Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/32ed1779ee9042246f7d111e783a16/fi_workdir/RGB_RLP_lowDV_1ststrand_40C_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/3ecd01cc419a9cbaad86373964db54/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/3ecd01cc419a9cbaad86373964db54/.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: 3867
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3867
=> 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:3867
=> 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:
ASPH--LINC02842 HAVANA gene 1045 33265 . + . FI_gene_label "ASPH^ENSG00000198363.18" ; ID "ASPH--LINC02842^ASPH^ENSG00000198363.18" ; ccdsid "CCDS43742.1" ; exon_id "ENSE00002130497.1" ; exon_number 1 ; gene_id "ASPH--LINC02842^ASPH^ENSG00000198363.18" ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13" ; havana_transcript "OTTHUMT00000378511.2" ; hgnc_id "HGNC:757" ; level 2 ; orig_coord_info "chr8,61714269,61714371,-" ; protein_id "ENSP00000348841.5" ; tag basic CCDS ; transcript_id "ASPH--LINC02842^ENST00000356457.9" ; transcript_name "ASPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
ASPH--LINC02842 HAVANA mRNA 1045 33265 . + . FI_gene_label "ASPH^ENSG00000198363.18" ; ID "ASPH--LINC02842^ENST00000356457.9" ; Parent "ASPH--LINC02842^ASPH^ENSG00000198363.18" ; ccdsid "CCDS43742.1" ; exon_id "ENSE00002130497.1" ; exon_number 1 ; gene_id "ASPH--LINC02842^ASPH^ENSG00000198363.18" ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13" ; havana_transcript "OTTHUMT00000378511.2" ; hgnc_id "HGNC:757" ; level 2 ; orig_coord_info "chr8,61714269,61714371,-" ; protein_id "ENSP00000348841.5" ; tag basic CCDS ; transcript_id "ASPH--LINC02842^ENST00000356457.9" ; transcript_name "ASPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATP11A--AL359649.1 ENSEMBL gene 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--AL359649.1^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--AL359649.1 ENSEMBL mRNA 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--AL359649.1^ENST00000375630.6" ; Parent "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--AL359649.1^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--AL359649.1^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ATP11A--LINC00354 ENSEMBL gene 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--LINC00354^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--LINC00354^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--LINC00354^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--LINC00354 ENSEMBL mRNA 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--LINC00354^ENST00000375630.6" ; Parent "ATP11A--LINC00354^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--LINC00354^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--LINC00354^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ATP11A--MCF2L HAVANA gene 94647 104280 . + . FI_gene_label "MCF2L^ENSG00000126217.21" ; ID "ATP11A--MCF2L^MCF2L^ENSG00000126217.21" ; exon_id "ENSE00001643016.1" ; exon_number 1 ; gene_id "ATP11A--MCF2L^MCF2L^ENSG00000126217.21" ; gene_name MCF2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000017377.18" ; havana_transcript "OTTHUMT00000339076.1" ; hgnc_id "HGNC:14576" ; level 2 ; orig_coord_info "chr13,113087350,113087456,+" ; protein_id "ENSP00000261963.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ATP11A--MCF2L^ENST00000261963.11" ; transcript_name "MCF2L-201" ; transcript_support_level 1 ; transcript_type protein_coding
ATP11A--MCF2L HAVANA mRNA 94647 104280 . + . FI_gene_label "MCF2L^ENSG00000126217.21" ; ID "ATP11A--MCF2L^ENST00000261963.11" ; Parent "ATP11A--MCF2L^MCF2L^ENSG00000126217.21" ; exon_id "ENSE00001643016.1" ; exon_number 1 ; gene_id "ATP11A--MCF2L^MCF2L^ENSG00000126217.21" ; gene_name MCF2L ; gene_type protein_coding ; havana_gene "OTTHUMG00000017377.18" ; havana_transcript "OTTHUMT00000339076.1" ; hgnc_id "HGNC:14576" ; level 2 ; orig_coord_info "chr13,113087350,113087456,+" ; protein_id "ENSP00000261963.7" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ATP11A--MCF2L^ENST00000261963.11" ; transcript_name "MCF2L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ATP11A--MCF2L ENSEMBL gene 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--MCF2L^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--MCF2L^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--MCF2L^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
ATP11A--MCF2L ENSEMBL mRNA 1001 44637 . + . FI_gene_label "ATP11A^ENSG00000068650.18" ; ID "ATP11A--MCF2L^ENST00000375630.6" ; Parent "ATP11A--MCF2L^ATP11A^ENSG00000068650.18" ; exon_id "ENSE00001740661.1" ; exon_number 1 ; gene_id "ATP11A--MCF2L^ATP11A^ENSG00000068650.18" ; gene_name ATP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017371.10" ; hgnc_id "HGNC:13552" ; level 3 ; orig_coord_info "chr13,112690417,112690455,+" ; protein_id "ENSP00000364781.2" ; tag basic appris_alternative_2 ; transcript_id "ATP11A--MCF2L^ENST00000375630.6" ; transcript_name "ATP11A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CAB39--ARFIP1 HAVANA gene 1001 15013 . + . FI_gene_label "CAB39^ENSG00000135932.11" ; ID "CAB39--ARFIP1^CAB39^ENSG00000135932.11" ; ccdsid "CCDS2478.1" ; exon_id "ENSE00001174710.1" ; exon_number 2 ; gene_id "CAB39--ARFIP1^CAB39^ENSG00000135932.11" ; gene_name CAB39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133220.4" ; havana_transcript "OTTHUMT00000256955.3" ; hgnc_id "HGNC:20292" ; level 2 ; orig_coord_info "chr2,230760002,230760115,+" ; protein_id "ENSP00000258418.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000258418.10" ; transcript_name "CAB39-201" ; transcript_support_level 1 ; transcript_type protein_coding
CAB39--ARFIP1 HAVANA mRNA 1001 15013 . + . FI_gene_label "CAB39^ENSG00000135932.11" ; ID "CAB39--ARFIP1^ENST00000258418.10" ; Parent "CAB39--ARFIP1^CAB39^ENSG00000135932.11" ; ccdsid "CCDS2478.1" ; exon_id "ENSE00001174710.1" ; exon_number 2 ; gene_id "CAB39--ARFIP1^CAB39^ENSG00000135932.11" ; gene_name CAB39 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133220.4" ; havana_transcript "OTTHUMT00000256955.3" ; hgnc_id "HGNC:20292" ; level 2 ; orig_coord_info "chr2,230760002,230760115,+" ; protein_id "ENSP00000258418.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000258418.10" ; transcript_name "CAB39-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CAB39--ARFIP1 HAVANA gene 18031 33854 . + . FI_gene_label "ARFIP1^ENSG00000164144.16" ; ID "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16" ; ccdsid "CCDS34080.1" ; exon_id "ENSE00003895784.1" ; exon_number 2 ; gene_id "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16" ; gene_name ARFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161468.3" ; havana_transcript "OTTHUMT00000504379.2" ; hgnc_id "HGNC:21496" ; level 2 ; orig_coord_info "chr4,152829634,152829726,+" ; protein_id "ENSP00000296557.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_4 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000353617.7" ; transcript_name "ARFIP1-201" ; transcript_support_level 5 ; transcript_type protein_coding
CAB39--ARFIP1 HAVANA mRNA 18031 33854 . + . FI_gene_label "ARFIP1^ENSG00000164144.16" ; ID "CAB39--ARFIP1^ENST00000353617.7" ; Parent "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16" ; ccdsid "CCDS34080.1" ; exon_id "ENSE00003895784.1" ; exon_number 2 ; gene_id "CAB39--ARFIP1^ARFIP1^ENSG00000164144.16" ; gene_name ARFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000161468.3" ; havana_transcript "OTTHUMT00000504379.2" ; hgnc_id "HGNC:21496" ; level 2 ; orig_coord_info "chr4,152829634,152829726,+" ; protein_id "ENSP00000296557.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_4 CCDS ; transcript_id "CAB39--ARFIP1^ENST00000353617.7" ; transcript_name "ARFIP1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHA13 HAVANA gene 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHA13 HAVANA mRNA 8595 17035 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA3--PCDHA13^ENST00000289272.3" ; Parent "PCDHA3--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHA13 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHA13 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHA13^ENST00000532566.3" ; Parent "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHA13^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHA13^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC1 HAVANA gene 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHAC1 HAVANA mRNA 8595 18610 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA3--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA3--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC1 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHAC1 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC1^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC1^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC1^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC2 HAVANA gene 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA3--PCDHAC2 HAVANA mRNA 8601 19336 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA3--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA3--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA3--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 "PCDHA3--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA3--PCDHAC2 HAVANA gene 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA3--PCDHAC2 HAVANA mRNA 1001 5594 . + . FI_gene_label "PCDHA3^ENSG00000255408.4" ; ID "PCDHA3--PCDHAC2^ENST00000532566.3" ; Parent "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; exon_id "ENSE00002153432.3" ; exon_number 1 ; gene_id "PCDHA3--PCDHAC2^PCDHA3^ENSG00000255408.4" ; gene_name PCDHA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163357.4" ; havana_transcript "OTTHUMT00000477482.1" ; hgnc_id "HGNC:8669" ; level 2 ; orig_coord_info "chr5,140801198,140803669,+" ; protein_id "ENSP00000434086.2" ; tag RNA_Seq_supported_partial basic ; transcript_id "PCDHA3--PCDHAC2^ENST00000532566.3" ; transcript_name "PCDHA3-202" ; transcript_support_level NA ; 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:
PCDHA6--PCDHA13 HAVANA gene 7268 15708 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHA13 HAVANA mRNA 7268 15708 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA6--PCDHA13^ENST00000289272.3" ; Parent "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHA13 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHA13 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHA13^ENST00000378126.4" ; Parent "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC1 HAVANA gene 7268 17283 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC1 HAVANA mRNA 7268 17283 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA6--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC1 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC1 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC1^ENST00000378126.4" ; Parent "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC2 HAVANA gene 7274 18009 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC2 HAVANA mRNA 7274 18009 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA6--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA6--PCDHAC2 HAVANA gene 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC2 HAVANA mRNA 1001 4267 . + . FI_gene_label "PCDHA6^ENSG00000081842.18" ; ID "PCDHA6--PCDHAC2^ENST00000378126.4" ; Parent "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; exon_id "ENSE00001476364.4" ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18" ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5" ; havana_transcript "OTTHUMT00000477550.1" ; hgnc_id "HGNC:8672" ; level 2 ; orig_coord_info "chr5,140828092,140830500,+" ; protein_id "ENSP00000367366.4" ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4" ; transcript_name "PCDHA6-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
SMIM14--CECR2 ENSEMBL gene 18633 42307 . + . FI_gene_label "CECR2^ENSG00000099954.18" ; ID "SMIM14--CECR2^CECR2^ENSG00000099954.18" ; exon_id "ENSE00003472152.1" ; exon_number 4 ; gene_id "SMIM14--CECR2^CECR2^ENSG00000099954.18" ; gene_name CECR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150072.9" ; hgnc_id "HGNC:1840" ; level 3 ; orig_coord_info "chr22,17499494,17499549,+" ; protein_id "ENSP00000262608.10" ; tag basic appris_alternative_2 ; transcript_id "SMIM14--CECR2^ENST00000262608.12" ; transcript_name "CECR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SMIM14--CECR2 ENSEMBL mRNA 18633 42307 . + . FI_gene_label "CECR2^ENSG00000099954.18" ; ID "SMIM14--CECR2^ENST00000262608.12" ; Parent "SMIM14--CECR2^CECR2^ENSG00000099954.18" ; exon_id "ENSE00003472152.1" ; exon_number 4 ; gene_id "SMIM14--CECR2^CECR2^ENSG00000099954.18" ; gene_name CECR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150072.9" ; hgnc_id "HGNC:1840" ; level 3 ; orig_coord_info "chr22,17499494,17499549,+" ; protein_id "ENSP00000262608.10" ; tag basic appris_alternative_2 ; transcript_id "SMIM14--CECR2^ENST00000262608.12" ; transcript_name "CECR2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SMIM14--CECR2 HAVANA gene 1038 14035 . + . FI_gene_label "SMIM14^ENSG00000163683.12" ; ID "SMIM14--CECR2^SMIM14^ENSG00000163683.12" ; ccdsid "CCDS3456.1" ; exon_id "ENSE00001123004.1" ; exon_number 2 ; gene_id "SMIM14--CECR2^SMIM14^ENSG00000163683.12" ; gene_name SMIM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128581.8" ; havana_transcript "OTTHUMT00000250434.5" ; hgnc_id "HGNC:27321" ; level 1 ; orig_coord_info "chr4,39605071,39605145,-" ; protein_id "ENSP00000295958.4" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "SMIM14--CECR2^ENST00000295958.10" ; transcript_name "SMIM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
SMIM14--CECR2 HAVANA mRNA 1038 14035 . + . FI_gene_label "SMIM14^ENSG00000163683.12" ; ID "SMIM14--CECR2^ENST00000295958.10" ; Parent "SMIM14--CECR2^SMIM14^ENSG00000163683.12" ; ccdsid "CCDS3456.1" ; exon_id "ENSE00001123004.1" ; exon_number 2 ; gene_id "SMIM14--CECR2^SMIM14^ENSG00000163683.12" ; gene_name SMIM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128581.8" ; havana_transcript "OTTHUMT00000250434.5" ; hgnc_id "HGNC:27321" ; level 1 ; orig_coord_info "chr4,39605071,39605145,-" ; protein_id "ENSP00000295958.4" ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "SMIM14--CECR2^ENST00000295958.10" ; transcript_name "SMIM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SREBF1--NCOR1 ENSEMBL gene 1001 12895 . + . FI_gene_label "SREBF1^ENSG00000072310.17" ; ID "SREBF1--NCOR1^SREBF1^ENSG00000072310.17" ; ccdsid "CCDS11189.1" ; exon_id "ENSE00003873048.1" ; exon_number 1 ; gene_id "SREBF1--NCOR1^SREBF1^ENSG00000072310.17" ; gene_name SREBF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059313.9" ; hgnc_id "HGNC:11289" ; level 3 ; orig_coord_info "chr17,17836727,17836817,-" ; protein_id "ENSP00000261646.5" ; tag basic appris_principal_2 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000261646.10" ; transcript_name "SREBF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SREBF1--NCOR1 ENSEMBL mRNA 1001 12895 . + . FI_gene_label "SREBF1^ENSG00000072310.17" ; ID "SREBF1--NCOR1^ENST00000261646.10" ; Parent "SREBF1--NCOR1^SREBF1^ENSG00000072310.17" ; ccdsid "CCDS11189.1" ; exon_id "ENSE00003873048.1" ; exon_number 1 ; gene_id "SREBF1--NCOR1^SREBF1^ENSG00000072310.17" ; gene_name SREBF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059313.9" ; hgnc_id "HGNC:11289" ; level 3 ; orig_coord_info "chr17,17836727,17836817,-" ; protein_id "ENSP00000261646.5" ; tag basic appris_principal_2 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000261646.10" ; transcript_name "SREBF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SREBF1--NCOR1 HAVANA gene 18731 74680 . + . FI_gene_label "NCOR1^ENSG00000141027.21" ; ID "SREBF1--NCOR1^NCOR1^ENSG00000141027.21" ; ccdsid "CCDS11175.1" ; exon_id "ENSE00003656730.1" ; exon_number 2 ; gene_id "SREBF1--NCOR1^NCOR1^ENSG00000141027.21" ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12" ; havana_transcript "OTTHUMT00000131751.6" ; hgnc_id "HGNC:7672" ; level 2 ; orig_coord_info "chr17,16194462,16194569,-" ; protein_id "ENSP00000268712.2" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000268712.8" ; transcript_name "NCOR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SREBF1--NCOR1 HAVANA mRNA 18731 74680 . + . FI_gene_label "NCOR1^ENSG00000141027.21" ; ID "SREBF1--NCOR1^ENST00000268712.8" ; Parent "SREBF1--NCOR1^NCOR1^ENSG00000141027.21" ; ccdsid "CCDS11175.1" ; exon_id "ENSE00003656730.1" ; exon_number 2 ; gene_id "SREBF1--NCOR1^NCOR1^ENSG00000141027.21" ; gene_name NCOR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059309.12" ; havana_transcript "OTTHUMT00000131751.6" ; hgnc_id "HGNC:7672" ; level 2 ; orig_coord_info "chr17,16194462,16194569,-" ; protein_id "ENSP00000268712.2" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SREBF1--NCOR1^ENST00000268712.8" ; transcript_name "NCOR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SRGAP2B--SEC22B3P HAVANA gene 1001 17112 . + . FI_gene_label "SRGAP2B^ENSG00000196369.11" ; ID "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11" ; exon_id "ENSE00001848190.1" ; exon_number 2 ; gene_id "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11" ; gene_name SRGAP2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000041442.8" ; havana_transcript "OTTHUMT00000099258.6" ; hgnc_id "HGNC:35237" ; level 2 ; orig_coord_info "chr1,145092835,145092901,-" ; protein_id "ENSP00000477776.1" ; tag basic appris_alternative_2 ; transcript_id "SRGAP2B--SEC22B3P^ENST00000612199.4" ; transcript_name "SRGAP2B-204" ; transcript_support_level 1 ; transcript_type protein_coding
SRGAP2B--SEC22B3P HAVANA mRNA 1001 17112 . + . FI_gene_label "SRGAP2B^ENSG00000196369.11" ; ID "SRGAP2B--SEC22B3P^ENST00000612199.4" ; Parent "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11" ; exon_id "ENSE00001848190.1" ; exon_number 2 ; gene_id "SRGAP2B--SEC22B3P^SRGAP2B^ENSG00000196369.11" ; gene_name SRGAP2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000041442.8" ; havana_transcript "OTTHUMT00000099258.6" ; hgnc_id "HGNC:35237" ; level 2 ; orig_coord_info "chr1,145092835,145092901,-" ; protein_id "ENSP00000477776.1" ; tag basic appris_alternative_2 ; transcript_id "SRGAP2B--SEC22B3P^ENST00000612199.4" ; transcript_name "SRGAP2B-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STARD13--AL139005.1 HAVANA gene 7683 28646 . + . FI_gene_label "STARD13^ENSG00000133121.21" ; ID "STARD13--AL139005.1^STARD13^ENSG00000133121.21" ; ccdsid "CCDS9349.1" ; exon_id "ENSE00001333091.2" ; exon_number 1 ; gene_id "STARD13--AL139005.1^STARD13^ENSG00000133121.21" ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8" ; havana_transcript "OTTHUMT00000044439.3" ; hgnc_id "HGNC:19164" ; level 2 ; orig_coord_info "chr13,33185878,33186022,-" ; protein_id "ENSP00000255486.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--AL139005.1^ENST00000255486.8" ; transcript_name "STARD13-201" ; transcript_support_level 1 ; transcript_type protein_coding
STARD13--AL139005.1 HAVANA mRNA 7683 28646 . + . FI_gene_label "STARD13^ENSG00000133121.21" ; ID "STARD13--AL139005.1^ENST00000255486.8" ; Parent "STARD13--AL139005.1^STARD13^ENSG00000133121.21" ; ccdsid "CCDS9349.1" ; exon_id "ENSE00001333091.2" ; exon_number 1 ; gene_id "STARD13--AL139005.1^STARD13^ENSG00000133121.21" ; gene_name STARD13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016708.8" ; havana_transcript "OTTHUMT00000044439.3" ; hgnc_id "HGNC:19164" ; level 2 ; orig_coord_info "chr13,33185878,33186022,-" ; protein_id "ENSP00000255486.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "STARD13--AL139005.1^ENST00000255486.8" ; transcript_name "STARD13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SUZ12P1--AFMID HAVANA gene 20691 30890 . + . FI_gene_label "AFMID^ENSG00000183077.15" ; ID "SUZ12P1--AFMID^AFMID^ENSG00000183077.15" ; ccdsid "CCDS45801.1" ; exon_id "ENSE00003668375.1" ; exon_number 1 ; gene_id "SUZ12P1--AFMID^AFMID^ENSG00000183077.15" ; gene_name AFMID ; gene_type protein_coding ; havana_gene "OTTHUMG00000153957.4" ; havana_transcript "OTTHUMT00000333203.1" ; hgnc_id "HGNC:20910" ; level 2 ; orig_coord_info "chr17,78187371,78187433,+" ; protein_id "ENSP00000328938.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "SUZ12P1--AFMID^ENST00000327898.9" ; transcript_name "AFMID-201" ; transcript_support_level 1 ; transcript_type protein_coding
SUZ12P1--AFMID HAVANA mRNA 20691 30890 . + . FI_gene_label "AFMID^ENSG00000183077.15" ; ID "SUZ12P1--AFMID^ENST00000327898.9" ; Parent "SUZ12P1--AFMID^AFMID^ENSG00000183077.15" ; ccdsid "CCDS45801.1" ; exon_id "ENSE00003668375.1" ; exon_number 1 ; gene_id "SUZ12P1--AFMID^AFMID^ENSG00000183077.15" ; gene_name AFMID ; gene_type protein_coding ; havana_gene "OTTHUMG00000153957.4" ; havana_transcript "OTTHUMT00000333203.1" ; hgnc_id "HGNC:20910" ; level 2 ; orig_coord_info "chr17,78187371,78187433,+" ; protein_id "ENSP00000328938.5" ; tag basic appris_alternative_2 CCDS ; transcript_id "SUZ12P1--AFMID^ENST00000327898.9" ; transcript_name "AFMID-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:
ASPH--LINC02842 HAVANA gene 58793 62237 . + . FI_gene_label "LINC02842^ENSG00000254119.5" ; ID "ASPH--LINC02842^LINC02842^ENSG00000254119.5" ; exon_id "ENSE00002098747.1" ; exon_number 1 ; gene_id "ASPH--LINC02842^LINC02842^ENSG00000254119.5" ; gene_name LINC02842 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164339.3" ; havana_transcript "OTTHUMT00000378340.1" ; hgnc_id "HGNC:54378" ; level 2 ; orig_coord_info "chr8,61834917,61834996,+" ; tag basic ; transcript_id "ASPH--LINC02842^ENST00000517953.5" ; transcript_name "LINC02842-201" ; transcript_support_level 3 ; transcript_type lncRNA
ASPH--LINC02842 HAVANA RNA 58793 62237 . + . FI_gene_label "LINC02842^ENSG00000254119.5" ; ID "ASPH--LINC02842^ENST00000517953.5" ; Parent "ASPH--LINC02842^LINC02842^ENSG00000254119.5" ; exon_id "ENSE00002098747.1" ; exon_number 1 ; gene_id "ASPH--LINC02842^LINC02842^ENSG00000254119.5" ; gene_name LINC02842 ; gene_type lncRNA ; havana_gene "OTTHUMG00000164339.3" ; havana_transcript "OTTHUMT00000378340.1" ; hgnc_id "HGNC:54378" ; level 2 ; orig_coord_info "chr8,61834917,61834996,+" ; tag basic ; transcript_id "ASPH--LINC02842^ENST00000517953.5" ; transcript_name "LINC02842-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
ATP11A--AL359649.1 HAVANA gene 47728 52767 . + . FI_gene_label "AL359649.1^ENSG00000204398.5" ; ID "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5" ; exon_id "ENSE00001468102.1" ; exon_number 1 ; gene_id "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5" ; gene_name "AL359649.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017360.3" ; havana_transcript "OTTHUMT00000045814.2" ; level 2 ; orig_coord_info "chr13,111588291,111588344,+" ; tag basic ; transcript_id "ATP11A--AL359649.1^ENST00000375713.1" ; transcript_name "AL359649.1-202" ; transcript_support_level 5 ; transcript_type lncRNA
ATP11A--AL359649.1 HAVANA RNA 47728 52767 . + . FI_gene_label "AL359649.1^ENSG00000204398.5" ; ID "ATP11A--AL359649.1^ENST00000375713.1" ; Parent "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5" ; exon_id "ENSE00001468102.1" ; exon_number 1 ; gene_id "ATP11A--AL359649.1^AL359649.1^ENSG00000204398.5" ; gene_name "AL359649.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017360.3" ; havana_transcript "OTTHUMT00000045814.2" ; level 2 ; orig_coord_info "chr13,111588291,111588344,+" ; tag basic ; transcript_id "ATP11A--AL359649.1^ENST00000375713.1" ; transcript_name "AL359649.1-202" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
ATP11A--LINC00354 HAVANA gene 51573 52521 . + . FI_gene_label "LINC00354^ENSG00000226903.2" ; ID "ATP11A--LINC00354^LINC00354^ENSG00000226903.2" ; exon_id "ENSE00001724879.1" ; exon_number 1 ; gene_id "ATP11A--LINC00354^LINC00354^ENSG00000226903.2" ; gene_name LINC00354 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017361.10" ; havana_transcript "OTTHUMT00000045815.1" ; hgnc_id "HGNC:42672" ; level 2 ; orig_coord_info "chr13,111899988,111900083,+" ; transcript_id "ATP11A--LINC00354^ENST00000412119.1" ; transcript_name "LINC00354-201" ; transcript_support_level 5 ; transcript_type lncRNA
ATP11A--LINC00354 HAVANA RNA 51573 52521 . + . FI_gene_label "LINC00354^ENSG00000226903.2" ; ID "ATP11A--LINC00354^ENST00000412119.1" ; Parent "ATP11A--LINC00354^LINC00354^ENSG00000226903.2" ; exon_id "ENSE00001724879.1" ; exon_number 1 ; gene_id "ATP11A--LINC00354^LINC00354^ENSG00000226903.2" ; gene_name LINC00354 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017361.10" ; havana_transcript "OTTHUMT00000045815.1" ; hgnc_id "HGNC:42672" ; level 2 ; orig_coord_info "chr13,111899988,111900083,+" ; transcript_id "ATP11A--LINC00354^ENST00000412119.1" ; transcript_name "LINC00354-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
SRGAP2B--SEC22B3P HAVANA gene 20113 23688 . + . FI_gene_label "SEC22B3P^ENSG00000275140.1" ; ID "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1" ; exon_id "ENSE00003747856.1" ; exon_number 1 ; gene_id "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1" ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1" ; havana_transcript "OTTHUMT00000477871.1" ; hgnc_id "HGNC:53891" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr1,148784482,148784594,-" ; tag basic ; transcript_id "SRGAP2B--SEC22B3P^ENST00000616023.1" ; transcript_name "SEC22B3P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
SRGAP2B--SEC22B3P HAVANA RNA 20113 23688 . + . FI_gene_label "SEC22B3P^ENSG00000275140.1" ; ID "SRGAP2B--SEC22B3P^ENST00000616023.1" ; Parent "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1" ; exon_id "ENSE00003747856.1" ; exon_number 1 ; gene_id "SRGAP2B--SEC22B3P^SEC22B3P^ENSG00000275140.1" ; gene_name SEC22B3P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188674.1" ; havana_transcript "OTTHUMT00000477871.1" ; hgnc_id "HGNC:53891" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr1,148784482,148784594,-" ; tag basic ; transcript_id "SRGAP2B--SEC22B3P^ENST00000616023.1" ; transcript_name "SEC22B3P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
STARD13--AL139005.1 HAVANA gene 31680 33314 . + . FI_gene_label "AL139005.1^ENSG00000279393.1" ; ID "STARD13--AL139005.1^AL139005.1^ENSG00000279393.1" ; exon_id "ENSE00003759365.1" ; exon_number 1 ; gene_id "STARD13--AL139005.1^AL139005.1^ENSG00000279393.1" ; gene_name "AL139005.1" ; gene_type TEC ; havana_gene "OTTHUMG00000175973.1" ; havana_transcript "OTTHUMT00000431332.1" ; level 2 ; orig_coord_info "chr13,28495633,28497267,+" ; tag basic ; transcript_id "STARD13--AL139005.1^ENST00000623899.1" ; transcript_name "AL139005.1-201" ; transcript_support_level NA ; transcript_type TEC
STARD13--AL139005.1 HAVANA RNA 31680 33314 . + . FI_gene_label "AL139005.1^ENSG00000279393.1" ; ID "STARD13--AL139005.1^ENST00000623899.1" ; Parent "STARD13--AL139005.1^AL139005.1^ENSG00000279393.1" ; exon_id "ENSE00003759365.1" ; exon_number 1 ; gene_id "STARD13--AL139005.1^AL139005.1^ENSG00000279393.1" ; gene_name "AL139005.1" ; gene_type TEC ; havana_gene "OTTHUMG00000175973.1" ; havana_transcript "OTTHUMT00000431332.1" ; level 2 ; orig_coord_info "chr13,28495633,28497267,+" ; tag basic ; transcript_id "STARD13--AL139005.1^ENST00000623899.1" ; transcript_name "AL139005.1-201" ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created:
SUZ12P1--AFMID HAVANA gene 2514 7684 . + . FI_gene_label "SUZ12P1^ENSG00000264538.6" ; ID "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6" ; exon_id "ENSE00002690561.1" ; exon_number 1 ; gene_id "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6" ; gene_name SUZ12P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000178989.2" ; havana_transcript "OTTHUMT00000444258.1" ; hgnc_id "HGNC:32421" ; level 2 ; orig_coord_info "chr17,30731706,30732123,+" ; transcript_id "SUZ12P1--AFMID^ENST00000497969.6" ; transcript_name "SUZ12P1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
SUZ12P1--AFMID HAVANA RNA 2514 7684 . + . FI_gene_label "SUZ12P1^ENSG00000264538.6" ; ID "SUZ12P1--AFMID^ENST00000497969.6" ; Parent "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6" ; exon_id "ENSE00002690561.1" ; exon_number 1 ; gene_id "SUZ12P1--AFMID^SUZ12P1^ENSG00000264538.6" ; gene_name SUZ12P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000178989.2" ; havana_transcript "OTTHUMT00000444258.1" ; hgnc_id "HGNC:32421" ; level 2 ; orig_coord_info "chr17,30731706,30732123,+" ; transcript_id "SUZ12P1--AFMID^ENST00000497969.6" ; transcript_name "SUZ12P1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
317 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 ------------------------------
386 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