 27100 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA10--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA10--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 "PCDHA10--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA10--PCDHAC2 HAVANA gene 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC2 HAVANA mRNA 1001 13358 . + . FI_gene_label "PCDHA10^ENSG00000250120.8" ; ID "PCDHA10--PCDHAC2^ENST00000562220.2" ; Parent "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; ccdsid "CCDS75325.1" ; exon_id "ENSE00002616704.2" ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8" ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5" ; havana_transcript "OTTHUMT00000477562.1" ; hgnc_id "HGNC:8664" ; level 2 ; orig_coord_info "chr5,140856049,140858580,+" ; protein_id "ENSP00000478748.1" ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2" ; transcript_name "PCDHA10-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PHKB--ITFG1 HAVANA gene 1204 44448 . + . FI_gene_label "PHKB^ENSG00000102893.16" ; ID "PHKB--ITFG1^PHKB^ENSG00000102893.16" ; exon_id "ENSE00002601441.1" ; exon_number 1 ; gene_id "PHKB--ITFG1^PHKB^ENSG00000102893.16" ; gene_name PHKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000133102.6" ; havana_transcript "OTTHUMT00000256767.3" ; hgnc_id "HGNC:8927" ; level 2 ; orig_coord_info "chr16,47461351,47461426,+" ; protein_id "ENSP00000299167.8" ; tag alternative_5_UTR basic ; transcript_id "PHKB--ITFG1^ENST00000299167.12" ; transcript_name "PHKB-201" ; transcript_support_level 5 ; transcript_type protein_coding
PHKB--ITFG1 HAVANA mRNA 1204 44448 . + . FI_gene_label "PHKB^ENSG00000102893.16" ; ID "PHKB--ITFG1^ENST00000299167.12" ; Parent "PHKB--ITFG1^PHKB^ENSG00000102893.16" ; exon_id "ENSE00002601441.1" ; exon_number 1 ; gene_id "PHKB--ITFG1^PHKB^ENSG00000102893.16" ; gene_name PHKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000133102.6" ; havana_transcript "OTTHUMT00000256767.3" ; hgnc_id "HGNC:8927" ; level 2 ; orig_coord_info "chr16,47461351,47461426,+" ; protein_id "ENSP00000299167.8" ; tag alternative_5_UTR basic ; transcript_id "PHKB--ITFG1^ENST00000299167.12" ; transcript_name "PHKB-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PHKB--ITFG1 HAVANA gene 48858 77339 . + . FI_gene_label "ITFG1^ENSG00000129636.13" ; ID "PHKB--ITFG1^ITFG1^ENSG00000129636.13" ; ccdsid "CCDS10728.1" ; exon_id "ENSE00001404558.4" ; exon_number 1 ; gene_id "PHKB--ITFG1^ITFG1^ENSG00000129636.13" ; gene_name ITFG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133103.6" ; havana_transcript "OTTHUMT00000256768.4" ; hgnc_id "HGNC:30697" ; level 2 ; orig_coord_info "chr16,47460838,47461045,-" ; protein_id "ENSP00000319918.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHKB--ITFG1^ENST00000320640.11" ; transcript_name "ITFG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PHKB--ITFG1 HAVANA mRNA 48858 77339 . + . FI_gene_label "ITFG1^ENSG00000129636.13" ; ID "PHKB--ITFG1^ENST00000320640.11" ; Parent "PHKB--ITFG1^ITFG1^ENSG00000129636.13" ; ccdsid "CCDS10728.1" ; exon_id "ENSE00001404558.4" ; exon_number 1 ; gene_id "PHKB--ITFG1^ITFG1^ENSG00000129636.13" ; gene_name ITFG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133103.6" ; havana_transcript "OTTHUMT00000256768.4" ; hgnc_id "HGNC:30697" ; level 2 ; orig_coord_info "chr16,47460838,47461045,-" ; protein_id "ENSP00000319918.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PHKB--ITFG1^ENST00000320640.11" ; transcript_name "ITFG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRG--NARS1 HAVANA gene 47890 59817 . + . FI_gene_label "NARS1^ENSG00000134440.12" ; ID "PTPRG--NARS1^NARS1^ENSG00000134440.12" ; ccdsid "CCDS32837.1" ; exon_id "ENSE00001225301.5" ; exon_number 1 ; gene_id "PTPRG--NARS1^NARS1^ENSG00000134440.12" ; gene_name NARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180125.7" ; havana_transcript "OTTHUMT00000449872.3" ; hgnc_id "HGNC:7643" ; level 2 ; orig_coord_info "chr18,57621708,57621717,-" ; protein_id "ENSP00000256854.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPRG--NARS1^ENST00000256854.10" ; transcript_name "NARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRG--NARS1 HAVANA mRNA 47890 59817 . + . FI_gene_label "NARS1^ENSG00000134440.12" ; ID "PTPRG--NARS1^ENST00000256854.10" ; Parent "PTPRG--NARS1^NARS1^ENSG00000134440.12" ; ccdsid "CCDS32837.1" ; exon_id "ENSE00001225301.5" ; exon_number 1 ; gene_id "PTPRG--NARS1^NARS1^ENSG00000134440.12" ; gene_name NARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180125.7" ; havana_transcript "OTTHUMT00000449872.3" ; hgnc_id "HGNC:7643" ; level 2 ; orig_coord_info "chr18,57621708,57621717,-" ; protein_id "ENSP00000256854.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPRG--NARS1^ENST00000256854.10" ; transcript_name "NARS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRG--NARS1 HAVANA gene 1343 40232 . + . FI_gene_label "PTPRG^ENSG00000144724.20" ; ID "PTPRG--NARS1^PTPRG^ENSG00000144724.20" ; exon_id "ENSE00001873446.1" ; exon_number 1 ; gene_id "PTPRG--NARS1^PTPRG^ENSG00000144724.20" ; gene_name PTPRG ; gene_type protein_coding ; havana_gene "OTTHUMG00000158660.2" ; havana_transcript "OTTHUMT00000351675.1" ; hgnc_id "HGNC:9671" ; level 2 ; orig_coord_info "chr3,61562288,61562372,+" ; protein_id "ENSP00000295874.10" ; tag basic appris_alternative_2 ; transcript_id "PTPRG--NARS1^ENST00000295874.14" ; transcript_name "PTPRG-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRG--NARS1 HAVANA mRNA 1343 40232 . + . FI_gene_label "PTPRG^ENSG00000144724.20" ; ID "PTPRG--NARS1^ENST00000295874.14" ; Parent "PTPRG--NARS1^PTPRG^ENSG00000144724.20" ; exon_id "ENSE00001873446.1" ; exon_number 1 ; gene_id "PTPRG--NARS1^PTPRG^ENSG00000144724.20" ; gene_name PTPRG ; gene_type protein_coding ; havana_gene "OTTHUMG00000158660.2" ; havana_transcript "OTTHUMT00000351675.1" ; hgnc_id "HGNC:9671" ; level 2 ; orig_coord_info "chr3,61562288,61562372,+" ; protein_id "ENSP00000295874.10" ; tag basic appris_alternative_2 ; transcript_id "PTPRG--NARS1^ENST00000295874.14" ; transcript_name "PTPRG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM6--SELENOI HAVANA gene 35008 52145 . + . FI_gene_label "SELENOI^ENSG00000138018.18" ; ID "RBM6--SELENOI^SELENOI^ENSG00000138018.18" ; ccdsid "CCDS46240.1" ; exon_id "ENSE00001136464.6" ; exon_number 1 ; gene_id "RBM6--SELENOI^SELENOI^ENSG00000138018.18" ; gene_name SELENOI ; gene_type protein_coding ; havana_gene "OTTHUMG00000151931.5" ; havana_transcript "OTTHUMT00000324484.4" ; hgnc_id "HGNC:29361" ; level 2 ; orig_coord_info "chr2,26346233,26346289,+" ; protein_id "ENSP00000260585.7" ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "RBM6--SELENOI^ENST00000260585.12" ; transcript_name "SELENOI-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM6--SELENOI HAVANA mRNA 35008 52145 . + . FI_gene_label "SELENOI^ENSG00000138018.18" ; ID "RBM6--SELENOI^ENST00000260585.12" ; Parent "RBM6--SELENOI^SELENOI^ENSG00000138018.18" ; ccdsid "CCDS46240.1" ; exon_id "ENSE00001136464.6" ; exon_number 1 ; gene_id "RBM6--SELENOI^SELENOI^ENSG00000138018.18" ; gene_name SELENOI ; gene_type protein_coding ; havana_gene "OTTHUMG00000151931.5" ; havana_transcript "OTTHUMT00000324484.4" ; hgnc_id "HGNC:29361" ; level 2 ; orig_coord_info "chr2,26346233,26346289,+" ; protein_id "ENSP00000260585.7" ; tag basic MANE_Select appris_principal_2 CCDS seleno ; transcript_id "RBM6--SELENOI^ENST00000260585.12" ; transcript_name "SELENOI-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM6--SELENOI HAVANA gene 1144 26383 . + . FI_gene_label "RBM6^ENSG00000004534.15" ; ID "RBM6--SELENOI^RBM6^ENSG00000004534.15" ; ccdsid "CCDS2809.1" ; exon_id "ENSE00003569056.1" ; exon_number 2 ; gene_id "RBM6--SELENOI^RBM6^ENSG00000004534.15" ; gene_name RBM6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156736.13" ; havana_transcript "OTTHUMT00000345528.6" ; hgnc_id "HGNC:9903" ; level 2 ; orig_coord_info "chr3,49962642,49962685,+" ; protein_id "ENSP00000266022.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RBM6--SELENOI^ENST00000266022.9" ; transcript_name "RBM6-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM6--SELENOI HAVANA mRNA 1144 26383 . + . FI_gene_label "RBM6^ENSG00000004534.15" ; ID "RBM6--SELENOI^ENST00000266022.9" ; Parent "RBM6--SELENOI^RBM6^ENSG00000004534.15" ; ccdsid "CCDS2809.1" ; exon_id "ENSE00003569056.1" ; exon_number 2 ; gene_id "RBM6--SELENOI^RBM6^ENSG00000004534.15" ; gene_name RBM6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156736.13" ; havana_transcript "OTTHUMT00000345528.6" ; hgnc_id "HGNC:9903" ; level 2 ; orig_coord_info "chr3,49962642,49962685,+" ; protein_id "ENSP00000266022.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RBM6--SELENOI^ENST00000266022.9" ; transcript_name "RBM6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RUNDC3A-AS1--SLC25A39 HAVANA gene 14933 20178 . + . FI_gene_label "SLC25A39^ENSG00000013306.16" ; ID "RUNDC3A-AS1--SLC25A39^SLC25A39^ENSG00000013306.16" ; ccdsid "CCDS11482.1" ; exon_id "ENSE00003601221.1" ; exon_number 2 ; gene_id "RUNDC3A-AS1--SLC25A39^SLC25A39^ENSG00000013306.16" ; gene_name SLC25A39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132628.4" ; havana_transcript "OTTHUMT00000255875.1" ; hgnc_id "HGNC:24279" ; level 2 ; orig_coord_info "chr17,44323478,44323562,-" ; protein_id "ENSP00000225308.8" ; tag basic appris_principal_4 CCDS ; transcript_id "RUNDC3A-AS1--SLC25A39^ENST00000225308.12" ; transcript_name "SLC25A39-201" ; transcript_support_level 1 ; transcript_type protein_coding
RUNDC3A-AS1--SLC25A39 HAVANA mRNA 14933 20178 . + . FI_gene_label "SLC25A39^ENSG00000013306.16" ; ID "RUNDC3A-AS1--SLC25A39^ENST00000225308.12" ; Parent "RUNDC3A-AS1--SLC25A39^SLC25A39^ENSG00000013306.16" ; ccdsid "CCDS11482.1" ; exon_id "ENSE00003601221.1" ; exon_number 2 ; gene_id "RUNDC3A-AS1--SLC25A39^SLC25A39^ENSG00000013306.16" ; gene_name SLC25A39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132628.4" ; havana_transcript "OTTHUMT00000255875.1" ; hgnc_id "HGNC:24279" ; level 2 ; orig_coord_info "chr17,44323478,44323562,-" ; protein_id "ENSP00000225308.8" ; tag basic appris_principal_4 CCDS ; transcript_id "RUNDC3A-AS1--SLC25A39^ENST00000225308.12" ; transcript_name "SLC25A39-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SIM2--ASS1 HAVANA gene 1001 18670 . + . FI_gene_label "SIM2^ENSG00000159263.16" ; ID "SIM2--ASS1^SIM2^ENSG00000159263.16" ; ccdsid "CCDS13646.1" ; exon_id "ENSE00003579996.2" ; exon_number 1 ; gene_id "SIM2--ASS1^SIM2^ENSG00000159263.16" ; gene_name SIM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086637.4" ; havana_transcript "OTTHUMT00000194692.2" ; hgnc_id "HGNC:10883" ; level 2 ; orig_coord_info "chr21,36699747,36699921,+" ; protein_id "ENSP00000290399.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SIM2--ASS1^ENST00000290399.11" ; transcript_name "SIM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SIM2--ASS1 HAVANA mRNA 1001 18670 . + . FI_gene_label "SIM2^ENSG00000159263.16" ; ID "SIM2--ASS1^ENST00000290399.11" ; Parent "SIM2--ASS1^SIM2^ENSG00000159263.16" ; ccdsid "CCDS13646.1" ; exon_id "ENSE00003579996.2" ; exon_number 1 ; gene_id "SIM2--ASS1^SIM2^ENSG00000159263.16" ; gene_name SIM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086637.4" ; havana_transcript "OTTHUMT00000194692.2" ; hgnc_id "HGNC:10883" ; level 2 ; orig_coord_info "chr21,36699747,36699921,+" ; protein_id "ENSP00000290399.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SIM2--ASS1^ENST00000290399.11" ; transcript_name "SIM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SIM2--ASS1 HAVANA gene 21671 39091 . + . FI_gene_label "ASS1^ENSG00000130707.18" ; ID "SIM2--ASS1^ASS1^ENSG00000130707.18" ; ccdsid "CCDS6933.1" ; exon_id "ENSE00002397383.1" ; exon_number 2 ; gene_id "SIM2--ASS1^ASS1^ENSG00000130707.18" ; gene_name ASS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020806.5" ; havana_transcript "OTTHUMT00000054650.2" ; hgnc_id "HGNC:758" ; level 2 ; orig_coord_info "chr9,130452229,130452333,+" ; protein_id "ENSP00000253004.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SIM2--ASS1^ENST00000352480.10" ; transcript_name "ASS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SIM2--ASS1 HAVANA mRNA 21671 39091 . + . FI_gene_label "ASS1^ENSG00000130707.18" ; ID "SIM2--ASS1^ENST00000352480.10" ; Parent "SIM2--ASS1^ASS1^ENSG00000130707.18" ; ccdsid "CCDS6933.1" ; exon_id "ENSE00002397383.1" ; exon_number 2 ; gene_id "SIM2--ASS1^ASS1^ENSG00000130707.18" ; gene_name ASS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020806.5" ; havana_transcript "OTTHUMT00000054650.2" ; hgnc_id "HGNC:758" ; level 2 ; orig_coord_info "chr9,130452229,130452333,+" ; protein_id "ENSP00000253004.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SIM2--ASS1^ENST00000352480.10" ; transcript_name "ASS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STK24--LINC01722 HAVANA gene 3947 19671 . + . FI_gene_label "STK24^ENSG00000102572.15" ; ID "STK24--LINC01722^STK24^ENSG00000102572.15" ; ccdsid "CCDS9488.1" ; exon_id "ENSE00001470887.3" ; exon_number 1 ; gene_id "STK24--LINC01722^STK24^ENSG00000102572.15" ; gene_name STK24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017250.3" ; havana_transcript "OTTHUMT00000045549.2" ; hgnc_id "HGNC:11403" ; level 2 ; orig_coord_info "chr13,98521775,98521852,-" ; protein_id "ENSP00000365730.3" ; tag basic CCDS ; transcript_id "STK24--LINC01722^ENST00000376547.7" ; transcript_name "STK24-201" ; transcript_support_level 1 ; transcript_type protein_coding
STK24--LINC01722 HAVANA mRNA 3947 19671 . + . FI_gene_label "STK24^ENSG00000102572.15" ; ID "STK24--LINC01722^ENST00000376547.7" ; Parent "STK24--LINC01722^STK24^ENSG00000102572.15" ; ccdsid "CCDS9488.1" ; exon_id "ENSE00001470887.3" ; exon_number 1 ; gene_id "STK24--LINC01722^STK24^ENSG00000102572.15" ; gene_name STK24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017250.3" ; havana_transcript "OTTHUMT00000045549.2" ; hgnc_id "HGNC:11403" ; level 2 ; orig_coord_info "chr13,98521775,98521852,-" ; protein_id "ENSP00000365730.3" ; tag basic CCDS ; transcript_id "STK24--LINC01722^ENST00000376547.7" ; transcript_name "STK24-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STK24--PA2G4P2 HAVANA gene 3947 19671 . + . FI_gene_label "STK24^ENSG00000102572.15" ; ID "STK24--PA2G4P2^STK24^ENSG00000102572.15" ; ccdsid "CCDS9488.1" ; exon_id "ENSE00001470887.3" ; exon_number 1 ; gene_id "STK24--PA2G4P2^STK24^ENSG00000102572.15" ; gene_name STK24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017250.3" ; havana_transcript "OTTHUMT00000045549.2" ; hgnc_id "HGNC:11403" ; level 2 ; orig_coord_info "chr13,98521775,98521852,-" ; protein_id "ENSP00000365730.3" ; tag basic CCDS ; transcript_id "STK24--PA2G4P2^ENST00000376547.7" ; transcript_name "STK24-201" ; transcript_support_level 1 ; transcript_type protein_coding
STK24--PA2G4P2 HAVANA mRNA 3947 19671 . + . FI_gene_label "STK24^ENSG00000102572.15" ; ID "STK24--PA2G4P2^ENST00000376547.7" ; Parent "STK24--PA2G4P2^STK24^ENSG00000102572.15" ; ccdsid "CCDS9488.1" ; exon_id "ENSE00001470887.3" ; exon_number 1 ; gene_id "STK24--PA2G4P2^STK24^ENSG00000102572.15" ; gene_name STK24 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017250.3" ; havana_transcript "OTTHUMT00000045549.2" ; hgnc_id "HGNC:11403" ; level 2 ; orig_coord_info "chr13,98521775,98521852,-" ; protein_id "ENSP00000365730.3" ; tag basic CCDS ; transcript_id "STK24--PA2G4P2^ENST00000376547.7" ; transcript_name "STK24-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TALDO1--AC131934.1 HAVANA gene 1050 9536 . + . FI_gene_label "TALDO1^ENSG00000177156.11" ; ID "TALDO1--AC131934.1^TALDO1^ENSG00000177156.11" ; ccdsid "CCDS7712.1" ; exon_id "ENSE00001297974.7" ; exon_number 1 ; gene_id "TALDO1--AC131934.1^TALDO1^ENSG00000177156.11" ; gene_name TALDO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133318.5" ; havana_transcript "OTTHUMT00000257116.2" ; hgnc_id "HGNC:11559" ; level 2 ; orig_coord_info "chr11,747482,747578,+" ; protein_id "ENSP00000321259.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--AC131934.1^ENST00000319006.8" ; transcript_name "TALDO1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TALDO1--AC131934.1 HAVANA mRNA 1050 9536 . + . FI_gene_label "TALDO1^ENSG00000177156.11" ; ID "TALDO1--AC131934.1^ENST00000319006.8" ; Parent "TALDO1--AC131934.1^TALDO1^ENSG00000177156.11" ; ccdsid "CCDS7712.1" ; exon_id "ENSE00001297974.7" ; exon_number 1 ; gene_id "TALDO1--AC131934.1^TALDO1^ENSG00000177156.11" ; gene_name TALDO1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133318.5" ; havana_transcript "OTTHUMT00000257116.2" ; hgnc_id "HGNC:11559" ; level 2 ; orig_coord_info "chr11,747482,747578,+" ; protein_id "ENSP00000321259.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TALDO1--AC131934.1^ENST00000319006.8" ; transcript_name "TALDO1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TEAD2--ZNF106 HAVANA gene 21486 48475 . + . FI_gene_label "ZNF106^ENSG00000103994.18" ; ID "TEAD2--ZNF106^ZNF106^ENSG00000103994.18" ; ccdsid "CCDS32208.1" ; exon_id "ENSE00002323335.1" ; exon_number 1 ; gene_id "TEAD2--ZNF106^ZNF106^ENSG00000103994.18" ; gene_name ZNF106 ; gene_type protein_coding ; havana_gene "OTTHUMG00000173244.7" ; havana_transcript "OTTHUMT00000422587.1" ; hgnc_id "HGNC:12886" ; level 2 ; orig_coord_info "chr15,42456958,42457205,-" ; protein_id "ENSP00000263805.4" ; tag basic CCDS ; transcript_id "TEAD2--ZNF106^ENST00000263805.8" ; transcript_name "ZNF106-201" ; transcript_support_level 1 ; transcript_type protein_coding
TEAD2--ZNF106 HAVANA mRNA 21486 48475 . + . FI_gene_label "ZNF106^ENSG00000103994.18" ; ID "TEAD2--ZNF106^ENST00000263805.8" ; Parent "TEAD2--ZNF106^ZNF106^ENSG00000103994.18" ; ccdsid "CCDS32208.1" ; exon_id "ENSE00002323335.1" ; exon_number 1 ; gene_id "TEAD2--ZNF106^ZNF106^ENSG00000103994.18" ; gene_name ZNF106 ; gene_type protein_coding ; havana_gene "OTTHUMG00000173244.7" ; havana_transcript "OTTHUMT00000422587.1" ; hgnc_id "HGNC:12886" ; level 2 ; orig_coord_info "chr15,42456958,42457205,-" ; protein_id "ENSP00000263805.4" ; tag basic CCDS ; transcript_id "TEAD2--ZNF106^ENST00000263805.8" ; transcript_name "ZNF106-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TEAD2--ZNF106 HAVANA gene 1001 14500 . + . FI_gene_label "TEAD2^ENSG00000074219.14" ; ID "TEAD2--ZNF106^TEAD2^ENSG00000074219.14" ; ccdsid "CCDS12761.1" ; exon_id "ENSE00000954740.1" ; exon_number 2 ; gene_id "TEAD2--ZNF106^TEAD2^ENSG00000074219.14" ; gene_name TEAD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183174.3" ; havana_transcript "OTTHUMT00000465465.1" ; hgnc_id "HGNC:11715" ; level 2 ; orig_coord_info "chr19,49359844,49360075,-" ; protein_id "ENSP00000310701.1" ; tag basic appris_principal_4 CCDS ; transcript_id "TEAD2--ZNF106^ENST00000311227.6" ; transcript_name "TEAD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TEAD2--ZNF106 HAVANA mRNA 1001 14500 . + . FI_gene_label "TEAD2^ENSG00000074219.14" ; ID "TEAD2--ZNF106^ENST00000311227.6" ; Parent "TEAD2--ZNF106^TEAD2^ENSG00000074219.14" ; ccdsid "CCDS12761.1" ; exon_id "ENSE00000954740.1" ; exon_number 2 ; gene_id "TEAD2--ZNF106^TEAD2^ENSG00000074219.14" ; gene_name TEAD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183174.3" ; havana_transcript "OTTHUMT00000465465.1" ; hgnc_id "HGNC:11715" ; level 2 ; orig_coord_info "chr19,49359844,49360075,-" ; protein_id "ENSP00000310701.1" ; tag basic appris_principal_4 CCDS ; transcript_id "TEAD2--ZNF106^ENST00000311227.6" ; transcript_name "TEAD2-201" ; 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:
TNS3--PKD1L1 HAVANA gene 48628 109174 . + . FI_gene_label "PKD1L1^ENSG00000158683.9" ; ID "TNS3--PKD1L1^PKD1L1^ENSG00000158683.9" ; ccdsid "CCDS34633.1" ; exon_id "ENSE00001175559.4" ; exon_number 1 ; gene_id "TNS3--PKD1L1^PKD1L1^ENSG00000158683.9" ; gene_name PKD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155649.2" ; havana_transcript "OTTHUMT00000340974.2" ; hgnc_id "HGNC:18053" ; level 2 ; orig_coord_info "chr7,47948397,47948440,-" ; protein_id "ENSP00000289672.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS3--PKD1L1^ENST00000289672.7" ; transcript_name "PKD1L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TNS3--PKD1L1 HAVANA mRNA 48628 109174 . + . FI_gene_label "PKD1L1^ENSG00000158683.9" ; ID "TNS3--PKD1L1^ENST00000289672.7" ; Parent "TNS3--PKD1L1^PKD1L1^ENSG00000158683.9" ; ccdsid "CCDS34633.1" ; exon_id "ENSE00001175559.4" ; exon_number 1 ; gene_id "TNS3--PKD1L1^PKD1L1^ENSG00000158683.9" ; gene_name PKD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155649.2" ; havana_transcript "OTTHUMT00000340974.2" ; hgnc_id "HGNC:18053" ; level 2 ; orig_coord_info "chr7,47948397,47948440,-" ; protein_id "ENSP00000289672.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS3--PKD1L1^ENST00000289672.7" ; transcript_name "PKD1L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TNS3--PKD1L1 HAVANA gene 1448 45627 . + . FI_gene_label "TNS3^ENSG00000136205.17" ; ID "TNS3--PKD1L1^TNS3^ENSG00000136205.17" ; ccdsid "CCDS5506.2" ; exon_id "ENSE00003480523.1" ; exon_number 6 ; gene_id "TNS3--PKD1L1^TNS3^ENSG00000136205.17" ; gene_name TNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074075.4" ; havana_transcript "OTTHUMT00000157253.2" ; hgnc_id "HGNC:21616" ; level 2 ; orig_coord_info "chr7,47439487,47439636,-" ; protein_id "ENSP00000312143.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS3--PKD1L1^ENST00000311160.14" ; transcript_name "TNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TNS3--PKD1L1 HAVANA mRNA 1448 45627 . + . FI_gene_label "TNS3^ENSG00000136205.17" ; ID "TNS3--PKD1L1^ENST00000311160.14" ; Parent "TNS3--PKD1L1^TNS3^ENSG00000136205.17" ; ccdsid "CCDS5506.2" ; exon_id "ENSE00003480523.1" ; exon_number 6 ; gene_id "TNS3--PKD1L1^TNS3^ENSG00000136205.17" ; gene_name TNS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074075.4" ; havana_transcript "OTTHUMT00000157253.2" ; hgnc_id "HGNC:21616" ; level 2 ; orig_coord_info "chr7,47439487,47439636,-" ; protein_id "ENSP00000312143.9" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS3--PKD1L1^ENST00000311160.14" ; transcript_name "TNS3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TTC39B--CCDC171 ENSEMBL gene 1001 26508 . + . FI_gene_label "TTC39B^ENSG00000155158.20" ; ID "TTC39B--CCDC171^TTC39B^ENSG00000155158.20" ; ccdsid "CCDS55295.1" ; exon_id "ENSE00003621952.1" ; exon_number 1 ; gene_id "TTC39B--CCDC171^TTC39B^ENSG00000155158.20" ; gene_name TTC39B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019581.7" ; hgnc_id "HGNC:23704" ; level 3 ; orig_coord_info "chr9,15307084,15307323,-" ; protein_id "ENSP00000297615.5" ; tag basic CCDS ; transcript_id "TTC39B--CCDC171^ENST00000297615.9" ; transcript_name "TTC39B-201" ; transcript_support_level 2 ; transcript_type protein_coding
TTC39B--CCDC171 ENSEMBL mRNA 1001 26508 . + . FI_gene_label "TTC39B^ENSG00000155158.20" ; ID "TTC39B--CCDC171^ENST00000297615.9" ; Parent "TTC39B--CCDC171^TTC39B^ENSG00000155158.20" ; ccdsid "CCDS55295.1" ; exon_id "ENSE00003621952.1" ; exon_number 1 ; gene_id "TTC39B--CCDC171^TTC39B^ENSG00000155158.20" ; gene_name TTC39B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019581.7" ; hgnc_id "HGNC:23704" ; level 3 ; orig_coord_info "chr9,15307084,15307323,-" ; protein_id "ENSP00000297615.5" ; tag basic CCDS ; transcript_id "TTC39B--CCDC171^ENST00000297615.9" ; transcript_name "TTC39B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TTC39B--CCDC171 HAVANA gene 36732 78692 . + . FI_gene_label "CCDC171^ENSG00000164989.17" ; ID "TTC39B--CCDC171^CCDC171^ENSG00000164989.17" ; ccdsid "CCDS6481.1" ; exon_id "ENSE00002733524.1" ; exon_number 2 ; gene_id "TTC39B--CCDC171^CCDC171^ENSG00000164989.17" ; gene_name CCDC171 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019584.7" ; havana_transcript "OTTHUMT00000051768.5" ; hgnc_id "HGNC:29828" ; level 2 ; orig_coord_info "chr9,15564089,15564129,+" ; protein_id "ENSP00000370077.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTC39B--CCDC171^ENST00000380701.8" ; transcript_name "CCDC171-201" ; transcript_support_level 1 ; transcript_type protein_coding
TTC39B--CCDC171 HAVANA mRNA 36732 78692 . + . FI_gene_label "CCDC171^ENSG00000164989.17" ; ID "TTC39B--CCDC171^ENST00000380701.8" ; Parent "TTC39B--CCDC171^CCDC171^ENSG00000164989.17" ; ccdsid "CCDS6481.1" ; exon_id "ENSE00002733524.1" ; exon_number 2 ; gene_id "TTC39B--CCDC171^CCDC171^ENSG00000164989.17" ; gene_name CCDC171 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019584.7" ; havana_transcript "OTTHUMT00000051768.5" ; hgnc_id "HGNC:29828" ; level 2 ; orig_coord_info "chr9,15564089,15564129,+" ; protein_id "ENSP00000370077.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TTC39B--CCDC171^ENST00000380701.8" ; transcript_name "CCDC171-201" ; 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:
ZNF81--AL807740.1 HAVANA gene 1045 5980 . + . FI_gene_label "ZNF81^ENSG00000197779.15" ; ID "ZNF81--AL807740.1^ZNF81^ENSG00000197779.15" ; exon_id "ENSE00001472254.1" ; exon_number 3 ; gene_id "ZNF81--AL807740.1^ZNF81^ENSG00000197779.15" ; gene_name ZNF81 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021462.3" ; havana_transcript "OTTHUMT00000130058.1" ; hgnc_id "HGNC:13156" ; level 2 ; orig_coord_info "chrX,47846268,47846321,+" ; protein_id "ENSP00000334641.4" ; tag basic ; transcript_id "ZNF81--AL807740.1^ENST00000334937.8" ; transcript_name "ZNF81-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF81--AL807740.1 HAVANA mRNA 1045 5980 . + . FI_gene_label "ZNF81^ENSG00000197779.15" ; ID "ZNF81--AL807740.1^ENST00000334937.8" ; Parent "ZNF81--AL807740.1^ZNF81^ENSG00000197779.15" ; exon_id "ENSE00001472254.1" ; exon_number 3 ; gene_id "ZNF81--AL807740.1^ZNF81^ENSG00000197779.15" ; gene_name ZNF81 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021462.3" ; havana_transcript "OTTHUMT00000130058.1" ; hgnc_id "HGNC:13156" ; level 2 ; orig_coord_info "chrX,47846268,47846321,+" ; protein_id "ENSP00000334641.4" ; tag basic ; transcript_id "ZNF81--AL807740.1^ENST00000334937.8" ; transcript_name "ZNF81-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF81--AL928596.1 HAVANA gene 1045 5980 . + . FI_gene_label "ZNF81^ENSG00000197779.15" ; ID "ZNF81--AL928596.1^ZNF81^ENSG00000197779.15" ; exon_id "ENSE00001472254.1" ; exon_number 3 ; gene_id "ZNF81--AL928596.1^ZNF81^ENSG00000197779.15" ; gene_name ZNF81 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021462.3" ; havana_transcript "OTTHUMT00000130058.1" ; hgnc_id "HGNC:13156" ; level 2 ; orig_coord_info "chrX,47846268,47846321,+" ; protein_id "ENSP00000334641.4" ; tag basic ; transcript_id "ZNF81--AL928596.1^ENST00000334937.8" ; transcript_name "ZNF81-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF81--AL928596.1 HAVANA mRNA 1045 5980 . + . FI_gene_label "ZNF81^ENSG00000197779.15" ; ID "ZNF81--AL928596.1^ENST00000334937.8" ; Parent "ZNF81--AL928596.1^ZNF81^ENSG00000197779.15" ; exon_id "ENSE00001472254.1" ; exon_number 3 ; gene_id "ZNF81--AL928596.1^ZNF81^ENSG00000197779.15" ; gene_name ZNF81 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021462.3" ; havana_transcript "OTTHUMT00000130058.1" ; hgnc_id "HGNC:13156" ; level 2 ; orig_coord_info "chrX,47846268,47846321,+" ; protein_id "ENSP00000334641.4" ; tag basic ; transcript_id "ZNF81--AL928596.1^ENST00000334937.8" ; transcript_name "ZNF81-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GK5--AC063938.1 HAVANA gene 30165 34836 . + . FI_gene_label "AC063938.1^ENSG00000241754.2" ; ID "GK5--AC063938.1^AC063938.1^ENSG00000241754.2" ; exon_id "ENSE00001872673.1" ; exon_number 1 ; gene_id "GK5--AC063938.1^AC063938.1^ENSG00000241754.2" ; gene_name "AC063938.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000159096.5" ; havana_transcript "OTTHUMT00000353284.2" ; level 2 ; orig_coord_info "chr3,102673754,102673913,-" ; tag TAGENE ; transcript_id "GK5--AC063938.1^ENST00000487772.2" ; transcript_name "AC063938.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
GK5--AC063938.1 HAVANA RNA 30165 34836 . + . FI_gene_label "AC063938.1^ENSG00000241754.2" ; ID "GK5--AC063938.1^ENST00000487772.2" ; Parent "GK5--AC063938.1^AC063938.1^ENSG00000241754.2" ; exon_id "ENSE00001872673.1" ; exon_number 1 ; gene_id "GK5--AC063938.1^AC063938.1^ENSG00000241754.2" ; gene_name "AC063938.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000159096.5" ; havana_transcript "OTTHUMT00000353284.2" ; level 2 ; orig_coord_info "chr3,102673754,102673913,-" ; tag TAGENE ; transcript_id "GK5--AC063938.1^ENST00000487772.2" ; transcript_name "AC063938.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
KLHL22--SMPD4P1 HAVANA gene 24014 36986 . + . FI_gene_label "SMPD4P1^ENSG00000223553.6" ; ID "KLHL22--SMPD4P1^SMPD4P1^ENSG00000223553.6" ; exon_id "ENSE00001676552.1" ; exon_number 1 ; gene_id "KLHL22--SMPD4P1^SMPD4P1^ENSG00000223553.6" ; gene_name SMPD4P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000030245.6" ; havana_transcript "OTTHUMT00000075099.6" ; hgnc_id "HGNC:39673" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr22,20626096,20626134,-" ; tag pseudo_consens basic ; transcript_id "KLHL22--SMPD4P1^ENST00000416717.6" ; transcript_name "SMPD4P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
KLHL22--SMPD4P1 HAVANA RNA 24014 36986 . + . FI_gene_label "SMPD4P1^ENSG00000223553.6" ; ID "KLHL22--SMPD4P1^ENST00000416717.6" ; Parent "KLHL22--SMPD4P1^SMPD4P1^ENSG00000223553.6" ; exon_id "ENSE00001676552.1" ; exon_number 1 ; gene_id "KLHL22--SMPD4P1^SMPD4P1^ENSG00000223553.6" ; gene_name SMPD4P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000030245.6" ; havana_transcript "OTTHUMT00000075099.6" ; hgnc_id "HGNC:39673" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr22,20626096,20626134,-" ; tag pseudo_consens basic ; transcript_id "KLHL22--SMPD4P1^ENST00000416717.6" ; transcript_name "SMPD4P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
LINC02071--SELENOP HAVANA gene 1001 6575 . + . FI_gene_label "LINC02071^ENSG00000249383.2" ; ID "LINC02071--SELENOP^LINC02071^ENSG00000249383.2" ; exon_id "ENSE00002028563.1" ; exon_number 1 ; gene_id "LINC02071--SELENOP^LINC02071^ENSG00000249383.2" ; gene_name LINC02071 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162372.2" ; havana_transcript "OTTHUMT00000368657.1" ; hgnc_id "HGNC:52917" ; level 2 ; orig_coord_info "chr17,51334346,51335165,-" ; tag basic ; transcript_id "LINC02071--SELENOP^ENST00000514726.1" ; transcript_name "LINC02071-201" ; transcript_support_level 1 ; transcript_type lncRNA
LINC02071--SELENOP HAVANA RNA 1001 6575 . + . FI_gene_label "LINC02071^ENSG00000249383.2" ; ID "LINC02071--SELENOP^ENST00000514726.1" ; Parent "LINC02071--SELENOP^LINC02071^ENSG00000249383.2" ; exon_id "ENSE00002028563.1" ; exon_number 1 ; gene_id "LINC02071--SELENOP^LINC02071^ENSG00000249383.2" ; gene_name LINC02071 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162372.2" ; havana_transcript "OTTHUMT00000368657.1" ; hgnc_id "HGNC:52917" ; level 2 ; orig_coord_info "chr17,51334346,51335165,-" ; tag basic ; transcript_id "LINC02071--SELENOP^ENST00000514726.1" ; transcript_name "LINC02071-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
RUNDC3A-AS1--SLC25A39 HAVANA gene 4361 8989 . + . FI_gene_label "RUNDC3A-AS1^ENSG00000267750.6" ; ID "RUNDC3A-AS1--SLC25A39^RUNDC3A-AS1^ENSG00000267750.6" ; exon_id "ENSE00002928820.1" ; exon_number 1 ; gene_id "RUNDC3A-AS1--SLC25A39^RUNDC3A-AS1^ENSG00000267750.6" ; gene_name "RUNDC3A-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000132629.4" ; havana_transcript "OTTHUMT00000457738.1" ; hgnc_id "HGNC:51344" ; level 2 ; orig_coord_info "chr17,44308257,44308393,-" ; transcript_id "RUNDC3A-AS1--SLC25A39^ENST00000586388.1" ; transcript_name "RUNDC3A-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA
RUNDC3A-AS1--SLC25A39 HAVANA RNA 4361 8989 . + . FI_gene_label "RUNDC3A-AS1^ENSG00000267750.6" ; ID "RUNDC3A-AS1--SLC25A39^ENST00000586388.1" ; Parent "RUNDC3A-AS1--SLC25A39^RUNDC3A-AS1^ENSG00000267750.6" ; exon_id "ENSE00002928820.1" ; exon_number 1 ; gene_id "RUNDC3A-AS1--SLC25A39^RUNDC3A-AS1^ENSG00000267750.6" ; gene_name "RUNDC3A-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000132629.4" ; havana_transcript "OTTHUMT00000457738.1" ; hgnc_id "HGNC:51344" ; level 2 ; orig_coord_info "chr17,44308257,44308393,-" ; transcript_id "RUNDC3A-AS1--SLC25A39^ENST00000586388.1" ; transcript_name "RUNDC3A-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
STK24--LINC01722 HAVANA gene 29646 43424 . + . FI_gene_label "LINC01722^ENSG00000233048.1" ; ID "STK24--LINC01722^LINC01722^ENSG00000233048.1" ; exon_id "ENSE00001596657.1" ; exon_number 1 ; gene_id "STK24--LINC01722^LINC01722^ENSG00000233048.1" ; gene_name LINC01722 ; gene_type lncRNA ; havana_gene "OTTHUMG00000031897.1" ; havana_transcript "OTTHUMT00000078030.1" ; hgnc_id "HGNC:52510" ; level 2 ; orig_coord_info "chr20,12951765,12952519,-" ; tag basic ; transcript_id "STK24--LINC01722^ENST00000456265.1" ; transcript_name "LINC01722-201" ; transcript_support_level 1 ; transcript_type lncRNA
STK24--LINC01722 HAVANA RNA 29646 43424 . + . FI_gene_label "LINC01722^ENSG00000233048.1" ; ID "STK24--LINC01722^ENST00000456265.1" ; Parent "STK24--LINC01722^LINC01722^ENSG00000233048.1" ; exon_id "ENSE00001596657.1" ; exon_number 1 ; gene_id "STK24--LINC01722^LINC01722^ENSG00000233048.1" ; gene_name LINC01722 ; gene_type lncRNA ; havana_gene "OTTHUMG00000031897.1" ; havana_transcript "OTTHUMT00000078030.1" ; hgnc_id "HGNC:52510" ; level 2 ; orig_coord_info "chr20,12951765,12952519,-" ; tag basic ; transcript_id "STK24--LINC01722^ENST00000456265.1" ; transcript_name "LINC01722-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
STK24--PA2G4P2 HAVANA gene 29646 30845 . + . FI_gene_label "PA2G4P2^ENSG00000235698.1" ; ID "STK24--PA2G4P2^PA2G4P2^ENSG00000235698.1" ; exon_id "ENSE00001777561.1" ; exon_number 1 ; gene_id "STK24--PA2G4P2^PA2G4P2^ENSG00000235698.1" ; gene_name PA2G4P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000031893.1" ; havana_transcript "OTTHUMT00000078026.1" ; hgnc_id "HGNC:16531" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr20,12380056,12381255,+" ; tag pseudo_consens basic ; transcript_id "STK24--PA2G4P2^ENST00000414718.1" ; transcript_name "PA2G4P2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
STK24--PA2G4P2 HAVANA RNA 29646 30845 . + . FI_gene_label "PA2G4P2^ENSG00000235698.1" ; ID "STK24--PA2G4P2^ENST00000414718.1" ; Parent "STK24--PA2G4P2^PA2G4P2^ENSG00000235698.1" ; exon_id "ENSE00001777561.1" ; exon_number 1 ; gene_id "STK24--PA2G4P2^PA2G4P2^ENSG00000235698.1" ; gene_name PA2G4P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000031893.1" ; havana_transcript "OTTHUMT00000078026.1" ; hgnc_id "HGNC:16531" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr20,12380056,12381255,+" ; tag pseudo_consens basic ; transcript_id "STK24--PA2G4P2^ENST00000414718.1" ; transcript_name "PA2G4P2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TALDO1--AC131934.1 HAVANA gene 12537 15448 . + . FI_gene_label "AC131934.1^ENSG00000255158.1" ; ID "TALDO1--AC131934.1^AC131934.1^ENSG00000255158.1" ; exon_id "ENSE00002144098.1" ; exon_number 1 ; gene_id "TALDO1--AC131934.1^AC131934.1^ENSG00000255158.1" ; gene_name "AC131934.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165430.1" ; havana_transcript "OTTHUMT00000384005.1" ; level 1 ; orig_coord_info "chr11,665910,666490,+" ; tag basic exp_conf ; transcript_id "TALDO1--AC131934.1^ENST00000527799.1" ; transcript_name "AC131934.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TALDO1--AC131934.1 HAVANA RNA 12537 15448 . + . FI_gene_label "AC131934.1^ENSG00000255158.1" ; ID "TALDO1--AC131934.1^ENST00000527799.1" ; Parent "TALDO1--AC131934.1^AC131934.1^ENSG00000255158.1" ; exon_id "ENSE00002144098.1" ; exon_number 1 ; gene_id "TALDO1--AC131934.1^AC131934.1^ENSG00000255158.1" ; gene_name "AC131934.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000165430.1" ; havana_transcript "OTTHUMT00000384005.1" ; level 1 ; orig_coord_info "chr11,665910,666490,+" ; tag basic exp_conf ; transcript_id "TALDO1--AC131934.1^ENST00000527799.1" ; transcript_name "AC131934.1-201" ; transcript_support_level 5 ; 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:
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
L1 and L2 created:
ZNF81--AL807740.1 HAVANA gene 22815 25538 . + . FI_gene_label "AL807740.1^ENSG00000283400.1" ; ID "ZNF81--AL807740.1^AL807740.1^ENSG00000283400.1" ; exon_id "ENSE00003794730.1" ; exon_number 1 ; gene_id "ZNF81--AL807740.1^AL807740.1^ENSG00000283400.1" ; gene_name "AL807740.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000191667.1" ; havana_transcript "OTTHUMT00000489190.1" ; level 2 ; orig_coord_info "chrX,20443326,20443626,+" ; tag basic ; transcript_id "ZNF81--AL807740.1^ENST00000636971.1" ; transcript_name "AL807740.1-201" ; transcript_support_level 4 ; transcript_type lncRNA
ZNF81--AL807740.1 HAVANA RNA 22815 25538 . + . FI_gene_label "AL807740.1^ENSG00000283400.1" ; ID "ZNF81--AL807740.1^ENST00000636971.1" ; Parent "ZNF81--AL807740.1^AL807740.1^ENSG00000283400.1" ; exon_id "ENSE00003794730.1" ; exon_number 1 ; gene_id "ZNF81--AL807740.1^AL807740.1^ENSG00000283400.1" ; gene_name "AL807740.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000191667.1" ; havana_transcript "OTTHUMT00000489190.1" ; level 2 ; orig_coord_info "chrX,20443326,20443626,+" ; tag basic ; transcript_id "ZNF81--AL807740.1^ENST00000636971.1" ; transcript_name "AL807740.1-201" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
ZNF81--AL928596.1 HAVANA gene 22815 24446 . + . FI_gene_label "AL928596.1^ENSG00000283631.1" ; ID "ZNF81--AL928596.1^AL928596.1^ENSG00000283631.1" ; exon_id "ENSE00003799756.1" ; exon_number 1 ; gene_id "ZNF81--AL928596.1^AL928596.1^ENSG00000283631.1" ; gene_name "AL928596.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000191666.1" ; havana_transcript "OTTHUMT00000489189.1" ; level 2 ; orig_coord_info "chrX,20317473,20317783,-" ; tag basic ; transcript_id "ZNF81--AL928596.1^ENST00000636738.1" ; transcript_name "AL928596.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
ZNF81--AL928596.1 HAVANA RNA 22815 24446 . + . FI_gene_label "AL928596.1^ENSG00000283631.1" ; ID "ZNF81--AL928596.1^ENST00000636738.1" ; Parent "ZNF81--AL928596.1^AL928596.1^ENSG00000283631.1" ; exon_id "ENSE00003799756.1" ; exon_number 1 ; gene_id "ZNF81--AL928596.1^AL928596.1^ENSG00000283631.1" ; gene_name "AL928596.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000191666.1" ; havana_transcript "OTTHUMT00000489189.1" ; level 2 ; orig_coord_info "chrX,20317473,20317783,-" ; tag basic ; transcript_id "ZNF81--AL928596.1^ENST00000636738.1" ; transcript_name "AL928596.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
464 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 ------------------------------
745 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 32 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed