Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/e988b921de5457cb140da40161ddcb/fi_workdir/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/70103ff3815668da2a6db978bfceab/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/70103ff3815668da2a6db978bfceab/.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: 7224
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 7224
=> 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:7224
=> 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:
AC079610.2--IKZF2 HAVANA gene 7237 23374 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "AC079610.2--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC079610.2--IKZF2 HAVANA mRNA 7237 23374 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "AC079610.2--IKZF2^ENST00000342002.6" ; Parent "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "AC079610.2--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DDHD2--ADAM32 HAVANA gene 29242 62192 . + . FI_gene_label "ADAM32^ENSG00000197140.15" ; ID "DDHD2--ADAM32^ADAM32^ENSG00000197140.15" ; ccdsid "CCDS47846.1" ; exon_id "ENSE00002129166.2" ; exon_number 1 ; gene_id "DDHD2--ADAM32^ADAM32^ENSG00000197140.15" ; gene_name ADAM32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164071.6" ; havana_transcript "OTTHUMT00000377089.2" ; hgnc_id "HGNC:15479" ; level 2 ; orig_coord_info "chr8,39107776,39107833,+" ; protein_id "ENSP00000369238.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDHD2--ADAM32^ENST00000379907.9" ; transcript_name "ADAM32-201" ; transcript_support_level 1 ; transcript_type protein_coding
DDHD2--ADAM32 HAVANA mRNA 29242 62192 . + . FI_gene_label "ADAM32^ENSG00000197140.15" ; ID "DDHD2--ADAM32^ENST00000379907.9" ; Parent "DDHD2--ADAM32^ADAM32^ENSG00000197140.15" ; ccdsid "CCDS47846.1" ; exon_id "ENSE00002129166.2" ; exon_number 1 ; gene_id "DDHD2--ADAM32^ADAM32^ENSG00000197140.15" ; gene_name ADAM32 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164071.6" ; havana_transcript "OTTHUMT00000377089.2" ; hgnc_id "HGNC:15479" ; level 2 ; orig_coord_info "chr8,39107776,39107833,+" ; protein_id "ENSP00000369238.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDHD2--ADAM32^ENST00000379907.9" ; transcript_name "ADAM32-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DDHD2--ADAM32 HAVANA gene 2193 21952 . + . FI_gene_label "DDHD2^ENSG00000085788.14" ; ID "DDHD2--ADAM32^DDHD2^ENSG00000085788.14" ; ccdsid "CCDS34883.1" ; exon_id "ENSE00003695665.1" ; exon_number 2 ; gene_id "DDHD2--ADAM32^DDHD2^ENSG00000085788.14" ; gene_name DDHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164095.7" ; havana_transcript "OTTHUMT00000377251.3" ; hgnc_id "HGNC:29106" ; level 2 ; orig_coord_info "chr8,38232995,38233214,+" ; protein_id "ENSP00000380352.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDHD2--ADAM32^ENST00000397166.7" ; transcript_name "DDHD2-201" ; transcript_support_level 2 ; transcript_type protein_coding
DDHD2--ADAM32 HAVANA mRNA 2193 21952 . + . FI_gene_label "DDHD2^ENSG00000085788.14" ; ID "DDHD2--ADAM32^ENST00000397166.7" ; Parent "DDHD2--ADAM32^DDHD2^ENSG00000085788.14" ; ccdsid "CCDS34883.1" ; exon_id "ENSE00003695665.1" ; exon_number 2 ; gene_id "DDHD2--ADAM32^DDHD2^ENSG00000085788.14" ; gene_name DDHD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164095.7" ; havana_transcript "OTTHUMT00000377251.3" ; hgnc_id "HGNC:29106" ; level 2 ; orig_coord_info "chr8,38232995,38233214,+" ; protein_id "ENSP00000380352.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DDHD2--ADAM32^ENST00000397166.7" ; transcript_name "DDHD2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ELAPOR1--VAV3 HAVANA gene 1437 25772 . + . FI_gene_label "ELAPOR1^ENSG00000116299.17" ; ID "ELAPOR1--VAV3^ELAPOR1^ENSG00000116299.17" ; ccdsid "CCDS794.1" ; exon_id "ENSE00002163328.2" ; exon_number 1 ; gene_id "ELAPOR1--VAV3^ELAPOR1^ENSG00000116299.17" ; gene_name ELAPOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011725.6" ; havana_transcript "OTTHUMT00000032389.3" ; hgnc_id "HGNC:29618" ; level 2 ; orig_coord_info "chr1,109114184,109114336,+" ; protein_id "ENSP00000358955.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ELAPOR1--VAV3^ENST00000369939.8" ; transcript_name "ELAPOR1-203" ; transcript_support_level 5 ; transcript_type protein_coding
ELAPOR1--VAV3 HAVANA mRNA 1437 25772 . + . FI_gene_label "ELAPOR1^ENSG00000116299.17" ; ID "ELAPOR1--VAV3^ENST00000369939.8" ; Parent "ELAPOR1--VAV3^ELAPOR1^ENSG00000116299.17" ; ccdsid "CCDS794.1" ; exon_id "ENSE00002163328.2" ; exon_number 1 ; gene_id "ELAPOR1--VAV3^ELAPOR1^ENSG00000116299.17" ; gene_name ELAPOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011725.6" ; havana_transcript "OTTHUMT00000032389.3" ; hgnc_id "HGNC:29618" ; level 2 ; orig_coord_info "chr1,109114184,109114336,+" ; protein_id "ENSP00000358955.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ELAPOR1--VAV3^ENST00000369939.8" ; transcript_name "ELAPOR1-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ELAPOR1--VAV3 HAVANA gene 28773 70654 . + . FI_gene_label "VAV3^ENSG00000134215.16" ; ID "ELAPOR1--VAV3^VAV3^ENSG00000134215.16" ; ccdsid "CCDS785.1" ; exon_id "ENSE00001894713.3" ; exon_number 1 ; gene_id "ELAPOR1--VAV3^VAV3^ENSG00000134215.16" ; gene_name VAV3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010995.5" ; havana_transcript "OTTHUMT00000030242.3" ; hgnc_id "HGNC:12659" ; level 2 ; orig_coord_info "chr1,107964666,107964869,-" ; protein_id "ENSP00000359073.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ELAPOR1--VAV3^ENST00000370056.9" ; transcript_name "VAV3-202" ; transcript_support_level 1 ; transcript_type protein_coding
ELAPOR1--VAV3 HAVANA mRNA 28773 70654 . + . FI_gene_label "VAV3^ENSG00000134215.16" ; ID "ELAPOR1--VAV3^ENST00000370056.9" ; Parent "ELAPOR1--VAV3^VAV3^ENSG00000134215.16" ; ccdsid "CCDS785.1" ; exon_id "ENSE00001894713.3" ; exon_number 1 ; gene_id "ELAPOR1--VAV3^VAV3^ENSG00000134215.16" ; gene_name VAV3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010995.5" ; havana_transcript "OTTHUMT00000030242.3" ; hgnc_id "HGNC:12659" ; level 2 ; orig_coord_info "chr1,107964666,107964869,-" ; protein_id "ENSP00000359073.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ELAPOR1--VAV3^ENST00000370056.9" ; transcript_name "VAV3-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERC1--ADAM2 HAVANA gene 44870 66552 . + . FI_gene_label "ADAM2^ENSG00000104755.15" ; ID "ERC1--ADAM2^ADAM2^ENSG00000104755.15" ; ccdsid "CCDS34884.1" ; exon_id "ENSE00002122139.1" ; exon_number 1 ; gene_id "ERC1--ADAM2^ADAM2^ENSG00000104755.15" ; gene_name ADAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164041.4" ; havana_transcript "OTTHUMT00000376926.2" ; hgnc_id "HGNC:198" ; level 2 ; orig_coord_info "chr8,39838131,39838185,-" ; protein_id "ENSP00000265708.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERC1--ADAM2^ENST00000265708.9" ; transcript_name "ADAM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERC1--ADAM2 HAVANA mRNA 44870 66552 . + . FI_gene_label "ADAM2^ENSG00000104755.15" ; ID "ERC1--ADAM2^ENST00000265708.9" ; Parent "ERC1--ADAM2^ADAM2^ENSG00000104755.15" ; ccdsid "CCDS34884.1" ; exon_id "ENSE00002122139.1" ; exon_number 1 ; gene_id "ERC1--ADAM2^ADAM2^ENSG00000104755.15" ; gene_name ADAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164041.4" ; havana_transcript "OTTHUMT00000376926.2" ; hgnc_id "HGNC:198" ; level 2 ; orig_coord_info "chr8,39838131,39838185,-" ; protein_id "ENSP00000265708.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERC1--ADAM2^ENST00000265708.9" ; transcript_name "ADAM2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERC1--ADAM2 HAVANA gene 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--ADAM2^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--ADAM2^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--ADAM2^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ERC1--ADAM2 HAVANA mRNA 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--ADAM2^ENST00000347735.10" ; Parent "ERC1--ADAM2^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--ADAM2^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--ADAM2^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ERCC1--EXOC3L2 HAVANA gene 6294 13820 . + . FI_gene_label "ERCC1^ENSG00000012061.16" ; ID "ERCC1--EXOC3L2^ERCC1^ENSG00000012061.16" ; ccdsid "CCDS12663.1" ; exon_id "ENSE00001373182.4" ; exon_number 1 ; gene_id "ERCC1--EXOC3L2^ERCC1^ENSG00000012061.16" ; gene_name ERCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182121.2" ; havana_transcript "OTTHUMT00000459549.1" ; hgnc_id "HGNC:3433" ; level 2 ; orig_coord_info "chr19,45423270,45423374,-" ; protein_id "ENSP00000013807.4" ; tag retained_intron_first basic CCDS ; transcript_id "ERCC1--EXOC3L2^ENST00000013807.9" ; transcript_name "ERCC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERCC1--EXOC3L2 HAVANA mRNA 6294 13820 . + . FI_gene_label "ERCC1^ENSG00000012061.16" ; ID "ERCC1--EXOC3L2^ENST00000013807.9" ; Parent "ERCC1--EXOC3L2^ERCC1^ENSG00000012061.16" ; ccdsid "CCDS12663.1" ; exon_id "ENSE00001373182.4" ; exon_number 1 ; gene_id "ERCC1--EXOC3L2^ERCC1^ENSG00000012061.16" ; gene_name ERCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182121.2" ; havana_transcript "OTTHUMT00000459549.1" ; hgnc_id "HGNC:3433" ; level 2 ; orig_coord_info "chr19,45423270,45423374,-" ; protein_id "ENSP00000013807.4" ; tag retained_intron_first basic CCDS ; transcript_id "ERCC1--EXOC3L2^ENST00000013807.9" ; transcript_name "ERCC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERCC1--EXOC3L2 HAVANA gene 20213 32207 . + . FI_gene_label "EXOC3L2^ENSG00000283632.4" ; ID "ERCC1--EXOC3L2^EXOC3L2^ENSG00000283632.4" ; exon_id "ENSE00002774868.2" ; exon_number 2 ; gene_id "ERCC1--EXOC3L2^EXOC3L2^ENSG00000283632.4" ; gene_name EXOC3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155018.2" ; havana_transcript "OTTHUMT00000338073.2" ; hgnc_id "HGNC:30162" ; level 2 ; orig_coord_info "chr19,45238523,45239045,-" ; protein_id "ENSP00000400713.2" ; tag basic MANE_Select appris_principal_1 ; transcript_id "ERCC1--EXOC3L2^ENST00000413988.3" ; transcript_name "EXOC3L2-201" ; transcript_support_level 5 ; transcript_type protein_coding
ERCC1--EXOC3L2 HAVANA mRNA 20213 32207 . + . FI_gene_label "EXOC3L2^ENSG00000283632.4" ; ID "ERCC1--EXOC3L2^ENST00000413988.3" ; Parent "ERCC1--EXOC3L2^EXOC3L2^ENSG00000283632.4" ; exon_id "ENSE00002774868.2" ; exon_number 2 ; gene_id "ERCC1--EXOC3L2^EXOC3L2^ENSG00000283632.4" ; gene_name EXOC3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155018.2" ; havana_transcript "OTTHUMT00000338073.2" ; hgnc_id "HGNC:30162" ; level 2 ; orig_coord_info "chr19,45238523,45239045,-" ; protein_id "ENSP00000400713.2" ; tag basic MANE_Select appris_principal_1 ; transcript_id "ERCC1--EXOC3L2^ENST00000413988.3" ; transcript_name "EXOC3L2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUCD1--UPB1 HAVANA gene 13962 28895 . + . FI_gene_label "UPB1^ENSG00000100024.15" ; ID "GUCD1--UPB1^UPB1^ENSG00000100024.15" ; ccdsid "CCDS13827.1" ; exon_id "ENSE00001921738.2" ; exon_number 1 ; gene_id "GUCD1--UPB1^UPB1^ENSG00000100024.15" ; gene_name UPB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150749.3" ; havana_transcript "OTTHUMT00000319869.2" ; hgnc_id "HGNC:16297" ; level 2 ; orig_coord_info "chr22,24495404,24495507,+" ; protein_id "ENSP00000324343.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GUCD1--UPB1^ENST00000326010.10" ; transcript_name "UPB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUCD1--UPB1 HAVANA mRNA 13962 28895 . + . FI_gene_label "UPB1^ENSG00000100024.15" ; ID "GUCD1--UPB1^ENST00000326010.10" ; Parent "GUCD1--UPB1^UPB1^ENSG00000100024.15" ; ccdsid "CCDS13827.1" ; exon_id "ENSE00001921738.2" ; exon_number 1 ; gene_id "GUCD1--UPB1^UPB1^ENSG00000100024.15" ; gene_name UPB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150749.3" ; havana_transcript "OTTHUMT00000319869.2" ; hgnc_id "HGNC:16297" ; level 2 ; orig_coord_info "chr22,24495404,24495507,+" ; protein_id "ENSP00000324343.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GUCD1--UPB1^ENST00000326010.10" ; transcript_name "UPB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUCD1--UPB1 HAVANA gene 1765 9717 . + . FI_gene_label "GUCD1^ENSG00000138867.17" ; ID "GUCD1--UPB1^GUCD1^ENSG00000138867.17" ; ccdsid "CCDS63426.1" ; exon_id "ENSE00001831631.1" ; exon_number 1 ; gene_id "GUCD1--UPB1^GUCD1^ENSG00000138867.17" ; gene_name GUCD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150728.3" ; havana_transcript "OTTHUMT00000319822.2" ; hgnc_id "HGNC:14237" ; level 2 ; orig_coord_info "chr22,24554949,24554991,-" ; protein_id "ENSP00000381297.4" ; tag dotter_confirmed CCDS ; transcript_id "GUCD1--UPB1^ENST00000398245.8" ; transcript_name "GUCD1-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
GUCD1--UPB1 HAVANA mRNA 1765 9717 . + . FI_gene_label "GUCD1^ENSG00000138867.17" ; ID "GUCD1--UPB1^ENST00000398245.8" ; Parent "GUCD1--UPB1^GUCD1^ENSG00000138867.17" ; ccdsid "CCDS63426.1" ; exon_id "ENSE00001831631.1" ; exon_number 1 ; gene_id "GUCD1--UPB1^GUCD1^ENSG00000138867.17" ; gene_name GUCD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150728.3" ; havana_transcript "OTTHUMT00000319822.2" ; hgnc_id "HGNC:14237" ; level 2 ; orig_coord_info "chr22,24554949,24554991,-" ; protein_id "ENSP00000381297.4" ; tag dotter_confirmed CCDS ; transcript_id "GUCD1--UPB1^ENST00000398245.8" ; transcript_name "GUCD1-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
LINC01953--IKZF2 HAVANA gene 7807 23944 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "LINC01953--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
LINC01953--IKZF2 HAVANA mRNA 7807 23944 . + . FI_gene_label "IKZF2^ENSG00000030419.16" ; ID "LINC01953--IKZF2^ENST00000342002.6" ; Parent "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; exon_id "ENSE00003626229.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^IKZF2^ENSG00000030419.16" ; gene_name IKZF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133005.7" ; havana_transcript "OTTHUMT00000256594.1" ; hgnc_id "HGNC:13177" ; level 2 ; orig_coord_info "chr2,213150181,213150183,-" ; protein_id "ENSP00000342876.2" ; tag basic appris_alternative_1 ; transcript_id "LINC01953--IKZF2^ENST00000342002.6" ; transcript_name "IKZF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NAGA--DGCR11 HAVANA gene 1031 10330 . + . FI_gene_label "NAGA^ENSG00000198951.12" ; ID "NAGA--DGCR11^NAGA^ENSG00000198951.12" ; ccdsid "CCDS14030.1" ; exon_id "ENSE00001370916.4" ; exon_number 1 ; gene_id "NAGA--DGCR11^NAGA^ENSG00000198951.12" ; gene_name NAGA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151276.4" ; havana_transcript "OTTHUMT00000322056.2" ; hgnc_id "HGNC:7631" ; level 2 ; orig_coord_info "chr22,42070282,42070297,-" ; protein_id "ENSP00000379680.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAGA--DGCR11^ENST00000396398.8" ; transcript_name "NAGA-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAGA--DGCR11 HAVANA mRNA 1031 10330 . + . FI_gene_label "NAGA^ENSG00000198951.12" ; ID "NAGA--DGCR11^ENST00000396398.8" ; Parent "NAGA--DGCR11^NAGA^ENSG00000198951.12" ; ccdsid "CCDS14030.1" ; exon_id "ENSE00001370916.4" ; exon_number 1 ; gene_id "NAGA--DGCR11^NAGA^ENSG00000198951.12" ; gene_name NAGA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151276.4" ; havana_transcript "OTTHUMT00000322056.2" ; hgnc_id "HGNC:7631" ; level 2 ; orig_coord_info "chr22,42070282,42070297,-" ; protein_id "ENSP00000379680.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAGA--DGCR11^ENST00000396398.8" ; transcript_name "NAGA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NAGA--DGCR2 HAVANA gene 13373 28614 . + . FI_gene_label "DGCR2^ENSG00000070413.20" ; ID "NAGA--DGCR2^DGCR2^ENSG00000070413.20" ; ccdsid "CCDS33598.1" ; exon_id "ENSE00003847150.1" ; exon_number 1 ; gene_id "NAGA--DGCR2^DGCR2^ENSG00000070413.20" ; gene_name DGCR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150141.3" ; havana_transcript "OTTHUMT00000316504.2" ; hgnc_id "HGNC:2845" ; level 2 ; orig_coord_info "chr22,19122128,19122206,-" ; protein_id "ENSP00000263196.7" ; tag non_canonical_conserved basic MANE_Select appris_principal_2 CCDS ; transcript_id "NAGA--DGCR2^ENST00000263196.12" ; transcript_name "DGCR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAGA--DGCR2 HAVANA mRNA 13373 28614 . + . FI_gene_label "DGCR2^ENSG00000070413.20" ; ID "NAGA--DGCR2^ENST00000263196.12" ; Parent "NAGA--DGCR2^DGCR2^ENSG00000070413.20" ; ccdsid "CCDS33598.1" ; exon_id "ENSE00003847150.1" ; exon_number 1 ; gene_id "NAGA--DGCR2^DGCR2^ENSG00000070413.20" ; gene_name DGCR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150141.3" ; havana_transcript "OTTHUMT00000316504.2" ; hgnc_id "HGNC:2845" ; level 2 ; orig_coord_info "chr22,19122128,19122206,-" ; protein_id "ENSP00000263196.7" ; tag non_canonical_conserved basic MANE_Select appris_principal_2 CCDS ; transcript_id "NAGA--DGCR2^ENST00000263196.12" ; transcript_name "DGCR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NAGA--DGCR2 HAVANA gene 1031 10330 . + . FI_gene_label "NAGA^ENSG00000198951.12" ; ID "NAGA--DGCR2^NAGA^ENSG00000198951.12" ; ccdsid "CCDS14030.1" ; exon_id "ENSE00001370916.4" ; exon_number 1 ; gene_id "NAGA--DGCR2^NAGA^ENSG00000198951.12" ; gene_name NAGA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151276.4" ; havana_transcript "OTTHUMT00000322056.2" ; hgnc_id "HGNC:7631" ; level 2 ; orig_coord_info "chr22,42070282,42070297,-" ; protein_id "ENSP00000379680.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAGA--DGCR2^ENST00000396398.8" ; transcript_name "NAGA-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAGA--DGCR2 HAVANA mRNA 1031 10330 . + . FI_gene_label "NAGA^ENSG00000198951.12" ; ID "NAGA--DGCR2^ENST00000396398.8" ; Parent "NAGA--DGCR2^NAGA^ENSG00000198951.12" ; ccdsid "CCDS14030.1" ; exon_id "ENSE00001370916.4" ; exon_number 1 ; gene_id "NAGA--DGCR2^NAGA^ENSG00000198951.12" ; gene_name NAGA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151276.4" ; havana_transcript "OTTHUMT00000322056.2" ; hgnc_id "HGNC:7631" ; level 2 ; orig_coord_info "chr22,42070282,42070297,-" ; protein_id "ENSP00000379680.3" ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "NAGA--DGCR2^ENST00000396398.8" ; transcript_name "NAGA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDUFA9--ACSM4 HAVANA gene 1020 22522 . + . FI_gene_label "NDUFA9^ENSG00000139180.11" ; ID "NDUFA9--ACSM4^NDUFA9^ENSG00000139180.11" ; ccdsid "CCDS8532.1" ; exon_id "ENSE00002204942.2" ; exon_number 1 ; gene_id "NDUFA9--ACSM4^NDUFA9^ENSG00000139180.11" ; gene_name NDUFA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168224.7" ; havana_transcript "OTTHUMT00000398900.4" ; hgnc_id "HGNC:7693" ; level 2 ; orig_coord_info "chr12,4649127,4649175,+" ; protein_id "ENSP00000266544.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFA9--ACSM4^ENST00000266544.10" ; transcript_name "NDUFA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDUFA9--ACSM4 HAVANA mRNA 1020 22522 . + . FI_gene_label "NDUFA9^ENSG00000139180.11" ; ID "NDUFA9--ACSM4^ENST00000266544.10" ; Parent "NDUFA9--ACSM4^NDUFA9^ENSG00000139180.11" ; ccdsid "CCDS8532.1" ; exon_id "ENSE00002204942.2" ; exon_number 1 ; gene_id "NDUFA9--ACSM4^NDUFA9^ENSG00000139180.11" ; gene_name NDUFA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168224.7" ; havana_transcript "OTTHUMT00000398900.4" ; hgnc_id "HGNC:7693" ; level 2 ; orig_coord_info "chr12,4649127,4649175,+" ; protein_id "ENSP00000266544.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFA9--ACSM4^ENST00000266544.10" ; transcript_name "NDUFA9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDUFA9--ACSM4 HAVANA gene 25523 37390 . + . FI_gene_label "ACSM4^ENSG00000215009.5" ; ID "NDUFA9--ACSM4^ACSM4^ENSG00000215009.5" ; ccdsid "CCDS44825.1" ; exon_id "ENSE00001538219.4" ; exon_number 1 ; gene_id "NDUFA9--ACSM4^ACSM4^ENSG00000215009.5" ; gene_name ACSM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154975.3" ; havana_transcript "OTTHUMT00000337866.2" ; hgnc_id "HGNC:32016" ; level 1 ; orig_coord_info "chr12,7304332,7304532,+" ; protein_id "ENSP00000382349.4" ; tag not_organism_supported basic appris_principal_1 exp_conf CCDS ; transcript_id "NDUFA9--ACSM4^ENST00000399422.4" ; transcript_name "ACSM4-201" ; transcript_support_level 5 ; transcript_type protein_coding
NDUFA9--ACSM4 HAVANA mRNA 25523 37390 . + . FI_gene_label "ACSM4^ENSG00000215009.5" ; ID "NDUFA9--ACSM4^ENST00000399422.4" ; Parent "NDUFA9--ACSM4^ACSM4^ENSG00000215009.5" ; ccdsid "CCDS44825.1" ; exon_id "ENSE00001538219.4" ; exon_number 1 ; gene_id "NDUFA9--ACSM4^ACSM4^ENSG00000215009.5" ; gene_name ACSM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154975.3" ; havana_transcript "OTTHUMT00000337866.2" ; hgnc_id "HGNC:32016" ; level 1 ; orig_coord_info "chr12,7304332,7304532,+" ; protein_id "ENSP00000382349.4" ; tag not_organism_supported basic appris_principal_1 exp_conf CCDS ; transcript_id "NDUFA9--ACSM4^ENST00000399422.4" ; transcript_name "ACSM4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
NEBL--LINC01153 HAVANA gene 25843 63335 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "NEBL--LINC01153^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "NEBL--LINC01153^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "NEBL--LINC01153^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
NEBL--LINC01153 HAVANA mRNA 25843 63335 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "NEBL--LINC01153^ENST00000377122.9" ; Parent "NEBL--LINC01153^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "NEBL--LINC01153^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "NEBL--LINC01153^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NEBL--RN7SKP167 HAVANA gene 25843 63335 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "NEBL--RN7SKP167^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "NEBL--RN7SKP167^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "NEBL--RN7SKP167^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
NEBL--RN7SKP167 HAVANA mRNA 25843 63335 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "NEBL--RN7SKP167^ENST00000377122.9" ; Parent "NEBL--RN7SKP167^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "NEBL--RN7SKP167^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "NEBL--RN7SKP167^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^ENST00000302641.8" ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^ENST00000606293.5" ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RIMKLB--AC007450.1 ENSEMBL gene 2965 14982 . + . FI_gene_label "RIMKLB^ENSG00000166532.16" ; ID "RIMKLB--AC007450.1^RIMKLB^ENSG00000166532.16" ; ccdsid "CCDS41748.1" ; exon_id "ENSE00003587193.1" ; exon_number 3 ; gene_id "RIMKLB--AC007450.1^RIMKLB^ENSG00000166532.16" ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4" ; hgnc_id "HGNC:29228" ; level 3 ; orig_coord_info "chr12,8713867,8714041,+" ; protein_id "ENSP00000350136.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--AC007450.1^ENST00000357529.7" ; transcript_name "RIMKLB-202" ; transcript_support_level 5 ; transcript_type protein_coding
RIMKLB--AC007450.1 ENSEMBL mRNA 2965 14982 . + . FI_gene_label "RIMKLB^ENSG00000166532.16" ; ID "RIMKLB--AC007450.1^ENST00000357529.7" ; Parent "RIMKLB--AC007450.1^RIMKLB^ENSG00000166532.16" ; ccdsid "CCDS41748.1" ; exon_id "ENSE00003587193.1" ; exon_number 3 ; gene_id "RIMKLB--AC007450.1^RIMKLB^ENSG00000166532.16" ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4" ; hgnc_id "HGNC:29228" ; level 3 ; orig_coord_info "chr12,8713867,8714041,+" ; protein_id "ENSP00000350136.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--AC007450.1^ENST00000357529.7" ; transcript_name "RIMKLB-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RIMKLB--LINC01252 ENSEMBL gene 2965 14982 . + . FI_gene_label "RIMKLB^ENSG00000166532.16" ; ID "RIMKLB--LINC01252^RIMKLB^ENSG00000166532.16" ; ccdsid "CCDS41748.1" ; exon_id "ENSE00003587193.1" ; exon_number 3 ; gene_id "RIMKLB--LINC01252^RIMKLB^ENSG00000166532.16" ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4" ; hgnc_id "HGNC:29228" ; level 3 ; orig_coord_info "chr12,8713867,8714041,+" ; protein_id "ENSP00000350136.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--LINC01252^ENST00000357529.7" ; transcript_name "RIMKLB-202" ; transcript_support_level 5 ; transcript_type protein_coding
RIMKLB--LINC01252 ENSEMBL mRNA 2965 14982 . + . FI_gene_label "RIMKLB^ENSG00000166532.16" ; ID "RIMKLB--LINC01252^ENST00000357529.7" ; Parent "RIMKLB--LINC01252^RIMKLB^ENSG00000166532.16" ; ccdsid "CCDS41748.1" ; exon_id "ENSE00003587193.1" ; exon_number 3 ; gene_id "RIMKLB--LINC01252^RIMKLB^ENSG00000166532.16" ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4" ; hgnc_id "HGNC:29228" ; level 3 ; orig_coord_info "chr12,8713867,8714041,+" ; protein_id "ENSP00000350136.3" ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--LINC01252^ENST00000357529.7" ; transcript_name "RIMKLB-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SGSM1--MYCL-AS1 HAVANA gene 1043 32478 . + . FI_gene_label "SGSM1^ENSG00000167037.19" ; ID "SGSM1--MYCL-AS1^SGSM1^ENSG00000167037.19" ; ccdsid "CCDS46675.1" ; exon_id "ENSE00001563186.3" ; exon_number 1 ; gene_id "SGSM1--MYCL-AS1^SGSM1^ENSG00000167037.19" ; gene_name SGSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150837.1" ; havana_transcript "OTTHUMT00000320279.1" ; hgnc_id "HGNC:29410" ; level 2 ; orig_coord_info "chr22,24806326,24806344,+" ; protein_id "ENSP00000383211.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SGSM1--MYCL-AS1^ENST00000400358.9" ; transcript_name "SGSM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SGSM1--MYCL-AS1 HAVANA mRNA 1043 32478 . + . FI_gene_label "SGSM1^ENSG00000167037.19" ; ID "SGSM1--MYCL-AS1^ENST00000400358.9" ; Parent "SGSM1--MYCL-AS1^SGSM1^ENSG00000167037.19" ; ccdsid "CCDS46675.1" ; exon_id "ENSE00001563186.3" ; exon_number 1 ; gene_id "SGSM1--MYCL-AS1^SGSM1^ENSG00000167037.19" ; gene_name SGSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150837.1" ; havana_transcript "OTTHUMT00000320279.1" ; hgnc_id "HGNC:29410" ; level 2 ; orig_coord_info "chr22,24806326,24806344,+" ; protein_id "ENSP00000383211.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SGSM1--MYCL-AS1^ENST00000400358.9" ; transcript_name "SGSM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SGSM1--MYCL HAVANA gene 35816 38123 . + . FI_gene_label "MYCL^ENSG00000116990.11" ; ID "SGSM1--MYCL^MYCL^ENSG00000116990.11" ; ccdsid "CCDS44117.2" ; exon_id "ENSE00001192335.5" ; exon_number 1 ; gene_id "SGSM1--MYCL^MYCL^ENSG00000116990.11" ; gene_name MYCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000009243.7" ; havana_transcript "OTTHUMT00000025625.3" ; hgnc_id "HGNC:7555" ; level 2 ; orig_coord_info "chr1,39901808,39901888,-" ; protein_id "ENSP00000361902.1" ; tag basic CCDS ; transcript_id "SGSM1--MYCL^ENST00000372815.1" ; transcript_name "MYCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
SGSM1--MYCL HAVANA mRNA 35816 38123 . + . FI_gene_label "MYCL^ENSG00000116990.11" ; ID "SGSM1--MYCL^ENST00000372815.1" ; Parent "SGSM1--MYCL^MYCL^ENSG00000116990.11" ; ccdsid "CCDS44117.2" ; exon_id "ENSE00001192335.5" ; exon_number 1 ; gene_id "SGSM1--MYCL^MYCL^ENSG00000116990.11" ; gene_name MYCL ; gene_type protein_coding ; havana_gene "OTTHUMG00000009243.7" ; havana_transcript "OTTHUMT00000025625.3" ; hgnc_id "HGNC:7555" ; level 2 ; orig_coord_info "chr1,39901808,39901888,-" ; protein_id "ENSP00000361902.1" ; tag basic CCDS ; transcript_id "SGSM1--MYCL^ENST00000372815.1" ; transcript_name "MYCL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SGSM1--MYCL HAVANA gene 1043 32478 . + . FI_gene_label "SGSM1^ENSG00000167037.19" ; ID "SGSM1--MYCL^SGSM1^ENSG00000167037.19" ; ccdsid "CCDS46675.1" ; exon_id "ENSE00001563186.3" ; exon_number 1 ; gene_id "SGSM1--MYCL^SGSM1^ENSG00000167037.19" ; gene_name SGSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150837.1" ; havana_transcript "OTTHUMT00000320279.1" ; hgnc_id "HGNC:29410" ; level 2 ; orig_coord_info "chr22,24806326,24806344,+" ; protein_id "ENSP00000383211.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SGSM1--MYCL^ENST00000400358.9" ; transcript_name "SGSM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SGSM1--MYCL HAVANA mRNA 1043 32478 . + . FI_gene_label "SGSM1^ENSG00000167037.19" ; ID "SGSM1--MYCL^ENST00000400358.9" ; Parent "SGSM1--MYCL^SGSM1^ENSG00000167037.19" ; ccdsid "CCDS46675.1" ; exon_id "ENSE00001563186.3" ; exon_number 1 ; gene_id "SGSM1--MYCL^SGSM1^ENSG00000167037.19" ; gene_name SGSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150837.1" ; havana_transcript "OTTHUMT00000320279.1" ; hgnc_id "HGNC:29410" ; level 2 ; orig_coord_info "chr22,24806326,24806344,+" ; protein_id "ENSP00000383211.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SGSM1--MYCL^ENST00000400358.9" ; transcript_name "SGSM1-201" ; 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:
SVIL--KIAA1217 HAVANA gene 69109 88779 . + . FI_gene_label "KIAA1217^ENSG00000120549.18" ; ID "SVIL--KIAA1217^KIAA1217^ENSG00000120549.18" ; ccdsid "CCDS60504.1" ; exon_id "ENSE00003758710.1" ; exon_number 2 ; gene_id "SVIL--KIAA1217^KIAA1217^ENSG00000120549.18" ; gene_name KIAA1217 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017824.8" ; havana_transcript "OTTHUMT00000047220.2" ; hgnc_id "HGNC:25428" ; level 1 ; orig_coord_info "chr10,24473228,24474060,+" ; protein_id "ENSP00000302343.6" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "SVIL--KIAA1217^ENST00000307544.10" ; transcript_name "KIAA1217-201" ; transcript_support_level 1 ; transcript_type protein_coding
SVIL--KIAA1217 HAVANA mRNA 69109 88779 . + . FI_gene_label "KIAA1217^ENSG00000120549.18" ; ID "SVIL--KIAA1217^ENST00000307544.10" ; Parent "SVIL--KIAA1217^KIAA1217^ENSG00000120549.18" ; ccdsid "CCDS60504.1" ; exon_id "ENSE00003758710.1" ; exon_number 2 ; gene_id "SVIL--KIAA1217^KIAA1217^ENSG00000120549.18" ; gene_name KIAA1217 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017824.8" ; havana_transcript "OTTHUMT00000047220.2" ; hgnc_id "HGNC:25428" ; level 1 ; orig_coord_info "chr10,24473228,24474060,+" ; protein_id "ENSP00000302343.6" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "SVIL--KIAA1217^ENST00000307544.10" ; transcript_name "KIAA1217-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SVIL--KIAA1217 HAVANA gene 9663 51851 . + . FI_gene_label "SVIL^ENSG00000197321.15" ; ID "SVIL--KIAA1217^SVIL^ENSG00000197321.15" ; ccdsid "CCDS7164.1" ; exon_id "ENSE00002704111.1" ; exon_number 4 ; gene_id "SVIL--KIAA1217^SVIL^ENSG00000197321.15" ; gene_name SVIL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017882.10" ; havana_transcript "OTTHUMT00000047395.1" ; hgnc_id "HGNC:11480" ; level 2 ; orig_coord_info "chr10,29555051,29555058,-" ; protein_id "ENSP00000348128.4" ; tag basic appris_principal_3 CCDS ; transcript_id "SVIL--KIAA1217^ENST00000355867.8" ; transcript_name "SVIL-201" ; transcript_support_level 1 ; transcript_type protein_coding
SVIL--KIAA1217 HAVANA mRNA 9663 51851 . + . FI_gene_label "SVIL^ENSG00000197321.15" ; ID "SVIL--KIAA1217^ENST00000355867.8" ; Parent "SVIL--KIAA1217^SVIL^ENSG00000197321.15" ; ccdsid "CCDS7164.1" ; exon_id "ENSE00002704111.1" ; exon_number 4 ; gene_id "SVIL--KIAA1217^SVIL^ENSG00000197321.15" ; gene_name SVIL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017882.10" ; havana_transcript "OTTHUMT00000047395.1" ; hgnc_id "HGNC:11480" ; level 2 ; orig_coord_info "chr10,29555051,29555058,-" ; protein_id "ENSP00000348128.4" ; tag basic appris_principal_3 CCDS ; transcript_id "SVIL--KIAA1217^ENST00000355867.8" ; transcript_name "SVIL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM134--GAB4 HAVANA gene 1022 8563 . + . FI_gene_label "TMEM134^ENSG00000172663.9" ; ID "TMEM134--GAB4^TMEM134^ENSG00000172663.9" ; ccdsid "CCDS8167.1" ; exon_id "ENSE00002268731.2" ; exon_number 1 ; gene_id "TMEM134--GAB4^TMEM134^ENSG00000172663.9" ; gene_name TMEM134 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168034.5" ; havana_transcript "OTTHUMT00000398994.3" ; hgnc_id "HGNC:26142" ; level 2 ; orig_coord_info "chr11,67469019,67469192,-" ; protein_id "ENSP00000312615.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM134--GAB4^ENST00000308022.7" ; transcript_name "TMEM134-201" ; transcript_support_level 2 ; transcript_type protein_coding
TMEM134--GAB4 HAVANA mRNA 1022 8563 . + . FI_gene_label "TMEM134^ENSG00000172663.9" ; ID "TMEM134--GAB4^ENST00000308022.7" ; Parent "TMEM134--GAB4^TMEM134^ENSG00000172663.9" ; ccdsid "CCDS8167.1" ; exon_id "ENSE00002268731.2" ; exon_number 1 ; gene_id "TMEM134--GAB4^TMEM134^ENSG00000172663.9" ; gene_name TMEM134 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168034.5" ; havana_transcript "OTTHUMT00000398994.3" ; hgnc_id "HGNC:26142" ; level 2 ; orig_coord_info "chr11,67469019,67469192,-" ; protein_id "ENSP00000312615.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM134--GAB4^ENST00000308022.7" ; transcript_name "TMEM134-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TMEM134--GAB4 HAVANA gene 11564 23386 . + . FI_gene_label "GAB4^ENSG00000215568.9" ; ID "TMEM134--GAB4^GAB4^ENSG00000215568.9" ; ccdsid "CCDS42976.1" ; exon_id "ENSE00001543684.1" ; exon_number 1 ; gene_id "TMEM134--GAB4^GAB4^ENSG00000215568.9" ; gene_name GAB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149992.6" ; havana_transcript "OTTHUMT00000315426.1" ; hgnc_id "HGNC:18325" ; level 2 ; orig_coord_info "chr22,17007941,17008114,-" ; protein_id "ENSP00000383431.1" ; tag basic appris_principal_4 CCDS ; transcript_id "TMEM134--GAB4^ENST00000400588.5" ; transcript_name "GAB4-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM134--GAB4 HAVANA mRNA 11564 23386 . + . FI_gene_label "GAB4^ENSG00000215568.9" ; ID "TMEM134--GAB4^ENST00000400588.5" ; Parent "TMEM134--GAB4^GAB4^ENSG00000215568.9" ; ccdsid "CCDS42976.1" ; exon_id "ENSE00001543684.1" ; exon_number 1 ; gene_id "TMEM134--GAB4^GAB4^ENSG00000215568.9" ; gene_name GAB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149992.6" ; havana_transcript "OTTHUMT00000315426.1" ; hgnc_id "HGNC:18325" ; level 2 ; orig_coord_info "chr22,17007941,17008114,-" ; protein_id "ENSP00000383431.1" ; tag basic appris_principal_4 CCDS ; transcript_id "TMEM134--GAB4^ENST00000400588.5" ; transcript_name "GAB4-201" ; 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:
WAC--AL355298.1 HAVANA gene 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--AL355298.1^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--AL355298.1^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--AL355298.1^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
WAC--AL355298.1 HAVANA mRNA 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--AL355298.1^ENST00000347934.8" ; Parent "WAC--AL355298.1^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--AL355298.1^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--AL355298.1^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
WAC--PLPP4 HAVANA gene 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--PLPP4^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--PLPP4^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--PLPP4^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
WAC--PLPP4 HAVANA mRNA 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--PLPP4^ENST00000347934.8" ; Parent "WAC--PLPP4^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--PLPP4^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--PLPP4^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
WAC--PLPP4 HAVANA gene 27991 38925 . + . FI_gene_label "PLPP4^ENSG00000203805.11" ; ID "WAC--PLPP4^PLPP4^ENSG00000203805.11" ; ccdsid "CCDS41573.1" ; exon_id "ENSE00001749139.2" ; exon_number 1 ; gene_id "WAC--PLPP4^PLPP4^ENSG00000203805.11" ; gene_name PLPP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019168.4" ; havana_transcript "OTTHUMT00000050702.4" ; hgnc_id "HGNC:23531" ; level 2 ; orig_coord_info "chr10,120457306,120457361,+" ; protein_id "ENSP00000381302.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WAC--PLPP4^ENST00000398250.6" ; transcript_name "PLPP4-202" ; transcript_support_level 1 ; transcript_type protein_coding
WAC--PLPP4 HAVANA mRNA 27991 38925 . + . FI_gene_label "PLPP4^ENSG00000203805.11" ; ID "WAC--PLPP4^ENST00000398250.6" ; Parent "WAC--PLPP4^PLPP4^ENSG00000203805.11" ; ccdsid "CCDS41573.1" ; exon_id "ENSE00001749139.2" ; exon_number 1 ; gene_id "WAC--PLPP4^PLPP4^ENSG00000203805.11" ; gene_name PLPP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019168.4" ; havana_transcript "OTTHUMT00000050702.4" ; hgnc_id "HGNC:23531" ; level 2 ; orig_coord_info "chr10,120457306,120457361,+" ; protein_id "ENSP00000381302.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WAC--PLPP4^ENST00000398250.6" ; transcript_name "PLPP4-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WAC--RPL21P16 HAVANA gene 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--RPL21P16^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--RPL21P16^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--RPL21P16^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
WAC--RPL21P16 HAVANA mRNA 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--RPL21P16^ENST00000347934.8" ; Parent "WAC--RPL21P16^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--RPL21P16^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--RPL21P16^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
WAC--ZRANB1 HAVANA gene 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--ZRANB1^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--ZRANB1^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--ZRANB1^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
WAC--ZRANB1 HAVANA mRNA 1821 22421 . + . FI_gene_label "WAC^ENSG00000095787.24" ; ID "WAC--ZRANB1^ENST00000347934.8" ; Parent "WAC--ZRANB1^WAC^ENSG00000095787.24" ; ccdsid "CCDS7160.1" ; exon_id "ENSE00001823796.1" ; exon_number 1 ; gene_id "WAC--ZRANB1^WAC^ENSG00000095787.24" ; gene_name WAC ; gene_type protein_coding ; havana_gene "OTTHUMG00000017872.11" ; havana_transcript "OTTHUMT00000047360.4" ; hgnc_id "HGNC:17327" ; level 1 ; orig_coord_info "chr10,28533580,28533620,+" ; protein_id "ENSP00000311106.4" ; tag basic appris_alternative_1 exp_conf CCDS ; transcript_id "WAC--ZRANB1^ENST00000347934.8" ; transcript_name "WAC-202" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
WAC--ZRANB1 HAVANA gene 27991 40620 . + . FI_gene_label "ZRANB1^ENSG00000019995.6" ; ID "WAC--ZRANB1^ZRANB1^ENSG00000019995.6" ; ccdsid "CCDS7642.1" ; exon_id "ENSE00001448061.1" ; exon_number 1 ; gene_id "WAC--ZRANB1^ZRANB1^ENSG00000019995.6" ; gene_name ZRANB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019223.1" ; havana_transcript "OTTHUMT00000050898.1" ; hgnc_id "HGNC:18224" ; level 2 ; orig_coord_info "chr10,124942494,124943307,+" ; protein_id "ENSP00000352676.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WAC--ZRANB1^ENST00000359653.4" ; transcript_name "ZRANB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
WAC--ZRANB1 HAVANA mRNA 27991 40620 . + . FI_gene_label "ZRANB1^ENSG00000019995.6" ; ID "WAC--ZRANB1^ENST00000359653.4" ; Parent "WAC--ZRANB1^ZRANB1^ENSG00000019995.6" ; ccdsid "CCDS7642.1" ; exon_id "ENSE00001448061.1" ; exon_number 1 ; gene_id "WAC--ZRANB1^ZRANB1^ENSG00000019995.6" ; gene_name ZRANB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019223.1" ; havana_transcript "OTTHUMT00000050898.1" ; hgnc_id "HGNC:18224" ; level 2 ; orig_coord_info "chr10,124942494,124943307,+" ; protein_id "ENSP00000352676.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WAC--ZRANB1^ENST00000359653.4" ; transcript_name "ZRANB1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC079610.2--IKZF2 HAVANA gene 1001 2147 . + . FI_gene_label "AC079610.2^ENSG00000272519.1" ; ID "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; exon_id "ENSE00003699505.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; gene_name "AC079610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000185531.1" ; havana_transcript "OTTHUMT00000470662.1" ; level 2 ; orig_coord_info "chr2,213276072,213276152,-" ; tag basic ; transcript_id "AC079610.2--IKZF2^ENST00000606960.1" ; transcript_name "AC079610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC079610.2--IKZF2 HAVANA RNA 1001 2147 . + . FI_gene_label "AC079610.2^ENSG00000272519.1" ; ID "AC079610.2--IKZF2^ENST00000606960.1" ; Parent "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; exon_id "ENSE00003699505.1" ; exon_number 1 ; gene_id "AC079610.2--IKZF2^AC079610.2^ENSG00000272519.1" ; gene_name "AC079610.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000185531.1" ; havana_transcript "OTTHUMT00000470662.1" ; level 2 ; orig_coord_info "chr2,213276072,213276152,-" ; tag basic ; transcript_id "AC079610.2--IKZF2^ENST00000606960.1" ; transcript_name "AC079610.2-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
LINC01953--IKZF2 HAVANA gene 1001 2717 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "LINC01953--IKZF2^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
LINC01953--IKZF2 HAVANA RNA 1001 2717 . + . FI_gene_label "LINC01953^ENSG00000236193.3" ; ID "LINC01953--IKZF2^ENST00000426870.1" ; Parent "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; exon_id "ENSE00001668924.1" ; exon_number 1 ; gene_id "LINC01953--IKZF2^LINC01953^ENSG00000236193.3" ; gene_name LINC01953 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186255.1" ; havana_transcript "OTTHUMT00000472502.1" ; hgnc_id "HGNC:52776" ; level 2 ; orig_coord_info "chr2,213167393,213167712,-" ; tag basic ; transcript_id "LINC01953--IKZF2^ENST00000426870.1" ; transcript_name "LINC01953-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
NAGA--DGCR11 HAVANA gene 13331 15544 . + . FI_gene_label "DGCR11^ENSG00000273311.1" ; ID "NAGA--DGCR11^DGCR11^ENSG00000273311.1" ; exon_id "ENSE00003703284.1" ; exon_number 1 ; gene_id "NAGA--DGCR11^DGCR11^ENSG00000273311.1" ; gene_name DGCR11 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186100.1" ; havana_transcript "OTTHUMT00000472255.1" ; hgnc_id "HGNC:17226" ; level 2 ; orig_coord_info "chr22,19046162,19048375,-" ; tag basic ; transcript_id "NAGA--DGCR11^ENST00000609958.1" ; transcript_name "DGCR11-201" ; transcript_support_level NA ; transcript_type lncRNA
NAGA--DGCR11 HAVANA RNA 13331 15544 . + . FI_gene_label "DGCR11^ENSG00000273311.1" ; ID "NAGA--DGCR11^ENST00000609958.1" ; Parent "NAGA--DGCR11^DGCR11^ENSG00000273311.1" ; exon_id "ENSE00003703284.1" ; exon_number 1 ; gene_id "NAGA--DGCR11^DGCR11^ENSG00000273311.1" ; gene_name DGCR11 ; gene_type lncRNA ; havana_gene "OTTHUMG00000186100.1" ; havana_transcript "OTTHUMT00000472255.1" ; hgnc_id "HGNC:17226" ; level 2 ; orig_coord_info "chr22,19046162,19048375,-" ; tag basic ; transcript_id "NAGA--DGCR11^ENST00000609958.1" ; transcript_name "DGCR11-201" ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created:
NEBL--LINC01153 HAVANA gene 66336 70199 . + . FI_gene_label "LINC01153^ENSG00000227143.1" ; ID "NEBL--LINC01153^LINC01153^ENSG00000227143.1" ; exon_id "ENSE00001607298.1" ; exon_number 1 ; gene_id "NEBL--LINC01153^LINC01153^ENSG00000227143.1" ; gene_name LINC01153 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019173.1" ; havana_transcript "OTTHUMT00000050713.1" ; hgnc_id "HGNC:49495" ; level 2 ; orig_coord_info "chr10,121178700,121178972,+" ; tag basic ; transcript_id "NEBL--LINC01153^ENST00000429809.1" ; transcript_name "LINC01153-201" ; transcript_support_level 1 ; transcript_type lncRNA
NEBL--LINC01153 HAVANA RNA 66336 70199 . + . FI_gene_label "LINC01153^ENSG00000227143.1" ; ID "NEBL--LINC01153^ENST00000429809.1" ; Parent "NEBL--LINC01153^LINC01153^ENSG00000227143.1" ; exon_id "ENSE00001607298.1" ; exon_number 1 ; gene_id "NEBL--LINC01153^LINC01153^ENSG00000227143.1" ; gene_name LINC01153 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019173.1" ; havana_transcript "OTTHUMT00000050713.1" ; hgnc_id "HGNC:49495" ; level 2 ; orig_coord_info "chr10,121178700,121178972,+" ; tag basic ; transcript_id "NEBL--LINC01153^ENST00000429809.1" ; transcript_name "LINC01153-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
NEBL--RN7SKP167 ENSEMBL gene 66336 66620 . + . FI_gene_label "RN7SKP167^ENSG00000222979.1" ; ID "NEBL--RN7SKP167^RN7SKP167^ENSG00000222979.1" ; exon_id "ENSE00001590865.1" ; exon_number 1 ; gene_id "NEBL--RN7SKP167^RN7SKP167^ENSG00000222979.1" ; gene_name RN7SKP167 ; gene_type misc_RNA ; hgnc_id "HGNC:45891" ; level 3 ; orig_coord_info "chr10,121410916,121411200,+" ; tag basic ; transcript_id "NEBL--RN7SKP167^ENST00000411047.1" ; transcript_name "RN7SKP167-201" ; transcript_support_level NA ; transcript_type misc_RNA
NEBL--RN7SKP167 ENSEMBL RNA 66336 66620 . + . FI_gene_label "RN7SKP167^ENSG00000222979.1" ; ID "NEBL--RN7SKP167^ENST00000411047.1" ; Parent "NEBL--RN7SKP167^RN7SKP167^ENSG00000222979.1" ; exon_id "ENSE00001590865.1" ; exon_number 1 ; gene_id "NEBL--RN7SKP167^RN7SKP167^ENSG00000222979.1" ; gene_name RN7SKP167 ; gene_type misc_RNA ; hgnc_id "HGNC:45891" ; level 3 ; orig_coord_info "chr10,121410916,121411200,+" ; tag basic ; transcript_id "NEBL--RN7SKP167^ENST00000411047.1" ; transcript_name "RN7SKP167-201" ; transcript_support_level NA ; transcript_type misc_RNA
L1 and L2 created:
RIMKLB--AC007450.1 HAVANA gene 22487 23674 . + . FI_gene_label "AC007450.1^ENSG00000256237.1" ; ID "RIMKLB--AC007450.1^AC007450.1^ENSG00000256237.1" ; exon_id "ENSE00002210709.1" ; exon_number 1 ; gene_id "RIMKLB--AC007450.1^AC007450.1^ENSG00000256237.1" ; gene_name "AC007450.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000168536.1" ; havana_transcript "OTTHUMT00000400126.1" ; level 2 ; orig_coord_info "chr12,11555783,11555838,-" ; tag basic ; transcript_id "RIMKLB--AC007450.1^ENST00000536492.1" ; transcript_name "AC007450.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
RIMKLB--AC007450.1 HAVANA RNA 22487 23674 . + . FI_gene_label "AC007450.1^ENSG00000256237.1" ; ID "RIMKLB--AC007450.1^ENST00000536492.1" ; Parent "RIMKLB--AC007450.1^AC007450.1^ENSG00000256237.1" ; exon_id "ENSE00002210709.1" ; exon_number 1 ; gene_id "RIMKLB--AC007450.1^AC007450.1^ENSG00000256237.1" ; gene_name "AC007450.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000168536.1" ; havana_transcript "OTTHUMT00000400126.1" ; level 2 ; orig_coord_info "chr12,11555783,11555838,-" ; tag basic ; transcript_id "RIMKLB--AC007450.1^ENST00000536492.1" ; transcript_name "AC007450.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
RIMKLB--LINC01252 HAVANA gene 22487 32280 . + . FI_gene_label "LINC01252^ENSG00000247157.7" ; ID "RIMKLB--LINC01252^LINC01252^ENSG00000247157.7" ; exon_id "ENSE00001970124.1" ; exon_number 1 ; gene_id "RIMKLB--LINC01252^LINC01252^ENSG00000247157.7" ; gene_name LINC01252 ; gene_type lncRNA ; havana_gene "OTTHUMG00000168537.4" ; havana_transcript "OTTHUMT00000400127.1" ; hgnc_id "HGNC:27888" ; level 2 ; orig_coord_info "chr12,11548030,11548360,+" ; tag basic ; transcript_id "RIMKLB--LINC01252^ENST00000499291.6" ; transcript_name "LINC01252-201" ; transcript_support_level 1 ; transcript_type lncRNA
RIMKLB--LINC01252 HAVANA RNA 22487 32280 . + . FI_gene_label "LINC01252^ENSG00000247157.7" ; ID "RIMKLB--LINC01252^ENST00000499291.6" ; Parent "RIMKLB--LINC01252^LINC01252^ENSG00000247157.7" ; exon_id "ENSE00001970124.1" ; exon_number 1 ; gene_id "RIMKLB--LINC01252^LINC01252^ENSG00000247157.7" ; gene_name LINC01252 ; gene_type lncRNA ; havana_gene "OTTHUMG00000168537.4" ; havana_transcript "OTTHUMT00000400127.1" ; hgnc_id "HGNC:27888" ; level 2 ; orig_coord_info "chr12,11548030,11548360,+" ; tag basic ; transcript_id "RIMKLB--LINC01252^ENST00000499291.6" ; transcript_name "LINC01252-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
SGSM1--MYCL-AS1 HAVANA gene 35479 36832 . + . FI_gene_label "MYCL-AS1^ENSG00000236546.1" ; ID "SGSM1--MYCL-AS1^MYCL-AS1^ENSG00000236546.1" ; exon_id "ENSE00001613777.1" ; exon_number 1 ; gene_id "SGSM1--MYCL-AS1^MYCL-AS1^ENSG00000236546.1" ; gene_name "MYCL-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000009292.1" ; havana_transcript "OTTHUMT00000025754.1" ; hgnc_id "HGNC:40386" ; level 2 ; orig_coord_info "chr1,39897745,39898066,+" ; tag basic ; transcript_id "SGSM1--MYCL-AS1^ENST00000418255.1" ; transcript_name "MYCL-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA
SGSM1--MYCL-AS1 HAVANA RNA 35479 36832 . + . FI_gene_label "MYCL-AS1^ENSG00000236546.1" ; ID "SGSM1--MYCL-AS1^ENST00000418255.1" ; Parent "SGSM1--MYCL-AS1^MYCL-AS1^ENSG00000236546.1" ; exon_id "ENSE00001613777.1" ; exon_number 1 ; gene_id "SGSM1--MYCL-AS1^MYCL-AS1^ENSG00000236546.1" ; gene_name "MYCL-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000009292.1" ; havana_transcript "OTTHUMT00000025754.1" ; hgnc_id "HGNC:40386" ; level 2 ; orig_coord_info "chr1,39897745,39898066,+" ; tag basic ; transcript_id "SGSM1--MYCL-AS1^ENST00000418255.1" ; transcript_name "MYCL-AS1-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
WAC--AL355298.1 HAVANA gene 27991 28170 . + . FI_gene_label "AL355298.1^ENSG00000223455.1" ; ID "WAC--AL355298.1^AL355298.1^ENSG00000223455.1" ; exon_id "ENSE00001596489.1" ; exon_number 1 ; gene_id "WAC--AL355298.1^AL355298.1^ENSG00000223455.1" ; gene_name "AL355298.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019163.1" ; havana_transcript "OTTHUMT00000050696.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr10,120069980,120070159,-" ; tag pseudo_consens basic ; transcript_id "WAC--AL355298.1^ENST00000425391.1" ; transcript_name "AL355298.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
WAC--AL355298.1 HAVANA RNA 27991 28170 . + . FI_gene_label "AL355298.1^ENSG00000223455.1" ; ID "WAC--AL355298.1^ENST00000425391.1" ; Parent "WAC--AL355298.1^AL355298.1^ENSG00000223455.1" ; exon_id "ENSE00001596489.1" ; exon_number 1 ; gene_id "WAC--AL355298.1^AL355298.1^ENSG00000223455.1" ; gene_name "AL355298.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019163.1" ; havana_transcript "OTTHUMT00000050696.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr10,120069980,120070159,-" ; tag pseudo_consens basic ; transcript_id "WAC--AL355298.1^ENST00000425391.1" ; transcript_name "AL355298.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
WAC--RPL21P16 HAVANA gene 27991 28473 . + . FI_gene_label "RPL21P16^ENSG00000220842.6" ; ID "WAC--RPL21P16^RPL21P16^ENSG00000220842.6" ; exon_id "ENSE00002525897.1" ; exon_number 1 ; gene_id "WAC--RPL21P16^RPL21P16^ENSG00000220842.6" ; gene_name RPL21P16 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019165.2" ; havana_transcript "OTTHUMT00000050698.2" ; hgnc_id "HGNC:31396" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr10,120354701,120355183,-" ; tag basic ; transcript_id "WAC--RPL21P16^ENST00000495531.1" ; transcript_name "RPL21P16-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
WAC--RPL21P16 HAVANA RNA 27991 28473 . + . FI_gene_label "RPL21P16^ENSG00000220842.6" ; ID "WAC--RPL21P16^ENST00000495531.1" ; Parent "WAC--RPL21P16^RPL21P16^ENSG00000220842.6" ; exon_id "ENSE00002525897.1" ; exon_number 1 ; gene_id "WAC--RPL21P16^RPL21P16^ENSG00000220842.6" ; gene_name RPL21P16 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000019165.2" ; havana_transcript "OTTHUMT00000050698.2" ; hgnc_id "HGNC:31396" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr10,120354701,120355183,-" ; tag basic ; transcript_id "WAC--RPL21P16^ENST00000495531.1" ; transcript_name "RPL21P16-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
550 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 ------------------------------
1233 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 1 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 39 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed