Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/6c41d9e458dd88f7bbbfd81985f26c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/2a8d082672db27d3809860aef8c4fc/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/6c41d9e458dd88f7bbbfd81985f26c/.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: 9390
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 9390
=> 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:9390
=> 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:
AC060809.1--ERBB4 HAVANA gene 7877 31109 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "AC060809.1--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "AC060809.1--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "AC060809.1--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC060809.1--ERBB4 HAVANA mRNA 7877 31109 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "AC060809.1--ERBB4^ENST00000260943.10" ; Parent "AC060809.1--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "AC060809.1--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "AC060809.1--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ARSG--DPH1 HAVANA gene 25289 36148 . + . FI_gene_label "DPH1^ENSG00000108963.19" ; ID "ARSG--DPH1^DPH1^ENSG00000108963.19" ; exon_id "ENSE00002639140.2" ; exon_number 1 ; gene_id "ARSG--DPH1^DPH1^ENSG00000108963.19" ; gene_name DPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177724.8" ; havana_transcript "OTTHUMT00000438660.2" ; hgnc_id "HGNC:3003" ; level 2 ; orig_coord_info "chr17,2030170,2030230,+" ; protein_id "ENSP00000263083.7" ; tag upstream_ATG basic MANE_Select appris_alternative_2 ; transcript_id "ARSG--DPH1^ENST00000263083.12" ; transcript_name "DPH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARSG--DPH1 HAVANA mRNA 25289 36148 . + . FI_gene_label "DPH1^ENSG00000108963.19" ; ID "ARSG--DPH1^ENST00000263083.12" ; Parent "ARSG--DPH1^DPH1^ENSG00000108963.19" ; exon_id "ENSE00002639140.2" ; exon_number 1 ; gene_id "ARSG--DPH1^DPH1^ENSG00000108963.19" ; gene_name DPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177724.8" ; havana_transcript "OTTHUMT00000438660.2" ; hgnc_id "HGNC:3003" ; level 2 ; orig_coord_info "chr17,2030170,2030230,+" ; protein_id "ENSP00000263083.7" ; tag upstream_ATG basic MANE_Select appris_alternative_2 ; transcript_id "ARSG--DPH1^ENST00000263083.12" ; transcript_name "DPH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARSG--DPH1 HAVANA gene 1001 22272 . + . FI_gene_label "ARSG^ENSG00000141337.13" ; ID "ARSG--DPH1^ARSG^ENSG00000141337.13" ; ccdsid "CCDS11676.1" ; exon_id "ENSE00001598531.1" ; exon_number 2 ; gene_id "ARSG--DPH1^ARSG^ENSG00000141337.13" ; gene_name ARSG ; gene_type protein_coding ; havana_gene "OTTHUMG00000179810.6" ; havana_transcript "OTTHUMT00000448369.1" ; hgnc_id "HGNC:24102" ; level 2 ; orig_coord_info "chr17,68307494,68307711,+" ; protein_id "ENSP00000407193.2" ; tag basic appris_principal_1 CCDS ; transcript_id "ARSG--DPH1^ENST00000448504.6" ; transcript_name "ARSG-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARSG--DPH1 HAVANA mRNA 1001 22272 . + . FI_gene_label "ARSG^ENSG00000141337.13" ; ID "ARSG--DPH1^ENST00000448504.6" ; Parent "ARSG--DPH1^ARSG^ENSG00000141337.13" ; ccdsid "CCDS11676.1" ; exon_id "ENSE00001598531.1" ; exon_number 2 ; gene_id "ARSG--DPH1^ARSG^ENSG00000141337.13" ; gene_name ARSG ; gene_type protein_coding ; havana_gene "OTTHUMG00000179810.6" ; havana_transcript "OTTHUMT00000448369.1" ; hgnc_id "HGNC:24102" ; level 2 ; orig_coord_info "chr17,68307494,68307711,+" ; protein_id "ENSP00000407193.2" ; tag basic appris_principal_1 CCDS ; transcript_id "ARSG--DPH1^ENST00000448504.6" ; transcript_name "ARSG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BMP2K--PTPRT HAVANA gene 28685 73944 . + . FI_gene_label "PTPRT^ENSG00000196090.12" ; ID "BMP2K--PTPRT^PTPRT^ENSG00000196090.12" ; exon_id "ENSE00001299020.1" ; exon_number 1 ; gene_id "BMP2K--PTPRT^PTPRT^ENSG00000196090.12" ; gene_name PTPRT ; gene_type protein_coding ; havana_gene "OTTHUMG00000033040.5" ; havana_transcript "OTTHUMT00000080317.1" ; hgnc_id "HGNC:9682" ; level 2 ; orig_coord_info "chr20,43189646,43189733,-" ; protein_id "ENSP00000348408.2" ; tag dotter_confirmed not_organism_supported basic appris_alternative_2 ; transcript_id "BMP2K--PTPRT^ENST00000356100.6" ; transcript_name "PTPRT-201" ; transcript_support_level 5 ; transcript_type protein_coding
BMP2K--PTPRT HAVANA mRNA 28685 73944 . + . FI_gene_label "PTPRT^ENSG00000196090.12" ; ID "BMP2K--PTPRT^ENST00000356100.6" ; Parent "BMP2K--PTPRT^PTPRT^ENSG00000196090.12" ; exon_id "ENSE00001299020.1" ; exon_number 1 ; gene_id "BMP2K--PTPRT^PTPRT^ENSG00000196090.12" ; gene_name PTPRT ; gene_type protein_coding ; havana_gene "OTTHUMG00000033040.5" ; havana_transcript "OTTHUMT00000080317.1" ; hgnc_id "HGNC:9682" ; level 2 ; orig_coord_info "chr20,43189646,43189733,-" ; protein_id "ENSP00000348408.2" ; tag dotter_confirmed not_organism_supported basic appris_alternative_2 ; transcript_id "BMP2K--PTPRT^ENST00000356100.6" ; transcript_name "PTPRT-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
BMP2K--PTPRT HAVANA gene 1001 17046 . + . FI_gene_label "BMP2K^ENSG00000138756.19" ; ID "BMP2K--PTPRT^BMP2K^ENSG00000138756.19" ; exon_id "ENSE00002038138.1" ; exon_number 1 ; gene_id "BMP2K--PTPRT^BMP2K^ENSG00000138756.19" ; gene_name BMP2K ; gene_type protein_coding ; havana_gene "OTTHUMG00000160900.2" ; havana_transcript "OTTHUMT00000362866.1" ; hgnc_id "HGNC:18041" ; level 2 ; orig_coord_info "chr4,78776544,78776721,+" ; protein_id "ENSP00000373662.3" ; transcript_id "BMP2K--PTPRT^ENST00000389010.7" ; transcript_name "BMP2K-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
BMP2K--PTPRT HAVANA mRNA 1001 17046 . + . FI_gene_label "BMP2K^ENSG00000138756.19" ; ID "BMP2K--PTPRT^ENST00000389010.7" ; Parent "BMP2K--PTPRT^BMP2K^ENSG00000138756.19" ; exon_id "ENSE00002038138.1" ; exon_number 1 ; gene_id "BMP2K--PTPRT^BMP2K^ENSG00000138756.19" ; gene_name BMP2K ; gene_type protein_coding ; havana_gene "OTTHUMG00000160900.2" ; havana_transcript "OTTHUMT00000362866.1" ; hgnc_id "HGNC:18041" ; level 2 ; orig_coord_info "chr4,78776544,78776721,+" ; protein_id "ENSP00000373662.3" ; transcript_id "BMP2K--PTPRT^ENST00000389010.7" ; transcript_name "BMP2K-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
CDK19--ROS1 HAVANA gene 1322 20698 . + . FI_gene_label "CDK19^ENSG00000155111.15" ; ID "CDK19--ROS1^CDK19^ENSG00000155111.15" ; ccdsid "CCDS75503.1" ; exon_id "ENSE00003470487.1" ; exon_number 3 ; gene_id "CDK19--ROS1^CDK19^ENSG00000155111.15" ; gene_name CDK19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015365.7" ; havana_transcript "OTTHUMT00000041805.1" ; hgnc_id "HGNC:19338" ; level 2 ; orig_coord_info "chr6,110746126,110746149,-" ; protein_id "ENSP00000317665.3" ; tag alternative_5_UTR basic CCDS ; transcript_id "CDK19--ROS1^ENST00000323817.7" ; transcript_name "CDK19-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDK19--ROS1 HAVANA mRNA 1322 20698 . + . FI_gene_label "CDK19^ENSG00000155111.15" ; ID "CDK19--ROS1^ENST00000323817.7" ; Parent "CDK19--ROS1^CDK19^ENSG00000155111.15" ; ccdsid "CCDS75503.1" ; exon_id "ENSE00003470487.1" ; exon_number 3 ; gene_id "CDK19--ROS1^CDK19^ENSG00000155111.15" ; gene_name CDK19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015365.7" ; havana_transcript "OTTHUMT00000041805.1" ; hgnc_id "HGNC:19338" ; level 2 ; orig_coord_info "chr6,110746126,110746149,-" ; protein_id "ENSP00000317665.3" ; tag alternative_5_UTR basic CCDS ; transcript_id "CDK19--ROS1^ENST00000323817.7" ; transcript_name "CDK19-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDK19--ROS1 HAVANA gene 23699 71078 . + . FI_gene_label "ROS1^ENSG00000047936.11" ; ID "CDK19--ROS1^ROS1^ENSG00000047936.11" ; exon_id "ENSE00003906517.1" ; exon_number 1 ; gene_id "CDK19--ROS1^ROS1^ENSG00000047936.11" ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1" ; havana_transcript "OTTHUMT00000043465.1" ; hgnc_id "HGNC:10261" ; level 2 ; orig_coord_info "chr6,117425534,117425656,-" ; protein_id "ENSP00000357493.3" ; tag basic MANE_Select appris_principal_4 ; transcript_id "CDK19--ROS1^ENST00000368507.8" ; transcript_name "ROS1-201" ; transcript_support_level 5 ; transcript_type protein_coding
CDK19--ROS1 HAVANA mRNA 23699 71078 . + . FI_gene_label "ROS1^ENSG00000047936.11" ; ID "CDK19--ROS1^ENST00000368507.8" ; Parent "CDK19--ROS1^ROS1^ENSG00000047936.11" ; exon_id "ENSE00003906517.1" ; exon_number 1 ; gene_id "CDK19--ROS1^ROS1^ENSG00000047936.11" ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1" ; havana_transcript "OTTHUMT00000043465.1" ; hgnc_id "HGNC:10261" ; level 2 ; orig_coord_info "chr6,117425534,117425656,-" ; protein_id "ENSP00000357493.3" ; tag basic MANE_Select appris_principal_4 ; transcript_id "CDK19--ROS1^ENST00000368507.8" ; transcript_name "ROS1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CEP43--ERBB4 HAVANA gene 32920 56152 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "CEP43--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "CEP43--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "CEP43--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
CEP43--ERBB4 HAVANA mRNA 32920 56152 . + . FI_gene_label "ERBB4^ENSG00000178568.15" ; ID "CEP43--ERBB4^ENST00000260943.10" ; Parent "CEP43--ERBB4^ERBB4^ENSG00000178568.15" ; exon_id "ENSE00001775290.1" ; exon_number 1 ; gene_id "CEP43--ERBB4^ERBB4^ENSG00000178568.15" ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6" ; havana_transcript "OTTHUMT00000336978.3" ; hgnc_id "HGNC:3432" ; level 2 ; orig_coord_info "chr2,212538449,212538529,-" ; protein_id "ENSP00000260943.6" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "CEP43--ERBB4^ENST00000260943.10" ; transcript_name "ERBB4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CEP43--ERBB4 HAVANA gene 1092 15349 . + . FI_gene_label "CEP43^ENSG00000213066.13" ; ID "CEP43--ERBB4^CEP43^ENSG00000213066.13" ; ccdsid "CCDS5297.1" ; exon_id "ENSE00001934670.1" ; exon_number 1 ; gene_id "CEP43--ERBB4^CEP43^ENSG00000213066.13" ; gene_name CEP43 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016011.4" ; havana_transcript "OTTHUMT00000043100.1" ; hgnc_id "HGNC:17012" ; level 2 ; orig_coord_info "chr6,166999413,166999514,+" ; protein_id "ENSP00000230248.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "CEP43--ERBB4^ENST00000349556.4" ; transcript_name "CEP43-201" ; transcript_support_level 1 ; transcript_type protein_coding
CEP43--ERBB4 HAVANA mRNA 1092 15349 . + . FI_gene_label "CEP43^ENSG00000213066.13" ; ID "CEP43--ERBB4^ENST00000349556.4" ; Parent "CEP43--ERBB4^CEP43^ENSG00000213066.13" ; ccdsid "CCDS5297.1" ; exon_id "ENSE00001934670.1" ; exon_number 1 ; gene_id "CEP43--ERBB4^CEP43^ENSG00000213066.13" ; gene_name CEP43 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016011.4" ; havana_transcript "OTTHUMT00000043100.1" ; hgnc_id "HGNC:17012" ; level 2 ; orig_coord_info "chr6,166999413,166999514,+" ; protein_id "ENSP00000230248.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "CEP43--ERBB4^ENST00000349556.4" ; transcript_name "CEP43-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DECR1--AP002847.1 HAVANA gene 1073 17559 . + . FI_gene_label "DECR1^ENSG00000104325.7" ; ID "DECR1--AP002847.1^DECR1^ENSG00000104325.7" ; ccdsid "CCDS6250.1" ; exon_id "ENSE00003845926.1" ; exon_number 1 ; gene_id "DECR1--AP002847.1^DECR1^ENSG00000104325.7" ; gene_name DECR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163829.4" ; havana_transcript "OTTHUMT00000375822.2" ; hgnc_id "HGNC:2753" ; level 2 ; orig_coord_info "chr8,90001493,90001561,+" ; protein_id "ENSP00000220764.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DECR1--AP002847.1^ENST00000220764.7" ; transcript_name "DECR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DECR1--AP002847.1 HAVANA mRNA 1073 17559 . + . FI_gene_label "DECR1^ENSG00000104325.7" ; ID "DECR1--AP002847.1^ENST00000220764.7" ; Parent "DECR1--AP002847.1^DECR1^ENSG00000104325.7" ; ccdsid "CCDS6250.1" ; exon_id "ENSE00003845926.1" ; exon_number 1 ; gene_id "DECR1--AP002847.1^DECR1^ENSG00000104325.7" ; gene_name DECR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163829.4" ; havana_transcript "OTTHUMT00000375822.2" ; hgnc_id "HGNC:2753" ; level 2 ; orig_coord_info "chr8,90001493,90001561,+" ; protein_id "ENSP00000220764.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DECR1--AP002847.1^ENST00000220764.7" ; transcript_name "DECR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DECR1--DPYS HAVANA gene 1073 17559 . + . FI_gene_label "DECR1^ENSG00000104325.7" ; ID "DECR1--DPYS^DECR1^ENSG00000104325.7" ; ccdsid "CCDS6250.1" ; exon_id "ENSE00003845926.1" ; exon_number 1 ; gene_id "DECR1--DPYS^DECR1^ENSG00000104325.7" ; gene_name DECR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163829.4" ; havana_transcript "OTTHUMT00000375822.2" ; hgnc_id "HGNC:2753" ; level 2 ; orig_coord_info "chr8,90001493,90001561,+" ; protein_id "ENSP00000220764.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DECR1--DPYS^ENST00000220764.7" ; transcript_name "DECR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DECR1--DPYS HAVANA mRNA 1073 17559 . + . FI_gene_label "DECR1^ENSG00000104325.7" ; ID "DECR1--DPYS^ENST00000220764.7" ; Parent "DECR1--DPYS^DECR1^ENSG00000104325.7" ; ccdsid "CCDS6250.1" ; exon_id "ENSE00003845926.1" ; exon_number 1 ; gene_id "DECR1--DPYS^DECR1^ENSG00000104325.7" ; gene_name DECR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163829.4" ; havana_transcript "OTTHUMT00000375822.2" ; hgnc_id "HGNC:2753" ; level 2 ; orig_coord_info "chr8,90001493,90001561,+" ; protein_id "ENSP00000220764.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "DECR1--DPYS^ENST00000220764.7" ; transcript_name "DECR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DECR1--DPYS HAVANA gene 20560 34780 . + . FI_gene_label "DPYS^ENSG00000147647.13" ; ID "DECR1--DPYS^DPYS^ENSG00000147647.13" ; ccdsid "CCDS6302.1" ; exon_id "ENSE00002092993.2" ; exon_number 1 ; gene_id "DECR1--DPYS^DPYS^ENSG00000147647.13" ; gene_name DPYS ; gene_type protein_coding ; havana_gene "OTTHUMG00000164891.5" ; havana_transcript "OTTHUMT00000380814.2" ; hgnc_id "HGNC:3013" ; level 2 ; orig_coord_info "chr8,104466657,104466920,-" ; protein_id "ENSP00000276651.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DECR1--DPYS^ENST00000351513.7" ; transcript_name "DPYS-201" ; transcript_support_level 1 ; transcript_type protein_coding
DECR1--DPYS HAVANA mRNA 20560 34780 . + . FI_gene_label "DPYS^ENSG00000147647.13" ; ID "DECR1--DPYS^ENST00000351513.7" ; Parent "DECR1--DPYS^DPYS^ENSG00000147647.13" ; ccdsid "CCDS6302.1" ; exon_id "ENSE00002092993.2" ; exon_number 1 ; gene_id "DECR1--DPYS^DPYS^ENSG00000147647.13" ; gene_name DPYS ; gene_type protein_coding ; havana_gene "OTTHUMG00000164891.5" ; havana_transcript "OTTHUMT00000380814.2" ; hgnc_id "HGNC:3013" ; level 2 ; orig_coord_info "chr8,104466657,104466920,-" ; protein_id "ENSP00000276651.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DECR1--DPYS^ENST00000351513.7" ; transcript_name "DPYS-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DPH1--PIK3R6 HAVANA gene 1017 11876 . + . FI_gene_label "DPH1^ENSG00000108963.19" ; ID "DPH1--PIK3R6^DPH1^ENSG00000108963.19" ; exon_id "ENSE00002639140.2" ; exon_number 1 ; gene_id "DPH1--PIK3R6^DPH1^ENSG00000108963.19" ; gene_name DPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177724.8" ; havana_transcript "OTTHUMT00000438660.2" ; hgnc_id "HGNC:3003" ; level 2 ; orig_coord_info "chr17,2030170,2030230,+" ; protein_id "ENSP00000263083.7" ; tag upstream_ATG basic MANE_Select appris_alternative_2 ; transcript_id "DPH1--PIK3R6^ENST00000263083.12" ; transcript_name "DPH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
DPH1--PIK3R6 HAVANA mRNA 1017 11876 . + . FI_gene_label "DPH1^ENSG00000108963.19" ; ID "DPH1--PIK3R6^ENST00000263083.12" ; Parent "DPH1--PIK3R6^DPH1^ENSG00000108963.19" ; exon_id "ENSE00002639140.2" ; exon_number 1 ; gene_id "DPH1--PIK3R6^DPH1^ENSG00000108963.19" ; gene_name DPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177724.8" ; havana_transcript "OTTHUMT00000438660.2" ; hgnc_id "HGNC:3003" ; level 2 ; orig_coord_info "chr17,2030170,2030230,+" ; protein_id "ENSP00000263083.7" ; tag upstream_ATG basic MANE_Select appris_alternative_2 ; transcript_id "DPH1--PIK3R6^ENST00000263083.12" ; transcript_name "DPH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DPH1--PIK3R6 HAVANA gene 14894 32427 . + . FI_gene_label "PIK3R6^ENSG00000276231.5" ; ID "DPH1--PIK3R6^PIK3R6^ENSG00000276231.5" ; exon_id "ENSE00003728741.1" ; exon_number 2 ; gene_id "DPH1--PIK3R6^PIK3R6^ENSG00000276231.5" ; gene_name PIK3R6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132861.8" ; havana_transcript "OTTHUMT00000442555.3" ; hgnc_id "HGNC:27101" ; level 2 ; orig_coord_info "chr17,8849782,8849794,-" ; protein_id "ENSP00000480685.1" ; tag alternative_3_UTR ; transcript_id "DPH1--PIK3R6^ENST00000611951.4" ; transcript_name "PIK3R6-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
DPH1--PIK3R6 HAVANA mRNA 14894 32427 . + . FI_gene_label "PIK3R6^ENSG00000276231.5" ; ID "DPH1--PIK3R6^ENST00000611951.4" ; Parent "DPH1--PIK3R6^PIK3R6^ENSG00000276231.5" ; exon_id "ENSE00003728741.1" ; exon_number 2 ; gene_id "DPH1--PIK3R6^PIK3R6^ENSG00000276231.5" ; gene_name PIK3R6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132861.8" ; havana_transcript "OTTHUMT00000442555.3" ; hgnc_id "HGNC:27101" ; level 2 ; orig_coord_info "chr17,8849782,8849794,-" ; protein_id "ENSP00000480685.1" ; tag alternative_3_UTR ; transcript_id "DPH1--PIK3R6^ENST00000611951.4" ; transcript_name "PIK3R6-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
EXOC4--NUP205 HAVANA gene 1006 38283 . + . FI_gene_label "EXOC4^ENSG00000131558.15" ; ID "EXOC4--NUP205^EXOC4^ENSG00000131558.15" ; ccdsid "CCDS5829.1" ; exon_id "ENSE00003845393.1" ; exon_number 1 ; gene_id "EXOC4--NUP205^EXOC4^ENSG00000131558.15" ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5" ; havana_transcript "OTTHUMT00000339182.2" ; hgnc_id "HGNC:30389" ; level 2 ; orig_coord_info "chr7,133253102,133253187,+" ; protein_id "ENSP00000253861.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--NUP205^ENST00000253861.5" ; transcript_name "EXOC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC4--NUP205 HAVANA mRNA 1006 38283 . + . FI_gene_label "EXOC4^ENSG00000131558.15" ; ID "EXOC4--NUP205^ENST00000253861.5" ; Parent "EXOC4--NUP205^EXOC4^ENSG00000131558.15" ; ccdsid "CCDS5829.1" ; exon_id "ENSE00003845393.1" ; exon_number 1 ; gene_id "EXOC4--NUP205^EXOC4^ENSG00000131558.15" ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5" ; havana_transcript "OTTHUMT00000339182.2" ; hgnc_id "HGNC:30389" ; level 2 ; orig_coord_info "chr7,133253102,133253187,+" ; protein_id "ENSP00000253861.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--NUP205^ENST00000253861.5" ; transcript_name "EXOC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC4--NUP205 HAVANA gene 42112 83427 . + . FI_gene_label "NUP205^ENSG00000155561.15" ; ID "EXOC4--NUP205^NUP205^ENSG00000155561.15" ; ccdsid "CCDS34759.1" ; exon_id "ENSE00001611881.3" ; exon_number 1 ; gene_id "EXOC4--NUP205^NUP205^ENSG00000155561.15" ; gene_name NUP205 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155497.5" ; havana_transcript "OTTHUMT00000340358.2" ; hgnc_id "HGNC:18658" ; level 2 ; orig_coord_info "chr7,135557945,135557972,+" ; protein_id "ENSP00000285968.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--NUP205^ENST00000285968.11" ; transcript_name "NUP205-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC4--NUP205 HAVANA mRNA 42112 83427 . + . FI_gene_label "NUP205^ENSG00000155561.15" ; ID "EXOC4--NUP205^ENST00000285968.11" ; Parent "EXOC4--NUP205^NUP205^ENSG00000155561.15" ; ccdsid "CCDS34759.1" ; exon_id "ENSE00001611881.3" ; exon_number 1 ; gene_id "EXOC4--NUP205^NUP205^ENSG00000155561.15" ; gene_name NUP205 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155497.5" ; havana_transcript "OTTHUMT00000340358.2" ; hgnc_id "HGNC:18658" ; level 2 ; orig_coord_info "chr7,135557945,135557972,+" ; protein_id "ENSP00000285968.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--NUP205^ENST00000285968.11" ; transcript_name "NUP205-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC4--TMEM212-AS1 HAVANA gene 1006 38283 . + . FI_gene_label "EXOC4^ENSG00000131558.15" ; ID "EXOC4--TMEM212-AS1^EXOC4^ENSG00000131558.15" ; ccdsid "CCDS5829.1" ; exon_id "ENSE00003845393.1" ; exon_number 1 ; gene_id "EXOC4--TMEM212-AS1^EXOC4^ENSG00000131558.15" ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5" ; havana_transcript "OTTHUMT00000339182.2" ; hgnc_id "HGNC:30389" ; level 2 ; orig_coord_info "chr7,133253102,133253187,+" ; protein_id "ENSP00000253861.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--TMEM212-AS1^ENST00000253861.5" ; transcript_name "EXOC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC4--TMEM212-AS1 HAVANA mRNA 1006 38283 . + . FI_gene_label "EXOC4^ENSG00000131558.15" ; ID "EXOC4--TMEM212-AS1^ENST00000253861.5" ; Parent "EXOC4--TMEM212-AS1^EXOC4^ENSG00000131558.15" ; ccdsid "CCDS5829.1" ; exon_id "ENSE00003845393.1" ; exon_number 1 ; gene_id "EXOC4--TMEM212-AS1^EXOC4^ENSG00000131558.15" ; gene_name EXOC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155259.5" ; havana_transcript "OTTHUMT00000339182.2" ; hgnc_id "HGNC:30389" ; level 2 ; orig_coord_info "chr7,133253102,133253187,+" ; protein_id "ENSP00000253861.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC4--TMEM212-AS1^ENST00000253861.5" ; transcript_name "EXOC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FAM227B--SEMA3D HAVANA gene 32564 56650 . + . FI_gene_label "SEMA3D^ENSG00000153993.13" ; ID "FAM227B--SEMA3D^SEMA3D^ENSG00000153993.13" ; ccdsid "CCDS34676.1" ; exon_id "ENSE00001809975.1" ; exon_number 1 ; gene_id "FAM227B--SEMA3D^SEMA3D^ENSG00000153993.13" ; gene_name SEMA3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154569.4" ; havana_transcript "OTTHUMT00000336084.2" ; hgnc_id "HGNC:10726" ; level 2 ; orig_coord_info "chr7,85121741,85121891,-" ; protein_id "ENSP00000284136.6" ; tag basic appris_principal_1 CCDS ; transcript_id "FAM227B--SEMA3D^ENST00000284136.10" ; transcript_name "SEMA3D-201" ; transcript_support_level 5 ; transcript_type protein_coding
FAM227B--SEMA3D HAVANA mRNA 32564 56650 . + . FI_gene_label "SEMA3D^ENSG00000153993.13" ; ID "FAM227B--SEMA3D^ENST00000284136.10" ; Parent "FAM227B--SEMA3D^SEMA3D^ENSG00000153993.13" ; ccdsid "CCDS34676.1" ; exon_id "ENSE00001809975.1" ; exon_number 1 ; gene_id "FAM227B--SEMA3D^SEMA3D^ENSG00000153993.13" ; gene_name SEMA3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154569.4" ; havana_transcript "OTTHUMT00000336084.2" ; hgnc_id "HGNC:10726" ; level 2 ; orig_coord_info "chr7,85121741,85121891,-" ; protein_id "ENSP00000284136.6" ; tag basic appris_principal_1 CCDS ; transcript_id "FAM227B--SEMA3D^ENST00000284136.10" ; transcript_name "SEMA3D-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
FAM227B--SEMA3D HAVANA gene 1112 27245 . + . FI_gene_label "FAM227B^ENSG00000166262.16" ; ID "FAM227B--SEMA3D^FAM227B^ENSG00000166262.16" ; ccdsid "CCDS32237.1" ; exon_id "ENSE00003614479.1" ; exon_number 2 ; gene_id "FAM227B--SEMA3D^FAM227B^ENSG00000166262.16" ; gene_name FAM227B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172328.3" ; havana_transcript "OTTHUMT00000417872.2" ; hgnc_id "HGNC:26543" ; level 2 ; orig_coord_info "chr15,49615121,49615171,-" ; protein_id "ENSP00000299338.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "FAM227B--SEMA3D^ENST00000299338.11" ; transcript_name "FAM227B-201" ; transcript_support_level 2 ; transcript_type protein_coding
FAM227B--SEMA3D HAVANA mRNA 1112 27245 . + . FI_gene_label "FAM227B^ENSG00000166262.16" ; ID "FAM227B--SEMA3D^ENST00000299338.11" ; Parent "FAM227B--SEMA3D^FAM227B^ENSG00000166262.16" ; ccdsid "CCDS32237.1" ; exon_id "ENSE00003614479.1" ; exon_number 2 ; gene_id "FAM227B--SEMA3D^FAM227B^ENSG00000166262.16" ; gene_name FAM227B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172328.3" ; havana_transcript "OTTHUMT00000417872.2" ; hgnc_id "HGNC:26543" ; level 2 ; orig_coord_info "chr15,49615121,49615171,-" ; protein_id "ENSP00000299338.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "FAM227B--SEMA3D^ENST00000299338.11" ; transcript_name "FAM227B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
HSPD1--AC068489.1 HAVANA gene 2129 14369 . + . FI_gene_label "HSPD1^ENSG00000144381.18" ; ID "HSPD1--AC068489.1^HSPD1^ENSG00000144381.18" ; ccdsid "CCDS33357.1" ; exon_id "ENSE00003603043.1" ; exon_number 2 ; gene_id "HSPD1--AC068489.1^HSPD1^ENSG00000144381.18" ; gene_name HSPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154463.5" ; hgnc_id "HGNC:5261" ; level 2 ; orig_coord_info "chr2,197498675,197498848,-" ; protein_id "ENSP00000340019.2" ; tag basic appris_principal_1 CCDS ; transcript_id "HSPD1--AC068489.1^ENST00000345042.6" ; transcript_name "HSPD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
HSPD1--AC068489.1 HAVANA mRNA 2129 14369 . + . FI_gene_label "HSPD1^ENSG00000144381.18" ; ID "HSPD1--AC068489.1^ENST00000345042.6" ; Parent "HSPD1--AC068489.1^HSPD1^ENSG00000144381.18" ; ccdsid "CCDS33357.1" ; exon_id "ENSE00003603043.1" ; exon_number 2 ; gene_id "HSPD1--AC068489.1^HSPD1^ENSG00000144381.18" ; gene_name HSPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154463.5" ; hgnc_id "HGNC:5261" ; level 2 ; orig_coord_info "chr2,197498675,197498848,-" ; protein_id "ENSP00000340019.2" ; tag basic appris_principal_1 CCDS ; transcript_id "HSPD1--AC068489.1^ENST00000345042.6" ; transcript_name "HSPD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
HSPD1--LLPHP3 HAVANA gene 2129 14369 . + . FI_gene_label "HSPD1^ENSG00000144381.18" ; ID "HSPD1--LLPHP3^HSPD1^ENSG00000144381.18" ; ccdsid "CCDS33357.1" ; exon_id "ENSE00003603043.1" ; exon_number 2 ; gene_id "HSPD1--LLPHP3^HSPD1^ENSG00000144381.18" ; gene_name HSPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154463.5" ; hgnc_id "HGNC:5261" ; level 2 ; orig_coord_info "chr2,197498675,197498848,-" ; protein_id "ENSP00000340019.2" ; tag basic appris_principal_1 CCDS ; transcript_id "HSPD1--LLPHP3^ENST00000345042.6" ; transcript_name "HSPD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
HSPD1--LLPHP3 HAVANA mRNA 2129 14369 . + . FI_gene_label "HSPD1^ENSG00000144381.18" ; ID "HSPD1--LLPHP3^ENST00000345042.6" ; Parent "HSPD1--LLPHP3^HSPD1^ENSG00000144381.18" ; ccdsid "CCDS33357.1" ; exon_id "ENSE00003603043.1" ; exon_number 2 ; gene_id "HSPD1--LLPHP3^HSPD1^ENSG00000144381.18" ; gene_name HSPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154463.5" ; hgnc_id "HGNC:5261" ; level 2 ; orig_coord_info "chr2,197498675,197498848,-" ; protein_id "ENSP00000340019.2" ; tag basic appris_principal_1 CCDS ; transcript_id "HSPD1--LLPHP3^ENST00000345042.6" ; transcript_name "HSPD1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
KIAA1109--SPATA5 HAVANA gene 1003 92861 . + . FI_gene_label "KIAA1109^ENSG00000138688.16" ; ID "KIAA1109--SPATA5^KIAA1109^ENSG00000138688.16" ; ccdsid "CCDS43267.1" ; exon_id "ENSE00001535991.1" ; exon_number 3 ; gene_id "KIAA1109--SPATA5^KIAA1109^ENSG00000138688.16" ; gene_name KIAA1109 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150116.4" ; havana_transcript "OTTHUMT00000316415.1" ; hgnc_id "HGNC:26953" ; level 2 ; orig_coord_info "chr4,122170648,122170744,+" ; protein_id "ENSP00000264501.4" ; tag basic appris_principal_2 CCDS ; transcript_id "KIAA1109--SPATA5^ENST00000264501.8" ; transcript_name "KIAA1109-201" ; transcript_support_level 5 ; transcript_type protein_coding
KIAA1109--SPATA5 HAVANA mRNA 1003 92861 . + . FI_gene_label "KIAA1109^ENSG00000138688.16" ; ID "KIAA1109--SPATA5^ENST00000264501.8" ; Parent "KIAA1109--SPATA5^KIAA1109^ENSG00000138688.16" ; ccdsid "CCDS43267.1" ; exon_id "ENSE00001535991.1" ; exon_number 3 ; gene_id "KIAA1109--SPATA5^KIAA1109^ENSG00000138688.16" ; gene_name KIAA1109 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150116.4" ; havana_transcript "OTTHUMT00000316415.1" ; hgnc_id "HGNC:26953" ; level 2 ; orig_coord_info "chr4,122170648,122170744,+" ; protein_id "ENSP00000264501.4" ; tag basic appris_principal_2 CCDS ; transcript_id "KIAA1109--SPATA5^ENST00000264501.8" ; transcript_name "KIAA1109-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
KIAA1109--SPATA5 HAVANA gene 95876 121127 . + . FI_gene_label "SPATA5^ENSG00000145375.9" ; ID "KIAA1109--SPATA5^SPATA5^ENSG00000145375.9" ; ccdsid "CCDS3730.1" ; exon_id "ENSE00001895453.2" ; exon_number 1 ; gene_id "KIAA1109--SPATA5^SPATA5^ENSG00000145375.9" ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5" ; havana_transcript "OTTHUMT00000256714.3" ; hgnc_id "HGNC:18119" ; level 2 ; orig_coord_info "chr4,122923143,122923305,+" ; protein_id "ENSP00000274008.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KIAA1109--SPATA5^ENST00000274008.5" ; transcript_name "SPATA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
KIAA1109--SPATA5 HAVANA mRNA 95876 121127 . + . FI_gene_label "SPATA5^ENSG00000145375.9" ; ID "KIAA1109--SPATA5^ENST00000274008.5" ; Parent "KIAA1109--SPATA5^SPATA5^ENSG00000145375.9" ; ccdsid "CCDS3730.1" ; exon_id "ENSE00001895453.2" ; exon_number 1 ; gene_id "KIAA1109--SPATA5^SPATA5^ENSG00000145375.9" ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5" ; havana_transcript "OTTHUMT00000256714.3" ; hgnc_id "HGNC:18119" ; level 2 ; orig_coord_info "chr4,122923143,122923305,+" ; protein_id "ENSP00000274008.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KIAA1109--SPATA5^ENST00000274008.5" ; transcript_name "SPATA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MEIS2--AC066614.1 HAVANA gene 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--AC066614.1^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--AC066614.1^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--AC066614.1^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
MEIS2--AC066614.1 HAVANA mRNA 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--AC066614.1^ENST00000314177.12" ; Parent "MEIS2--AC066614.1^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--AC066614.1^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--AC066614.1^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
MEIS2--FAM227B HAVANA gene 28404 54537 . + . FI_gene_label "FAM227B^ENSG00000166262.16" ; ID "MEIS2--FAM227B^FAM227B^ENSG00000166262.16" ; ccdsid "CCDS32237.1" ; exon_id "ENSE00003614479.1" ; exon_number 2 ; gene_id "MEIS2--FAM227B^FAM227B^ENSG00000166262.16" ; gene_name FAM227B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172328.3" ; havana_transcript "OTTHUMT00000417872.2" ; hgnc_id "HGNC:26543" ; level 2 ; orig_coord_info "chr15,49615121,49615171,-" ; protein_id "ENSP00000299338.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "MEIS2--FAM227B^ENST00000299338.11" ; transcript_name "FAM227B-201" ; transcript_support_level 2 ; transcript_type protein_coding
MEIS2--FAM227B HAVANA mRNA 28404 54537 . + . FI_gene_label "FAM227B^ENSG00000166262.16" ; ID "MEIS2--FAM227B^ENST00000299338.11" ; Parent "MEIS2--FAM227B^FAM227B^ENSG00000166262.16" ; ccdsid "CCDS32237.1" ; exon_id "ENSE00003614479.1" ; exon_number 2 ; gene_id "MEIS2--FAM227B^FAM227B^ENSG00000166262.16" ; gene_name FAM227B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172328.3" ; havana_transcript "OTTHUMT00000417872.2" ; hgnc_id "HGNC:26543" ; level 2 ; orig_coord_info "chr15,49615121,49615171,-" ; protein_id "ENSP00000299338.6" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "MEIS2--FAM227B^ENST00000299338.11" ; transcript_name "FAM227B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
MEIS2--FAM227B HAVANA gene 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--FAM227B^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--FAM227B^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--FAM227B^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
MEIS2--FAM227B HAVANA mRNA 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--FAM227B^ENST00000314177.12" ; Parent "MEIS2--FAM227B^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--FAM227B^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--FAM227B^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
MEIS2--LINC02490 HAVANA gene 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--LINC02490^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--LINC02490^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--LINC02490^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
MEIS2--LINC02490 HAVANA mRNA 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--LINC02490^ENST00000314177.12" ; Parent "MEIS2--LINC02490^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--LINC02490^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--LINC02490^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
MEIS2--SEMA3D HAVANA gene 30603 54689 . + . FI_gene_label "SEMA3D^ENSG00000153993.13" ; ID "MEIS2--SEMA3D^SEMA3D^ENSG00000153993.13" ; ccdsid "CCDS34676.1" ; exon_id "ENSE00001809975.1" ; exon_number 1 ; gene_id "MEIS2--SEMA3D^SEMA3D^ENSG00000153993.13" ; gene_name SEMA3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154569.4" ; havana_transcript "OTTHUMT00000336084.2" ; hgnc_id "HGNC:10726" ; level 2 ; orig_coord_info "chr7,85121741,85121891,-" ; protein_id "ENSP00000284136.6" ; tag basic appris_principal_1 CCDS ; transcript_id "MEIS2--SEMA3D^ENST00000284136.10" ; transcript_name "SEMA3D-201" ; transcript_support_level 5 ; transcript_type protein_coding
MEIS2--SEMA3D HAVANA mRNA 30603 54689 . + . FI_gene_label "SEMA3D^ENSG00000153993.13" ; ID "MEIS2--SEMA3D^ENST00000284136.10" ; Parent "MEIS2--SEMA3D^SEMA3D^ENSG00000153993.13" ; ccdsid "CCDS34676.1" ; exon_id "ENSE00001809975.1" ; exon_number 1 ; gene_id "MEIS2--SEMA3D^SEMA3D^ENSG00000153993.13" ; gene_name SEMA3D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154569.4" ; havana_transcript "OTTHUMT00000336084.2" ; hgnc_id "HGNC:10726" ; level 2 ; orig_coord_info "chr7,85121741,85121891,-" ; protein_id "ENSP00000284136.6" ; tag basic appris_principal_1 CCDS ; transcript_id "MEIS2--SEMA3D^ENST00000284136.10" ; transcript_name "SEMA3D-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
MEIS2--SEMA3D HAVANA gene 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--SEMA3D^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--SEMA3D^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--SEMA3D^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
MEIS2--SEMA3D HAVANA mRNA 2579 23411 . + . FI_gene_label "MEIS2^ENSG00000134138.20" ; ID "MEIS2--SEMA3D^ENST00000314177.12" ; Parent "MEIS2--SEMA3D^MEIS2^ENSG00000134138.20" ; exon_id "ENSE00002536875.1" ; exon_number 1 ; gene_id "MEIS2--SEMA3D^MEIS2^ENSG00000134138.20" ; gene_name MEIS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129781.7" ; havana_transcript "OTTHUMT00000417553.1" ; hgnc_id "HGNC:7001" ; level 2 ; orig_coord_info "chr15,37099455,37099466,-" ; protein_id "ENSP00000326296.8" ; transcript_id "MEIS2--SEMA3D^ENST00000314177.12" ; transcript_name "MEIS2-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
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:
PIK3CA--TBC1D32 HAVANA gene 1244 32228 . + . FI_gene_label "PIK3CA^ENSG00000121879.6" ; ID "PIK3CA--TBC1D32^PIK3CA^ENSG00000121879.6" ; ccdsid "CCDS43171.1" ; exon_id "ENSE00001139995.2" ; exon_number 2 ; gene_id "PIK3CA--TBC1D32^PIK3CA^ENSG00000121879.6" ; gene_name PIK3CA ; gene_type protein_coding ; havana_gene "OTTHUMG00000157311.5" ; havana_transcript "OTTHUMT00000348409.3" ; hgnc_id "HGNC:8975" ; level 1 ; orig_coord_info "chr3,179198826,179199177,+" ; protein_id "ENSP00000263967.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "PIK3CA--TBC1D32^ENST00000263967.4" ; transcript_name "PIK3CA-201" ; transcript_support_level 2 ; transcript_type protein_coding
PIK3CA--TBC1D32 HAVANA mRNA 1244 32228 . + . FI_gene_label "PIK3CA^ENSG00000121879.6" ; ID "PIK3CA--TBC1D32^ENST00000263967.4" ; Parent "PIK3CA--TBC1D32^PIK3CA^ENSG00000121879.6" ; ccdsid "CCDS43171.1" ; exon_id "ENSE00001139995.2" ; exon_number 2 ; gene_id "PIK3CA--TBC1D32^PIK3CA^ENSG00000121879.6" ; gene_name PIK3CA ; gene_type protein_coding ; havana_gene "OTTHUMG00000157311.5" ; havana_transcript "OTTHUMT00000348409.3" ; hgnc_id "HGNC:8975" ; level 1 ; orig_coord_info "chr3,179198826,179199177,+" ; protein_id "ENSP00000263967.3" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "PIK3CA--TBC1D32^ENST00000263967.4" ; transcript_name "PIK3CA-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PIK3CA--TBC1D32 HAVANA gene 35544 76928 . + . FI_gene_label "TBC1D32^ENSG00000146350.14" ; ID "PIK3CA--TBC1D32^TBC1D32^ENSG00000146350.14" ; exon_id "ENSE00001706723.1" ; exon_number 1 ; gene_id "PIK3CA--TBC1D32^TBC1D32^ENSG00000146350.14" ; gene_name TBC1D32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015474.6" ; havana_transcript "OTTHUMT00000042017.3" ; hgnc_id "HGNC:21485" ; level 2 ; orig_coord_info "chr6,121334276,121334430,-" ; protein_id "ENSP00000275159.6" ; tag non_canonical_conserved basic appris_principal_1 ; transcript_id "PIK3CA--TBC1D32^ENST00000275159.10" ; transcript_name "TBC1D32-201" ; transcript_support_level 5 ; transcript_type protein_coding
PIK3CA--TBC1D32 HAVANA mRNA 35544 76928 . + . FI_gene_label "TBC1D32^ENSG00000146350.14" ; ID "PIK3CA--TBC1D32^ENST00000275159.10" ; Parent "PIK3CA--TBC1D32^TBC1D32^ENSG00000146350.14" ; exon_id "ENSE00001706723.1" ; exon_number 1 ; gene_id "PIK3CA--TBC1D32^TBC1D32^ENSG00000146350.14" ; gene_name TBC1D32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015474.6" ; havana_transcript "OTTHUMT00000042017.3" ; hgnc_id "HGNC:21485" ; level 2 ; orig_coord_info "chr6,121334276,121334430,-" ; protein_id "ENSP00000275159.6" ; tag non_canonical_conserved basic appris_principal_1 ; transcript_id "PIK3CA--TBC1D32^ENST00000275159.10" ; transcript_name "TBC1D32-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RDH10--SPAG1 HAVANA gene 1001 10455 . + . FI_gene_label "RDH10^ENSG00000121039.10" ; ID "RDH10--SPAG1^RDH10^ENSG00000121039.10" ; ccdsid "CCDS6213.1" ; exon_id "ENSE00001122881.6" ; exon_number 1 ; gene_id "RDH10--SPAG1^RDH10^ENSG00000121039.10" ; gene_name RDH10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164492.3" ; havana_transcript "OTTHUMT00000378982.2" ; hgnc_id "HGNC:19975" ; level 2 ; orig_coord_info "chr8,73295290,73295578,+" ; protein_id "ENSP00000240285.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RDH10--SPAG1^ENST00000240285.10" ; transcript_name "RDH10-201" ; transcript_support_level 1 ; transcript_type protein_coding
RDH10--SPAG1 HAVANA mRNA 1001 10455 . + . FI_gene_label "RDH10^ENSG00000121039.10" ; ID "RDH10--SPAG1^ENST00000240285.10" ; Parent "RDH10--SPAG1^RDH10^ENSG00000121039.10" ; ccdsid "CCDS6213.1" ; exon_id "ENSE00001122881.6" ; exon_number 1 ; gene_id "RDH10--SPAG1^RDH10^ENSG00000121039.10" ; gene_name RDH10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164492.3" ; havana_transcript "OTTHUMT00000378982.2" ; hgnc_id "HGNC:19975" ; level 2 ; orig_coord_info "chr8,73295290,73295578,+" ; protein_id "ENSP00000240285.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RDH10--SPAG1^ENST00000240285.10" ; transcript_name "RDH10-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RDH10--SPAG1 ENSEMBL gene 13585 34080 . + . FI_gene_label "SPAG1^ENSG00000104450.13" ; ID "RDH10--SPAG1^SPAG1^ENSG00000104450.13" ; ccdsid "CCDS34930.1" ; exon_id "ENSE00001250023.3" ; exon_number 2 ; gene_id "RDH10--SPAG1^SPAG1^ENSG00000104450.13" ; gene_name SPAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164706.3" ; hgnc_id "HGNC:11212" ; level 3 ; orig_coord_info "chr8,100162281,100162420,+" ; protein_id "ENSP00000251809.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RDH10--SPAG1^ENST00000251809.4" ; transcript_name "SPAG1-201" ; transcript_support_level 5 ; transcript_type protein_coding
RDH10--SPAG1 ENSEMBL mRNA 13585 34080 . + . FI_gene_label "SPAG1^ENSG00000104450.13" ; ID "RDH10--SPAG1^ENST00000251809.4" ; Parent "RDH10--SPAG1^SPAG1^ENSG00000104450.13" ; ccdsid "CCDS34930.1" ; exon_id "ENSE00001250023.3" ; exon_number 2 ; gene_id "RDH10--SPAG1^SPAG1^ENSG00000104450.13" ; gene_name SPAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164706.3" ; hgnc_id "HGNC:11212" ; level 3 ; orig_coord_info "chr8,100162281,100162420,+" ; protein_id "ENSP00000251809.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RDH10--SPAG1^ENST00000251809.4" ; transcript_name "SPAG1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--AC061997.1 HAVANA gene 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC061997.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC061997.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC061997.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--AC061997.1 HAVANA mRNA 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC061997.1^ENST00000338508.8" ; Parent "SHANK2--AC061997.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC061997.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC061997.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--AC104042.1 HAVANA gene 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC104042.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC104042.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC104042.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--AC104042.1 HAVANA mRNA 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--AC104042.1^ENST00000338508.8" ; Parent "SHANK2--AC104042.1^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--AC104042.1^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--AC104042.1^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SKIL--NCEH1 HAVANA gene 1038 14980 . + . FI_gene_label "SKIL^ENSG00000136603.14" ; ID "SKIL--NCEH1^SKIL^ENSG00000136603.14" ; ccdsid "CCDS33890.1" ; exon_id "ENSE00001594946.1" ; exon_number 2 ; gene_id "SKIL--NCEH1^SKIL^ENSG00000136603.14" ; gene_name SKIL ; gene_type protein_coding ; havana_gene "OTTHUMG00000158831.7" ; havana_transcript "OTTHUMT00000352413.3" ; hgnc_id "HGNC:10897" ; level 2 ; orig_coord_info "chr3,170360332,170361429,+" ; protein_id "ENSP00000259119.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SKIL--NCEH1^ENST00000259119.9" ; transcript_name "SKIL-201" ; transcript_support_level 1 ; transcript_type protein_coding
SKIL--NCEH1 HAVANA mRNA 1038 14980 . + . FI_gene_label "SKIL^ENSG00000136603.14" ; ID "SKIL--NCEH1^ENST00000259119.9" ; Parent "SKIL--NCEH1^SKIL^ENSG00000136603.14" ; ccdsid "CCDS33890.1" ; exon_id "ENSE00001594946.1" ; exon_number 2 ; gene_id "SKIL--NCEH1^SKIL^ENSG00000136603.14" ; gene_name SKIL ; gene_type protein_coding ; havana_gene "OTTHUMG00000158831.7" ; havana_transcript "OTTHUMT00000352413.3" ; hgnc_id "HGNC:10897" ; level 2 ; orig_coord_info "chr3,170360332,170361429,+" ; protein_id "ENSP00000259119.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_2 CCDS ; transcript_id "SKIL--NCEH1^ENST00000259119.9" ; transcript_name "SKIL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SKIL--NCEH1 HAVANA gene 18087 23038 . + . FI_gene_label "NCEH1^ENSG00000144959.11" ; ID "SKIL--NCEH1^NCEH1^ENSG00000144959.11" ; exon_id "ENSE00001705780.1" ; exon_number 1 ; gene_id "SKIL--NCEH1^NCEH1^ENSG00000144959.11" ; gene_name NCEH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156872.8" ; havana_transcript "OTTHUMT00000346480.3" ; hgnc_id "HGNC:29260" ; level 2 ; orig_coord_info "chr3,172710847,172710984,-" ; protein_id "ENSP00000402196.2" ; transcript_id "SKIL--NCEH1^ENST00000421723.2" ; transcript_name "NCEH1-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
SKIL--NCEH1 HAVANA mRNA 18087 23038 . + . FI_gene_label "NCEH1^ENSG00000144959.11" ; ID "SKIL--NCEH1^ENST00000421723.2" ; Parent "SKIL--NCEH1^NCEH1^ENSG00000144959.11" ; exon_id "ENSE00001705780.1" ; exon_number 1 ; gene_id "SKIL--NCEH1^NCEH1^ENSG00000144959.11" ; gene_name NCEH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156872.8" ; havana_transcript "OTTHUMT00000346480.3" ; hgnc_id "HGNC:29260" ; level 2 ; orig_coord_info "chr3,172710847,172710984,-" ; protein_id "ENSP00000402196.2" ; transcript_id "SKIL--NCEH1^ENST00000421723.2" ; transcript_name "NCEH1-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
SPATA5--DCHS2 HAVANA gene 1009 26260 . + . FI_gene_label "SPATA5^ENSG00000145375.9" ; ID "SPATA5--DCHS2^SPATA5^ENSG00000145375.9" ; ccdsid "CCDS3730.1" ; exon_id "ENSE00001895453.2" ; exon_number 1 ; gene_id "SPATA5--DCHS2^SPATA5^ENSG00000145375.9" ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5" ; havana_transcript "OTTHUMT00000256714.3" ; hgnc_id "HGNC:18119" ; level 2 ; orig_coord_info "chr4,122923143,122923305,+" ; protein_id "ENSP00000274008.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SPATA5--DCHS2^ENST00000274008.5" ; transcript_name "SPATA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPATA5--DCHS2 HAVANA mRNA 1009 26260 . + . FI_gene_label "SPATA5^ENSG00000145375.9" ; ID "SPATA5--DCHS2^ENST00000274008.5" ; Parent "SPATA5--DCHS2^SPATA5^ENSG00000145375.9" ; ccdsid "CCDS3730.1" ; exon_id "ENSE00001895453.2" ; exon_number 1 ; gene_id "SPATA5--DCHS2^SPATA5^ENSG00000145375.9" ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5" ; havana_transcript "OTTHUMT00000256714.3" ; hgnc_id "HGNC:18119" ; level 2 ; orig_coord_info "chr4,122923143,122923305,+" ; protein_id "ENSP00000274008.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SPATA5--DCHS2^ENST00000274008.5" ; transcript_name "SPATA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPATA5--DCHS2 HAVANA gene 29344 52436 . + . FI_gene_label "DCHS2^ENSG00000197410.14" ; ID "SPATA5--DCHS2^DCHS2^ENSG00000197410.14" ; ccdsid "CCDS47150.1" ; exon_id "ENSE00001376479.1" ; exon_number 1 ; gene_id "SPATA5--DCHS2^DCHS2^ENSG00000197410.14" ; gene_name DCHS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161556.7" ; havana_transcript "OTTHUMT00000365282.3" ; hgnc_id "HGNC:23111" ; level 2 ; orig_coord_info "chr4,154489304,154491355,-" ; protein_id "ENSP00000345062.1" ; tag basic CCDS ; transcript_id "SPATA5--DCHS2^ENST00000339452.2" ; transcript_name "DCHS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPATA5--DCHS2 HAVANA mRNA 29344 52436 . + . FI_gene_label "DCHS2^ENSG00000197410.14" ; ID "SPATA5--DCHS2^ENST00000339452.2" ; Parent "SPATA5--DCHS2^DCHS2^ENSG00000197410.14" ; ccdsid "CCDS47150.1" ; exon_id "ENSE00001376479.1" ; exon_number 1 ; gene_id "SPATA5--DCHS2^DCHS2^ENSG00000197410.14" ; gene_name DCHS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161556.7" ; havana_transcript "OTTHUMT00000365282.3" ; hgnc_id "HGNC:23111" ; level 2 ; orig_coord_info "chr4,154489304,154491355,-" ; protein_id "ENSP00000345062.1" ; tag basic CCDS ; transcript_id "SPATA5--DCHS2^ENST00000339452.2" ; transcript_name "DCHS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPIDR--ZNF595 HAVANA gene 1061 36568 . + . FI_gene_label "SPIDR^ENSG00000164808.17" ; ID "SPIDR--ZNF595^SPIDR^ENSG00000164808.17" ; ccdsid "CCDS43737.1" ; exon_id "ENSE00002119316.2" ; exon_number 1 ; gene_id "SPIDR--ZNF595^SPIDR^ENSG00000164808.17" ; gene_name SPIDR ; gene_type protein_coding ; havana_gene "OTTHUMG00000164176.7" ; havana_transcript "OTTHUMT00000377611.2" ; hgnc_id "HGNC:28971" ; level 2 ; orig_coord_info "chr8,47260959,47260991,+" ; protein_id "ENSP00000297423.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPIDR--ZNF595^ENST00000297423.9" ; transcript_name "SPIDR-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPIDR--ZNF595 HAVANA mRNA 1061 36568 . + . FI_gene_label "SPIDR^ENSG00000164808.17" ; ID "SPIDR--ZNF595^ENST00000297423.9" ; Parent "SPIDR--ZNF595^SPIDR^ENSG00000164808.17" ; ccdsid "CCDS43737.1" ; exon_id "ENSE00002119316.2" ; exon_number 1 ; gene_id "SPIDR--ZNF595^SPIDR^ENSG00000164808.17" ; gene_name SPIDR ; gene_type protein_coding ; havana_gene "OTTHUMG00000164176.7" ; havana_transcript "OTTHUMT00000377611.2" ; hgnc_id "HGNC:28971" ; level 2 ; orig_coord_info "chr8,47260959,47260991,+" ; protein_id "ENSP00000297423.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPIDR--ZNF595^ENST00000297423.9" ; transcript_name "SPIDR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPIDR--ZNF595 HAVANA gene 39587 43520 . + . FI_gene_label "ZNF595^ENSG00000272602.6" ; ID "SPIDR--ZNF595^ZNF595^ENSG00000272602.6" ; exon_id "ENSE00002066979.1" ; exon_number 1 ; gene_id "SPIDR--ZNF595^ZNF595^ENSG00000272602.6" ; gene_name ZNF595 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159865.6" ; havana_transcript "OTTHUMT00000357817.2" ; hgnc_id "HGNC:27196" ; level 1 ; orig_coord_info "chr4,53489,53491,+" ; protein_id "ENSP00000434858.1" ; tag basic exp_conf ; transcript_id "SPIDR--ZNF595^ENST00000509152.3" ; transcript_name "ZNF595-202" ; transcript_support_level 1 ; transcript_type protein_coding
SPIDR--ZNF595 HAVANA mRNA 39587 43520 . + . FI_gene_label "ZNF595^ENSG00000272602.6" ; ID "SPIDR--ZNF595^ENST00000509152.3" ; Parent "SPIDR--ZNF595^ZNF595^ENSG00000272602.6" ; exon_id "ENSE00002066979.1" ; exon_number 1 ; gene_id "SPIDR--ZNF595^ZNF595^ENSG00000272602.6" ; gene_name ZNF595 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159865.6" ; havana_transcript "OTTHUMT00000357817.2" ; hgnc_id "HGNC:27196" ; level 1 ; orig_coord_info "chr4,53489,53491,+" ; protein_id "ENSP00000434858.1" ; tag basic exp_conf ; transcript_id "SPIDR--ZNF595^ENST00000509152.3" ; transcript_name "ZNF595-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TUBGCP2--AC104640.2 HAVANA gene 2981 22940 . + . FI_gene_label "TUBGCP2^ENSG00000130640.14" ; ID "TUBGCP2--AC104640.2^TUBGCP2^ENSG00000130640.14" ; ccdsid "CCDS7676.1" ; exon_id "ENSE00003692697.1" ; exon_number 2 ; gene_id "TUBGCP2--AC104640.2^TUBGCP2^ENSG00000130640.14" ; gene_name TUBGCP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019319.6" ; havana_transcript "OTTHUMT00000051148.2" ; hgnc_id "HGNC:18599" ; level 2 ; orig_coord_info "chr10,133302792,133302941,-" ; protein_id "ENSP00000252936.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TUBGCP2--AC104640.2^ENST00000252936.8" ; transcript_name "TUBGCP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
TUBGCP2--AC104640.2 HAVANA mRNA 2981 22940 . + . FI_gene_label "TUBGCP2^ENSG00000130640.14" ; ID "TUBGCP2--AC104640.2^ENST00000252936.8" ; Parent "TUBGCP2--AC104640.2^TUBGCP2^ENSG00000130640.14" ; ccdsid "CCDS7676.1" ; exon_id "ENSE00003692697.1" ; exon_number 2 ; gene_id "TUBGCP2--AC104640.2^TUBGCP2^ENSG00000130640.14" ; gene_name TUBGCP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019319.6" ; havana_transcript "OTTHUMT00000051148.2" ; hgnc_id "HGNC:18599" ; level 2 ; orig_coord_info "chr10,133302792,133302941,-" ; protein_id "ENSP00000252936.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TUBGCP2--AC104640.2^ENST00000252936.8" ; transcript_name "TUBGCP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TUBGCP2--AC117434.1 HAVANA gene 2981 22940 . + . FI_gene_label "TUBGCP2^ENSG00000130640.14" ; ID "TUBGCP2--AC117434.1^TUBGCP2^ENSG00000130640.14" ; ccdsid "CCDS7676.1" ; exon_id "ENSE00003692697.1" ; exon_number 2 ; gene_id "TUBGCP2--AC117434.1^TUBGCP2^ENSG00000130640.14" ; gene_name TUBGCP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019319.6" ; havana_transcript "OTTHUMT00000051148.2" ; hgnc_id "HGNC:18599" ; level 2 ; orig_coord_info "chr10,133302792,133302941,-" ; protein_id "ENSP00000252936.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TUBGCP2--AC117434.1^ENST00000252936.8" ; transcript_name "TUBGCP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
TUBGCP2--AC117434.1 HAVANA mRNA 2981 22940 . + . FI_gene_label "TUBGCP2^ENSG00000130640.14" ; ID "TUBGCP2--AC117434.1^ENST00000252936.8" ; Parent "TUBGCP2--AC117434.1^TUBGCP2^ENSG00000130640.14" ; ccdsid "CCDS7676.1" ; exon_id "ENSE00003692697.1" ; exon_number 2 ; gene_id "TUBGCP2--AC117434.1^TUBGCP2^ENSG00000130640.14" ; gene_name TUBGCP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019319.6" ; havana_transcript "OTTHUMT00000051148.2" ; hgnc_id "HGNC:18599" ; level 2 ; orig_coord_info "chr10,133302792,133302941,-" ; protein_id "ENSP00000252936.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TUBGCP2--AC117434.1^ENST00000252936.8" ; transcript_name "TUBGCP2-201" ; transcript_support_level 2 ; 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:
UAP1--INO80 ENSEMBL gene 1001 14719 . + . FI_gene_label "UAP1^ENSG00000117143.13" ; ID "UAP1--INO80^UAP1^ENSG00000117143.13" ; ccdsid "CCDS81393.1" ; exon_id "ENSE00001004734.3" ; exon_number 2 ; gene_id "UAP1--INO80^UAP1^ENSG00000117143.13" ; gene_name UAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034419.4" ; hgnc_id "HGNC:12457" ; level 3 ; orig_coord_info "chr1,162566069,162566348,+" ; protein_id "ENSP00000271469.3" ; tag basic appris_alternative_1 CCDS ; transcript_id "UAP1--INO80^ENST00000271469.7" ; transcript_name "UAP1-201" ; transcript_support_level 5 ; transcript_type protein_coding
UAP1--INO80 ENSEMBL mRNA 1001 14719 . + . FI_gene_label "UAP1^ENSG00000117143.13" ; ID "UAP1--INO80^ENST00000271469.7" ; Parent "UAP1--INO80^UAP1^ENSG00000117143.13" ; ccdsid "CCDS81393.1" ; exon_id "ENSE00001004734.3" ; exon_number 2 ; gene_id "UAP1--INO80^UAP1^ENSG00000117143.13" ; gene_name UAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000034419.4" ; hgnc_id "HGNC:12457" ; level 3 ; orig_coord_info "chr1,162566069,162566348,+" ; protein_id "ENSP00000271469.3" ; tag basic appris_alternative_1 CCDS ; transcript_id "UAP1--INO80^ENST00000271469.7" ; transcript_name "UAP1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
UAP1--INO80 ENSEMBL gene 17847 56468 . + . FI_gene_label "INO80^ENSG00000128908.17" ; ID "UAP1--INO80^INO80^ENSG00000128908.17" ; ccdsid "CCDS10071.1" ; exon_id "ENSE00002244371.1" ; exon_number 2 ; gene_id "UAP1--INO80^INO80^ENSG00000128908.17" ; gene_name INO80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130209.6" ; hgnc_id "HGNC:26956" ; level 3 ; orig_coord_info "chr15,41096168,41096310,-" ; protein_id "ENSP00000384686.3" ; tag basic appris_principal_1 CCDS ; transcript_id "UAP1--INO80^ENST00000401393.7" ; transcript_name "INO80-201" ; transcript_support_level 1 ; transcript_type protein_coding
UAP1--INO80 ENSEMBL mRNA 17847 56468 . + . FI_gene_label "INO80^ENSG00000128908.17" ; ID "UAP1--INO80^ENST00000401393.7" ; Parent "UAP1--INO80^INO80^ENSG00000128908.17" ; ccdsid "CCDS10071.1" ; exon_id "ENSE00002244371.1" ; exon_number 2 ; gene_id "UAP1--INO80^INO80^ENSG00000128908.17" ; gene_name INO80 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130209.6" ; hgnc_id "HGNC:26956" ; level 3 ; orig_coord_info "chr15,41096168,41096310,-" ; protein_id "ENSP00000384686.3" ; tag basic appris_principal_1 CCDS ; transcript_id "UAP1--INO80^ENST00000401393.7" ; transcript_name "INO80-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZCCHC14--IGH-@-ext ENSEMBL gene 2171 19711 . + . FI_gene_label "ZCCHC14^ENSG00000140948.13" ; ID "ZCCHC14--IGH-@-ext^ZCCHC14^ENSG00000140948.13" ; ccdsid "CCDS10961.1" ; exon_id "ENSE00001826524.2" ; exon_number 1 ; gene_id "ZCCHC14--IGH-@-ext^ZCCHC14^ENSG00000140948.13" ; gene_name ZCCHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137655.4" ; hgnc_id "HGNC:24134" ; level 3 ; orig_coord_info "chr16,87491669,87491827,-" ; protein_id "ENSP00000268616.4" ; tag basic appris_principal_4 CCDS ; transcript_id "ZCCHC14--IGH-@-ext^ENST00000268616.9" ; transcript_name "ZCCHC14-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZCCHC14--IGH-@-ext ENSEMBL mRNA 2171 19711 . + . FI_gene_label "ZCCHC14^ENSG00000140948.13" ; ID "ZCCHC14--IGH-@-ext^ENST00000268616.9" ; Parent "ZCCHC14--IGH-@-ext^ZCCHC14^ENSG00000140948.13" ; ccdsid "CCDS10961.1" ; exon_id "ENSE00001826524.2" ; exon_number 1 ; gene_id "ZCCHC14--IGH-@-ext^ZCCHC14^ENSG00000140948.13" ; gene_name ZCCHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137655.4" ; hgnc_id "HGNC:24134" ; level 3 ; orig_coord_info "chr16,87491669,87491827,-" ; protein_id "ENSP00000268616.4" ; tag basic appris_principal_4 CCDS ; transcript_id "ZCCHC14--IGH-@-ext^ENST00000268616.9" ; transcript_name "ZCCHC14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC060809.1--ERBB4 HAVANA gene 1001 4564 . + . FI_gene_label "AC060809.1^ENSG00000259543.1" ; ID "AC060809.1--ERBB4^AC060809.1^ENSG00000259543.1" ; exon_id "ENSE00002544347.1" ; exon_number 1 ; gene_id "AC060809.1--ERBB4^AC060809.1^ENSG00000259543.1" ; gene_name "AC060809.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172164.1" ; havana_transcript "OTTHUMT00000417157.1" ; level 2 ; orig_coord_info "chr15,81427448,81427545,+" ; tag basic ; transcript_id "AC060809.1--ERBB4^ENST00000559211.1" ; transcript_name "AC060809.1-201" ; transcript_support_level 4 ; transcript_type lncRNA
AC060809.1--ERBB4 HAVANA RNA 1001 4564 . + . FI_gene_label "AC060809.1^ENSG00000259543.1" ; ID "AC060809.1--ERBB4^ENST00000559211.1" ; Parent "AC060809.1--ERBB4^AC060809.1^ENSG00000259543.1" ; exon_id "ENSE00002544347.1" ; exon_number 1 ; gene_id "AC060809.1--ERBB4^AC060809.1^ENSG00000259543.1" ; gene_name "AC060809.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172164.1" ; havana_transcript "OTTHUMT00000417157.1" ; level 2 ; orig_coord_info "chr15,81427448,81427545,+" ; tag basic ; transcript_id "AC060809.1--ERBB4^ENST00000559211.1" ; transcript_name "AC060809.1-201" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
DECR1--AP002847.1 HAVANA gene 20560 22804 . + . FI_gene_label "AP002847.1^ENSG00000279138.1" ; ID "DECR1--AP002847.1^AP002847.1^ENSG00000279138.1" ; exon_id "ENSE00003756842.1" ; exon_number 1 ; gene_id "DECR1--AP002847.1^AP002847.1^ENSG00000279138.1" ; gene_name "AP002847.1" ; gene_type TEC ; havana_gene "OTTHUMG00000173419.1" ; havana_transcript "OTTHUMT00000423042.1" ; level 2 ; orig_coord_info "chr8,104478539,104480783,-" ; tag basic ; transcript_id "DECR1--AP002847.1^ENST00000625136.1" ; transcript_name "AP002847.1-201" ; transcript_support_level NA ; transcript_type TEC
DECR1--AP002847.1 HAVANA RNA 20560 22804 . + . FI_gene_label "AP002847.1^ENSG00000279138.1" ; ID "DECR1--AP002847.1^ENST00000625136.1" ; Parent "DECR1--AP002847.1^AP002847.1^ENSG00000279138.1" ; exon_id "ENSE00003756842.1" ; exon_number 1 ; gene_id "DECR1--AP002847.1^AP002847.1^ENSG00000279138.1" ; gene_name "AP002847.1" ; gene_type TEC ; havana_gene "OTTHUMG00000173419.1" ; havana_transcript "OTTHUMT00000423042.1" ; level 2 ; orig_coord_info "chr8,104478539,104480783,-" ; tag basic ; transcript_id "DECR1--AP002847.1^ENST00000625136.1" ; transcript_name "AP002847.1-201" ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created:
EXOC4--TMEM212-AS1 HAVANA gene 42112 45979 . + . FI_gene_label "TMEM212-AS1^ENSG00000234717.2" ; ID "EXOC4--TMEM212-AS1^TMEM212-AS1^ENSG00000234717.2" ; exon_id "ENSE00001666209.2" ; exon_number 1 ; gene_id "EXOC4--TMEM212-AS1^TMEM212-AS1^ENSG00000234717.2" ; gene_name "TMEM212-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000156879.2" ; havana_transcript "OTTHUMT00000346408.2" ; hgnc_id "HGNC:41939" ; level 2 ; orig_coord_info "chr3,171900451,171900749,-" ; tag basic TAGENE ; transcript_id "EXOC4--TMEM212-AS1^ENST00000449106.2" ; transcript_name "TMEM212-AS1-201" ; transcript_support_level 3 ; transcript_type lncRNA
EXOC4--TMEM212-AS1 HAVANA RNA 42112 45979 . + . FI_gene_label "TMEM212-AS1^ENSG00000234717.2" ; ID "EXOC4--TMEM212-AS1^ENST00000449106.2" ; Parent "EXOC4--TMEM212-AS1^TMEM212-AS1^ENSG00000234717.2" ; exon_id "ENSE00001666209.2" ; exon_number 1 ; gene_id "EXOC4--TMEM212-AS1^TMEM212-AS1^ENSG00000234717.2" ; gene_name "TMEM212-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000156879.2" ; havana_transcript "OTTHUMT00000346408.2" ; hgnc_id "HGNC:41939" ; level 2 ; orig_coord_info "chr3,171900451,171900749,-" ; tag basic TAGENE ; transcript_id "EXOC4--TMEM212-AS1^ENST00000449106.2" ; transcript_name "TMEM212-AS1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
HSPD1--AC068489.1 HAVANA gene 18491 19751 . + . FI_gene_label "AC068489.1^ENSG00000234446.3" ; ID "HSPD1--AC068489.1^AC068489.1^ENSG00000234446.3" ; exon_id "ENSE00001694416.1" ; exon_number 1 ; gene_id "HSPD1--AC068489.1^AC068489.1^ENSG00000234446.3" ; gene_name "AC068489.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154090.4" ; havana_transcript "OTTHUMT00000333848.2" ; level 2 ; orig_coord_info "chr2,221637543,221637597,+" ; transcript_id "HSPD1--AC068489.1^ENST00000453706.2" ; transcript_name "AC068489.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
HSPD1--AC068489.1 HAVANA RNA 18491 19751 . + . FI_gene_label "AC068489.1^ENSG00000234446.3" ; ID "HSPD1--AC068489.1^ENST00000453706.2" ; Parent "HSPD1--AC068489.1^AC068489.1^ENSG00000234446.3" ; exon_id "ENSE00001694416.1" ; exon_number 1 ; gene_id "HSPD1--AC068489.1^AC068489.1^ENSG00000234446.3" ; gene_name "AC068489.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154090.4" ; havana_transcript "OTTHUMT00000333848.2" ; level 2 ; orig_coord_info "chr2,221637543,221637597,+" ; transcript_id "HSPD1--AC068489.1^ENST00000453706.2" ; transcript_name "AC068489.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
HSPD1--LLPHP3 HAVANA gene 17372 17761 . + . FI_gene_label "LLPHP3^ENSG00000233868.1" ; ID "HSPD1--LLPHP3^LLPHP3^ENSG00000233868.1" ; exon_id "ENSE00001664898.1" ; exon_number 1 ; gene_id "HSPD1--LLPHP3^LLPHP3^ENSG00000233868.1" ; gene_name LLPHP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153408.1" ; havana_transcript "OTTHUMT00000331058.1" ; hgnc_id "HGNC:54775" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr2,221944223,221944612,+" ; tag basic ; transcript_id "HSPD1--LLPHP3^ENST00000417147.1" ; transcript_name "LLPHP3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
HSPD1--LLPHP3 HAVANA RNA 17372 17761 . + . FI_gene_label "LLPHP3^ENSG00000233868.1" ; ID "HSPD1--LLPHP3^ENST00000417147.1" ; Parent "HSPD1--LLPHP3^LLPHP3^ENSG00000233868.1" ; exon_id "ENSE00001664898.1" ; exon_number 1 ; gene_id "HSPD1--LLPHP3^LLPHP3^ENSG00000233868.1" ; gene_name LLPHP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000153408.1" ; havana_transcript "OTTHUMT00000331058.1" ; hgnc_id "HGNC:54775" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr2,221944223,221944612,+" ; tag basic ; transcript_id "HSPD1--LLPHP3^ENST00000417147.1" ; transcript_name "LLPHP3-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
MEIS2--AC066614.1 HAVANA gene 28293 30207 . + . FI_gene_label "AC066614.1^ENSG00000287596.1" ; ID "MEIS2--AC066614.1^AC066614.1^ENSG00000287596.1" ; exon_id "ENSE00003862299.1" ; exon_number 1 ; gene_id "MEIS2--AC066614.1^AC066614.1^ENSG00000287596.1" ; gene_name "AC066614.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195881.1" ; havana_transcript "OTTHUMT00000529215.1" ; level 2 ; orig_coord_info "chr15,53419865,53420669,+" ; tag basic TAGENE ; transcript_id "MEIS2--AC066614.1^ENST00000662193.1" ; transcript_name "AC066614.1-201" ; transcript_type lncRNA
MEIS2--AC066614.1 HAVANA RNA 28293 30207 . + . FI_gene_label "AC066614.1^ENSG00000287596.1" ; ID "MEIS2--AC066614.1^ENST00000662193.1" ; Parent "MEIS2--AC066614.1^AC066614.1^ENSG00000287596.1" ; exon_id "ENSE00003862299.1" ; exon_number 1 ; gene_id "MEIS2--AC066614.1^AC066614.1^ENSG00000287596.1" ; gene_name "AC066614.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195881.1" ; havana_transcript "OTTHUMT00000529215.1" ; level 2 ; orig_coord_info "chr15,53419865,53420669,+" ; tag basic TAGENE ; transcript_id "MEIS2--AC066614.1^ENST00000662193.1" ; transcript_name "AC066614.1-201" ; transcript_type lncRNA
L1 and L2 created:
MEIS2--LINC02490 HAVANA gene 28293 30893 . + . FI_gene_label "LINC02490^ENSG00000259237.1" ; ID "MEIS2--LINC02490^LINC02490^ENSG00000259237.1" ; exon_id "ENSE00002569592.1" ; exon_number 1 ; gene_id "MEIS2--LINC02490^LINC02490^ENSG00000259237.1" ; gene_name LINC02490 ; gene_type lncRNA ; havana_gene "OTTHUMG00000172483.1" ; havana_transcript "OTTHUMT00000418736.1" ; hgnc_id "HGNC:53471" ; level 2 ; orig_coord_info "chr15,53116365,53116458,+" ; tag basic ; transcript_id "MEIS2--LINC02490^ENST00000559915.1" ; transcript_name "LINC02490-201" ; transcript_support_level 3 ; transcript_type lncRNA
MEIS2--LINC02490 HAVANA RNA 28293 30893 . + . FI_gene_label "LINC02490^ENSG00000259237.1" ; ID "MEIS2--LINC02490^ENST00000559915.1" ; Parent "MEIS2--LINC02490^LINC02490^ENSG00000259237.1" ; exon_id "ENSE00002569592.1" ; exon_number 1 ; gene_id "MEIS2--LINC02490^LINC02490^ENSG00000259237.1" ; gene_name LINC02490 ; gene_type lncRNA ; havana_gene "OTTHUMG00000172483.1" ; havana_transcript "OTTHUMT00000418736.1" ; hgnc_id "HGNC:53471" ; level 2 ; orig_coord_info "chr15,53116365,53116458,+" ; tag basic ; transcript_id "MEIS2--LINC02490^ENST00000559915.1" ; transcript_name "LINC02490-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
SHANK2--AC061997.1 ENSEMBL gene 61945 62040 . + . FI_gene_label "AC061997.1^ENSG00000251838.1" ; ID "SHANK2--AC061997.1^AC061997.1^ENSG00000251838.1" ; exon_id "ENSE00002088306.1" ; exon_number 1 ; gene_id "SHANK2--AC061997.1^AC061997.1^ENSG00000251838.1" ; gene_name "AC061997.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chr11,37702125,37702220,-" ; tag basic ; transcript_id "SHANK2--AC061997.1^ENST00000516029.1" ; transcript_name "AC061997.1-201" ; transcript_support_level NA ; transcript_type snoRNA
SHANK2--AC061997.1 ENSEMBL RNA 61945 62040 . + . FI_gene_label "AC061997.1^ENSG00000251838.1" ; ID "SHANK2--AC061997.1^ENST00000516029.1" ; Parent "SHANK2--AC061997.1^AC061997.1^ENSG00000251838.1" ; exon_id "ENSE00002088306.1" ; exon_number 1 ; gene_id "SHANK2--AC061997.1^AC061997.1^ENSG00000251838.1" ; gene_name "AC061997.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chr11,37702125,37702220,-" ; tag basic ; transcript_id "SHANK2--AC061997.1^ENST00000516029.1" ; transcript_name "AC061997.1-201" ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created:
SHANK2--AC104042.1 HAVANA gene 61945 63495 . + . FI_gene_label "AC104042.1^ENSG00000254498.1" ; ID "SHANK2--AC104042.1^AC104042.1^ENSG00000254498.1" ; exon_id "ENSE00002168998.1" ; exon_number 1 ; gene_id "SHANK2--AC104042.1^AC104042.1^ENSG00000254498.1" ; gene_name "AC104042.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166332.1" ; havana_transcript "OTTHUMT00000389187.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr11,36696317,36697090,+" ; tag pseudo_consens basic ; transcript_id "SHANK2--AC104042.1^ENST00000524806.1" ; transcript_name "AC104042.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
SHANK2--AC104042.1 HAVANA RNA 61945 63495 . + . FI_gene_label "AC104042.1^ENSG00000254498.1" ; ID "SHANK2--AC104042.1^ENST00000524806.1" ; Parent "SHANK2--AC104042.1^AC104042.1^ENSG00000254498.1" ; exon_id "ENSE00002168998.1" ; exon_number 1 ; gene_id "SHANK2--AC104042.1^AC104042.1^ENSG00000254498.1" ; gene_name "AC104042.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166332.1" ; havana_transcript "OTTHUMT00000389187.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr11,36696317,36697090,+" ; tag pseudo_consens basic ; transcript_id "SHANK2--AC104042.1^ENST00000524806.1" ; transcript_name "AC104042.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TUBGCP2--AC104640.2 HAVANA gene 25941 26086 . + . FI_gene_label "AC104640.2^ENSG00000271413.1" ; ID "TUBGCP2--AC104640.2^AC104640.2^ENSG00000271413.1" ; exon_id "ENSE00003686525.1" ; exon_number 1 ; gene_id "TUBGCP2--AC104640.2^AC104640.2^ENSG00000271413.1" ; gene_name "AC104640.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184291.1" ; havana_transcript "OTTHUMT00000468566.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr3,176069107,176069252,+" ; tag pseudo_consens basic ; transcript_id "TUBGCP2--AC104640.2^ENST00000604457.1" ; transcript_name "AC104640.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TUBGCP2--AC104640.2 HAVANA RNA 25941 26086 . + . FI_gene_label "AC104640.2^ENSG00000271413.1" ; ID "TUBGCP2--AC104640.2^ENST00000604457.1" ; Parent "TUBGCP2--AC104640.2^AC104640.2^ENSG00000271413.1" ; exon_id "ENSE00003686525.1" ; exon_number 1 ; gene_id "TUBGCP2--AC104640.2^AC104640.2^ENSG00000271413.1" ; gene_name "AC104640.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000184291.1" ; havana_transcript "OTTHUMT00000468566.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr3,176069107,176069252,+" ; tag pseudo_consens basic ; transcript_id "TUBGCP2--AC104640.2^ENST00000604457.1" ; transcript_name "AC104640.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TUBGCP2--AC117434.1 HAVANA gene 25941 26776 . + . FI_gene_label "AC117434.1^ENSG00000238026.1" ; ID "TUBGCP2--AC117434.1^AC117434.1^ENSG00000238026.1" ; exon_id "ENSE00001785372.1" ; exon_number 1 ; gene_id "TUBGCP2--AC117434.1^AC117434.1^ENSG00000238026.1" ; gene_name "AC117434.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157230.1" ; havana_transcript "OTTHUMT00000348093.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr3,176113702,176114537,-" ; tag pseudo_consens basic ; transcript_id "TUBGCP2--AC117434.1^ENST00000419971.1" ; transcript_name "AC117434.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TUBGCP2--AC117434.1 HAVANA RNA 25941 26776 . + . FI_gene_label "AC117434.1^ENSG00000238026.1" ; ID "TUBGCP2--AC117434.1^ENST00000419971.1" ; Parent "TUBGCP2--AC117434.1^AC117434.1^ENSG00000238026.1" ; exon_id "ENSE00001785372.1" ; exon_number 1 ; gene_id "TUBGCP2--AC117434.1^AC117434.1^ENSG00000238026.1" ; gene_name "AC117434.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000157230.1" ; havana_transcript "OTTHUMT00000348093.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr3,176113702,176114537,-" ; tag pseudo_consens basic ; transcript_id "TUBGCP2--AC117434.1^ENST00000419971.1" ; transcript_name "AC117434.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
ZCCHC14--IGH-@-ext SuperLocus-ext gene 22712 1314052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "ZCCHC14--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "ZCCHC14--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "ZCCHC14--IGH-@-ext^IGH-.t@-ext"
ZCCHC14--IGH-@-ext SuperLocus-ext RNA 22712 1314052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "ZCCHC14--IGH-@-ext^IGH-.t@-ext" ; Parent "ZCCHC14--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "ZCCHC14--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "ZCCHC14--IGH-@-ext^IGH-.t@-ext"
644 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
1248 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 46 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