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: 4017
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4017
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:4017
=> 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:
AC004980.3--UPK3BL1 HAVANA gene 6366 11192 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC004980.3--UPK3BL1 HAVANA mRNA 6366 11192 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "AC004980.3--UPK3BL1^ENST00000340457.8" ; Parent "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CPSF6--ANKRD36C HAVANA gene 1048 12978 . + . FI_gene_label "CPSF6^ENSG00000111605.18" ; ID "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18" ; ccdsid "CCDS73494.1" ; exon_id "ENSE00002424959.1" ; exon_number 1 ; gene_id "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18" ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4" ; havana_transcript "OTTHUMT00000403613.1" ; hgnc_id "HGNC:13871" ; level 2 ; orig_coord_info "chr12,69239647,69239706,+" ; protein_id "ENSP00000266679.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--ANKRD36C^ENST00000266679.8" ; transcript_name "CPSF6-201" ; transcript_support_level 1 ; transcript_type protein_coding
CPSF6--ANKRD36C HAVANA mRNA 1048 12978 . + . FI_gene_label "CPSF6^ENSG00000111605.18" ; ID "CPSF6--ANKRD36C^ENST00000266679.8" ; Parent "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18" ; ccdsid "CCDS73494.1" ; exon_id "ENSE00002424959.1" ; exon_number 1 ; gene_id "CPSF6--ANKRD36C^CPSF6^ENSG00000111605.18" ; gene_name CPSF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169340.4" ; havana_transcript "OTTHUMT00000403613.1" ; hgnc_id "HGNC:13871" ; level 2 ; orig_coord_info "chr12,69239647,69239706,+" ; protein_id "ENSP00000266679.8" ; tag basic appris_alternative_1 CCDS ; transcript_id "CPSF6--ANKRD36C^ENST00000266679.8" ; transcript_name "CPSF6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CPSF6--ANKRD36C ENSEMBL gene 35506 73554 . + . FI_gene_label "ANKRD36C^ENSG00000174501.14" ; ID "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14" ; exon_id "ENSE00003729919.1" ; exon_number 5 ; gene_id "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14" ; gene_name ANKRD36C ; gene_type protein_coding ; havana_gene "OTTHUMG00000155211.2" ; hgnc_id "HGNC:32946" ; level 3 ; orig_coord_info "chr2,95935454,95935487,-" ; protein_id "ENSP00000295246.6" ; tag basic ; transcript_id "CPSF6--ANKRD36C^ENST00000295246.6" ; transcript_name "ANKRD36C-201" ; transcript_support_level 5 ; transcript_type protein_coding
CPSF6--ANKRD36C ENSEMBL mRNA 35506 73554 . + . FI_gene_label "ANKRD36C^ENSG00000174501.14" ; ID "CPSF6--ANKRD36C^ENST00000295246.6" ; Parent "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14" ; exon_id "ENSE00003729919.1" ; exon_number 5 ; gene_id "CPSF6--ANKRD36C^ANKRD36C^ENSG00000174501.14" ; gene_name ANKRD36C ; gene_type protein_coding ; havana_gene "OTTHUMG00000155211.2" ; hgnc_id "HGNC:32946" ; level 3 ; orig_coord_info "chr2,95935454,95935487,-" ; protein_id "ENSP00000295246.6" ; tag basic ; transcript_id "CPSF6--ANKRD36C^ENST00000295246.6" ; transcript_name "ANKRD36C-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
EFL1--GOLGA6L11P HAVANA gene 1001 25062 . + . FI_gene_label "EFL1^ENSG00000140598.15" ; ID "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; ccdsid "CCDS42071.1" ; exon_id "ENSE00003786417.1" ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5" ; havana_transcript "OTTHUMT00000419252.2" ; hgnc_id "HGNC:25789" ; level 2 ; orig_coord_info "chr15,82261688,82261778,-" ; protein_id "ENSP00000268206.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12" ; transcript_name "EFL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
EFL1--GOLGA6L11P HAVANA mRNA 1001 25062 . + . FI_gene_label "EFL1^ENSG00000140598.15" ; ID "EFL1--GOLGA6L11P^ENST00000268206.12" ; Parent "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; ccdsid "CCDS42071.1" ; exon_id "ENSE00003786417.1" ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15" ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5" ; havana_transcript "OTTHUMT00000419252.2" ; hgnc_id "HGNC:25789" ; level 2 ; orig_coord_info "chr15,82261688,82261778,-" ; protein_id "ENSP00000268206.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12" ; transcript_name "EFL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EIF4G3--HP1BP3 HAVANA gene 10142 51670 . + . FI_gene_label "EIF4G3^ENSG00000075151.22" ; ID "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22" ; ccdsid "CCDS214.1" ; exon_id "ENSE00003337316.1" ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22" ; gene_name EIF4G3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002624.7" ; havana_transcript "OTTHUMT00000007467.3" ; hgnc_id "HGNC:3298" ; level 2 ; orig_coord_info "chr1,21002713,21002742,-" ; protein_id "ENSP00000264211.7" ; tag basic appris_principal_4 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000264211.12" ; transcript_name "EIF4G3-201" ; transcript_support_level 5 ; transcript_type protein_coding
EIF4G3--HP1BP3 HAVANA mRNA 10142 51670 . + . FI_gene_label "EIF4G3^ENSG00000075151.22" ; ID "EIF4G3--HP1BP3^ENST00000264211.12" ; Parent "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22" ; ccdsid "CCDS214.1" ; exon_id "ENSE00003337316.1" ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^EIF4G3^ENSG00000075151.22" ; gene_name EIF4G3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002624.7" ; havana_transcript "OTTHUMT00000007467.3" ; hgnc_id "HGNC:3298" ; level 2 ; orig_coord_info "chr1,21002713,21002742,-" ; protein_id "ENSP00000264211.7" ; tag basic appris_principal_4 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000264211.12" ; transcript_name "EIF4G3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
EIF4G3--HP1BP3 HAVANA gene 55520 73106 . + . FI_gene_label "HP1BP3^ENSG00000127483.19" ; ID "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19" ; ccdsid "CCDS30621.1" ; exon_id "ENSE00002245255.1" ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19" ; gene_name HP1BP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002622.10" ; havana_transcript "OTTHUMT00000007457.3" ; hgnc_id "HGNC:24973" ; level 2 ; orig_coord_info "chr1,20780345,20780440,-" ; protein_id "ENSP00000312625.5" ; tag basic appris_principal_2 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000312239.10" ; transcript_name "HP1BP3-201" ; transcript_support_level 2 ; transcript_type protein_coding
EIF4G3--HP1BP3 HAVANA mRNA 55520 73106 . + . FI_gene_label "HP1BP3^ENSG00000127483.19" ; ID "EIF4G3--HP1BP3^ENST00000312239.10" ; Parent "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19" ; ccdsid "CCDS30621.1" ; exon_id "ENSE00002245255.1" ; exon_number 2 ; gene_id "EIF4G3--HP1BP3^HP1BP3^ENSG00000127483.19" ; gene_name HP1BP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002622.10" ; havana_transcript "OTTHUMT00000007457.3" ; hgnc_id "HGNC:24973" ; level 2 ; orig_coord_info "chr1,20780345,20780440,-" ; protein_id "ENSP00000312625.5" ; tag basic appris_principal_2 CCDS ; transcript_id "EIF4G3--HP1BP3^ENST00000312239.10" ; transcript_name "HP1BP3-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
GINS2--AC025822.2 HAVANA gene 2120 8183 . + . FI_gene_label "GINS2^ENSG00000131153.9" ; ID "GINS2--AC025822.2^GINS2^ENSG00000131153.9" ; ccdsid "CCDS10953.1" ; exon_id "ENSE00001303150.3" ; exon_number 1 ; gene_id "GINS2--AC025822.2^GINS2^ENSG00000131153.9" ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4" ; havana_transcript "OTTHUMT00000269098.2" ; hgnc_id "HGNC:24575" ; level 2 ; orig_coord_info "chr16,85688809,85688898,-" ; protein_id "ENSP00000253462.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--AC025822.2^ENST00000253462.8" ; transcript_name "GINS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GINS2--AC025822.2 HAVANA mRNA 2120 8183 . + . FI_gene_label "GINS2^ENSG00000131153.9" ; ID "GINS2--AC025822.2^ENST00000253462.8" ; Parent "GINS2--AC025822.2^GINS2^ENSG00000131153.9" ; ccdsid "CCDS10953.1" ; exon_id "ENSE00001303150.3" ; exon_number 1 ; gene_id "GINS2--AC025822.2^GINS2^ENSG00000131153.9" ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4" ; havana_transcript "OTTHUMT00000269098.2" ; hgnc_id "HGNC:24575" ; level 2 ; orig_coord_info "chr16,85688809,85688898,-" ; protein_id "ENSP00000253462.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--AC025822.2^ENST00000253462.8" ; transcript_name "GINS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GINS2--LINC00702 HAVANA gene 2120 8183 . + . FI_gene_label "GINS2^ENSG00000131153.9" ; ID "GINS2--LINC00702^GINS2^ENSG00000131153.9" ; ccdsid "CCDS10953.1" ; exon_id "ENSE00001303150.3" ; exon_number 1 ; gene_id "GINS2--LINC00702^GINS2^ENSG00000131153.9" ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4" ; havana_transcript "OTTHUMT00000269098.2" ; hgnc_id "HGNC:24575" ; level 2 ; orig_coord_info "chr16,85688809,85688898,-" ; protein_id "ENSP00000253462.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--LINC00702^ENST00000253462.8" ; transcript_name "GINS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GINS2--LINC00702 HAVANA mRNA 2120 8183 . + . FI_gene_label "GINS2^ENSG00000131153.9" ; ID "GINS2--LINC00702^ENST00000253462.8" ; Parent "GINS2--LINC00702^GINS2^ENSG00000131153.9" ; ccdsid "CCDS10953.1" ; exon_id "ENSE00001303150.3" ; exon_number 1 ; gene_id "GINS2--LINC00702^GINS2^ENSG00000131153.9" ; gene_name GINS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137646.4" ; havana_transcript "OTTHUMT00000269098.2" ; hgnc_id "HGNC:24575" ; level 2 ; orig_coord_info "chr16,85688809,85688898,-" ; protein_id "ENSP00000253462.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GINS2--LINC00702^ENST00000253462.8" ; transcript_name "GINS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^ENST00000289272.3" ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^ENST00000616325.1" ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PKD1--NPIPB12 HAVANA gene 1001 30973 . + . FI_gene_label "PKD1^ENSG00000008710.20" ; ID "PKD1--NPIPB12^PKD1^ENSG00000008710.20" ; ccdsid "CCDS32369.1" ; exon_id "ENSE00002710399.1" ; exon_number 1 ; gene_id "PKD1--NPIPB12^PKD1^ENSG00000008710.20" ; gene_name PKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155795.6" ; havana_transcript "OTTHUMT00000341688.2" ; hgnc_id "HGNC:9008" ; level 2 ; orig_coord_info "chr16,2135475,2135689,-" ; protein_id "ENSP00000262304.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PKD1--NPIPB12^ENST00000262304.9" ; transcript_name "PKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PKD1--NPIPB12 HAVANA mRNA 1001 30973 . + . FI_gene_label "PKD1^ENSG00000008710.20" ; ID "PKD1--NPIPB12^ENST00000262304.9" ; Parent "PKD1--NPIPB12^PKD1^ENSG00000008710.20" ; ccdsid "CCDS32369.1" ; exon_id "ENSE00002710399.1" ; exon_number 1 ; gene_id "PKD1--NPIPB12^PKD1^ENSG00000008710.20" ; gene_name PKD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155795.6" ; havana_transcript "OTTHUMT00000341688.2" ; hgnc_id "HGNC:9008" ; level 2 ; orig_coord_info "chr16,2135475,2135689,-" ; protein_id "ENSP00000262304.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PKD1--NPIPB12^ENST00000262304.9" ; transcript_name "PKD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PKD1--NPIPB12 ENSEMBL gene 42932 45149 . + . FI_gene_label "NPIPB12^ENSG00000169203.16" ; ID "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16" ; exon_id "ENSE00001744303.2" ; exon_number 1 ; gene_id "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16" ; gene_name NPIPB12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163547.2" ; hgnc_id "HGNC:37491" ; level 3 ; orig_coord_info "chr16,29485263,29485827,-" ; protein_id "ENSP00000399107.3" ; tag basic appris_alternative_2 ; transcript_id "PKD1--NPIPB12^ENST00000458643.3" ; transcript_name "NPIPB12-201" ; transcript_support_level 5 ; transcript_type protein_coding
PKD1--NPIPB12 ENSEMBL mRNA 42932 45149 . + . FI_gene_label "NPIPB12^ENSG00000169203.16" ; ID "PKD1--NPIPB12^ENST00000458643.3" ; Parent "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16" ; exon_id "ENSE00001744303.2" ; exon_number 1 ; gene_id "PKD1--NPIPB12^NPIPB12^ENSG00000169203.16" ; gene_name NPIPB12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163547.2" ; hgnc_id "HGNC:37491" ; level 3 ; orig_coord_info "chr16,29485263,29485827,-" ; protein_id "ENSP00000399107.3" ; tag basic appris_alternative_2 ; transcript_id "PKD1--NPIPB12^ENST00000458643.3" ; transcript_name "NPIPB12-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PMS2P1--UPK3BL1 HAVANA gene 14962 19788 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P1--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P1--UPK3BL1 HAVANA mRNA 14962 19788 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "PMS2P1--UPK3BL1^ENST00000340457.8" ; Parent "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P1--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PSG5--CD177 HAVANA gene 1001 12284 . + . FI_gene_label "PSG5^ENSG00000204941.14" ; ID "PSG5--CD177^PSG5^ENSG00000204941.14" ; ccdsid "CCDS12617.1" ; exon_id "ENSE00001564066.1" ; exon_number 1 ; gene_id "PSG5--CD177^PSG5^ENSG00000204941.14" ; gene_name PSG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151539.3" ; havana_transcript "OTTHUMT00000323057.1" ; hgnc_id "HGNC:9522" ; level 2 ; orig_coord_info "chr19,43186342,43186405,-" ; protein_id "ENSP00000344413.6" ; tag alternative_3_UTR basic MANE_Select CCDS ; transcript_id "PSG5--CD177^ENST00000342951.11" ; transcript_name "PSG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
PSG5--CD177 HAVANA mRNA 1001 12284 . + . FI_gene_label "PSG5^ENSG00000204941.14" ; ID "PSG5--CD177^ENST00000342951.11" ; Parent "PSG5--CD177^PSG5^ENSG00000204941.14" ; ccdsid "CCDS12617.1" ; exon_id "ENSE00001564066.1" ; exon_number 1 ; gene_id "PSG5--CD177^PSG5^ENSG00000204941.14" ; gene_name PSG5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151539.3" ; havana_transcript "OTTHUMT00000323057.1" ; hgnc_id "HGNC:9522" ; level 2 ; orig_coord_info "chr19,43186342,43186405,-" ; protein_id "ENSP00000344413.6" ; tag alternative_3_UTR basic MANE_Select CCDS ; transcript_id "PSG5--CD177^ENST00000342951.11" ; transcript_name "PSG5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PSG5--CD177 HAVANA gene 16801 22302 . + . FI_gene_label "CD177^ENSG00000204936.10" ; ID "PSG5--CD177^CD177^ENSG00000204936.10" ; exon_id "ENSE00003739430.1" ; exon_number 1 ; gene_id "PSG5--CD177^CD177^ENSG00000204936.10" ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4" ; havana_transcript "OTTHUMT00000470164.2" ; hgnc_id "HGNC:30072" ; level 2 ; orig_coord_info "chr19,43353715,43353766,+" ; protein_id "ENSP00000367251.2" ; transcript_id "PSG5--CD177^ENST00000378012.3" ; transcript_name "CD177-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
PSG5--CD177 HAVANA mRNA 16801 22302 . + . FI_gene_label "CD177^ENSG00000204936.10" ; ID "PSG5--CD177^ENST00000378012.3" ; Parent "PSG5--CD177^CD177^ENSG00000204936.10" ; exon_id "ENSE00003739430.1" ; exon_number 1 ; gene_id "PSG5--CD177^CD177^ENSG00000204936.10" ; gene_name CD177 ; gene_type protein_coding ; havana_gene "OTTHUMG00000185320.4" ; havana_transcript "OTTHUMT00000470164.2" ; hgnc_id "HGNC:30072" ; level 2 ; orig_coord_info "chr19,43353715,43353766,+" ; protein_id "ENSP00000367251.2" ; transcript_id "PSG5--CD177^ENST00000378012.3" ; transcript_name "CD177-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
PUM1--NKAIN1 HAVANA gene 1294 30447 . + . FI_gene_label "PUM1^ENSG00000134644.16" ; ID "PUM1--NKAIN1^PUM1^ENSG00000134644.16" ; ccdsid "CCDS338.1" ; exon_id "ENSE00003607854.1" ; exon_number 2 ; gene_id "PUM1--NKAIN1^PUM1^ENSG00000134644.16" ; gene_name PUM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003795.5" ; havana_transcript "OTTHUMT00000010671.1" ; hgnc_id "HGNC:14957" ; level 2 ; orig_coord_info "chr1,31059204,31059566,-" ; protein_id "ENSP00000257075.5" ; tag basic appris_principal_4 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000257075.9" ; transcript_name "PUM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PUM1--NKAIN1 HAVANA mRNA 1294 30447 . + . FI_gene_label "PUM1^ENSG00000134644.16" ; ID "PUM1--NKAIN1^ENST00000257075.9" ; Parent "PUM1--NKAIN1^PUM1^ENSG00000134644.16" ; ccdsid "CCDS338.1" ; exon_id "ENSE00003607854.1" ; exon_number 2 ; gene_id "PUM1--NKAIN1^PUM1^ENSG00000134644.16" ; gene_name PUM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003795.5" ; havana_transcript "OTTHUMT00000010671.1" ; hgnc_id "HGNC:14957" ; level 2 ; orig_coord_info "chr1,31059204,31059566,-" ; protein_id "ENSP00000257075.5" ; tag basic appris_principal_4 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000257075.9" ; transcript_name "PUM1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PUM1--NKAIN1 HAVANA gene 33448 42502 . + . FI_gene_label "NKAIN1^ENSG00000084628.10" ; ID "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10" ; ccdsid "CCDS339.2" ; exon_id "ENSE00001461423.3" ; exon_number 1 ; gene_id "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10" ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5" ; havana_transcript "OTTHUMT00000010655.3" ; hgnc_id "HGNC:25743" ; level 2 ; orig_coord_info "chr1,31239494,31239547,-" ; protein_id "ENSP00000362841.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000373736.7" ; transcript_name "NKAIN1-201" ; transcript_support_level 2 ; transcript_type protein_coding
PUM1--NKAIN1 HAVANA mRNA 33448 42502 . + . FI_gene_label "NKAIN1^ENSG00000084628.10" ; ID "PUM1--NKAIN1^ENST00000373736.7" ; Parent "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10" ; ccdsid "CCDS339.2" ; exon_id "ENSE00001461423.3" ; exon_number 1 ; gene_id "PUM1--NKAIN1^NKAIN1^ENSG00000084628.10" ; gene_name NKAIN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003788.5" ; havana_transcript "OTTHUMT00000010655.3" ; hgnc_id "HGNC:25743" ; level 2 ; orig_coord_info "chr1,31239494,31239547,-" ; protein_id "ENSP00000362841.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PUM1--NKAIN1^ENST00000373736.7" ; transcript_name "NKAIN1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
RAB3B--SSBP3 HAVANA gene 22749 45544 . + . FI_gene_label "SSBP3^ENSG00000157216.16" ; ID "RAB3B--SSBP3^SSBP3^ENSG00000157216.16" ; ccdsid "CCDS590.1" ; exon_id "ENSE00001894230.1" ; exon_number 1 ; gene_id "RAB3B--SSBP3^SSBP3^ENSG00000157216.16" ; gene_name SSBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008264.5" ; havana_transcript "OTTHUMT00000022720.2" ; hgnc_id "HGNC:15674" ; level 2 ; orig_coord_info "chr1,54405953,54406008,-" ; protein_id "ENSP00000350067.4" ; tag basic CCDS ; transcript_id "RAB3B--SSBP3^ENST00000357475.9" ; transcript_name "SSBP3-202" ; transcript_support_level 1 ; transcript_type protein_coding
RAB3B--SSBP3 HAVANA mRNA 22749 45544 . + . FI_gene_label "SSBP3^ENSG00000157216.16" ; ID "RAB3B--SSBP3^ENST00000357475.9" ; Parent "RAB3B--SSBP3^SSBP3^ENSG00000157216.16" ; ccdsid "CCDS590.1" ; exon_id "ENSE00001894230.1" ; exon_number 1 ; gene_id "RAB3B--SSBP3^SSBP3^ENSG00000157216.16" ; gene_name SSBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008264.5" ; havana_transcript "OTTHUMT00000022720.2" ; hgnc_id "HGNC:15674" ; level 2 ; orig_coord_info "chr1,54405953,54406008,-" ; protein_id "ENSP00000350067.4" ; tag basic CCDS ; transcript_id "RAB3B--SSBP3^ENST00000357475.9" ; transcript_name "SSBP3-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RAB3B--SSBP3 HAVANA gene 1001 17780 . + . FI_gene_label "RAB3B^ENSG00000169213.7" ; ID "RAB3B--SSBP3^RAB3B^ENSG00000169213.7" ; ccdsid "CCDS560.1" ; exon_id "ENSE00003281431.1" ; exon_number 2 ; gene_id "RAB3B--SSBP3^RAB3B^ENSG00000169213.7" ; gene_name RAB3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000008627.2" ; havana_transcript "OTTHUMT00000023816.2" ; hgnc_id "HGNC:9778" ; level 2 ; orig_coord_info "chr1,51976890,51977117,-" ; protein_id "ENSP00000360718.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB3B--SSBP3^ENST00000371655.4" ; transcript_name "RAB3B-201" ; transcript_support_level 1 ; transcript_type protein_coding
RAB3B--SSBP3 HAVANA mRNA 1001 17780 . + . FI_gene_label "RAB3B^ENSG00000169213.7" ; ID "RAB3B--SSBP3^ENST00000371655.4" ; Parent "RAB3B--SSBP3^RAB3B^ENSG00000169213.7" ; ccdsid "CCDS560.1" ; exon_id "ENSE00003281431.1" ; exon_number 2 ; gene_id "RAB3B--SSBP3^RAB3B^ENSG00000169213.7" ; gene_name RAB3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000008627.2" ; havana_transcript "OTTHUMT00000023816.2" ; hgnc_id "HGNC:9778" ; level 2 ; orig_coord_info "chr1,51976890,51977117,-" ; protein_id "ENSP00000360718.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAB3B--SSBP3^ENST00000371655.4" ; transcript_name "RAB3B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SBF2--RIC3 HAVANA gene 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--RIC3^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--RIC3^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--RIC3^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--RIC3 HAVANA mRNA 1001 59812 . + . FI_gene_label "SBF2^ENSG00000133812.17" ; ID "SBF2--RIC3^ENST00000256190.13" ; Parent "SBF2--RIC3^SBF2^ENSG00000133812.17" ; ccdsid "CCDS31427.1" ; exon_id "ENSE00003900171.1" ; exon_number 1 ; gene_id "SBF2--RIC3^SBF2^ENSG00000133812.17" ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3" ; havana_transcript "OTTHUMT00000386911.2" ; hgnc_id "HGNC:2135" ; level 2 ; orig_coord_info "chr11,10294015,10294069,-" ; protein_id "ENSP00000256190.8" ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--RIC3^ENST00000256190.13" ; transcript_name "SBF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SBF2--RIC3 HAVANA gene 62844 77582 . + . FI_gene_label "RIC3^ENSG00000166405.15" ; ID "SBF2--RIC3^RIC3^ENSG00000166405.15" ; ccdsid "CCDS55742.1" ; exon_id "ENSE00003848333.1" ; exon_number 1 ; gene_id "SBF2--RIC3^RIC3^ENSG00000166405.15" ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6" ; havana_transcript "OTTHUMT00000385900.3" ; hgnc_id "HGNC:30338" ; level 2 ; orig_coord_info "chr11,8168866,8168989,-" ; protein_id "ENSP00000308820.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SBF2--RIC3^ENST00000309737.11" ; transcript_name "RIC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--RIC3 HAVANA mRNA 62844 77582 . + . FI_gene_label "RIC3^ENSG00000166405.15" ; ID "SBF2--RIC3^ENST00000309737.11" ; Parent "SBF2--RIC3^RIC3^ENSG00000166405.15" ; ccdsid "CCDS55742.1" ; exon_id "ENSE00003848333.1" ; exon_number 1 ; gene_id "SBF2--RIC3^RIC3^ENSG00000166405.15" ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6" ; havana_transcript "OTTHUMT00000385900.3" ; hgnc_id "HGNC:30338" ; level 2 ; orig_coord_info "chr11,8168866,8168989,-" ; protein_id "ENSP00000308820.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "SBF2--RIC3^ENST00000309737.11" ; transcript_name "RIC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLFN11--SLFN12 HAVANA gene 14962 22369 . + . FI_gene_label "SLFN12^ENSG00000172123.13" ; ID "SLFN11--SLFN12^SLFN12^ENSG00000172123.13" ; ccdsid "CCDS11295.1" ; exon_id "ENSE00001160241.4" ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN12^ENSG00000172123.13" ; gene_name SLFN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132952.3" ; havana_transcript "OTTHUMT00000256490.1" ; hgnc_id "HGNC:25500" ; level 2 ; orig_coord_info "chr17,35421990,35423028,-" ; protein_id "ENSP00000302077.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000304905.10" ; transcript_name "SLFN12-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLFN11--SLFN12 HAVANA mRNA 14962 22369 . + . FI_gene_label "SLFN12^ENSG00000172123.13" ; ID "SLFN11--SLFN12^ENST00000304905.10" ; Parent "SLFN11--SLFN12^SLFN12^ENSG00000172123.13" ; ccdsid "CCDS11295.1" ; exon_id "ENSE00001160241.4" ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN12^ENSG00000172123.13" ; gene_name SLFN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132952.3" ; havana_transcript "OTTHUMT00000256490.1" ; hgnc_id "HGNC:25500" ; level 2 ; orig_coord_info "chr17,35421990,35423028,-" ; protein_id "ENSP00000302077.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000304905.10" ; transcript_name "SLFN12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLFN11--SLFN12 HAVANA gene 1095 11178 . + . FI_gene_label "SLFN11^ENSG00000172716.16" ; ID "SLFN11--SLFN12^SLFN11^ENSG00000172716.16" ; ccdsid "CCDS11294.1" ; exon_id "ENSE00001186651.3" ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN11^ENSG00000172716.16" ; gene_name SLFN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132948.3" ; havana_transcript "OTTHUMT00000256481.1" ; hgnc_id "HGNC:26633" ; level 2 ; orig_coord_info "chr17,35362739,35363807,-" ; protein_id "ENSP00000312402.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000308377.8" ; transcript_name "SLFN11-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLFN11--SLFN12 HAVANA mRNA 1095 11178 . + . FI_gene_label "SLFN11^ENSG00000172716.16" ; ID "SLFN11--SLFN12^ENST00000308377.8" ; Parent "SLFN11--SLFN12^SLFN11^ENSG00000172716.16" ; ccdsid "CCDS11294.1" ; exon_id "ENSE00001186651.3" ; exon_number 2 ; gene_id "SLFN11--SLFN12^SLFN11^ENSG00000172716.16" ; gene_name SLFN11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132948.3" ; havana_transcript "OTTHUMT00000256481.1" ; hgnc_id "HGNC:26633" ; level 2 ; orig_coord_info "chr17,35362739,35363807,-" ; protein_id "ENSP00000312402.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SLFN11--SLFN12^ENST00000308377.8" ; transcript_name "SLFN11-201" ; 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:
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:
AC004980.3--UPK3BL1 HAVANA gene 1001 3365 . + . FI_gene_label "AC004980.3^ENSG00000230305.2" ; ID "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; exon_id "ENSE00002500030.1" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; gene_name "AC004980.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2" ; havana_transcript "OTTHUMT00000341407.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76524515,76524698,+" ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1" ; transcript_name "AC004980.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC004980.3--UPK3BL1 HAVANA RNA 1001 3365 . + . FI_gene_label "AC004980.3^ENSG00000230305.2" ; ID "AC004980.3--UPK3BL1^ENST00000447046.1" ; Parent "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; exon_id "ENSE00002500030.1" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; gene_name "AC004980.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2" ; havana_transcript "OTTHUMT00000341407.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76524515,76524698,+" ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1" ; transcript_name "AC004980.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
EFL1--GOLGA6L11P HAVANA gene 28063 33687 . + . FI_gene_label "GOLGA6L11P^ENSG00000223698.3" ; ID "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; exon_id "ENSE00001742768.1" ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2" ; havana_transcript "OTTHUMT00000104689.2" ; hgnc_id "HGNC:23958" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chrY,24168187,24168270,+" ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2" ; transcript_name "GOLGA6L11P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EFL1--GOLGA6L11P HAVANA RNA 28063 33687 . + . FI_gene_label "GOLGA6L11P^ENSG00000223698.3" ; ID "EFL1--GOLGA6L11P^ENST00000417252.2" ; Parent "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; exon_id "ENSE00001742768.1" ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3" ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2" ; havana_transcript "OTTHUMT00000104689.2" ; hgnc_id "HGNC:23958" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chrY,24168187,24168270,+" ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2" ; transcript_name "GOLGA6L11P-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
GINS2--AC025822.2 HAVANA gene 11184 15782 . + . FI_gene_label "AC025822.2^ENSG00000236990.1" ; ID "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1" ; exon_id "ENSE00001647260.1" ; exon_number 1 ; gene_id "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1" ; gene_name "AC025822.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017571.1" ; havana_transcript "OTTHUMT00000046505.1" ; level 2 ; orig_coord_info "chr10,4051726,4052157,+" ; tag basic ; transcript_id "GINS2--AC025822.2^ENST00000455199.1" ; transcript_name "AC025822.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
GINS2--AC025822.2 HAVANA RNA 11184 15782 . + . FI_gene_label "AC025822.2^ENSG00000236990.1" ; ID "GINS2--AC025822.2^ENST00000455199.1" ; Parent "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1" ; exon_id "ENSE00001647260.1" ; exon_number 1 ; gene_id "GINS2--AC025822.2^AC025822.2^ENSG00000236990.1" ; gene_name "AC025822.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000017571.1" ; havana_transcript "OTTHUMT00000046505.1" ; level 2 ; orig_coord_info "chr10,4051726,4052157,+" ; tag basic ; transcript_id "GINS2--AC025822.2^ENST00000455199.1" ; transcript_name "AC025822.2-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
GINS2--LINC00702 HAVANA gene 11307 12146 . + . FI_gene_label "LINC00702^ENSG00000233117.4" ; ID "GINS2--LINC00702^LINC00702^ENSG00000233117.4" ; exon_id "ENSE00001727453.1" ; exon_number 1 ; gene_id "GINS2--LINC00702^LINC00702^ENSG00000233117.4" ; gene_name LINC00702 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017572.17" ; havana_transcript "OTTHUMT00000046506.1" ; hgnc_id "HGNC:44676" ; level 1 ; orig_coord_info "chr10,4243504,4243789,-" ; tag exp_conf ; transcript_id "GINS2--LINC00702^ENST00000418372.1" ; transcript_name "LINC00702-201" ; transcript_support_level 3 ; transcript_type lncRNA
GINS2--LINC00702 HAVANA RNA 11307 12146 . + . FI_gene_label "LINC00702^ENSG00000233117.4" ; ID "GINS2--LINC00702^ENST00000418372.1" ; Parent "GINS2--LINC00702^LINC00702^ENSG00000233117.4" ; exon_id "ENSE00001727453.1" ; exon_number 1 ; gene_id "GINS2--LINC00702^LINC00702^ENSG00000233117.4" ; gene_name LINC00702 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017572.17" ; havana_transcript "OTTHUMT00000046506.1" ; hgnc_id "HGNC:44676" ; level 1 ; orig_coord_info "chr10,4243504,4243789,-" ; tag exp_conf ; transcript_id "GINS2--LINC00702^ENST00000418372.1" ; transcript_name "LINC00702-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
PMS2P1--UPK3BL1 HAVANA gene 1448 6845 . + . FI_gene_label "PMS2P1^ENSG00000078319.10" ; ID "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10" ; exon_id "ENSE00003899279.1" ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10" ; gene_name PMS2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156885.3" ; havana_transcript "OTTHUMT00000346451.2" ; hgnc_id "HGNC:9123" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr7,100335838,100335860,-" ; tag basic ; transcript_id "PMS2P1--UPK3BL1^ENST00000431037.3" ; transcript_name "PMS2P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
PMS2P1--UPK3BL1 HAVANA RNA 1448 6845 . + . FI_gene_label "PMS2P1^ENSG00000078319.10" ; ID "PMS2P1--UPK3BL1^ENST00000431037.3" ; Parent "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10" ; exon_id "ENSE00003899279.1" ; exon_number 1 ; gene_id "PMS2P1--UPK3BL1^PMS2P1^ENSG00000078319.10" ; gene_name PMS2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156885.3" ; havana_transcript "OTTHUMT00000346451.2" ; hgnc_id "HGNC:9123" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr7,100335838,100335860,-" ; tag basic ; transcript_id "PMS2P1--UPK3BL1^ENST00000431037.3" ; transcript_name "PMS2P1-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
323 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
647 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 22 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed