Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/bc3d9b48fabf17f02256dc29545fcd/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/e1afd428b4843c8e35c21ace445bcd/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/e1afd428b4843c8e35c21ace445bcd/.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: 3450
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3450
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:3450
=> 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:
ADCY9--AC007610.2 HAVANA gene 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--AC007610.2^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--AC007610.2^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--AC007610.2^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADCY9--AC007610.2 HAVANA mRNA 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--AC007610.2^ENST00000294016.8" ; Parent "ADCY9--AC007610.2^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--AC007610.2^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--AC007610.2^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADCY9--AC007610.5 HAVANA gene 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--AC007610.5^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--AC007610.5^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--AC007610.5^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADCY9--AC007610.5 HAVANA mRNA 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--AC007610.5^ENST00000294016.8" ; Parent "ADCY9--AC007610.5^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--AC007610.5^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--AC007610.5^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADCY9--MSRB1 HAVANA gene 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--MSRB1^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--MSRB1^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--MSRB1^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADCY9--MSRB1 HAVANA mRNA 1001 22672 . + . FI_gene_label "ADCY9^ENSG00000162104.10" ; ID "ADCY9--MSRB1^ENST00000294016.8" ; Parent "ADCY9--MSRB1^ADCY9^ENSG00000162104.10" ; ccdsid "CCDS32382.1" ; exon_id "ENSE00001062629.1" ; exon_number 2 ; gene_id "ADCY9--MSRB1^ADCY9^ENSG00000162104.10" ; gene_name ADCY9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177612.3" ; havana_transcript "OTTHUMT00000438076.2" ; hgnc_id "HGNC:240" ; level 2 ; orig_coord_info "chr16,4113750,4115442,-" ; protein_id "ENSP00000294016.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADCY9--MSRB1^ENST00000294016.8" ; transcript_name "ADCY9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADCY9--MSRB1 HAVANA gene 26897 31071 . + . FI_gene_label "MSRB1^ENSG00000198736.12" ; ID "ADCY9--MSRB1^MSRB1^ENSG00000198736.12" ; ccdsid "CCDS42100.1" ; exon_id "ENSE00002604473.1" ; exon_number 1 ; gene_id "ADCY9--MSRB1^MSRB1^ENSG00000198736.12" ; gene_name MSRB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129143.2" ; havana_transcript "OTTHUMT00000251203.1" ; hgnc_id "HGNC:14133" ; level 2 ; orig_coord_info "chr16,1943102,1943156,-" ; protein_id "ENSP00000355084.3" ; tag basic MANE_Select appris_principal_4 CCDS seleno ; transcript_id "ADCY9--MSRB1^ENST00000361871.8" ; transcript_name "MSRB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADCY9--MSRB1 HAVANA mRNA 26897 31071 . + . FI_gene_label "MSRB1^ENSG00000198736.12" ; ID "ADCY9--MSRB1^ENST00000361871.8" ; Parent "ADCY9--MSRB1^MSRB1^ENSG00000198736.12" ; ccdsid "CCDS42100.1" ; exon_id "ENSE00002604473.1" ; exon_number 1 ; gene_id "ADCY9--MSRB1^MSRB1^ENSG00000198736.12" ; gene_name MSRB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129143.2" ; havana_transcript "OTTHUMT00000251203.1" ; hgnc_id "HGNC:14133" ; level 2 ; orig_coord_info "chr16,1943102,1943156,-" ; protein_id "ENSP00000355084.3" ; tag basic MANE_Select appris_principal_4 CCDS seleno ; transcript_id "ADCY9--MSRB1^ENST00000361871.8" ; transcript_name "MSRB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AP1B1--GPAT4 HAVANA gene 1001 23709 . + . FI_gene_label "AP1B1^ENSG00000100280.17" ; ID "AP1B1--GPAT4^AP1B1^ENSG00000100280.17" ; ccdsid "CCDS54515.1" ; exon_id "ENSE00002296219.1" ; exon_number 2 ; gene_id "AP1B1--GPAT4^AP1B1^ENSG00000100280.17" ; gene_name AP1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151109.4" ; havana_transcript "OTTHUMT00000321375.2" ; hgnc_id "HGNC:554" ; level 2 ; orig_coord_info "chr22,29367207,29367243,-" ; protein_id "ENSP00000319361.7" ; tag basic CCDS ; transcript_id "AP1B1--GPAT4^ENST00000317368.11" ; transcript_name "AP1B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AP1B1--GPAT4 HAVANA mRNA 1001 23709 . + . FI_gene_label "AP1B1^ENSG00000100280.17" ; ID "AP1B1--GPAT4^ENST00000317368.11" ; Parent "AP1B1--GPAT4^AP1B1^ENSG00000100280.17" ; ccdsid "CCDS54515.1" ; exon_id "ENSE00002296219.1" ; exon_number 2 ; gene_id "AP1B1--GPAT4^AP1B1^ENSG00000100280.17" ; gene_name AP1B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151109.4" ; havana_transcript "OTTHUMT00000321375.2" ; hgnc_id "HGNC:554" ; level 2 ; orig_coord_info "chr22,29367207,29367243,-" ; protein_id "ENSP00000319361.7" ; tag basic CCDS ; transcript_id "AP1B1--GPAT4^ENST00000317368.11" ; transcript_name "AP1B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AP1B1--GPAT4 HAVANA gene 27908 44494 . + . FI_gene_label "GPAT4^ENSG00000158669.11" ; ID "AP1B1--GPAT4^GPAT4^ENSG00000158669.11" ; ccdsid "CCDS6117.1" ; exon_id "ENSE00001526992.1" ; exon_number 2 ; gene_id "AP1B1--GPAT4^GPAT4^ENSG00000158669.11" ; gene_name GPAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164082.4" ; havana_transcript "OTTHUMT00000377158.1" ; hgnc_id "HGNC:20880" ; level 2 ; orig_coord_info "chr8,41599140,41599304,+" ; protein_id "ENSP00000380184.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AP1B1--GPAT4^ENST00000396987.7" ; transcript_name "GPAT4-201" ; transcript_support_level 1 ; transcript_type protein_coding
AP1B1--GPAT4 HAVANA mRNA 27908 44494 . + . FI_gene_label "GPAT4^ENSG00000158669.11" ; ID "AP1B1--GPAT4^ENST00000396987.7" ; Parent "AP1B1--GPAT4^GPAT4^ENSG00000158669.11" ; ccdsid "CCDS6117.1" ; exon_id "ENSE00001526992.1" ; exon_number 2 ; gene_id "AP1B1--GPAT4^GPAT4^ENSG00000158669.11" ; gene_name GPAT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164082.4" ; havana_transcript "OTTHUMT00000377158.1" ; hgnc_id "HGNC:20880" ; level 2 ; orig_coord_info "chr8,41599140,41599304,+" ; protein_id "ENSP00000380184.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AP1B1--GPAT4^ENST00000396987.7" ; transcript_name "GPAT4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARHGAP21--TBC1D22A ENSEMBL gene 2898 32111 . + . FI_gene_label "ARHGAP21^ENSG00000107863.19" ; ID "ARHGAP21--TBC1D22A^ARHGAP21^ENSG00000107863.19" ; exon_id "ENSE00003748160.1" ; exon_number 1 ; gene_id "ARHGAP21--TBC1D22A^ARHGAP21^ENSG00000107863.19" ; gene_name ARHGAP21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017825.8" ; hgnc_id "HGNC:23725" ; level 3 ; orig_coord_info "chr10,24721837,24721896,-" ; protein_id "ENSP00000365604.5" ; tag basic ; transcript_id "ARHGAP21--TBC1D22A^ENST00000320481.10" ; transcript_name "ARHGAP21-201" ; transcript_support_level 5 ; transcript_type protein_coding
ARHGAP21--TBC1D22A ENSEMBL mRNA 2898 32111 . + . FI_gene_label "ARHGAP21^ENSG00000107863.19" ; ID "ARHGAP21--TBC1D22A^ENST00000320481.10" ; Parent "ARHGAP21--TBC1D22A^ARHGAP21^ENSG00000107863.19" ; exon_id "ENSE00003748160.1" ; exon_number 1 ; gene_id "ARHGAP21--TBC1D22A^ARHGAP21^ENSG00000107863.19" ; gene_name ARHGAP21 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017825.8" ; hgnc_id "HGNC:23725" ; level 3 ; orig_coord_info "chr10,24721837,24721896,-" ; protein_id "ENSP00000365604.5" ; tag basic ; transcript_id "ARHGAP21--TBC1D22A^ENST00000320481.10" ; transcript_name "ARHGAP21-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ARHGAP21--TBC1D22A HAVANA gene 35923 58086 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "ARHGAP21--TBC1D22A^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "ARHGAP21--TBC1D22A^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP21--TBC1D22A^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP21--TBC1D22A HAVANA mRNA 35923 58086 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "ARHGAP21--TBC1D22A^ENST00000337137.9" ; Parent "ARHGAP21--TBC1D22A^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "ARHGAP21--TBC1D22A^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP21--TBC1D22A^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BOLA2--AC025279.2 HAVANA gene 1001 2372 . + . FI_gene_label "BOLA2^ENSG00000183336.8" ; ID "BOLA2--AC025279.2^BOLA2^ENSG00000183336.8" ; ccdsid "CCDS32426.1" ; exon_id "ENSE00001605967.1" ; exon_number 1 ; gene_id "BOLA2--AC025279.2^BOLA2^ENSG00000183336.8" ; gene_name BOLA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176757.2" ; havana_transcript "OTTHUMT00000433254.1" ; hgnc_id "HGNC:29488" ; level 2 ; orig_coord_info "chr16,29454191,29454451,-" ; protein_id "ENSP00000331127.3" ; tag basic appris_principal_1 CCDS ; transcript_id "BOLA2--AC025279.2^ENST00000330978.3" ; transcript_name "BOLA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
BOLA2--AC025279.2 HAVANA mRNA 1001 2372 . + . FI_gene_label "BOLA2^ENSG00000183336.8" ; ID "BOLA2--AC025279.2^ENST00000330978.3" ; Parent "BOLA2--AC025279.2^BOLA2^ENSG00000183336.8" ; ccdsid "CCDS32426.1" ; exon_id "ENSE00001605967.1" ; exon_number 1 ; gene_id "BOLA2--AC025279.2^BOLA2^ENSG00000183336.8" ; gene_name BOLA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176757.2" ; havana_transcript "OTTHUMT00000433254.1" ; hgnc_id "HGNC:29488" ; level 2 ; orig_coord_info "chr16,29454191,29454451,-" ; protein_id "ENSP00000331127.3" ; tag basic appris_principal_1 CCDS ; transcript_id "BOLA2--AC025279.2^ENST00000330978.3" ; transcript_name "BOLA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
C16orf87--AC007493.1 HAVANA gene 1001 12460 . + . FI_gene_label "C16orf87^ENSG00000155330.10" ; ID "C16orf87--AC007493.1^C16orf87^ENSG00000155330.10" ; ccdsid "CCDS10724.1" ; exon_id "ENSE00001862260.3" ; exon_number 1 ; gene_id "C16orf87--AC007493.1^C16orf87^ENSG00000155330.10" ; gene_name C16orf87 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132538.3" ; havana_transcript "OTTHUMT00000255738.3" ; hgnc_id "HGNC:33754" ; level 2 ; orig_coord_info "chr16,46831084,46831149,-" ; protein_id "ENSP00000285697.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "C16orf87--AC007493.1^ENST00000285697.9" ; transcript_name "C16orf87-201" ; transcript_support_level 1 ; transcript_type protein_coding
C16orf87--AC007493.1 HAVANA mRNA 1001 12460 . + . FI_gene_label "C16orf87^ENSG00000155330.10" ; ID "C16orf87--AC007493.1^ENST00000285697.9" ; Parent "C16orf87--AC007493.1^C16orf87^ENSG00000155330.10" ; ccdsid "CCDS10724.1" ; exon_id "ENSE00001862260.3" ; exon_number 1 ; gene_id "C16orf87--AC007493.1^C16orf87^ENSG00000155330.10" ; gene_name C16orf87 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132538.3" ; havana_transcript "OTTHUMT00000255738.3" ; hgnc_id "HGNC:33754" ; level 2 ; orig_coord_info "chr16,46831084,46831149,-" ; protein_id "ENSP00000285697.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "C16orf87--AC007493.1^ENST00000285697.9" ; transcript_name "C16orf87-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GOLGA6L10--GOLGA2P6 HAVANA gene 1001 9781 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
GOLGA6L10--GOLGA2P6 HAVANA mRNA 1001 9781 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; Parent "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUCY1B2--NKAIN2 HAVANA mRNA 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^ENST00000368416.5" ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MET--5_8S_rRNA HAVANA gene 1001 27300 . + . FI_gene_label "MET^ENSG00000105976.16" ; ID "MET--5_8S_rRNA^MET^ENSG00000105976.16" ; ccdsid "CCDS47689.1" ; exon_id "ENSE00001238915.3" ; exon_number 2 ; gene_id "MET--5_8S_rRNA^MET^ENSG00000105976.16" ; gene_name MET ; gene_type protein_coding ; havana_gene "OTTHUMG00000023299.10" ; havana_transcript "OTTHUMT00000059620.4" ; hgnc_id "HGNC:7029" ; level 2 ; orig_coord_info "chr7,116699085,116700284,+" ; protein_id "ENSP00000317272.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "MET--5_8S_rRNA^ENST00000318493.11" ; transcript_name "MET-201" ; transcript_support_level 1 ; transcript_type protein_coding
MET--5_8S_rRNA HAVANA mRNA 1001 27300 . + . FI_gene_label "MET^ENSG00000105976.16" ; ID "MET--5_8S_rRNA^ENST00000318493.11" ; Parent "MET--5_8S_rRNA^MET^ENSG00000105976.16" ; ccdsid "CCDS47689.1" ; exon_id "ENSE00001238915.3" ; exon_number 2 ; gene_id "MET--5_8S_rRNA^MET^ENSG00000105976.16" ; gene_name MET ; gene_type protein_coding ; havana_gene "OTTHUMG00000023299.10" ; havana_transcript "OTTHUMT00000059620.4" ; hgnc_id "HGNC:7029" ; level 2 ; orig_coord_info "chr7,116699085,116700284,+" ; protein_id "ENSP00000317272.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "MET--5_8S_rRNA^ENST00000318493.11" ; transcript_name "MET-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--AC022167.4 HAVANA gene 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--AC022167.4^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--AC022167.4^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--AC022167.4^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NKD1--AC022167.4 HAVANA mRNA 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--AC022167.4^ENST00000268459.6" ; Parent "NKD1--AC022167.4^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--AC022167.4^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--AC022167.4^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--AC138904.1 HAVANA gene 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--AC138904.1^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--AC138904.1^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--AC138904.1^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NKD1--AC138904.1 HAVANA mRNA 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--AC138904.1^ENST00000268459.6" ; Parent "NKD1--AC138904.1^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--AC138904.1^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--AC138904.1^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--CARHSP1 HAVANA gene 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--CARHSP1^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--CARHSP1^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--CARHSP1^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NKD1--CARHSP1 HAVANA mRNA 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--CARHSP1^ENST00000268459.6" ; Parent "NKD1--CARHSP1^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--CARHSP1^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--CARHSP1^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--CARHSP1 HAVANA gene 29451 39600 . + . FI_gene_label "CARHSP1^ENSG00000153048.11" ; ID "NKD1--CARHSP1^CARHSP1^ENSG00000153048.11" ; ccdsid "CCDS10537.1" ; exon_id "ENSE00003650612.1" ; exon_number 2 ; gene_id "NKD1--CARHSP1^CARHSP1^ENSG00000153048.11" ; gene_name CARHSP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129695.5" ; havana_transcript "OTTHUMT00000434250.2" ; hgnc_id "HGNC:17150" ; level 2 ; orig_coord_info "chr16,8859171,8859328,-" ; protein_id "ENSP00000311847.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--CARHSP1^ENST00000311052.10" ; transcript_name "CARHSP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NKD1--CARHSP1 HAVANA mRNA 29451 39600 . + . FI_gene_label "CARHSP1^ENSG00000153048.11" ; ID "NKD1--CARHSP1^ENST00000311052.10" ; Parent "NKD1--CARHSP1^CARHSP1^ENSG00000153048.11" ; ccdsid "CCDS10537.1" ; exon_id "ENSE00003650612.1" ; exon_number 2 ; gene_id "NKD1--CARHSP1^CARHSP1^ENSG00000153048.11" ; gene_name CARHSP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129695.5" ; havana_transcript "OTTHUMT00000434250.2" ; hgnc_id "HGNC:17150" ; level 2 ; orig_coord_info "chr16,8859171,8859328,-" ; protein_id "ENSP00000311847.4" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--CARHSP1^ENST00000311052.10" ; transcript_name "CARHSP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--LITAFD HAVANA gene 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--LITAFD^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--LITAFD^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--LITAFD^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NKD1--LITAFD HAVANA mRNA 1001 26444 . + . FI_gene_label "NKD1^ENSG00000140807.7" ; ID "NKD1--LITAFD^ENST00000268459.6" ; Parent "NKD1--LITAFD^NKD1^ENSG00000140807.7" ; ccdsid "CCDS10743.1" ; exon_id "ENSE00001320873.3" ; exon_number 1 ; gene_id "NKD1--LITAFD^NKD1^ENSG00000140807.7" ; gene_name NKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133169.7" ; havana_transcript "OTTHUMT00000256873.4" ; hgnc_id "HGNC:17045" ; level 2 ; orig_coord_info "chr16,50548554,50548578,+" ; protein_id "ENSP00000268459.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NKD1--LITAFD^ENST00000268459.6" ; transcript_name "NKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NKD1--LITAFD HAVANA gene 29445 33114 . + . FI_gene_label "LITAFD^ENSG00000283516.1" ; ID "NKD1--LITAFD^LITAFD^ENSG00000283516.1" ; exon_id "ENSE00003794227.1" ; exon_number 3 ; gene_id "NKD1--LITAFD^LITAFD^ENSG00000283516.1" ; gene_name LITAFD ; gene_type protein_coding ; havana_gene "OTTHUMG00000176581.3" ; havana_transcript "OTTHUMT00000490125.1" ; hgnc_id "HGNC:53927" ; level 2 ; orig_coord_info "chr16,8884356,8884465,+" ; protein_id "ENSP00000490685.1" ; tag alternative_5_UTR basic appris_principal_1 ; transcript_id "NKD1--LITAFD^ENST00000636296.1" ; transcript_name "LITAFD-201" ; transcript_support_level 5 ; transcript_type protein_coding
NKD1--LITAFD HAVANA mRNA 29445 33114 . + . FI_gene_label "LITAFD^ENSG00000283516.1" ; ID "NKD1--LITAFD^ENST00000636296.1" ; Parent "NKD1--LITAFD^LITAFD^ENSG00000283516.1" ; exon_id "ENSE00003794227.1" ; exon_number 3 ; gene_id "NKD1--LITAFD^LITAFD^ENSG00000283516.1" ; gene_name LITAFD ; gene_type protein_coding ; havana_gene "OTTHUMG00000176581.3" ; havana_transcript "OTTHUMT00000490125.1" ; hgnc_id "HGNC:53927" ; level 2 ; orig_coord_info "chr16,8884356,8884465,+" ; protein_id "ENSP00000490685.1" ; tag alternative_5_UTR basic appris_principal_1 ; transcript_id "NKD1--LITAFD^ENST00000636296.1" ; transcript_name "LITAFD-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PANX2--AC087698.1 HAVANA gene 1001 6631 . + . FI_gene_label "PANX2^ENSG00000073150.14" ; ID "PANX2--AC087698.1^PANX2^ENSG00000073150.14" ; ccdsid "CCDS54544.1" ; exon_id "ENSE00002266289.1" ; exon_number 1 ; gene_id "PANX2--AC087698.1^PANX2^ENSG00000073150.14" ; gene_name PANX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044649.5" ; havana_transcript "OTTHUMT00000317003.2" ; hgnc_id "HGNC:8600" ; level 2 ; orig_coord_info "chr22,50170731,50170956,+" ; protein_id "ENSP00000159647.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "PANX2--AC087698.1^ENST00000159647.9" ; transcript_name "PANX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PANX2--AC087698.1 HAVANA mRNA 1001 6631 . + . FI_gene_label "PANX2^ENSG00000073150.14" ; ID "PANX2--AC087698.1^ENST00000159647.9" ; Parent "PANX2--AC087698.1^PANX2^ENSG00000073150.14" ; ccdsid "CCDS54544.1" ; exon_id "ENSE00002266289.1" ; exon_number 1 ; gene_id "PANX2--AC087698.1^PANX2^ENSG00000073150.14" ; gene_name PANX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044649.5" ; havana_transcript "OTTHUMT00000317003.2" ; hgnc_id "HGNC:8600" ; level 2 ; orig_coord_info "chr22,50170731,50170956,+" ; protein_id "ENSP00000159647.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "PANX2--AC087698.1^ENST00000159647.9" ; transcript_name "PANX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PANX2--AC090152.1 HAVANA gene 1001 6631 . + . FI_gene_label "PANX2^ENSG00000073150.14" ; ID "PANX2--AC090152.1^PANX2^ENSG00000073150.14" ; ccdsid "CCDS54544.1" ; exon_id "ENSE00002266289.1" ; exon_number 1 ; gene_id "PANX2--AC090152.1^PANX2^ENSG00000073150.14" ; gene_name PANX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044649.5" ; havana_transcript "OTTHUMT00000317003.2" ; hgnc_id "HGNC:8600" ; level 2 ; orig_coord_info "chr22,50170731,50170956,+" ; protein_id "ENSP00000159647.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "PANX2--AC090152.1^ENST00000159647.9" ; transcript_name "PANX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PANX2--AC090152.1 HAVANA mRNA 1001 6631 . + . FI_gene_label "PANX2^ENSG00000073150.14" ; ID "PANX2--AC090152.1^ENST00000159647.9" ; Parent "PANX2--AC090152.1^PANX2^ENSG00000073150.14" ; ccdsid "CCDS54544.1" ; exon_id "ENSE00002266289.1" ; exon_number 1 ; gene_id "PANX2--AC090152.1^PANX2^ENSG00000073150.14" ; gene_name PANX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000044649.5" ; havana_transcript "OTTHUMT00000317003.2" ; hgnc_id "HGNC:8600" ; level 2 ; orig_coord_info "chr22,50170731,50170956,+" ; protein_id "ENSP00000159647.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "PANX2--AC090152.1^ENST00000159647.9" ; transcript_name "PANX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC7A5P1--N4BP1 HAVANA gene 5839 20348 . + . FI_gene_label "N4BP1^ENSG00000102921.8" ; ID "SLC7A5P1--N4BP1^N4BP1^ENSG00000102921.8" ; ccdsid "CCDS45479.1" ; exon_id "ENSE00001231868.2" ; exon_number 1 ; gene_id "SLC7A5P1--N4BP1^N4BP1^ENSG00000102921.8" ; gene_name N4BP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175421.5" ; havana_transcript "OTTHUMT00000429920.2" ; hgnc_id "HGNC:29850" ; level 2 ; orig_coord_info "chr16,48609775,48609972,-" ; protein_id "ENSP00000262384.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A5P1--N4BP1^ENST00000262384.4" ; transcript_name "N4BP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC7A5P1--N4BP1 HAVANA mRNA 5839 20348 . + . FI_gene_label "N4BP1^ENSG00000102921.8" ; ID "SLC7A5P1--N4BP1^ENST00000262384.4" ; Parent "SLC7A5P1--N4BP1^N4BP1^ENSG00000102921.8" ; ccdsid "CCDS45479.1" ; exon_id "ENSE00001231868.2" ; exon_number 1 ; gene_id "SLC7A5P1--N4BP1^N4BP1^ENSG00000102921.8" ; gene_name N4BP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175421.5" ; havana_transcript "OTTHUMT00000429920.2" ; hgnc_id "HGNC:29850" ; level 2 ; orig_coord_info "chr16,48609775,48609972,-" ; protein_id "ENSP00000262384.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A5P1--N4BP1^ENST00000262384.4" ; transcript_name "N4BP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SUPV3L1--SPIDR HAVANA gene 21333 56840 . + . FI_gene_label "SPIDR^ENSG00000164808.17" ; ID "SUPV3L1--SPIDR^SPIDR^ENSG00000164808.17" ; ccdsid "CCDS43737.1" ; exon_id "ENSE00002119316.2" ; exon_number 1 ; gene_id "SUPV3L1--SPIDR^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 "SUPV3L1--SPIDR^ENST00000297423.9" ; transcript_name "SPIDR-201" ; transcript_support_level 1 ; transcript_type protein_coding
SUPV3L1--SPIDR HAVANA mRNA 21333 56840 . + . FI_gene_label "SPIDR^ENSG00000164808.17" ; ID "SUPV3L1--SPIDR^ENST00000297423.9" ; Parent "SUPV3L1--SPIDR^SPIDR^ENSG00000164808.17" ; ccdsid "CCDS43737.1" ; exon_id "ENSE00002119316.2" ; exon_number 1 ; gene_id "SUPV3L1--SPIDR^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 "SUPV3L1--SPIDR^ENST00000297423.9" ; transcript_name "SPIDR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SUPV3L1--SPIDR HAVANA gene 1001 18266 . + . FI_gene_label "SUPV3L1^ENSG00000156502.14" ; ID "SUPV3L1--SPIDR^SUPV3L1^ENSG00000156502.14" ; ccdsid "CCDS7287.1" ; exon_id "ENSE00001864569.2" ; exon_number 1 ; gene_id "SUPV3L1--SPIDR^SUPV3L1^ENSG00000156502.14" ; gene_name SUPV3L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018375.4" ; havana_transcript "OTTHUMT00000048396.3" ; hgnc_id "HGNC:11471" ; level 2 ; orig_coord_info "chr10,69180292,69180562,+" ; protein_id "ENSP00000352678.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUPV3L1--SPIDR^ENST00000359655.9" ; transcript_name "SUPV3L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SUPV3L1--SPIDR HAVANA mRNA 1001 18266 . + . FI_gene_label "SUPV3L1^ENSG00000156502.14" ; ID "SUPV3L1--SPIDR^ENST00000359655.9" ; Parent "SUPV3L1--SPIDR^SUPV3L1^ENSG00000156502.14" ; ccdsid "CCDS7287.1" ; exon_id "ENSE00001864569.2" ; exon_number 1 ; gene_id "SUPV3L1--SPIDR^SUPV3L1^ENSG00000156502.14" ; gene_name SUPV3L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018375.4" ; havana_transcript "OTTHUMT00000048396.3" ; hgnc_id "HGNC:11471" ; level 2 ; orig_coord_info "chr10,69180292,69180562,+" ; protein_id "ENSP00000352678.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUPV3L1--SPIDR^ENST00000359655.9" ; transcript_name "SUPV3L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TBC1D22A--AC022535.2 HAVANA gene 1034 23197 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "TBC1D22A--AC022535.2^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.2^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TBC1D22A--AC022535.2^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBC1D22A--AC022535.2 HAVANA mRNA 1034 23197 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "TBC1D22A--AC022535.2^ENST00000337137.9" ; Parent "TBC1D22A--AC022535.2^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.2^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TBC1D22A--AC022535.2^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TBC1D22A--AC022535.3 HAVANA gene 1034 23197 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "TBC1D22A--AC022535.3^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.3^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TBC1D22A--AC022535.3^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBC1D22A--AC022535.3 HAVANA mRNA 1034 23197 . + . FI_gene_label "TBC1D22A^ENSG00000054611.14" ; ID "TBC1D22A--AC022535.3^ENST00000337137.9" ; Parent "TBC1D22A--AC022535.3^TBC1D22A^ENSG00000054611.14" ; ccdsid "CCDS14078.1" ; exon_id "ENSE00001916547.2" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.3^TBC1D22A^ENSG00000054611.14" ; gene_name TBC1D22A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150332.4" ; havana_transcript "OTTHUMT00000317600.4" ; hgnc_id "HGNC:1309" ; level 2 ; orig_coord_info "chr22,46762787,46762848,+" ; protein_id "ENSP00000336724.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TBC1D22A--AC022535.3^ENST00000337137.9" ; transcript_name "TBC1D22A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF668--BCL7C HAVANA gene 10441 14083 . + . FI_gene_label "BCL7C^ENSG00000099385.12" ; ID "ZNF668--BCL7C^BCL7C^ENSG00000099385.12" ; ccdsid "CCDS10693.1" ; exon_id "ENSE00002656701.2" ; exon_number 1 ; gene_id "ZNF668--BCL7C^BCL7C^ENSG00000099385.12" ; gene_name BCL7C ; gene_type protein_coding ; havana_gene "OTTHUMG00000177719.2" ; havana_transcript "OTTHUMT00000255547.3" ; hgnc_id "HGNC:1006" ; level 2 ; orig_coord_info "chr16,30893853,30893944,-" ; protein_id "ENSP00000215115.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ZNF668--BCL7C^ENST00000215115.5" ; transcript_name "BCL7C-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF668--BCL7C HAVANA mRNA 10441 14083 . + . FI_gene_label "BCL7C^ENSG00000099385.12" ; ID "ZNF668--BCL7C^ENST00000215115.5" ; Parent "ZNF668--BCL7C^BCL7C^ENSG00000099385.12" ; ccdsid "CCDS10693.1" ; exon_id "ENSE00002656701.2" ; exon_number 1 ; gene_id "ZNF668--BCL7C^BCL7C^ENSG00000099385.12" ; gene_name BCL7C ; gene_type protein_coding ; havana_gene "OTTHUMG00000177719.2" ; havana_transcript "OTTHUMT00000255547.3" ; hgnc_id "HGNC:1006" ; level 2 ; orig_coord_info "chr16,30893853,30893944,-" ; protein_id "ENSP00000215115.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ZNF668--BCL7C^ENST00000215115.5" ; transcript_name "BCL7C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZNF668--BCL7C HAVANA gene 1001 7211 . + . FI_gene_label "ZNF668^ENSG00000167394.13" ; ID "ZNF668--BCL7C^ZNF668^ENSG00000167394.13" ; ccdsid "CCDS10701.1" ; exon_id "ENSE00003624600.1" ; exon_number 2 ; gene_id "ZNF668--BCL7C^ZNF668^ENSG00000167394.13" ; gene_name ZNF668 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047357.6" ; havana_transcript "OTTHUMT00000108516.4" ; hgnc_id "HGNC:25821" ; level 2 ; orig_coord_info "chr16,31063813,31064459,-" ; protein_id "ENSP00000300849.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF668--BCL7C^ENST00000300849.5" ; transcript_name "ZNF668-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZNF668--BCL7C HAVANA mRNA 1001 7211 . + . FI_gene_label "ZNF668^ENSG00000167394.13" ; ID "ZNF668--BCL7C^ENST00000300849.5" ; Parent "ZNF668--BCL7C^ZNF668^ENSG00000167394.13" ; ccdsid "CCDS10701.1" ; exon_id "ENSE00003624600.1" ; exon_number 2 ; gene_id "ZNF668--BCL7C^ZNF668^ENSG00000167394.13" ; gene_name ZNF668 ; gene_type protein_coding ; havana_gene "OTTHUMG00000047357.6" ; havana_transcript "OTTHUMT00000108516.4" ; hgnc_id "HGNC:25821" ; level 2 ; orig_coord_info "chr16,31063813,31064459,-" ; protein_id "ENSP00000300849.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF668--BCL7C^ENST00000300849.5" ; transcript_name "ZNF668-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC135050.3--SMG1P4 HAVANA gene 21687 25908 . + . FI_gene_label "SMG1P4^ENSG00000185710.9" ; ID "AC135050.3--SMG1P4^SMG1P4^ENSG00000185710.9" ; exon_id "ENSE00002234515.1" ; exon_number 1 ; gene_id "AC135050.3--SMG1P4^SMG1P4^ENSG00000185710.9" ; gene_name SMG1P4 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000164330.2" ; havana_transcript "OTTHUMT00000402430.1" ; hgnc_id "HGNC:49861" ; level 2 ; orig_coord_info "chr16,21889252,21889287,-" ; transcript_id "AC135050.3--SMG1P4^ENST00000380598.4" ; transcript_name "SMG1P4-201" ; transcript_support_level 5 ; transcript_type processed_transcript
AC135050.3--SMG1P4 HAVANA RNA 21687 25908 . + . FI_gene_label "SMG1P4^ENSG00000185710.9" ; ID "AC135050.3--SMG1P4^ENST00000380598.4" ; Parent "AC135050.3--SMG1P4^SMG1P4^ENSG00000185710.9" ; exon_id "ENSE00002234515.1" ; exon_number 1 ; gene_id "AC135050.3--SMG1P4^SMG1P4^ENSG00000185710.9" ; gene_name SMG1P4 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000164330.2" ; havana_transcript "OTTHUMT00000402430.1" ; hgnc_id "HGNC:49861" ; level 2 ; orig_coord_info "chr16,21889252,21889287,-" ; transcript_id "AC135050.3--SMG1P4^ENST00000380598.4" ; transcript_name "SMG1P4-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
AC135050.3--SMG1P4 HAVANA gene 1001 2449 . + . FI_gene_label "AC135050.3^ENSG00000260911.2" ; ID "AC135050.3--SMG1P4^AC135050.3^ENSG00000260911.2" ; exon_id "ENSE00002604405.1" ; exon_number 1 ; gene_id "AC135050.3--SMG1P4^AC135050.3^ENSG00000260911.2" ; gene_name "AC135050.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000176730.2" ; havana_transcript "OTTHUMT00000433356.2" ; level 2 ; orig_coord_info "chr16,31043150,31043242,+" ; tag basic ; transcript_id "AC135050.3--SMG1P4^ENST00000570266.2" ; transcript_name "AC135050.3-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC135050.3--SMG1P4 HAVANA RNA 1001 2449 . + . FI_gene_label "AC135050.3^ENSG00000260911.2" ; ID "AC135050.3--SMG1P4^ENST00000570266.2" ; Parent "AC135050.3--SMG1P4^AC135050.3^ENSG00000260911.2" ; exon_id "ENSE00002604405.1" ; exon_number 1 ; gene_id "AC135050.3--SMG1P4^AC135050.3^ENSG00000260911.2" ; gene_name "AC135050.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000176730.2" ; havana_transcript "OTTHUMT00000433356.2" ; level 2 ; orig_coord_info "chr16,31043150,31043242,+" ; tag basic ; transcript_id "AC135050.3--SMG1P4^ENST00000570266.2" ; transcript_name "AC135050.3-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
ADCY9--AC007610.2 HAVANA gene 26803 29468 . + . FI_gene_label "AC007610.2^ENSG00000260381.2" ; ID "ADCY9--AC007610.2^AC007610.2^ENSG00000260381.2" ; exon_id "ENSE00002583764.1" ; exon_number 1 ; gene_id "ADCY9--AC007610.2^AC007610.2^ENSG00000260381.2" ; gene_name "AC007610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000173451.1" ; havana_transcript "OTTHUMT00000423146.1" ; level 2 ; orig_coord_info "chr16,50121819,50121943,-" ; tag basic ; transcript_id "ADCY9--AC007610.2^ENST00000566770.1" ; transcript_name "AC007610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
ADCY9--AC007610.2 HAVANA RNA 26803 29468 . + . FI_gene_label "AC007610.2^ENSG00000260381.2" ; ID "ADCY9--AC007610.2^ENST00000566770.1" ; Parent "ADCY9--AC007610.2^AC007610.2^ENSG00000260381.2" ; exon_id "ENSE00002583764.1" ; exon_number 1 ; gene_id "ADCY9--AC007610.2^AC007610.2^ENSG00000260381.2" ; gene_name "AC007610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000173451.1" ; havana_transcript "OTTHUMT00000423146.1" ; level 2 ; orig_coord_info "chr16,50121819,50121943,-" ; tag basic ; transcript_id "ADCY9--AC007610.2^ENST00000566770.1" ; transcript_name "AC007610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
ADCY9--AC007610.5 HAVANA gene 26803 28906 . + . FI_gene_label "AC007610.5^ENSG00000287444.1" ; ID "ADCY9--AC007610.5^AC007610.5^ENSG00000287444.1" ; exon_id "ENSE00003881393.1" ; exon_number 1 ; gene_id "ADCY9--AC007610.5^AC007610.5^ENSG00000287444.1" ; gene_name "AC007610.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195255.1" ; havana_transcript "OTTHUMT00000525609.1" ; level 2 ; orig_coord_info "chr16,50120064,50120155,+" ; tag basic TAGENE ; transcript_id "ADCY9--AC007610.5^ENST00000657788.1" ; transcript_name "AC007610.5-201" ; transcript_type lncRNA
ADCY9--AC007610.5 HAVANA RNA 26803 28906 . + . FI_gene_label "AC007610.5^ENSG00000287444.1" ; ID "ADCY9--AC007610.5^ENST00000657788.1" ; Parent "ADCY9--AC007610.5^AC007610.5^ENSG00000287444.1" ; exon_id "ENSE00003881393.1" ; exon_number 1 ; gene_id "ADCY9--AC007610.5^AC007610.5^ENSG00000287444.1" ; gene_name "AC007610.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195255.1" ; havana_transcript "OTTHUMT00000525609.1" ; level 2 ; orig_coord_info "chr16,50120064,50120155,+" ; tag basic TAGENE ; transcript_id "ADCY9--AC007610.5^ENST00000657788.1" ; transcript_name "AC007610.5-201" ; transcript_type lncRNA
L1 and L2 created:
BOLA2--AC025279.2 HAVANA gene 5373 10025 . + . FI_gene_label "AC025279.2^ENSG00000260413.1" ; ID "BOLA2--AC025279.2^AC025279.2^ENSG00000260413.1" ; exon_id "ENSE00003499573.1" ; exon_number 1 ; gene_id "BOLA2--AC025279.2^AC025279.2^ENSG00000260413.1" ; gene_name "AC025279.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000176714.1" ; havana_transcript "OTTHUMT00000433250.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,29312350,29312589,+" ; tag basic ; transcript_id "BOLA2--AC025279.2^ENST00000569730.1" ; transcript_name "AC025279.2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
BOLA2--AC025279.2 HAVANA RNA 5373 10025 . + . FI_gene_label "AC025279.2^ENSG00000260413.1" ; ID "BOLA2--AC025279.2^ENST00000569730.1" ; Parent "BOLA2--AC025279.2^AC025279.2^ENSG00000260413.1" ; exon_id "ENSE00003499573.1" ; exon_number 1 ; gene_id "BOLA2--AC025279.2^AC025279.2^ENSG00000260413.1" ; gene_name "AC025279.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000176714.1" ; havana_transcript "OTTHUMT00000433250.1" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,29312350,29312589,+" ; tag basic ; transcript_id "BOLA2--AC025279.2^ENST00000569730.1" ; transcript_name "AC025279.2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
C16orf87--AC007493.1 HAVANA gene 15978 16790 . + . FI_gene_label "AC007493.1^ENSG00000260573.4" ; ID "C16orf87--AC007493.1^AC007493.1^ENSG00000260573.4" ; exon_id "ENSE00002576588.1" ; exon_number 1 ; gene_id "C16orf87--AC007493.1^AC007493.1^ENSG00000260573.4" ; gene_name "AC007493.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000173394.6" ; havana_transcript "OTTHUMT00000422973.2" ; level 2 ; orig_coord_info "chr16,50407701,50407944,+" ; tag basic ; transcript_id "C16orf87--AC007493.1^ENST00000567899.1" ; transcript_name "AC007493.1-205" ; transcript_support_level 2 ; transcript_type lncRNA
C16orf87--AC007493.1 HAVANA RNA 15978 16790 . + . FI_gene_label "AC007493.1^ENSG00000260573.4" ; ID "C16orf87--AC007493.1^ENST00000567899.1" ; Parent "C16orf87--AC007493.1^AC007493.1^ENSG00000260573.4" ; exon_id "ENSE00002576588.1" ; exon_number 1 ; gene_id "C16orf87--AC007493.1^AC007493.1^ENSG00000260573.4" ; gene_name "AC007493.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000173394.6" ; havana_transcript "OTTHUMT00000422973.2" ; level 2 ; orig_coord_info "chr16,50407701,50407944,+" ; tag basic ; transcript_id "C16orf87--AC007493.1^ENST00000567899.1" ; transcript_name "AC007493.1-205" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
GOLGA6L10--GOLGA2P6 HAVANA gene 12782 20364 . + . FI_gene_label "GOLGA2P6^ENSG00000241621.1" ; ID "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; exon_id "ENSE00001603136.1" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1" ; havana_transcript "OTTHUMT00000047421.1" ; hgnc_id "HGNC:44948" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr10,30374327,30374386,-" ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; transcript_name "GOLGA2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GOLGA6L10--GOLGA2P6 HAVANA RNA 12782 20364 . + . FI_gene_label "GOLGA2P6^ENSG00000241621.1" ; ID "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; Parent "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; exon_id "ENSE00001603136.1" ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1" ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1" ; havana_transcript "OTTHUMT00000047421.1" ; hgnc_id "HGNC:44948" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr10,30374327,30374386,-" ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4" ; transcript_name "GOLGA2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
GUCY1B2--NKAIN2 HAVANA RNA 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^ENST00000389600.6" ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
MET--5_8S_rRNA ENSEMBL gene 30301 30451 . + . FI_gene_label "5_8S_rRNA^ENSG00000283274.1" ; ID "MET--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; exon_id "ENSE00003799578.1" ; exon_number 1 ; gene_id "MET--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+" ; tag basic ; transcript_id "MET--5_8S_rRNA^ENST00000636054.1" ; transcript_name "5_8S_rRNA.7-201" ; transcript_support_level NA ; transcript_type rRNA
MET--5_8S_rRNA ENSEMBL RNA 30301 30451 . + . FI_gene_label "5_8S_rRNA^ENSG00000283274.1" ; ID "MET--5_8S_rRNA^ENST00000636054.1" ; Parent "MET--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; exon_id "ENSE00003799578.1" ; exon_number 1 ; gene_id "MET--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1" ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+" ; tag basic ; transcript_id "MET--5_8S_rRNA^ENST00000636054.1" ; transcript_name "5_8S_rRNA.7-201" ; transcript_support_level NA ; transcript_type rRNA
L1 and L2 created:
NKD1--AC022167.4 HAVANA gene 29445 30226 . + . FI_gene_label "AC022167.4^ENSG00000261481.1" ; ID "NKD1--AC022167.4^AC022167.4^ENSG00000261481.1" ; exon_id "ENSE00002605631.1" ; exon_number 1 ; gene_id "NKD1--AC022167.4^AC022167.4^ENSG00000261481.1" ; gene_name "AC022167.4" ; gene_type lncRNA ; havana_gene "OTTHUMG00000176902.1" ; havana_transcript "OTTHUMT00000434267.1" ; level 2 ; orig_coord_info "chr16,8869251,8869328,+" ; tag basic ; transcript_id "NKD1--AC022167.4^ENST00000570290.1" ; transcript_name "AC022167.4-201" ; transcript_support_level 3 ; transcript_type lncRNA
NKD1--AC022167.4 HAVANA RNA 29445 30226 . + . FI_gene_label "AC022167.4^ENSG00000261481.1" ; ID "NKD1--AC022167.4^ENST00000570290.1" ; Parent "NKD1--AC022167.4^AC022167.4^ENSG00000261481.1" ; exon_id "ENSE00002605631.1" ; exon_number 1 ; gene_id "NKD1--AC022167.4^AC022167.4^ENSG00000261481.1" ; gene_name "AC022167.4" ; gene_type lncRNA ; havana_gene "OTTHUMG00000176902.1" ; havana_transcript "OTTHUMT00000434267.1" ; level 2 ; orig_coord_info "chr16,8869251,8869328,+" ; tag basic ; transcript_id "NKD1--AC022167.4^ENST00000570290.1" ; transcript_name "AC022167.4-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
NKD1--AC138904.1 HAVANA gene 29445 32925 . + . FI_gene_label "AC138904.1^ENSG00000246465.1" ; ID "NKD1--AC138904.1^AC138904.1^ENSG00000246465.1" ; exon_id "ENSE00001627948.2" ; exon_number 1 ; gene_id "NKD1--AC138904.1^AC138904.1^ENSG00000246465.1" ; gene_name "AC138904.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166065.1" ; havana_transcript "OTTHUMT00000387676.1" ; level 1 ; orig_coord_info "chr16,28291767,28292064,-" ; tag basic exp_conf ; transcript_id "NKD1--AC138904.1^ENST00000501520.1" ; transcript_name "AC138904.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
NKD1--AC138904.1 HAVANA RNA 29445 32925 . + . FI_gene_label "AC138904.1^ENSG00000246465.1" ; ID "NKD1--AC138904.1^ENST00000501520.1" ; Parent "NKD1--AC138904.1^AC138904.1^ENSG00000246465.1" ; exon_id "ENSE00001627948.2" ; exon_number 1 ; gene_id "NKD1--AC138904.1^AC138904.1^ENSG00000246465.1" ; gene_name "AC138904.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000166065.1" ; havana_transcript "OTTHUMT00000387676.1" ; level 1 ; orig_coord_info "chr16,28291767,28292064,-" ; tag basic exp_conf ; transcript_id "NKD1--AC138904.1^ENST00000501520.1" ; transcript_name "AC138904.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
PANX2--AC087698.1 ENSEMBL gene 9635 9765 . + . FI_gene_label "AC087698.1^ENSG00000206853.1" ; ID "PANX2--AC087698.1^AC087698.1^ENSG00000206853.1" ; exon_id "ENSE00001499136.1" ; exon_number 1 ; gene_id "PANX2--AC087698.1^AC087698.1^ENSG00000206853.1" ; gene_name "AC087698.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chr8,59137372,59137502,-" ; tag basic ; transcript_id "PANX2--AC087698.1^ENST00000384126.1" ; transcript_name "AC087698.1-201" ; transcript_support_level NA ; transcript_type snoRNA
PANX2--AC087698.1 ENSEMBL RNA 9635 9765 . + . FI_gene_label "AC087698.1^ENSG00000206853.1" ; ID "PANX2--AC087698.1^ENST00000384126.1" ; Parent "PANX2--AC087698.1^AC087698.1^ENSG00000206853.1" ; exon_id "ENSE00001499136.1" ; exon_number 1 ; gene_id "PANX2--AC087698.1^AC087698.1^ENSG00000206853.1" ; gene_name "AC087698.1" ; gene_type snoRNA ; level 3 ; orig_coord_info "chr8,59137372,59137502,-" ; tag basic ; transcript_id "PANX2--AC087698.1^ENST00000384126.1" ; transcript_name "AC087698.1-201" ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created:
PANX2--AC090152.1 HAVANA gene 10541 11910 . + . FI_gene_label "AC090152.1^ENSG00000167912.6" ; ID "PANX2--AC090152.1^AC090152.1^ENSG00000167912.6" ; exon_id "ENSE00002125581.1" ; exon_number 1 ; gene_id "PANX2--AC090152.1^AC090152.1^ENSG00000167912.6" ; gene_name "AC090152.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164333.2" ; havana_transcript "OTTHUMT00000378312.1" ; level 2 ; orig_coord_info "chr8,59119946,59120071,+" ; transcript_id "PANX2--AC090152.1^ENST00000517898.1" ; transcript_name "AC090152.1-203" ; transcript_support_level 2 ; transcript_type lncRNA
PANX2--AC090152.1 HAVANA RNA 10541 11910 . + . FI_gene_label "AC090152.1^ENSG00000167912.6" ; ID "PANX2--AC090152.1^ENST00000517898.1" ; Parent "PANX2--AC090152.1^AC090152.1^ENSG00000167912.6" ; exon_id "ENSE00002125581.1" ; exon_number 1 ; gene_id "PANX2--AC090152.1^AC090152.1^ENSG00000167912.6" ; gene_name "AC090152.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164333.2" ; havana_transcript "OTTHUMT00000378312.1" ; level 2 ; orig_coord_info "chr8,59119946,59120071,+" ; transcript_id "PANX2--AC090152.1^ENST00000517898.1" ; transcript_name "AC090152.1-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
SLC7A5P1--N4BP1 HAVANA gene 1001 1538 . + . FI_gene_label "SLC7A5P1^ENSG00000260727.2" ; ID "SLC7A5P1--N4BP1^SLC7A5P1^ENSG00000260727.2" ; exon_id "ENSE00002599076.2" ; exon_number 1 ; gene_id "SLC7A5P1--N4BP1^SLC7A5P1^ENSG00000260727.2" ; gene_name SLC7A5P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000176771.1" ; havana_transcript "OTTHUMT00000433672.1" ; hgnc_id "HGNC:29458" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,29613103,29613640,-" ; tag pseudo_consens basic ; transcript_id "SLC7A5P1--N4BP1^ENST00000568957.2" ; transcript_name "SLC7A5P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
SLC7A5P1--N4BP1 HAVANA RNA 1001 1538 . + . FI_gene_label "SLC7A5P1^ENSG00000260727.2" ; ID "SLC7A5P1--N4BP1^ENST00000568957.2" ; Parent "SLC7A5P1--N4BP1^SLC7A5P1^ENSG00000260727.2" ; exon_id "ENSE00002599076.2" ; exon_number 1 ; gene_id "SLC7A5P1--N4BP1^SLC7A5P1^ENSG00000260727.2" ; gene_name SLC7A5P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000176771.1" ; havana_transcript "OTTHUMT00000433672.1" ; hgnc_id "HGNC:29458" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,29613103,29613640,-" ; tag pseudo_consens basic ; transcript_id "SLC7A5P1--N4BP1^ENST00000568957.2" ; transcript_name "SLC7A5P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
TBC1D22A--AC022535.2 HAVANA gene 26204 30061 . + . FI_gene_label "AC022535.2^ENSG00000286687.1" ; ID "TBC1D22A--AC022535.2^AC022535.2^ENSG00000286687.1" ; exon_id "ENSE00003877621.1" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.2^AC022535.2^ENSG00000286687.1" ; gene_name "AC022535.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000193971.1" ; havana_transcript "OTTHUMT00000507922.1" ; level 2 ; orig_coord_info "chr10,4497449,4497475,+" ; tag basic TAGENE ; transcript_id "TBC1D22A--AC022535.2^ENST00000660243.1" ; transcript_name "AC022535.2-201" ; transcript_type lncRNA
TBC1D22A--AC022535.2 HAVANA RNA 26204 30061 . + . FI_gene_label "AC022535.2^ENSG00000286687.1" ; ID "TBC1D22A--AC022535.2^ENST00000660243.1" ; Parent "TBC1D22A--AC022535.2^AC022535.2^ENSG00000286687.1" ; exon_id "ENSE00003877621.1" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.2^AC022535.2^ENSG00000286687.1" ; gene_name "AC022535.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000193971.1" ; havana_transcript "OTTHUMT00000507922.1" ; level 2 ; orig_coord_info "chr10,4497449,4497475,+" ; tag basic TAGENE ; transcript_id "TBC1D22A--AC022535.2^ENST00000660243.1" ; transcript_name "AC022535.2-201" ; transcript_type lncRNA
L1 and L2 created:
TBC1D22A--AC022535.3 HAVANA gene 26204 28959 . + . FI_gene_label "AC022535.3^ENSG00000287246.1" ; ID "TBC1D22A--AC022535.3^AC022535.3^ENSG00000287246.1" ; exon_id "ENSE00003856034.1" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.3^AC022535.3^ENSG00000287246.1" ; gene_name "AC022535.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195085.1" ; havana_transcript "OTTHUMT00000524368.1" ; level 2 ; orig_coord_info "chr10,4437102,4437265,+" ; tag basic TAGENE ; transcript_id "TBC1D22A--AC022535.3^ENST00000668998.1" ; transcript_name "AC022535.3-201" ; transcript_type lncRNA
TBC1D22A--AC022535.3 HAVANA RNA 26204 28959 . + . FI_gene_label "AC022535.3^ENSG00000287246.1" ; ID "TBC1D22A--AC022535.3^ENST00000668998.1" ; Parent "TBC1D22A--AC022535.3^AC022535.3^ENSG00000287246.1" ; exon_id "ENSE00003856034.1" ; exon_number 1 ; gene_id "TBC1D22A--AC022535.3^AC022535.3^ENSG00000287246.1" ; gene_name "AC022535.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195085.1" ; havana_transcript "OTTHUMT00000524368.1" ; level 2 ; orig_coord_info "chr10,4437102,4437265,+" ; tag basic TAGENE ; transcript_id "TBC1D22A--AC022535.3^ENST00000668998.1" ; transcript_name "AC022535.3-201" ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
311 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
543 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 30 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
Lets remove isoform AP1B1--GPAT4^ENST00000432560.6
1 identical isoforms removed
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GFF3 file parsed