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: 5300
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5300
=> 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:5300
=> 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:
AC015911.9--SLFN12L HAVANA gene 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L HAVANA mRNA 4692 11059 . + . FI_gene_label "SLFN12L^ENSG00000205045.11" ; ID "AC015911.9--SLFN12L^ENST00000260908.12" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; exon_id "ENSE00003850559.1" ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11" ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1" ; havana_transcript "OTTHUMT00000395748.3" ; hgnc_id "HGNC:33920" ; level 2 ; orig_coord_info "chr17,35479117,35480155,-" ; protein_id "ENSP00000437635.2" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12" ; transcript_name "SLFN12L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ADAMTS6--CENPK ENSEMBL gene 40958 52671 . + . FI_gene_label "CENPK^ENSG00000123219.13" ; ID "ADAMTS6--CENPK^CENPK^ENSG00000123219.13" ; ccdsid "CCDS3984.1" ; exon_id "ENSE00001382668.3" ; exon_number 1 ; gene_id "ADAMTS6--CENPK^CENPK^ENSG00000123219.13" ; gene_name CENPK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131227.5" ; hgnc_id "HGNC:29479" ; level 3 ; orig_coord_info "chr5,65554797,65554907,-" ; protein_id "ENSP00000242872.3" ; tag basic appris_principal_1 CCDS ; transcript_id "ADAMTS6--CENPK^ENST00000242872.7" ; transcript_name "CENPK-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADAMTS6--CENPK ENSEMBL mRNA 40958 52671 . + . FI_gene_label "CENPK^ENSG00000123219.13" ; ID "ADAMTS6--CENPK^ENST00000242872.7" ; Parent "ADAMTS6--CENPK^CENPK^ENSG00000123219.13" ; ccdsid "CCDS3984.1" ; exon_id "ENSE00001382668.3" ; exon_number 1 ; gene_id "ADAMTS6--CENPK^CENPK^ENSG00000123219.13" ; gene_name CENPK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131227.5" ; hgnc_id "HGNC:29479" ; level 3 ; orig_coord_info "chr5,65554797,65554907,-" ; protein_id "ENSP00000242872.3" ; tag basic appris_principal_1 CCDS ; transcript_id "ADAMTS6--CENPK^ENST00000242872.7" ; transcript_name "CENPK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADAMTS6--CENPK HAVANA gene 1504 34689 . + . FI_gene_label "ADAMTS6^ENSG00000049192.15" ; ID "ADAMTS6--CENPK^ADAMTS6^ENSG00000049192.15" ; exon_id "ENSE00001487392.1" ; exon_number 2 ; gene_id "ADAMTS6--CENPK^ADAMTS6^ENSG00000049192.15" ; gene_name ADAMTS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074079.8" ; havana_transcript "OTTHUMT00000368524.2" ; hgnc_id "HGNC:222" ; level 2 ; orig_coord_info "chr5,65473577,65473673,-" ; protein_id "ENSP00000424377.1" ; transcript_id "ADAMTS6--CENPK^ENST00000381052.8" ; transcript_name "ADAMTS6-202" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ADAMTS6--CENPK HAVANA mRNA 1504 34689 . + . FI_gene_label "ADAMTS6^ENSG00000049192.15" ; ID "ADAMTS6--CENPK^ENST00000381052.8" ; Parent "ADAMTS6--CENPK^ADAMTS6^ENSG00000049192.15" ; exon_id "ENSE00001487392.1" ; exon_number 2 ; gene_id "ADAMTS6--CENPK^ADAMTS6^ENSG00000049192.15" ; gene_name ADAMTS6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074079.8" ; havana_transcript "OTTHUMT00000368524.2" ; hgnc_id "HGNC:222" ; level 2 ; orig_coord_info "chr5,65473577,65473673,-" ; protein_id "ENSP00000424377.1" ; transcript_id "ADAMTS6--CENPK^ENST00000381052.8" ; transcript_name "ADAMTS6-202" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
CAPZB--OR4F3 HAVANA gene 1001 28676 . + . FI_gene_label "CAPZB^ENSG00000077549.19" ; ID "CAPZB--OR4F3^CAPZB^ENSG00000077549.19" ; ccdsid "CCDS41277.1" ; exon_id "ENSE00001546290.4" ; exon_number 1 ; gene_id "CAPZB--OR4F3^CAPZB^ENSG00000077549.19" ; gene_name CAPZB ; gene_type protein_coding ; havana_gene "OTTHUMG00000002556.12" ; havana_transcript "OTTHUMT00000476514.3" ; hgnc_id "HGNC:1491" ; level 2 ; orig_coord_info "chr1,19485436,19485438,-" ; protein_id "ENSP00000264202.7" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CAPZB--OR4F3^ENST00000264202.8" ; transcript_name "CAPZB-201" ; transcript_support_level 1 ; transcript_type protein_coding
CAPZB--OR4F3 HAVANA mRNA 1001 28676 . + . FI_gene_label "CAPZB^ENSG00000077549.19" ; ID "CAPZB--OR4F3^ENST00000264202.8" ; Parent "CAPZB--OR4F3^CAPZB^ENSG00000077549.19" ; ccdsid "CCDS41277.1" ; exon_id "ENSE00001546290.4" ; exon_number 1 ; gene_id "CAPZB--OR4F3^CAPZB^ENSG00000077549.19" ; gene_name CAPZB ; gene_type protein_coding ; havana_gene "OTTHUMG00000002556.12" ; havana_transcript "OTTHUMT00000476514.3" ; hgnc_id "HGNC:1491" ; level 2 ; orig_coord_info "chr1,19485436,19485438,-" ; protein_id "ENSP00000264202.7" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CAPZB--OR4F3^ENST00000264202.8" ; transcript_name "CAPZB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CAPZB--OR4F3 HAVANA gene 31677 32671 . + . FI_gene_label "OR4F3^ENSG00000230178.1" ; ID "CAPZB--OR4F3^OR4F3^ENSG00000230178.1" ; ccdsid "CCDS43415.1" ; exon_id "ENSE00002321347.1" ; exon_number 1 ; gene_id "CAPZB--OR4F3^OR4F3^ENSG00000230178.1" ; gene_name OR4F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162081.1" ; havana_transcript "OTTHUMT00000367138.1" ; hgnc_id "HGNC:8300" ; level 2 ; orig_coord_info "chr5,181367287,181368222,+" ; protein_id "ENSP00000394282.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CAPZB--OR4F3^ENST00000456475.1" ; transcript_name "OR4F3-201" ; transcript_support_level NA ; transcript_type protein_coding
CAPZB--OR4F3 HAVANA mRNA 31677 32671 . + . FI_gene_label "OR4F3^ENSG00000230178.1" ; ID "CAPZB--OR4F3^ENST00000456475.1" ; Parent "CAPZB--OR4F3^OR4F3^ENSG00000230178.1" ; ccdsid "CCDS43415.1" ; exon_id "ENSE00002321347.1" ; exon_number 1 ; gene_id "CAPZB--OR4F3^OR4F3^ENSG00000230178.1" ; gene_name OR4F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162081.1" ; havana_transcript "OTTHUMT00000367138.1" ; hgnc_id "HGNC:8300" ; level 2 ; orig_coord_info "chr5,181367287,181368222,+" ; protein_id "ENSP00000394282.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CAPZB--OR4F3^ENST00000456475.1" ; transcript_name "OR4F3-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
CAPZB--SEPTIN14P5 HAVANA gene 1001 28676 . + . FI_gene_label "CAPZB^ENSG00000077549.19" ; ID "CAPZB--SEPTIN14P5^CAPZB^ENSG00000077549.19" ; ccdsid "CCDS41277.1" ; exon_id "ENSE00001546290.4" ; exon_number 1 ; gene_id "CAPZB--SEPTIN14P5^CAPZB^ENSG00000077549.19" ; gene_name CAPZB ; gene_type protein_coding ; havana_gene "OTTHUMG00000002556.12" ; havana_transcript "OTTHUMT00000476514.3" ; hgnc_id "HGNC:1491" ; level 2 ; orig_coord_info "chr1,19485436,19485438,-" ; protein_id "ENSP00000264202.7" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CAPZB--SEPTIN14P5^ENST00000264202.8" ; transcript_name "CAPZB-201" ; transcript_support_level 1 ; transcript_type protein_coding
CAPZB--SEPTIN14P5 HAVANA mRNA 1001 28676 . + . FI_gene_label "CAPZB^ENSG00000077549.19" ; ID "CAPZB--SEPTIN14P5^ENST00000264202.8" ; Parent "CAPZB--SEPTIN14P5^CAPZB^ENSG00000077549.19" ; ccdsid "CCDS41277.1" ; exon_id "ENSE00001546290.4" ; exon_number 1 ; gene_id "CAPZB--SEPTIN14P5^CAPZB^ENSG00000077549.19" ; gene_name CAPZB ; gene_type protein_coding ; havana_gene "OTTHUMG00000002556.12" ; havana_transcript "OTTHUMT00000476514.3" ; hgnc_id "HGNC:1491" ; level 2 ; orig_coord_info "chr1,19485436,19485438,-" ; protein_id "ENSP00000264202.7" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "CAPZB--SEPTIN14P5^ENST00000264202.8" ; transcript_name "CAPZB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDKAL1--STK4 HAVANA gene 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--STK4^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--STK4^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--STK4^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDKAL1--STK4 HAVANA mRNA 1001 21482 . + . FI_gene_label "CDKAL1^ENSG00000145996.11" ; ID "CDKAL1--STK4^ENST00000274695.8" ; Parent "CDKAL1--STK4^CDKAL1^ENSG00000145996.11" ; ccdsid "CCDS4546.1" ; exon_id "ENSE00003893317.1" ; exon_number 3 ; gene_id "CDKAL1--STK4^CDKAL1^ENSG00000145996.11" ; gene_name CDKAL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014340.2" ; havana_transcript "OTTHUMT00000504200.1" ; hgnc_id "HGNC:21050" ; level 2 ; orig_coord_info "chr6,20546351,20546523,+" ; protein_id "ENSP00000274695.4" ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDKAL1--STK4^ENST00000274695.8" ; transcript_name "CDKAL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDKAL1--STK4 HAVANA gene 24526 41799 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "CDKAL1--STK4^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "CDKAL1--STK4^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "CDKAL1--STK4^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
CDKAL1--STK4 HAVANA mRNA 24526 41799 . + . FI_gene_label "STK4^ENSG00000101109.12" ; ID "CDKAL1--STK4^ENST00000372801.5" ; Parent "CDKAL1--STK4^STK4^ENSG00000101109.12" ; ccdsid "CCDS86957.1" ; exon_id "ENSE00001458687.1" ; exon_number 1 ; gene_id "CDKAL1--STK4^STK4^ENSG00000101109.12" ; gene_name STK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033059.6" ; havana_transcript "OTTHUMT00000127823.1" ; hgnc_id "HGNC:11408" ; level 2 ; orig_coord_info "chr20,44966569,44966603,+" ; protein_id "ENSP00000361887.1" ; tag basic CCDS ; transcript_id "CDKAL1--STK4^ENST00000372801.5" ; transcript_name "STK4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
DHX9--MTARC2 HAVANA gene 29543 39034 . + . FI_gene_label "MTARC2^ENSG00000117791.16" ; ID "DHX9--MTARC2^MTARC2^ENSG00000117791.16" ; ccdsid "CCDS81425.1" ; exon_id "ENSE00001404577.1" ; exon_number 1 ; gene_id "DHX9--MTARC2^MTARC2^ENSG00000117791.16" ; gene_name MTARC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037354.6" ; havana_transcript "OTTHUMT00000090912.1" ; hgnc_id "HGNC:26064" ; level 2 ; orig_coord_info "chr1,220748532,220748803,+" ; protein_id "ENSP00000352266.2" ; tag basic CCDS ; transcript_id "DHX9--MTARC2^ENST00000359316.6" ; transcript_name "MTARC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHX9--MTARC2 HAVANA mRNA 29543 39034 . + . FI_gene_label "MTARC2^ENSG00000117791.16" ; ID "DHX9--MTARC2^ENST00000359316.6" ; Parent "DHX9--MTARC2^MTARC2^ENSG00000117791.16" ; ccdsid "CCDS81425.1" ; exon_id "ENSE00001404577.1" ; exon_number 1 ; gene_id "DHX9--MTARC2^MTARC2^ENSG00000117791.16" ; gene_name MTARC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037354.6" ; havana_transcript "OTTHUMT00000090912.1" ; hgnc_id "HGNC:26064" ; level 2 ; orig_coord_info "chr1,220748532,220748803,+" ; protein_id "ENSP00000352266.2" ; tag basic CCDS ; transcript_id "DHX9--MTARC2^ENST00000359316.6" ; transcript_name "MTARC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DHX9--MTARC2 HAVANA gene 1001 26498 . + . FI_gene_label "DHX9^ENSG00000135829.17" ; ID "DHX9--MTARC2^DHX9^ENSG00000135829.17" ; ccdsid "CCDS41444.1" ; exon_id "ENSE00003559534.1" ; exon_number 2 ; gene_id "DHX9--MTARC2^DHX9^ENSG00000135829.17" ; gene_name DHX9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035337.6" ; havana_transcript "OTTHUMT00000085522.3" ; hgnc_id "HGNC:2750" ; level 2 ; orig_coord_info "chr1,182842567,182842677,+" ; protein_id "ENSP00000356520.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX9--MTARC2^ENST00000367549.4" ; transcript_name "DHX9-201" ; transcript_support_level 1 ; transcript_type protein_coding
DHX9--MTARC2 HAVANA mRNA 1001 26498 . + . FI_gene_label "DHX9^ENSG00000135829.17" ; ID "DHX9--MTARC2^ENST00000367549.4" ; Parent "DHX9--MTARC2^DHX9^ENSG00000135829.17" ; ccdsid "CCDS41444.1" ; exon_id "ENSE00003559534.1" ; exon_number 2 ; gene_id "DHX9--MTARC2^DHX9^ENSG00000135829.17" ; gene_name DHX9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035337.6" ; havana_transcript "OTTHUMT00000085522.3" ; hgnc_id "HGNC:2750" ; level 2 ; orig_coord_info "chr1,182842567,182842677,+" ; protein_id "ENSP00000356520.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DHX9--MTARC2^ENST00000367549.4" ; transcript_name "DHX9-201" ; transcript_support_level 1 ; 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:
JADE3--KRBOX4 HAVANA gene 19078 26729 . + . FI_gene_label "KRBOX4^ENSG00000147121.16" ; ID "JADE3--KRBOX4^KRBOX4^ENSG00000147121.16" ; ccdsid "CCDS14267.1" ; exon_id "ENSE00001093022.1" ; exon_number 3 ; gene_id "JADE3--KRBOX4^KRBOX4^ENSG00000147121.16" ; gene_name KRBOX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021421.4" ; havana_transcript "OTTHUMT00000356709.1" ; hgnc_id "HGNC:26007" ; level 2 ; orig_coord_info "chrX,46450461,46450475,+" ; protein_id "ENSP00000298190.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "JADE3--KRBOX4^ENST00000298190.10" ; transcript_name "KRBOX4-201" ; transcript_support_level 2 ; transcript_type protein_coding
JADE3--KRBOX4 HAVANA mRNA 19078 26729 . + . FI_gene_label "KRBOX4^ENSG00000147121.16" ; ID "JADE3--KRBOX4^ENST00000298190.10" ; Parent "JADE3--KRBOX4^KRBOX4^ENSG00000147121.16" ; ccdsid "CCDS14267.1" ; exon_id "ENSE00001093022.1" ; exon_number 3 ; gene_id "JADE3--KRBOX4^KRBOX4^ENSG00000147121.16" ; gene_name KRBOX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021421.4" ; havana_transcript "OTTHUMT00000356709.1" ; hgnc_id "HGNC:26007" ; level 2 ; orig_coord_info "chrX,46450461,46450475,+" ; protein_id "ENSP00000298190.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "JADE3--KRBOX4^ENST00000298190.10" ; transcript_name "KRBOX4-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
JADE3--KRBOX4 HAVANA gene 1001 7000 . + . FI_gene_label "JADE3^ENSG00000102221.14" ; ID "JADE3--KRBOX4^JADE3^ENSG00000102221.14" ; exon_id "ENSE00001138472.1" ; exon_number 2 ; gene_id "JADE3--KRBOX4^JADE3^ENSG00000102221.14" ; gene_name JADE3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021431.6" ; havana_transcript "OTTHUMT00000318538.2" ; hgnc_id "HGNC:22982" ; level 2 ; orig_coord_info "chrX,46984895,46984940,+" ; protein_id "ENSP00000391009.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "JADE3--KRBOX4^ENST00000424392.5" ; transcript_name "JADE3-201" ; transcript_support_level 3 ; transcript_type protein_coding
JADE3--KRBOX4 HAVANA mRNA 1001 7000 . + . FI_gene_label "JADE3^ENSG00000102221.14" ; ID "JADE3--KRBOX4^ENST00000424392.5" ; Parent "JADE3--KRBOX4^JADE3^ENSG00000102221.14" ; exon_id "ENSE00001138472.1" ; exon_number 2 ; gene_id "JADE3--KRBOX4^JADE3^ENSG00000102221.14" ; gene_name JADE3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021431.6" ; havana_transcript "OTTHUMT00000318538.2" ; hgnc_id "HGNC:22982" ; level 2 ; orig_coord_info "chrX,46984895,46984940,+" ; protein_id "ENSP00000391009.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "JADE3--KRBOX4^ENST00000424392.5" ; transcript_name "JADE3-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
KCNQ1--ZNF157 HAVANA gene 1325 22441 . + . FI_gene_label "KCNQ1^ENSG00000053918.18" ; ID "KCNQ1--ZNF157^KCNQ1^ENSG00000053918.18" ; ccdsid "CCDS7736.1" ; exon_id "ENSE00001339597.3" ; exon_number 1 ; gene_id "KCNQ1--ZNF157^KCNQ1^ENSG00000053918.18" ; gene_name KCNQ1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009900.11" ; havana_transcript "OTTHUMT00000027382.5" ; hgnc_id "HGNC:6294" ; level 2 ; orig_coord_info "chr11,2445099,2445484,+" ; protein_id "ENSP00000155840.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KCNQ1--ZNF157^ENST00000155840.12" ; transcript_name "KCNQ1-201" ; transcript_support_level 1 ; transcript_type protein_coding
KCNQ1--ZNF157 HAVANA mRNA 1325 22441 . + . FI_gene_label "KCNQ1^ENSG00000053918.18" ; ID "KCNQ1--ZNF157^ENST00000155840.12" ; Parent "KCNQ1--ZNF157^KCNQ1^ENSG00000053918.18" ; ccdsid "CCDS7736.1" ; exon_id "ENSE00001339597.3" ; exon_number 1 ; gene_id "KCNQ1--ZNF157^KCNQ1^ENSG00000053918.18" ; gene_name KCNQ1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000009900.11" ; havana_transcript "OTTHUMT00000027382.5" ; hgnc_id "HGNC:6294" ; level 2 ; orig_coord_info "chr11,2445099,2445484,+" ; protein_id "ENSP00000155840.2" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KCNQ1--ZNF157^ENST00000155840.12" ; transcript_name "KCNQ1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KCNQ1--ZNF157 HAVANA gene 25442 30234 . + . FI_gene_label "ZNF157^ENSG00000147117.8" ; ID "KCNQ1--ZNF157^ZNF157^ENSG00000147117.8" ; ccdsid "CCDS14278.1" ; exon_id "ENSE00001472701.4" ; exon_number 1 ; gene_id "KCNQ1--ZNF157^ZNF157^ENSG00000147117.8" ; gene_name ZNF157 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021443.1" ; havana_transcript "OTTHUMT00000056415.1" ; hgnc_id "HGNC:12942" ; level 2 ; orig_coord_info "chrX,47370669,47370740,+" ; protein_id "ENSP00000366273.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KCNQ1--ZNF157^ENST00000377073.4" ; transcript_name "ZNF157-201" ; transcript_support_level 1 ; transcript_type protein_coding
KCNQ1--ZNF157 HAVANA mRNA 25442 30234 . + . FI_gene_label "ZNF157^ENSG00000147117.8" ; ID "KCNQ1--ZNF157^ENST00000377073.4" ; Parent "KCNQ1--ZNF157^ZNF157^ENSG00000147117.8" ; ccdsid "CCDS14278.1" ; exon_id "ENSE00001472701.4" ; exon_number 1 ; gene_id "KCNQ1--ZNF157^ZNF157^ENSG00000147117.8" ; gene_name ZNF157 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021443.1" ; havana_transcript "OTTHUMT00000056415.1" ; hgnc_id "HGNC:12942" ; level 2 ; orig_coord_info "chrX,47370669,47370740,+" ; protein_id "ENSP00000366273.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KCNQ1--ZNF157^ENST00000377073.4" ; transcript_name "ZNF157-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 HAVANA gene 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13 HAVANA mRNA 14666 23106 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA4--PCDHA13^ENST00000289272.3" ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHA13 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHA13^ENST00000378125.4" ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 HAVANA gene 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1 HAVANA mRNA 14666 24681 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA4--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC1 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC1^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 HAVANA gene 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2 HAVANA mRNA 14672 25407 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA4--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA4--PCDHAC2 ENSEMBL gene 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2 ENSEMBL mRNA 1001 3590 . + . FI_gene_label "PCDHA4^ENSG00000204967.12" ; ID "PCDHA4--PCDHAC2^ENST00000378125.4" ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; exon_id "ENSE00003735925.1" ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12" ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5" ; hgnc_id "HGNC:8670" ; level 3 ; orig_coord_info "chr5,140806929,140806945,+" ; protein_id "ENSP00000367365.4" ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4" ; transcript_name "PCDHA4-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHA13 HAVANA gene 6617 15057 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA8--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA8--PCDHA13 HAVANA mRNA 6617 15057 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA8--PCDHA13^ENST00000289272.3" ; Parent "PCDHA8--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHA13 HAVANA gene 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHA13^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHA13^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHA13^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA8--PCDHA13 HAVANA mRNA 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHA13^ENST00000378123.4" ; Parent "PCDHA8--PCDHA13^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHA13^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHA13^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHAC1 HAVANA gene 6617 16632 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA8--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA8--PCDHAC1 HAVANA mRNA 6617 16632 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA8--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA8--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHAC1 HAVANA gene 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHAC1^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHAC1^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHAC1^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA8--PCDHAC1 HAVANA mRNA 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHAC1^ENST00000378123.4" ; Parent "PCDHA8--PCDHAC1^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHAC1^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHAC1^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHAC2 HAVANA gene 6623 17358 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA8--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA8--PCDHAC2 HAVANA mRNA 6623 17358 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA8--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA8--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA8--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 "PCDHA8--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA8--PCDHAC2 HAVANA gene 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHAC2^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHAC2^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHAC2^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA8--PCDHAC2 HAVANA mRNA 1001 3616 . + . FI_gene_label "PCDHA8^ENSG00000204962.6" ; ID "PCDHA8--PCDHAC2^ENST00000378123.4" ; Parent "PCDHA8--PCDHAC2^PCDHA8^ENSG00000204962.6" ; exon_id "ENSE00001476361.4" ; exon_number 1 ; gene_id "PCDHA8--PCDHAC2^PCDHA8^ENSG00000204962.6" ; gene_name PCDHA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163354.4" ; havana_transcript "OTTHUMT00000477552.1" ; hgnc_id "HGNC:8674" ; level 2 ; orig_coord_info "chr5,140841322,140843763,+" ; protein_id "ENSP00000367363.3" ; tag basic ; transcript_id "PCDHA8--PCDHAC2^ENST00000378123.4" ; transcript_name "PCDHA8-201" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PIP5K1C--AP000547.3 HAVANA gene 1001 26998 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "PIP5K1C--AP000547.3^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "PIP5K1C--AP000547.3^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PIP5K1C--AP000547.3^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
PIP5K1C--AP000547.3 HAVANA mRNA 1001 26998 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "PIP5K1C--AP000547.3^ENST00000335312.8" ; Parent "PIP5K1C--AP000547.3^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "PIP5K1C--AP000547.3^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PIP5K1C--AP000547.3^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PIP5K1C--TPTEP1 HAVANA gene 1001 26998 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "PIP5K1C--TPTEP1^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "PIP5K1C--TPTEP1^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PIP5K1C--TPTEP1^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
PIP5K1C--TPTEP1 HAVANA mRNA 1001 26998 . + . FI_gene_label "PIP5K1C^ENSG00000186111.11" ; ID "PIP5K1C--TPTEP1^ENST00000335312.8" ; Parent "PIP5K1C--TPTEP1^PIP5K1C^ENSG00000186111.11" ; ccdsid "CCDS32872.1" ; exon_id "ENSE00002751293.2" ; exon_number 1 ; gene_id "PIP5K1C--TPTEP1^PIP5K1C^ENSG00000186111.11" ; gene_name PIP5K1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000180870.4" ; havana_transcript "OTTHUMT00000453432.2" ; hgnc_id "HGNC:8996" ; level 2 ; orig_coord_info "chr19,3700297,3700390,-" ; protein_id "ENSP00000335333.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "PIP5K1C--TPTEP1^ENST00000335312.8" ; transcript_name "PIP5K1C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPIG--LINC01807 HAVANA gene 1010 21125 . + . FI_gene_label "PPIG^ENSG00000138398.17" ; ID "PPIG--LINC01807^PPIG^ENSG00000138398.17" ; ccdsid "CCDS2235.1" ; exon_id "ENSE00003522833.1" ; exon_number 3 ; gene_id "PPIG--LINC01807^PPIG^ENSG00000138398.17" ; gene_name PPIG ; gene_type protein_coding ; havana_gene "OTTHUMG00000132206.6" ; havana_transcript "OTTHUMT00000255264.3" ; hgnc_id "HGNC:14650" ; level 2 ; orig_coord_info "chr2,169604042,169604102,+" ; protein_id "ENSP00000260970.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPIG--LINC01807^ENST00000260970.8" ; transcript_name "PPIG-201" ; transcript_support_level 1 ; transcript_type protein_coding
PPIG--LINC01807 HAVANA mRNA 1010 21125 . + . FI_gene_label "PPIG^ENSG00000138398.17" ; ID "PPIG--LINC01807^ENST00000260970.8" ; Parent "PPIG--LINC01807^PPIG^ENSG00000138398.17" ; ccdsid "CCDS2235.1" ; exon_id "ENSE00003522833.1" ; exon_number 3 ; gene_id "PPIG--LINC01807^PPIG^ENSG00000138398.17" ; gene_name PPIG ; gene_type protein_coding ; havana_gene "OTTHUMG00000132206.6" ; havana_transcript "OTTHUMT00000255264.3" ; hgnc_id "HGNC:14650" ; level 2 ; orig_coord_info "chr2,169604042,169604102,+" ; protein_id "ENSP00000260970.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPIG--LINC01807^ENST00000260970.8" ; transcript_name "PPIG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPIG--PID1 HAVANA gene 1010 21125 . + . FI_gene_label "PPIG^ENSG00000138398.17" ; ID "PPIG--PID1^PPIG^ENSG00000138398.17" ; ccdsid "CCDS2235.1" ; exon_id "ENSE00003522833.1" ; exon_number 3 ; gene_id "PPIG--PID1^PPIG^ENSG00000138398.17" ; gene_name PPIG ; gene_type protein_coding ; havana_gene "OTTHUMG00000132206.6" ; havana_transcript "OTTHUMT00000255264.3" ; hgnc_id "HGNC:14650" ; level 2 ; orig_coord_info "chr2,169604042,169604102,+" ; protein_id "ENSP00000260970.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPIG--PID1^ENST00000260970.8" ; transcript_name "PPIG-201" ; transcript_support_level 1 ; transcript_type protein_coding
PPIG--PID1 HAVANA mRNA 1010 21125 . + . FI_gene_label "PPIG^ENSG00000138398.17" ; ID "PPIG--PID1^ENST00000260970.8" ; Parent "PPIG--PID1^PPIG^ENSG00000138398.17" ; ccdsid "CCDS2235.1" ; exon_id "ENSE00003522833.1" ; exon_number 3 ; gene_id "PPIG--PID1^PPIG^ENSG00000138398.17" ; gene_name PPIG ; gene_type protein_coding ; havana_gene "OTTHUMG00000132206.6" ; havana_transcript "OTTHUMT00000255264.3" ; hgnc_id "HGNC:14650" ; level 2 ; orig_coord_info "chr2,169604042,169604102,+" ; protein_id "ENSP00000260970.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPIG--PID1^ENST00000260970.8" ; transcript_name "PPIG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPIG--PID1 HAVANA gene 27820 31765 . + . FI_gene_label "PID1^ENSG00000153823.19" ; ID "PPIG--PID1^PID1^ENSG00000153823.19" ; ccdsid "CCDS82577.1" ; exon_id "ENSE00001409871.2" ; exon_number 1 ; gene_id "PPIG--PID1^PID1^ENSG00000153823.19" ; gene_name PID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133191.5" ; havana_transcript "OTTHUMT00000331810.2" ; hgnc_id "HGNC:26084" ; level 2 ; orig_coord_info "chr2,229231926,229232054,-" ; protein_id "ENSP00000283937.8" ; tag basic CCDS ; transcript_id "PPIG--PID1^ENST00000354069.6" ; transcript_name "PID1-201" ; transcript_support_level 3 ; transcript_type protein_coding
PPIG--PID1 HAVANA mRNA 27820 31765 . + . FI_gene_label "PID1^ENSG00000153823.19" ; ID "PPIG--PID1^ENST00000354069.6" ; Parent "PPIG--PID1^PID1^ENSG00000153823.19" ; ccdsid "CCDS82577.1" ; exon_id "ENSE00001409871.2" ; exon_number 1 ; gene_id "PPIG--PID1^PID1^ENSG00000153823.19" ; gene_name PID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133191.5" ; havana_transcript "OTTHUMT00000331810.2" ; hgnc_id "HGNC:26084" ; level 2 ; orig_coord_info "chr2,229231926,229232054,-" ; protein_id "ENSP00000283937.8" ; tag basic CCDS ; transcript_id "PPIG--PID1^ENST00000354069.6" ; transcript_name "PID1-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
PTPN20--BMS1P7 ENSEMBL gene 1043 20316 . + . FI_gene_label "PTPN20^ENSG00000204179.10" ; ID "PTPN20--BMS1P7^PTPN20^ENSG00000204179.10" ; ccdsid "CCDS73114.1" ; exon_id "ENSE00003719491.1" ; exon_number 4 ; gene_id "PTPN20--BMS1P7^PTPN20^ENSG00000204179.10" ; gene_name PTPN20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018094.10" ; hgnc_id "HGNC:23423" ; level 3 ; orig_coord_info "chr10,46946579,46946675,+" ; protein_id "ENSP00000363335.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "PTPN20--BMS1P7^ENST00000374218.6" ; transcript_name "PTPN20-201" ; transcript_support_level 5 ; transcript_type protein_coding
PTPN20--BMS1P7 ENSEMBL mRNA 1043 20316 . + . FI_gene_label "PTPN20^ENSG00000204179.10" ; ID "PTPN20--BMS1P7^ENST00000374218.6" ; Parent "PTPN20--BMS1P7^PTPN20^ENSG00000204179.10" ; ccdsid "CCDS73114.1" ; exon_id "ENSE00003719491.1" ; exon_number 4 ; gene_id "PTPN20--BMS1P7^PTPN20^ENSG00000204179.10" ; gene_name PTPN20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018094.10" ; hgnc_id "HGNC:23423" ; level 3 ; orig_coord_info "chr10,46946579,46946675,+" ; protein_id "ENSP00000363335.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "PTPN20--BMS1P7^ENST00000374218.6" ; transcript_name "PTPN20-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4 HAVANA gene 15043 21268 . + . FI_gene_label "RBM4^ENSG00000173933.21" ; ID "RBM14--RBM4^RBM4^ENSG00000173933.21" ; ccdsid "CCDS41676.1" ; exon_id "ENSE00003513724.1" ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21" ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7" ; havana_transcript "OTTHUMT00000334210.2" ; hgnc_id "HGNC:9901" ; level 2 ; orig_coord_info "chr11,66639712,66640123,+" ; protein_id "ENSP00000309166.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12" ; transcript_name "RBM4-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4 HAVANA mRNA 15043 21268 . + . FI_gene_label "RBM4^ENSG00000173933.21" ; ID "RBM14--RBM4^ENST00000310092.12" ; Parent "RBM14--RBM4^RBM4^ENSG00000173933.21" ; ccdsid "CCDS41676.1" ; exon_id "ENSE00003513724.1" ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21" ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7" ; havana_transcript "OTTHUMT00000334210.2" ; hgnc_id "HGNC:9901" ; level 2 ; orig_coord_info "chr11,66639712,66640123,+" ; protein_id "ENSP00000309166.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12" ; transcript_name "RBM4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBM14--RBM4 HAVANA gene 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4 HAVANA mRNA 1005 12006 . + . FI_gene_label "RBM14^ENSG00000239306.5" ; ID "RBM14--RBM4^ENST00000310137.5" ; Parent "RBM14--RBM4^RBM14^ENSG00000239306.5" ; ccdsid "CCDS8147.1" ; exon_id "ENSE00003902856.1" ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5" ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5" ; havana_transcript "OTTHUMT00000277128.1" ; hgnc_id "HGNC:14219" ; level 2 ; orig_coord_info "chr11,66616721,66617057,+" ; protein_id "ENSP00000311747.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5" ; transcript_name "RBM14-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SFXN5--KNTC1 HAVANA gene 2056 36272 . + . FI_gene_label "SFXN5^ENSG00000144040.13" ; ID "SFXN5--KNTC1^SFXN5^ENSG00000144040.13" ; ccdsid "CCDS1922.1" ; exon_id "ENSE00002304141.2" ; exon_number 1 ; gene_id "SFXN5--KNTC1^SFXN5^ENSG00000144040.13" ; gene_name SFXN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129775.9" ; havana_transcript "OTTHUMT00000251991.2" ; hgnc_id "HGNC:16073" ; level 2 ; orig_coord_info "chr2,73071604,73071705,-" ; protein_id "ENSP00000272433.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SFXN5--KNTC1^ENST00000272433.7" ; transcript_name "SFXN5-201" ; transcript_support_level 1 ; transcript_type protein_coding
SFXN5--KNTC1 HAVANA mRNA 2056 36272 . + . FI_gene_label "SFXN5^ENSG00000144040.13" ; ID "SFXN5--KNTC1^ENST00000272433.7" ; Parent "SFXN5--KNTC1^SFXN5^ENSG00000144040.13" ; ccdsid "CCDS1922.1" ; exon_id "ENSE00002304141.2" ; exon_number 1 ; gene_id "SFXN5--KNTC1^SFXN5^ENSG00000144040.13" ; gene_name SFXN5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129775.9" ; havana_transcript "OTTHUMT00000251991.2" ; hgnc_id "HGNC:16073" ; level 2 ; orig_coord_info "chr2,73071604,73071705,-" ; protein_id "ENSP00000272433.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SFXN5--KNTC1^ENST00000272433.7" ; transcript_name "SFXN5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SFXN5--KNTC1 HAVANA gene 39276 98096 . + . FI_gene_label "KNTC1^ENSG00000184445.12" ; ID "SFXN5--KNTC1^KNTC1^ENSG00000184445.12" ; ccdsid "CCDS45002.1" ; exon_id "ENSE00002214489.1" ; exon_number 2 ; gene_id "SFXN5--KNTC1^KNTC1^ENSG00000184445.12" ; gene_name KNTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168861.7" ; havana_transcript "OTTHUMT00000396110.3" ; hgnc_id "HGNC:17255" ; level 2 ; orig_coord_info "chr12,122530064,122530192,+" ; protein_id "ENSP00000328236.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SFXN5--KNTC1^ENST00000333479.12" ; transcript_name "KNTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SFXN5--KNTC1 HAVANA mRNA 39276 98096 . + . FI_gene_label "KNTC1^ENSG00000184445.12" ; ID "SFXN5--KNTC1^ENST00000333479.12" ; Parent "SFXN5--KNTC1^KNTC1^ENSG00000184445.12" ; ccdsid "CCDS45002.1" ; exon_id "ENSE00002214489.1" ; exon_number 2 ; gene_id "SFXN5--KNTC1^KNTC1^ENSG00000184445.12" ; gene_name KNTC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168861.7" ; havana_transcript "OTTHUMT00000396110.3" ; hgnc_id "HGNC:17255" ; level 2 ; orig_coord_info "chr12,122530064,122530192,+" ; protein_id "ENSP00000328236.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SFXN5--KNTC1^ENST00000333479.12" ; transcript_name "KNTC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--FCHSD2 HAVANA gene 62217 86507 . + . FI_gene_label "FCHSD2^ENSG00000137478.15" ; ID "SHANK2--FCHSD2^FCHSD2^ENSG00000137478.15" ; exon_id "ENSE00003654343.1" ; exon_number 3 ; gene_id "SHANK2--FCHSD2^FCHSD2^ENSG00000137478.15" ; gene_name FCHSD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153082.7" ; havana_transcript "OTTHUMT00000329378.4" ; hgnc_id "HGNC:29114" ; level 2 ; orig_coord_info "chr11,73015809,73015882,-" ; protein_id "ENSP00000308978.7" ; tag basic ; transcript_id "SHANK2--FCHSD2^ENST00000311172.11" ; transcript_name "FCHSD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SHANK2--FCHSD2 HAVANA mRNA 62217 86507 . + . FI_gene_label "FCHSD2^ENSG00000137478.15" ; ID "SHANK2--FCHSD2^ENST00000311172.11" ; Parent "SHANK2--FCHSD2^FCHSD2^ENSG00000137478.15" ; exon_id "ENSE00003654343.1" ; exon_number 3 ; gene_id "SHANK2--FCHSD2^FCHSD2^ENSG00000137478.15" ; gene_name FCHSD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153082.7" ; havana_transcript "OTTHUMT00000329378.4" ; hgnc_id "HGNC:29114" ; level 2 ; orig_coord_info "chr11,73015809,73015882,-" ; protein_id "ENSP00000308978.7" ; tag basic ; transcript_id "SHANK2--FCHSD2^ENST00000311172.11" ; transcript_name "FCHSD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SHANK2--FCHSD2 HAVANA gene 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--FCHSD2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--FCHSD2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--FCHSD2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
SHANK2--FCHSD2 HAVANA mRNA 33938 57363 . + . FI_gene_label "SHANK2^ENSG00000162105.20" ; ID "SHANK2--FCHSD2^ENST00000338508.8" ; Parent "SHANK2--FCHSD2^SHANK2^ENSG00000162105.20" ; ccdsid "CCDS76448.1" ; exon_id "ENSE00001714763.2" ; exon_number 1 ; gene_id "SHANK2--FCHSD2^SHANK2^ENSG00000162105.20" ; gene_name SHANK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154615.9" ; havana_transcript "OTTHUMT00000477858.2" ; hgnc_id "HGNC:14295" ; level 2 ; orig_coord_info "chr11,70661596,70661767,-" ; protein_id "ENSP00000345193.6" ; tag basic CCDS ; transcript_id "SHANK2--FCHSD2^ENST00000338508.8" ; transcript_name "SHANK2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
UBE2Q2P1--GOLGA6L10 HAVANA gene 16591 25371 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
UBE2Q2P1--GOLGA6L10 HAVANA mRNA 16591 25371 . + . FI_gene_label "GOLGA6L10^ENSG00000278662.5" ; ID "UBE2Q2P1--GOLGA6L10^ENST00000610657.2" ; Parent "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5" ; ccdsid "CCDS45325.2" ; exon_id "ENSE00002255247.2" ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^GOLGA6L10^ENSG00000278662.5" ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4" ; havana_transcript "OTTHUMT00000419277.4" ; hgnc_id "HGNC:37228" ; level 2 ; orig_coord_info "chr15,82349292,82349375,-" ; protein_id "ENSP00000479362.1" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000610657.2" ; transcript_name "GOLGA6L10-207" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
AC011997.1--AC022905.1 HAVANA gene 1001 5032 . + . FI_gene_label "AC011997.1^ENSG00000222017.1" ; ID "AC011997.1--AC022905.1^AC011997.1^ENSG00000222017.1" ; exon_id "ENSE00002442553.1" ; exon_number 1 ; gene_id "AC011997.1--AC022905.1^AC011997.1^ENSG00000222017.1" ; gene_name "AC011997.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154488.1" ; havana_transcript "OTTHUMT00000335479.1" ; level 2 ; orig_coord_info "chr2,197693106,197693216,+" ; tag basic ; transcript_id "AC011997.1--AC022905.1^ENST00000409845.1" ; transcript_name "AC011997.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
AC011997.1--AC022905.1 HAVANA RNA 1001 5032 . + . FI_gene_label "AC011997.1^ENSG00000222017.1" ; ID "AC011997.1--AC022905.1^ENST00000409845.1" ; Parent "AC011997.1--AC022905.1^AC011997.1^ENSG00000222017.1" ; exon_id "ENSE00002442553.1" ; exon_number 1 ; gene_id "AC011997.1--AC022905.1^AC011997.1^ENSG00000222017.1" ; gene_name "AC011997.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154488.1" ; havana_transcript "OTTHUMT00000335479.1" ; level 2 ; orig_coord_info "chr2,197693106,197693216,+" ; tag basic ; transcript_id "AC011997.1--AC022905.1^ENST00000409845.1" ; transcript_name "AC011997.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
AC011997.1--AC022905.1 HAVANA gene 8033 31602 . + . FI_gene_label "AC022905.1^ENSG00000250979.1" ; ID "AC011997.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; exon_id "ENSE00002030404.1" ; exon_number 1 ; gene_id "AC011997.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; gene_name "AC022905.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160469.1" ; havana_transcript "OTTHUMT00000360728.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,72251455,72251565,-" ; tag basic ; transcript_id "AC011997.1--AC022905.1^ENST00000503430.1" ; transcript_name "AC022905.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC011997.1--AC022905.1 HAVANA RNA 8033 31602 . + . FI_gene_label "AC022905.1^ENSG00000250979.1" ; ID "AC011997.1--AC022905.1^ENST00000503430.1" ; Parent "AC011997.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; exon_id "ENSE00002030404.1" ; exon_number 1 ; gene_id "AC011997.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; gene_name "AC022905.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160469.1" ; havana_transcript "OTTHUMT00000360728.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,72251455,72251565,-" ; tag basic ; transcript_id "AC011997.1--AC022905.1^ENST00000503430.1" ; transcript_name "AC022905.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L HAVANA gene 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L HAVANA RNA 1001 1691 . + . FI_gene_label "AC015911.9^ENSG00000286030.2" ; ID "AC015911.9--SLFN12L^ENST00000650652.2" ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; exon_id "ENSE00003850003.2" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2" ; gene_name "AC015911.9" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2" ; havana_transcript "OTTHUMT00000502481.2" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr17,35522279,35522969,-" ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2" ; transcript_name "AC015911.9-201" ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC015911.9--SLFN12L ENSEMBL gene 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
AC015911.9--SLFN12L ENSEMBL RNA 5824 9825 . + . FI_gene_label "SLFN12L^ENSG00000286065.2" ; ID "AC015911.9--SLFN12L^ENST00000675965.1" ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; exon_id "ENSE00003899764.1" ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2" ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2" ; hgnc_id "HGNC:33920" ; level 3 ; orig_coord_info "chr17,35480502,35480513,-" ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1" ; transcript_name "SLFN12L-206" ; transcript_type lncRNA
L1 and L2 created:
AC104041.1--AC022905.1 HAVANA gene 27146 50715 . + . FI_gene_label "AC022905.1^ENSG00000250979.1" ; ID "AC104041.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; exon_id "ENSE00002030404.1" ; exon_number 1 ; gene_id "AC104041.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; gene_name "AC022905.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160469.1" ; havana_transcript "OTTHUMT00000360728.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,72251455,72251565,-" ; tag basic ; transcript_id "AC104041.1--AC022905.1^ENST00000503430.1" ; transcript_name "AC022905.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC104041.1--AC022905.1 HAVANA RNA 27146 50715 . + . FI_gene_label "AC022905.1^ENSG00000250979.1" ; ID "AC104041.1--AC022905.1^ENST00000503430.1" ; Parent "AC104041.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; exon_id "ENSE00002030404.1" ; exon_number 1 ; gene_id "AC104041.1--AC022905.1^AC022905.1^ENSG00000250979.1" ; gene_name "AC022905.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000160469.1" ; havana_transcript "OTTHUMT00000360728.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,72251455,72251565,-" ; tag basic ; transcript_id "AC104041.1--AC022905.1^ENST00000503430.1" ; transcript_name "AC022905.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC104041.1--AC022905.1 HAVANA gene 3640 17052 . + . FI_gene_label "AC104041.1^ENSG00000259692.6" ; ID "AC104041.1--AC022905.1^AC104041.1^ENSG00000259692.6" ; exon_id "ENSE00002541371.1" ; exon_number 1 ; gene_id "AC104041.1--AC022905.1^AC104041.1^ENSG00000259692.6" ; gene_name "AC104041.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172170.6" ; havana_transcript "OTTHUMT00000417173.2" ; level 2 ; orig_coord_info "chr15,81995427,81995666,-" ; tag basic ; transcript_id "AC104041.1--AC022905.1^ENST00000559299.2" ; transcript_name "AC104041.1-204" ; transcript_support_level 4 ; transcript_type lncRNA
AC104041.1--AC022905.1 HAVANA RNA 3640 17052 . + . FI_gene_label "AC104041.1^ENSG00000259692.6" ; ID "AC104041.1--AC022905.1^ENST00000559299.2" ; Parent "AC104041.1--AC022905.1^AC104041.1^ENSG00000259692.6" ; exon_id "ENSE00002541371.1" ; exon_number 1 ; gene_id "AC104041.1--AC022905.1^AC104041.1^ENSG00000259692.6" ; gene_name "AC104041.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172170.6" ; havana_transcript "OTTHUMT00000417173.2" ; level 2 ; orig_coord_info "chr15,81995427,81995666,-" ; tag basic ; transcript_id "AC104041.1--AC022905.1^ENST00000559299.2" ; transcript_name "AC104041.1-204" ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created:
CAPZB--SEPTIN14P5 HAVANA gene 31677 34403 . + . FI_gene_label "SEPTIN14P5^ENSG00000250765.6" ; ID "CAPZB--SEPTIN14P5^SEPTIN14P5^ENSG00000250765.6" ; exon_id "ENSE00002430372.1" ; exon_number 1 ; gene_id "CAPZB--SEPTIN14P5^SEPTIN14P5^ENSG00000250765.6" ; gene_name SEPTIN14P5 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162985.1" ; havana_transcript "OTTHUMT00000371259.1" ; hgnc_id "HGNC:51689" ; level 2 ; orig_coord_info "chr5,181329241,181329590,+" ; tag not_best_in_genome_evidence basic ; transcript_id "CAPZB--SEPTIN14P5^ENST00000509192.5" ; transcript_name "SEPTIN14P5-201" ; transcript_support_level 1 ; transcript_type lncRNA
CAPZB--SEPTIN14P5 HAVANA RNA 31677 34403 . + . FI_gene_label "SEPTIN14P5^ENSG00000250765.6" ; ID "CAPZB--SEPTIN14P5^ENST00000509192.5" ; Parent "CAPZB--SEPTIN14P5^SEPTIN14P5^ENSG00000250765.6" ; exon_id "ENSE00002430372.1" ; exon_number 1 ; gene_id "CAPZB--SEPTIN14P5^SEPTIN14P5^ENSG00000250765.6" ; gene_name SEPTIN14P5 ; gene_type lncRNA ; havana_gene "OTTHUMG00000162985.1" ; havana_transcript "OTTHUMT00000371259.1" ; hgnc_id "HGNC:51689" ; level 2 ; orig_coord_info "chr5,181329241,181329590,+" ; tag not_best_in_genome_evidence basic ; transcript_id "CAPZB--SEPTIN14P5^ENST00000509192.5" ; transcript_name "SEPTIN14P5-201" ; transcript_support_level 1 ; transcript_type lncRNA
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:
PIP5K1C--AP000547.3 HAVANA gene 32228 34750 . + . FI_gene_label "AP000547.3^ENSG00000283633.1" ; ID "PIP5K1C--AP000547.3^AP000547.3^ENSG00000283633.1" ; exon_id "ENSE00002951757.1" ; exon_number 1 ; gene_id "PIP5K1C--AP000547.3^AP000547.3^ENSG00000283633.1" ; gene_name "AP000547.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000141300.11" ; havana_transcript "OTTHUMT00000459903.5" ; level 2 ; orig_coord_info "chr22,16612582,16615104,+" ; tag basic ; transcript_id "PIP5K1C--AP000547.3^ENST00000588548.1" ; transcript_name "AP000547.3-204" ; transcript_support_level NA ; transcript_type lncRNA
PIP5K1C--AP000547.3 HAVANA RNA 32228 34750 . + . FI_gene_label "AP000547.3^ENSG00000283633.1" ; ID "PIP5K1C--AP000547.3^ENST00000588548.1" ; Parent "PIP5K1C--AP000547.3^AP000547.3^ENSG00000283633.1" ; exon_id "ENSE00002951757.1" ; exon_number 1 ; gene_id "PIP5K1C--AP000547.3^AP000547.3^ENSG00000283633.1" ; gene_name "AP000547.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000141300.11" ; havana_transcript "OTTHUMT00000459903.5" ; level 2 ; orig_coord_info "chr22,16612582,16615104,+" ; tag basic ; transcript_id "PIP5K1C--AP000547.3^ENST00000588548.1" ; transcript_name "AP000547.3-204" ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created:
PIP5K1C--TPTEP1 HAVANA gene 33666 47023 . + . FI_gene_label "TPTEP1^ENSG00000100181.22" ; ID "PIP5K1C--TPTEP1^TPTEP1^ENSG00000100181.22" ; exon_id "ENSE00001773127.1" ; exon_number 1 ; gene_id "PIP5K1C--TPTEP1^TPTEP1^ENSG00000100181.22" ; gene_name TPTEP1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191859.4" ; havana_transcript "OTTHUMT00000280577.1" ; hgnc_id "HGNC:43648" ; level 2 ; orig_coord_info "chr22,16619615,16619720,+" ; transcript_id "PIP5K1C--TPTEP1^ENST00000383140.7" ; transcript_name "TPTEP1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
PIP5K1C--TPTEP1 HAVANA RNA 33666 47023 . + . FI_gene_label "TPTEP1^ENSG00000100181.22" ; ID "PIP5K1C--TPTEP1^ENST00000383140.7" ; Parent "PIP5K1C--TPTEP1^TPTEP1^ENSG00000100181.22" ; exon_id "ENSE00001773127.1" ; exon_number 1 ; gene_id "PIP5K1C--TPTEP1^TPTEP1^ENSG00000100181.22" ; gene_name TPTEP1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191859.4" ; havana_transcript "OTTHUMT00000280577.1" ; hgnc_id "HGNC:43648" ; level 2 ; orig_coord_info "chr22,16619615,16619720,+" ; transcript_id "PIP5K1C--TPTEP1^ENST00000383140.7" ; transcript_name "TPTEP1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
PPIG--LINC01807 HAVANA gene 26491 31504 . + . FI_gene_label "LINC01807^ENSG00000232023.3" ; ID "PPIG--LINC01807^LINC01807^ENSG00000232023.3" ; exon_id "ENSE00001596043.1" ; exon_number 1 ; gene_id "PPIG--LINC01807^LINC01807^ENSG00000232023.3" ; gene_name LINC01807 ; gene_type lncRNA ; havana_gene "OTTHUMG00000153589.5" ; havana_transcript "OTTHUMT00000331758.2" ; hgnc_id "HGNC:52610" ; level 1 ; orig_coord_info "chr2,228611252,228611395,-" ; tag basic exp_conf ; transcript_id "PPIG--LINC01807^ENST00000432481.2" ; transcript_name "LINC01807-201" ; transcript_support_level 3 ; transcript_type lncRNA
PPIG--LINC01807 HAVANA RNA 26491 31504 . + . FI_gene_label "LINC01807^ENSG00000232023.3" ; ID "PPIG--LINC01807^ENST00000432481.2" ; Parent "PPIG--LINC01807^LINC01807^ENSG00000232023.3" ; exon_id "ENSE00001596043.1" ; exon_number 1 ; gene_id "PPIG--LINC01807^LINC01807^ENSG00000232023.3" ; gene_name LINC01807 ; gene_type lncRNA ; havana_gene "OTTHUMG00000153589.5" ; havana_transcript "OTTHUMT00000331758.2" ; hgnc_id "HGNC:52610" ; level 1 ; orig_coord_info "chr2,228611252,228611395,-" ; tag basic exp_conf ; transcript_id "PPIG--LINC01807^ENST00000432481.2" ; transcript_name "LINC01807-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
PTPN20--BMS1P7 HAVANA gene 23485 30059 . + . FI_gene_label "BMS1P7^ENSG00000270025.2" ; ID "PTPN20--BMS1P7^BMS1P7^ENSG00000270025.2" ; exon_id "ENSE00001675840.2" ; exon_number 1 ; gene_id "PTPN20--BMS1P7^BMS1P7^ENSG00000270025.2" ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3" ; havana_transcript "OTTHUMT00000047911.2" ; hgnc_id "HGNC:23655" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48059827,48060016,-" ; tag basic ; transcript_id "PTPN20--BMS1P7^ENST00000602440.2" ; transcript_name "BMS1P7-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
PTPN20--BMS1P7 HAVANA RNA 23485 30059 . + . FI_gene_label "BMS1P7^ENSG00000270025.2" ; ID "PTPN20--BMS1P7^ENST00000602440.2" ; Parent "PTPN20--BMS1P7^BMS1P7^ENSG00000270025.2" ; exon_id "ENSE00001675840.2" ; exon_number 1 ; gene_id "PTPN20--BMS1P7^BMS1P7^ENSG00000270025.2" ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3" ; havana_transcript "OTTHUMT00000047911.2" ; hgnc_id "HGNC:23655" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr10,48059827,48060016,-" ; tag basic ; transcript_id "PTPN20--BMS1P7^ENST00000602440.2" ; transcript_name "BMS1P7-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
UBE2Q2P1--GOLGA6L10 HAVANA gene 1422 13175 . + . FI_gene_label "UBE2Q2P1^ENSG00000189136.9" ; ID "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9" ; exon_id "ENSE00002026145.1" ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9" ; gene_name UBE2Q2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000148662.3" ; havana_transcript "OTTHUMT00000308970.2" ; hgnc_id "HGNC:37439" ; level 2 ; orig_coord_info "chr15,84569505,84570795,-" ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000339094.5" ; transcript_name "UBE2Q2P1-201" ; transcript_support_level 2 ; transcript_type processed_transcript
UBE2Q2P1--GOLGA6L10 HAVANA RNA 1422 13175 . + . FI_gene_label "UBE2Q2P1^ENSG00000189136.9" ; ID "UBE2Q2P1--GOLGA6L10^ENST00000339094.5" ; Parent "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9" ; exon_id "ENSE00002026145.1" ; exon_number 1 ; gene_id "UBE2Q2P1--GOLGA6L10^UBE2Q2P1^ENSG00000189136.9" ; gene_name UBE2Q2P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000148662.3" ; havana_transcript "OTTHUMT00000308970.2" ; hgnc_id "HGNC:37439" ; level 2 ; orig_coord_info "chr15,84569505,84570795,-" ; transcript_id "UBE2Q2P1--GOLGA6L10^ENST00000339094.5" ; transcript_name "UBE2Q2P1-201" ; transcript_support_level 2 ; transcript_type processed_transcript
445 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 1 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 ------------------------------
876 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 33 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed