Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/9d33cbf0182c7a718406be1ff3f4cf/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/fbb5b8944dcd5948b7bab7b5e40712/fi_workdir/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/9d33cbf0182c7a718406be1ff3f4cf/.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: 2976
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2976
=> 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:2976
=> 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 1 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:
C22orf39--MYO18B-AS1 HAVANA gene 1001 5839 . + . FI_gene_label "C22orf39^ENSG00000242259.9" ; ID "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9" ; exon_id "ENSE00003708298.2" ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9" ; gene_name C22orf39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150137.4" ; havana_transcript "OTTHUMT00000316494.3" ; hgnc_id "HGNC:27012" ; level 2 ; orig_coord_info "chr22,19447665,19447688,-" ; protein_id "ENSP00000382474.5" ; tag CAGE_supported_TSS upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "C22orf39--MYO18B-AS1^ENST00000399562.9" ; transcript_name "C22orf39-201" ; transcript_support_level 1 ; transcript_type protein_coding
C22orf39--MYO18B-AS1 HAVANA mRNA 1001 5839 . + . FI_gene_label "C22orf39^ENSG00000242259.9" ; ID "C22orf39--MYO18B-AS1^ENST00000399562.9" ; Parent "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9" ; exon_id "ENSE00003708298.2" ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^C22orf39^ENSG00000242259.9" ; gene_name C22orf39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150137.4" ; havana_transcript "OTTHUMT00000316494.3" ; hgnc_id "HGNC:27012" ; level 2 ; orig_coord_info "chr22,19447665,19447688,-" ; protein_id "ENSP00000382474.5" ; tag CAGE_supported_TSS upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "C22orf39--MYO18B-AS1^ENST00000399562.9" ; transcript_name "C22orf39-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DOK7--MICB HAVANA gene 17080 22456 . + . FI_gene_label "MICB^ENSG00000204516.10" ; ID "DOK7--MICB^MICB^ENSG00000204516.10" ; ccdsid "CCDS43449.1" ; exon_id "ENSE00001842955.2" ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10" ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4" ; havana_transcript "OTTHUMT00000076102.4" ; hgnc_id "HGNC:7091" ; level 2 ; orig_coord_info "chr6,31498194,31498263,+" ; protein_id "ENSP00000252229.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7" ; transcript_name "MICB-201" ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB HAVANA mRNA 17080 22456 . + . FI_gene_label "MICB^ENSG00000204516.10" ; ID "DOK7--MICB^ENST00000252229.7" ; Parent "DOK7--MICB^MICB^ENSG00000204516.10" ; ccdsid "CCDS43449.1" ; exon_id "ENSE00001842955.2" ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10" ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4" ; havana_transcript "OTTHUMT00000076102.4" ; hgnc_id "HGNC:7091" ; level 2 ; orig_coord_info "chr6,31498194,31498263,+" ; protein_id "ENSP00000252229.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7" ; transcript_name "MICB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DOK7--MICB HAVANA gene 1001 9638 . + . FI_gene_label "DOK7^ENSG00000175920.18" ; ID "DOK7--MICB^DOK7^ENSG00000175920.18" ; ccdsid "CCDS3370.2" ; exon_id "ENSE00003845135.1" ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18" ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8" ; havana_transcript "OTTHUMT00000313538.2" ; hgnc_id "HGNC:26594" ; level 2 ; orig_coord_info "chr4,3463376,3463429,+" ; protein_id "ENSP00000344432.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6" ; transcript_name "DOK7-201" ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB HAVANA mRNA 1001 9638 . + . FI_gene_label "DOK7^ENSG00000175920.18" ; ID "DOK7--MICB^ENST00000340083.6" ; Parent "DOK7--MICB^DOK7^ENSG00000175920.18" ; ccdsid "CCDS3370.2" ; exon_id "ENSE00003845135.1" ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18" ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8" ; havana_transcript "OTTHUMT00000313538.2" ; hgnc_id "HGNC:26594" ; level 2 ; orig_coord_info "chr4,3463376,3463429,+" ; protein_id "ENSP00000344432.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6" ; transcript_name "DOK7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC2--EPHA5 HAVANA gene 1001 32550 . + . FI_gene_label "EXOC2^ENSG00000112685.14" ; ID "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; ccdsid "CCDS34327.1" ; exon_id "ENSE00000679928.3" ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4" ; havana_transcript "OTTHUMT00000039627.2" ; hgnc_id "HGNC:24968" ; level 2 ; orig_coord_info "chr6,637701,637818,-" ; protein_id "ENSP00000230449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9" ; transcript_name "EXOC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5 HAVANA mRNA 1001 32550 . + . FI_gene_label "EXOC2^ENSG00000112685.14" ; ID "EXOC2--EPHA5^ENST00000230449.9" ; Parent "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; ccdsid "CCDS34327.1" ; exon_id "ENSE00000679928.3" ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4" ; havana_transcript "OTTHUMT00000039627.2" ; hgnc_id "HGNC:24968" ; level 2 ; orig_coord_info "chr6,637701,637818,-" ; protein_id "ENSP00000230449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9" ; transcript_name "EXOC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC2--EPHA5 HAVANA gene 35703 62112 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5 HAVANA mRNA 35703 62112 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EXOC2--EPHA5^ENST00000273854.7" ; Parent "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GTPBP2--AL008627.1 ENSEMBL gene 2477 9348 . + . FI_gene_label "GTPBP2^ENSG00000172432.19" ; ID "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19" ; ccdsid "CCDS69124.1" ; exon_id "ENSE00003534858.1" ; exon_number 3 ; gene_id "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19" ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13" ; hgnc_id "HGNC:4670" ; level 3 ; orig_coord_info "chr6,43626226,43626359,-" ; protein_id "ENSP00000304893.7" ; tag basic CCDS ; transcript_id "GTPBP2--AL008627.1^ENST00000307114.11" ; transcript_name "GTPBP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
GTPBP2--AL008627.1 ENSEMBL mRNA 2477 9348 . + . FI_gene_label "GTPBP2^ENSG00000172432.19" ; ID "GTPBP2--AL008627.1^ENST00000307114.11" ; Parent "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19" ; ccdsid "CCDS69124.1" ; exon_id "ENSE00003534858.1" ; exon_number 3 ; gene_id "GTPBP2--AL008627.1^GTPBP2^ENSG00000172432.19" ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13" ; hgnc_id "HGNC:4670" ; level 3 ; orig_coord_info "chr6,43626226,43626359,-" ; protein_id "ENSP00000304893.7" ; tag basic CCDS ; transcript_id "GTPBP2--AL008627.1^ENST00000307114.11" ; transcript_name "GTPBP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
GTPBP2--MBOAT1 ENSEMBL gene 2477 9348 . + . FI_gene_label "GTPBP2^ENSG00000172432.19" ; ID "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19" ; ccdsid "CCDS69124.1" ; exon_id "ENSE00003534858.1" ; exon_number 3 ; gene_id "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19" ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13" ; hgnc_id "HGNC:4670" ; level 3 ; orig_coord_info "chr6,43626226,43626359,-" ; protein_id "ENSP00000304893.7" ; tag basic CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000307114.11" ; transcript_name "GTPBP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
GTPBP2--MBOAT1 ENSEMBL mRNA 2477 9348 . + . FI_gene_label "GTPBP2^ENSG00000172432.19" ; ID "GTPBP2--MBOAT1^ENST00000307114.11" ; Parent "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19" ; ccdsid "CCDS69124.1" ; exon_id "ENSE00003534858.1" ; exon_number 3 ; gene_id "GTPBP2--MBOAT1^GTPBP2^ENSG00000172432.19" ; gene_name GTPBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014744.13" ; hgnc_id "HGNC:4670" ; level 3 ; orig_coord_info "chr6,43626226,43626359,-" ; protein_id "ENSP00000304893.7" ; tag basic CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000307114.11" ; transcript_name "GTPBP2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
GTPBP2--MBOAT1 HAVANA gene 13779 30103 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
GTPBP2--MBOAT1 HAVANA mRNA 13779 30103 . + . FI_gene_label "MBOAT1^ENSG00000172197.11" ; ID "GTPBP2--MBOAT1^ENST00000324607.8" ; Parent "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11" ; ccdsid "CCDS34346.1" ; exon_id "ENSE00001299453.6" ; exon_number 1 ; gene_id "GTPBP2--MBOAT1^MBOAT1^ENSG00000172197.11" ; gene_name MBOAT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014334.2" ; havana_transcript "OTTHUMT00000039980.2" ; hgnc_id "HGNC:21579" ; level 2 ; orig_coord_info "chr6,20212136,20212234,-" ; protein_id "ENSP00000324944.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTPBP2--MBOAT1^ENST00000324607.8" ; transcript_name "MBOAT1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUSB--NAIP ENSEMBL gene 16697 37876 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSB--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSB--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSB--NAIP^ENST00000194097.8" ; transcript_name "NAIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUSB--NAIP ENSEMBL mRNA 16697 37876 . + . FI_gene_label "NAIP^ENSG00000249437.8" ; ID "GUSB--NAIP^ENST00000194097.8" ; Parent "GUSB--NAIP^NAIP^ENSG00000249437.8" ; ccdsid "CCDS4009.1" ; exon_id "ENSE00002284906.1" ; exon_number 2 ; gene_id "GUSB--NAIP^NAIP^ENSG00000249437.8" ; gene_name NAIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000163318.7" ; hgnc_id "HGNC:7634" ; level 3 ; orig_coord_info "chr5,71012348,71012915,-" ; protein_id "ENSP00000443944.1" ; tag basic appris_principal_2 CCDS ; transcript_id "GUSB--NAIP^ENST00000194097.8" ; transcript_name "NAIP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUSB--NAIP HAVANA gene 1003 11674 . + . FI_gene_label "GUSB^ENSG00000169919.17" ; ID "GUSB--NAIP^GUSB^ENSG00000169919.17" ; ccdsid "CCDS5530.1" ; exon_id "ENSE00001554367.1" ; exon_number 1 ; gene_id "GUSB--NAIP^GUSB^ENSG00000169919.17" ; gene_name GUSB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023735.5" ; havana_transcript "OTTHUMT00000251637.4" ; hgnc_id "HGNC:4696" ; level 2 ; orig_coord_info "chr7,65981974,65982183,-" ; protein_id "ENSP00000302728.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GUSB--NAIP^ENST00000304895.9" ; transcript_name "GUSB-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUSB--NAIP HAVANA mRNA 1003 11674 . + . FI_gene_label "GUSB^ENSG00000169919.17" ; ID "GUSB--NAIP^ENST00000304895.9" ; Parent "GUSB--NAIP^GUSB^ENSG00000169919.17" ; ccdsid "CCDS5530.1" ; exon_id "ENSE00001554367.1" ; exon_number 1 ; gene_id "GUSB--NAIP^GUSB^ENSG00000169919.17" ; gene_name GUSB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023735.5" ; havana_transcript "OTTHUMT00000251637.4" ; hgnc_id "HGNC:4696" ; level 2 ; orig_coord_info "chr7,65981974,65982183,-" ; protein_id "ENSP00000302728.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GUSB--NAIP^ENST00000304895.9" ; transcript_name "GUSB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MSI2--CLTC HAVANA gene 57253 91788 . + . FI_gene_label "CLTC^ENSG00000141367.12" ; ID "MSI2--CLTC^CLTC^ENSG00000141367.12" ; ccdsid "CCDS32696.1" ; exon_id "ENSE00003895422.1" ; exon_number 1 ; gene_id "MSI2--CLTC^CLTC^ENSG00000141367.12" ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5" ; havana_transcript "OTTHUMT00000258859.2" ; hgnc_id "HGNC:2092" ; level 2 ; orig_coord_info "chr17,59620132,59620173,+" ; protein_id "ENSP00000269122.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000269122.8" ; transcript_name "CLTC-201" ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--CLTC HAVANA mRNA 57253 91788 . + . FI_gene_label "CLTC^ENSG00000141367.12" ; ID "MSI2--CLTC^ENST00000269122.8" ; Parent "MSI2--CLTC^CLTC^ENSG00000141367.12" ; ccdsid "CCDS32696.1" ; exon_id "ENSE00003895422.1" ; exon_number 1 ; gene_id "MSI2--CLTC^CLTC^ENSG00000141367.12" ; gene_name CLTC ; gene_type protein_coding ; havana_gene "OTTHUMG00000134279.5" ; havana_transcript "OTTHUMT00000258859.2" ; hgnc_id "HGNC:2092" ; level 2 ; orig_coord_info "chr17,59620132,59620173,+" ; protein_id "ENSP00000269122.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000269122.8" ; transcript_name "CLTC-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MSI2--CLTC HAVANA gene 1673 54046 . + . FI_gene_label "MSI2^ENSG00000153944.12" ; ID "MSI2--CLTC^MSI2^ENSG00000153944.12" ; ccdsid "CCDS11596.1" ; exon_id "ENSE00002219180.3" ; exon_number 1 ; gene_id "MSI2--CLTC^MSI2^ENSG00000153944.12" ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4" ; havana_transcript "OTTHUMT00000441813.2" ; hgnc_id "HGNC:18585" ; level 2 ; orig_coord_info "chr17,57256743,57256804,+" ; protein_id "ENSP00000284073.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000284073.7" ; transcript_name "MSI2-201" ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--CLTC HAVANA mRNA 1673 54046 . + . FI_gene_label "MSI2^ENSG00000153944.12" ; ID "MSI2--CLTC^ENST00000284073.7" ; Parent "MSI2--CLTC^MSI2^ENSG00000153944.12" ; ccdsid "CCDS11596.1" ; exon_id "ENSE00002219180.3" ; exon_number 1 ; gene_id "MSI2--CLTC^MSI2^ENSG00000153944.12" ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4" ; havana_transcript "OTTHUMT00000441813.2" ; hgnc_id "HGNC:18585" ; level 2 ; orig_coord_info "chr17,57256743,57256804,+" ; protein_id "ENSP00000284073.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--CLTC^ENST00000284073.7" ; transcript_name "MSI2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NARS2--GAB2 HAVANA gene 1011 17072 . + . FI_gene_label "NARS2^ENSG00000137513.10" ; ID "NARS2--GAB2^NARS2^ENSG00000137513.10" ; ccdsid "CCDS8261.1" ; exon_id "ENSE00001151727.6" ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10" ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4" ; havana_transcript "OTTHUMT00000391138.3" ; hgnc_id "HGNC:26274" ; level 2 ; orig_coord_info "chr11,78574348,78574488,-" ; protein_id "ENSP00000281038.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10" ; transcript_name "NARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2 HAVANA mRNA 1011 17072 . + . FI_gene_label "NARS2^ENSG00000137513.10" ; ID "NARS2--GAB2^ENST00000281038.10" ; Parent "NARS2--GAB2^NARS2^ENSG00000137513.10" ; ccdsid "CCDS8261.1" ; exon_id "ENSE00001151727.6" ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10" ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4" ; havana_transcript "OTTHUMT00000391138.3" ; hgnc_id "HGNC:26274" ; level 2 ; orig_coord_info "chr11,78574348,78574488,-" ; protein_id "ENSP00000281038.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10" ; transcript_name "NARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NARS2--GAB2 HAVANA gene 22864 39485 . + . FI_gene_label "GAB2^ENSG00000033327.13" ; ID "NARS2--GAB2^GAB2^ENSG00000033327.13" ; ccdsid "CCDS8260.1" ; exon_id "ENSE00003464974.1" ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13" ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3" ; havana_transcript "OTTHUMT00000391084.1" ; hgnc_id "HGNC:14458" ; level 2 ; orig_coord_info "chr11,78280601,78280862,-" ; protein_id "ENSP00000343959.2" ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6" ; transcript_name "GAB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2 HAVANA mRNA 22864 39485 . + . FI_gene_label "GAB2^ENSG00000033327.13" ; ID "NARS2--GAB2^ENST00000340149.6" ; Parent "NARS2--GAB2^GAB2^ENSG00000033327.13" ; ccdsid "CCDS8260.1" ; exon_id "ENSE00003464974.1" ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13" ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3" ; havana_transcript "OTTHUMT00000391084.1" ; hgnc_id "HGNC:14458" ; level 2 ; orig_coord_info "chr11,78280601,78280862,-" ; protein_id "ENSP00000343959.2" ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6" ; transcript_name "GAB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RIC1--FMNL1 HAVANA gene 1001 25077 . + . FI_gene_label "RIC1^ENSG00000107036.12" ; ID "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; ccdsid "CCDS47949.2" ; exon_id "ENSE00001626901.2" ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5" ; havana_transcript "OTTHUMT00000051635.3" ; hgnc_id "HGNC:17686" ; level 2 ; orig_coord_info "chr9,5629310,5629453,+" ; protein_id "ENSP00000251879.6" ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10" ; transcript_name "RIC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RIC1--FMNL1 HAVANA mRNA 1001 25077 . + . FI_gene_label "RIC1^ENSG00000107036.12" ; ID "RIC1--FMNL1^ENST00000251879.10" ; Parent "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; ccdsid "CCDS47949.2" ; exon_id "ENSE00001626901.2" ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5" ; havana_transcript "OTTHUMT00000051635.3" ; hgnc_id "HGNC:17686" ; level 2 ; orig_coord_info "chr9,5629310,5629453,+" ; protein_id "ENSP00000251879.6" ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10" ; transcript_name "RIC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RIC1--FMNL1 ENSEMBL gene 34309 51145 . + . FI_gene_label "FMNL1^ENSG00000184922.14" ; ID "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; exon_id "ENSE00001337921.3" ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5" ; hgnc_id "HGNC:1212" ; level 3 ; orig_coord_info "chr17,45222125,45222187,+" ; protein_id "ENSP00000327442.4" ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7" ; transcript_name "FMNL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
RIC1--FMNL1 ENSEMBL mRNA 34309 51145 . + . FI_gene_label "FMNL1^ENSG00000184922.14" ; ID "RIC1--FMNL1^ENST00000328118.7" ; Parent "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; exon_id "ENSE00001337921.3" ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5" ; hgnc_id "HGNC:1212" ; level 3 ; orig_coord_info "chr17,45222125,45222187,+" ; protein_id "ENSP00000327442.4" ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7" ; transcript_name "FMNL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
SHMT2--RACGAP1 HAVANA gene 11765 30952 . + . FI_gene_label "RACGAP1^ENSG00000161800.13" ; ID "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13" ; ccdsid "CCDS8795.1" ; exon_id "ENSE00003599562.1" ; exon_number 2 ; gene_id "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13" ; gene_name RACGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169811.7" ; havana_transcript "OTTHUMT00000405998.3" ; hgnc_id "HGNC:9804" ; level 2 ; orig_coord_info "chr12,50016631,50016715,-" ; protein_id "ENSP00000309871.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000312377.10" ; transcript_name "RACGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SHMT2--RACGAP1 HAVANA mRNA 11765 30952 . + . FI_gene_label "RACGAP1^ENSG00000161800.13" ; ID "SHMT2--RACGAP1^ENST00000312377.10" ; Parent "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13" ; ccdsid "CCDS8795.1" ; exon_id "ENSE00003599562.1" ; exon_number 2 ; gene_id "SHMT2--RACGAP1^RACGAP1^ENSG00000161800.13" ; gene_name RACGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169811.7" ; havana_transcript "OTTHUMT00000405998.3" ; hgnc_id "HGNC:9804" ; level 2 ; orig_coord_info "chr12,50016631,50016715,-" ; protein_id "ENSP00000309871.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000312377.10" ; transcript_name "RACGAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SHMT2--RACGAP1 HAVANA gene 1139 6363 . + . FI_gene_label "SHMT2^ENSG00000182199.11" ; ID "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11" ; ccdsid "CCDS8934.1" ; exon_id "ENSE00003673873.1" ; exon_number 1 ; gene_id "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11" ; gene_name SHMT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171246.15" ; havana_transcript "OTTHUMT00000412525.3" ; hgnc_id "HGNC:10852" ; level 2 ; orig_coord_info "chr12,57229779,57229811,+" ; protein_id "ENSP00000333667.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000328923.8" ; transcript_name "SHMT2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SHMT2--RACGAP1 HAVANA mRNA 1139 6363 . + . FI_gene_label "SHMT2^ENSG00000182199.11" ; ID "SHMT2--RACGAP1^ENST00000328923.8" ; Parent "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11" ; ccdsid "CCDS8934.1" ; exon_id "ENSE00003673873.1" ; exon_number 1 ; gene_id "SHMT2--RACGAP1^SHMT2^ENSG00000182199.11" ; gene_name SHMT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171246.15" ; havana_transcript "OTTHUMT00000412525.3" ; hgnc_id "HGNC:10852" ; level 2 ; orig_coord_info "chr12,57229779,57229811,+" ; protein_id "ENSP00000333667.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SHMT2--RACGAP1^ENST00000328923.8" ; transcript_name "SHMT2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
C22orf39--MYO18B-AS1 HAVANA gene 33040 44724 . + . FI_gene_label "MYO18B-AS1^ENSG00000231933.7" ; ID "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7" ; exon_id "ENSE00003705478.1" ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7" ; gene_name "MYO18B-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4" ; havana_transcript "OTTHUMT00000461522.3" ; hgnc_id "HGNC:40831" ; level 1 ; orig_coord_info "chr22,25900825,25901042,-" ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "C22orf39--MYO18B-AS1^ENST00000453457.7" ; transcript_name "MYO18B-AS1-201" ; transcript_support_level 5 ; transcript_type lncRNA
C22orf39--MYO18B-AS1 HAVANA RNA 33040 44724 . + . FI_gene_label "MYO18B-AS1^ENSG00000231933.7" ; ID "C22orf39--MYO18B-AS1^ENST00000453457.7" ; Parent "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7" ; exon_id "ENSE00003705478.1" ; exon_number 1 ; gene_id "C22orf39--MYO18B-AS1^MYO18B-AS1^ENSG00000231933.7" ; gene_name "MYO18B-AS1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000150907.4" ; havana_transcript "OTTHUMT00000461522.3" ; hgnc_id "HGNC:40831" ; level 1 ; orig_coord_info "chr22,25900825,25901042,-" ; tag mRNA_start_NF nested_454_RNA_Seq_supported RNA_Seq_supported_only exp_conf ; transcript_id "C22orf39--MYO18B-AS1^ENST00000453457.7" ; transcript_name "MYO18B-AS1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
GTPBP2--AL008627.1 HAVANA gene 13779 14264 . + . FI_gene_label "AL008627.1^ENSG00000229700.1" ; ID "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1" ; exon_id "ENSE00001629587.1" ; exon_number 1 ; gene_id "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1" ; gene_name "AL008627.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016195.1" ; havana_transcript "OTTHUMT00000043482.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr6,20042455,20042940,-" ; tag pseudo_consens basic ; transcript_id "GTPBP2--AL008627.1^ENST00000446953.1" ; transcript_name "AL008627.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
GTPBP2--AL008627.1 HAVANA RNA 13779 14264 . + . FI_gene_label "AL008627.1^ENSG00000229700.1" ; ID "GTPBP2--AL008627.1^ENST00000446953.1" ; Parent "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1" ; exon_id "ENSE00001629587.1" ; exon_number 1 ; gene_id "GTPBP2--AL008627.1^AL008627.1^ENSG00000229700.1" ; gene_name "AL008627.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016195.1" ; havana_transcript "OTTHUMT00000043482.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr6,20042455,20042940,-" ; tag pseudo_consens basic ; transcript_id "GTPBP2--AL008627.1^ENST00000446953.1" ; transcript_name "AL008627.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
258 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 ------------------------------
456 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 21 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed