Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/f578dbb4c87d503fe8c3730678e5e2/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/bf02b30f5709e60ae56858243e4e69/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/f578dbb4c87d503fe8c3730678e5e2/.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: 2828
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2828
=> 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:2828
=> 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:
AC005993.1--RGS6 ENSEMBL gene 16301 50680 . + . FI_gene_label "RGS6^ENSG00000182732.18" ; ID "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; exon_id "ENSE00003732696.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; gene_name RGS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171340.6" ; hgnc_id "HGNC:10002" ; level 3 ; orig_coord_info "chr14,72352116,72352194,+" ; protein_id "ENSP00000341199.7" ; tag basic ; transcript_id "AC005993.1--RGS6^ENST00000343854.10" ; transcript_name "RGS6-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC005993.1--RGS6 ENSEMBL mRNA 16301 50680 . + . FI_gene_label "RGS6^ENSG00000182732.18" ; ID "AC005993.1--RGS6^ENST00000343854.10" ; Parent "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; exon_id "ENSE00003732696.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^RGS6^ENSG00000182732.18" ; gene_name RGS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171340.6" ; hgnc_id "HGNC:10002" ; level 3 ; orig_coord_info "chr14,72352116,72352194,+" ; protein_id "ENSP00000341199.7" ; tag basic ; transcript_id "AC005993.1--RGS6^ENST00000343854.10" ; transcript_name "RGS6-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AGAP12P--FRMPD2 HAVANA gene 13554 48555 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding
AGAP12P--FRMPD2 HAVANA mRNA 13554 48555 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP12P--FRMPD2^ENST00000305531.3" ; Parent "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP12P--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AGAP4--FRMPD2 HAVANA gene 16607 51608 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP4--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP4--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP4--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding
AGAP4--FRMPD2 HAVANA mRNA 16607 51608 . + . FI_gene_label "FRMPD2^ENSG00000170324.21" ; ID "AGAP4--FRMPD2^ENST00000305531.3" ; Parent "AGAP4--FRMPD2^FRMPD2^ENSG00000170324.21" ; ccdsid "CCDS81460.1" ; exon_id "ENSE00001390154.1" ; exon_number 1 ; gene_id "AGAP4--FRMPD2^FRMPD2^ENSG00000170324.21" ; gene_name FRMPD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018171.7" ; havana_transcript "OTTHUMT00000277029.1" ; hgnc_id "HGNC:28572" ; level 2 ; orig_coord_info "chr10,48251566,48251710,-" ; protein_id "ENSP00000307079.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "AGAP4--FRMPD2^ENST00000305531.3" ; transcript_name "FRMPD2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
AGAP4--FRMPD2 HAVANA gene 3661 12452 . + . FI_gene_label "AGAP4^ENSG00000188234.14" ; ID "AGAP4--FRMPD2^AGAP4^ENSG00000188234.14" ; ccdsid "CCDS7215.1" ; exon_id "ENSE00002443810.1" ; exon_number 1 ; gene_id "AGAP4--FRMPD2^AGAP4^ENSG00000188234.14" ; gene_name AGAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018088.2" ; havana_transcript "OTTHUMT00000047799.1" ; hgnc_id "HGNC:23459" ; level 2 ; orig_coord_info "chr10,45847125,45847347,-" ; protein_id "ENSP00000392513.2" ; tag basic appris_principal_2 CCDS ; transcript_id "AGAP4--FRMPD2^ENST00000448048.7" ; transcript_name "AGAP4-202" ; transcript_support_level 1 ; transcript_type protein_coding
AGAP4--FRMPD2 HAVANA mRNA 3661 12452 . + . FI_gene_label "AGAP4^ENSG00000188234.14" ; ID "AGAP4--FRMPD2^ENST00000448048.7" ; Parent "AGAP4--FRMPD2^AGAP4^ENSG00000188234.14" ; ccdsid "CCDS7215.1" ; exon_id "ENSE00002443810.1" ; exon_number 1 ; gene_id "AGAP4--FRMPD2^AGAP4^ENSG00000188234.14" ; gene_name AGAP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018088.2" ; havana_transcript "OTTHUMT00000047799.1" ; hgnc_id "HGNC:23459" ; level 2 ; orig_coord_info "chr10,45847125,45847347,-" ; protein_id "ENSP00000392513.2" ; tag basic appris_principal_2 CCDS ; transcript_id "AGAP4--FRMPD2^ENST00000448048.7" ; transcript_name "AGAP4-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ETV6--POLE HAVANA gene 13392 15151 . + . FI_gene_label "ETV6^ENSG00000139083.11" ; ID "ETV6--POLE^ETV6^ENSG00000139083.11" ; exon_id "ENSE00002245284.1" ; exon_number 1 ; gene_id "ETV6--POLE^ETV6^ENSG00000139083.11" ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3" ; havana_transcript "OTTHUMT00000400134.1" ; hgnc_id "HGNC:3495" ; level 2 ; orig_coord_info "chr12,11885937,11886026,+" ; protein_id "ENSP00000266427.3" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--POLE^ENST00000266427.3" ; transcript_name "ETV6-201" ; transcript_support_level 3 ; transcript_type protein_coding
ETV6--POLE HAVANA mRNA 13392 15151 . + . FI_gene_label "ETV6^ENSG00000139083.11" ; ID "ETV6--POLE^ENST00000266427.3" ; Parent "ETV6--POLE^ETV6^ENSG00000139083.11" ; exon_id "ENSE00002245284.1" ; exon_number 1 ; gene_id "ETV6--POLE^ETV6^ENSG00000139083.11" ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3" ; havana_transcript "OTTHUMT00000400134.1" ; hgnc_id "HGNC:3495" ; level 2 ; orig_coord_info "chr12,11885937,11886026,+" ; protein_id "ENSP00000266427.3" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--POLE^ENST00000266427.3" ; transcript_name "ETV6-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
ETV6--POLE HAVANA gene 21953 59710 . + . FI_gene_label "POLE^ENSG00000177084.18" ; ID "ETV6--POLE^POLE^ENSG00000177084.18" ; ccdsid "CCDS9278.1" ; exon_id "ENSE00002699740.2" ; exon_number 1 ; gene_id "ETV6--POLE^POLE^ENSG00000177084.18" ; gene_name POLE ; gene_type protein_coding ; havana_gene "OTTHUMG00000168045.7" ; havana_transcript "OTTHUMT00000397689.3" ; hgnc_id "HGNC:9177" ; level 2 ; orig_coord_info "chr12,132687254,132687315,-" ; protein_id "ENSP00000322570.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ETV6--POLE^ENST00000320574.10" ; transcript_name "POLE-201" ; transcript_support_level 1 ; transcript_type protein_coding
ETV6--POLE HAVANA mRNA 21953 59710 . + . FI_gene_label "POLE^ENSG00000177084.18" ; ID "ETV6--POLE^ENST00000320574.10" ; Parent "ETV6--POLE^POLE^ENSG00000177084.18" ; ccdsid "CCDS9278.1" ; exon_id "ENSE00002699740.2" ; exon_number 1 ; gene_id "ETV6--POLE^POLE^ENSG00000177084.18" ; gene_name POLE ; gene_type protein_coding ; havana_gene "OTTHUMG00000168045.7" ; havana_transcript "OTTHUMT00000397689.3" ; hgnc_id "HGNC:9177" ; level 2 ; orig_coord_info "chr12,132687254,132687315,-" ; protein_id "ENSP00000322570.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ETV6--POLE^ENST00000320574.10" ; transcript_name "POLE-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHA13 HAVANA gene 8249 16689 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA5--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA5--PCDHA13 HAVANA mRNA 8249 16689 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA5--PCDHA13^ENST00000289272.3" ; Parent "PCDHA5--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHA13 HAVANA gene 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHA13^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHA13^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHA13^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA5--PCDHA13 HAVANA mRNA 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHA13^ENST00000614258.1" ; Parent "PCDHA5--PCDHA13^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHA13^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHA13^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHAC1 HAVANA gene 8249 18264 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA5--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA5--PCDHAC1 HAVANA mRNA 8249 18264 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA5--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA5--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHAC1 HAVANA gene 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHAC1^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHAC1^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHAC1^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA5--PCDHAC1 HAVANA mRNA 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHAC1^ENST00000614258.1" ; Parent "PCDHA5--PCDHAC1^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHAC1^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHAC1^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHAC2 HAVANA gene 8255 18990 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA5--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA5--PCDHAC2 HAVANA mRNA 8255 18990 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA5--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA5--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA5--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 "PCDHA5--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA5--PCDHAC2 HAVANA gene 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHAC2^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHAC2^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHAC2^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA5--PCDHAC2 HAVANA mRNA 1001 5248 . + . FI_gene_label "PCDHA5^ENSG00000204965.9" ; ID "PCDHA5--PCDHAC2^ENST00000614258.1" ; Parent "PCDHA5--PCDHAC2^PCDHA5^ENSG00000204965.9" ; exon_id "ENSE00003729378.1" ; exon_number 1 ; gene_id "PCDHA5--PCDHAC2^PCDHA5^ENSG00000204965.9" ; gene_name PCDHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163367.4" ; havana_transcript "OTTHUMT00000477514.1" ; hgnc_id "HGNC:8671" ; level 2 ; orig_coord_info "chr5,140821776,140824223,+" ; protein_id "ENSP00000484128.1" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA5--PCDHAC2^ENST00000614258.1" ; transcript_name "PCDHA5-203" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PDXDC2P--NPIPB3 HAVANA gene 27345 37259 . + . FI_gene_label "NPIPB3^ENSG00000169246.16" ; ID "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; exon_id "ENSE00003561690.1" ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5" ; havana_transcript "OTTHUMT00000400432.2" ; hgnc_id "HGNC:28989" ; level 2 ; orig_coord_info "chr16,21424979,21425003,-" ; protein_id "ENSP00000413141.2" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6" ; transcript_name "NPIPB3-201" ; transcript_support_level 3 ; transcript_type protein_coding
PDXDC2P--NPIPB3 HAVANA mRNA 27345 37259 . + . FI_gene_label "NPIPB3^ENSG00000169246.16" ; ID "PDXDC2P--NPIPB3^ENST00000419180.6" ; Parent "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; exon_id "ENSE00003561690.1" ; exon_number 2 ; gene_id "PDXDC2P--NPIPB3^NPIPB3^ENSG00000169246.16" ; gene_name NPIPB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163506.5" ; havana_transcript "OTTHUMT00000400432.2" ; hgnc_id "HGNC:28989" ; level 2 ; orig_coord_info "chr16,21424979,21425003,-" ; protein_id "ENSP00000413141.2" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PDXDC2P--NPIPB3^ENST00000419180.6" ; transcript_name "NPIPB3-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
SLCO1B3--SLCO1B7 ENSEMBL gene 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLCO1B3--SLCO1B7 ENSEMBL mRNA 3179 19485 . + . FI_gene_label "SLCO1B3^ENSG00000111700.13" ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6" ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; ccdsid "CCDS8684.1" ; exon_id "ENSE00003727652.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13" ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5" ; hgnc_id "HGNC:10961" ; level 3 ; orig_coord_info "chr12,20815739,20815822,+" ; protein_id "ENSP00000261196.2" ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6" ; transcript_name "SLCO1B3-201" ; 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:
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:
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:
AC005993.1--RGS6 HAVANA gene 1001 4837 . + . FI_gene_label "AC005993.1^ENSG00000266869.2" ; ID "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; exon_id "ENSE00002516676.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; gene_name "AC005993.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179238.4" ; havana_transcript "OTTHUMT00000445384.1" ; level 2 ; orig_coord_info "chr14,71848606,71848736,+" ; transcript_id "AC005993.1--RGS6^ENST00000555581.1" ; transcript_name "AC005993.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
AC005993.1--RGS6 HAVANA RNA 1001 4837 . + . FI_gene_label "AC005993.1^ENSG00000266869.2" ; ID "AC005993.1--RGS6^ENST00000555581.1" ; Parent "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; exon_id "ENSE00002516676.1" ; exon_number 1 ; gene_id "AC005993.1--RGS6^AC005993.1^ENSG00000266869.2" ; gene_name "AC005993.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000179238.4" ; havana_transcript "OTTHUMT00000445384.1" ; level 2 ; orig_coord_info "chr14,71848606,71848736,+" ; transcript_id "AC005993.1--RGS6^ENST00000555581.1" ; transcript_name "AC005993.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
AGAP12P--FRMPD2 HAVANA gene 1042 9399 . + . FI_gene_label "AGAP12P^ENSG00000265018.6" ; ID "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; exon_id "ENSE00002718806.2" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4" ; havana_transcript "OTTHUMT00000047912.4" ; hgnc_id "HGNC:23661" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48031376,48031599,-" ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6" ; transcript_name "AGAP12P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AGAP12P--FRMPD2 HAVANA RNA 1042 9399 . + . FI_gene_label "AGAP12P^ENSG00000265018.6" ; ID "AGAP12P--FRMPD2^ENST00000585227.6" ; Parent "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; exon_id "ENSE00002718806.2" ; exon_number 1 ; gene_id "AGAP12P--FRMPD2^AGAP12P^ENSG00000265018.6" ; gene_name AGAP12P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018164.4" ; havana_transcript "OTTHUMT00000047912.4" ; hgnc_id "HGNC:23661" ; level 1 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48031376,48031599,-" ; tag pseudo_consens basic ; transcript_id "AGAP12P--FRMPD2^ENST00000585227.6" ; transcript_name "AGAP12P-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
PDXDC2P--NPIPB3 HAVANA gene 1161 3891 . + . FI_gene_label "PDXDC2P^ENSG00000255185.6" ; ID "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; exon_id "ENSE00002159321.1" ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2" ; havana_transcript "OTTHUMT00000395272.1" ; hgnc_id "HGNC:27559" ; level 2 ; orig_coord_info "chr16,70065756,70065785,-" ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1" ; transcript_name "PDXDC2P-201" ; transcript_support_level 5 ; transcript_type processed_transcript
PDXDC2P--NPIPB3 HAVANA RNA 1161 3891 . + . FI_gene_label "PDXDC2P^ENSG00000255185.6" ; ID "PDXDC2P--NPIPB3^ENST00000525173.1" ; Parent "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; exon_id "ENSE00002159321.1" ; exon_number 1 ; gene_id "PDXDC2P--NPIPB3^PDXDC2P^ENSG00000255185.6" ; gene_name PDXDC2P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000167595.2" ; havana_transcript "OTTHUMT00000395272.1" ; hgnc_id "HGNC:27559" ; level 2 ; orig_coord_info "chr16,70065756,70065785,-" ; transcript_id "PDXDC2P--NPIPB3^ENST00000525173.1" ; transcript_name "PDXDC2P-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
SLCO1B3--SLCO1B7 HAVANA gene 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript
SLCO1B3--SLCO1B7 HAVANA RNA 34392 35949 . + . FI_gene_label "SLCO1B7^ENSG00000205754.12" ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1" ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; exon_id "ENSE00002290527.1" ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12" ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3" ; havana_transcript "OTTHUMT00000402068.1" ; hgnc_id "HGNC:32934" ; level 2 ; orig_coord_info "chr12,21067351,21067383,+" ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1" ; transcript_name "SLCO1B7-201" ; transcript_support_level 5 ; transcript_type processed_transcript
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
204 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 ------------------------------
444 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 20 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