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: 3032
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3032
=> 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:3032
=> 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:
COX6CP1--COX6C HAVANA gene 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding
COX6CP1--COX6C HAVANA mRNA 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^ENST00000297564.6" ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERC1--AC087341.1 HAVANA gene 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--AC087341.1^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--AC087341.1^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--AC087341.1^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ERC1--AC087341.1 HAVANA mRNA 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--AC087341.1^ENST00000347735.10" ; Parent "ERC1--AC087341.1^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--AC087341.1^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--AC087341.1^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ERC1--ADCY8 HAVANA gene 44808 66551 . + . FI_gene_label "ADCY8^ENSG00000155897.10" ; ID "ERC1--ADCY8^ADCY8^ENSG00000155897.10" ; ccdsid "CCDS6363.1" ; exon_id "ENSE00002098422.2" ; exon_number 1 ; gene_id "ERC1--ADCY8^ADCY8^ENSG00000155897.10" ; gene_name ADCY8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164756.3" ; havana_transcript "OTTHUMT00000380080.2" ; hgnc_id "HGNC:239" ; level 2 ; orig_coord_info "chr8,131039374,131040333,-" ; protein_id "ENSP00000286355.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERC1--ADCY8^ENST00000286355.10" ; transcript_name "ADCY8-201" ; transcript_support_level 1 ; transcript_type protein_coding
ERC1--ADCY8 HAVANA mRNA 44808 66551 . + . FI_gene_label "ADCY8^ENSG00000155897.10" ; ID "ERC1--ADCY8^ENST00000286355.10" ; Parent "ERC1--ADCY8^ADCY8^ENSG00000155897.10" ; ccdsid "CCDS6363.1" ; exon_id "ENSE00002098422.2" ; exon_number 1 ; gene_id "ERC1--ADCY8^ADCY8^ENSG00000155897.10" ; gene_name ADCY8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164756.3" ; havana_transcript "OTTHUMT00000380080.2" ; hgnc_id "HGNC:239" ; level 2 ; orig_coord_info "chr8,131039374,131040333,-" ; protein_id "ENSP00000286355.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ERC1--ADCY8^ENST00000286355.10" ; transcript_name "ADCY8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ERC1--ADCY8 HAVANA gene 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--ADCY8^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--ADCY8^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--ADCY8^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ERC1--ADCY8 HAVANA mRNA 1730 37441 . + . FI_gene_label "ERC1^ENSG00000082805.20" ; ID "ERC1--ADCY8^ENST00000347735.10" ; Parent "ERC1--ADCY8^ERC1^ENSG00000082805.20" ; exon_id "ENSE00001318114.5" ; exon_number 2 ; gene_id "ERC1--ADCY8^ERC1^ENSG00000082805.20" ; gene_name ERC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130138.14" ; havana_transcript "OTTHUMT00000398378.1" ; hgnc_id "HGNC:17072" ; level 2 ; orig_coord_info "chr12,1027904,1028572,+" ; protein_id "ENSP00000340054.6" ; transcript_id "ERC1--ADCY8^ENST00000347735.10" ; transcript_name "ERC1-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FBN3--IGH@-ext HAVANA gene 2827 51209 . + . FI_gene_label "FBN3^ENSG00000142449.13" ; ID "FBN3--IGH@-ext^FBN3^ENSG00000142449.13" ; ccdsid "CCDS12196.1" ; exon_id "ENSE00002311286.1" ; exon_number 1 ; gene_id "FBN3--IGH@-ext^FBN3^ENSG00000142449.13" ; gene_name FBN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182462.7" ; havana_transcript "OTTHUMT00000461469.1" ; hgnc_id "HGNC:18794" ; level 2 ; orig_coord_info "chr19,8147314,8147480,-" ; protein_id "ENSP00000270509.2" ; tag alternative_5_UTR basic CCDS ; transcript_id "FBN3--IGH@-ext^ENST00000270509.6" ; transcript_name "FBN3-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBN3--IGH@-ext HAVANA mRNA 2827 51209 . + . FI_gene_label "FBN3^ENSG00000142449.13" ; ID "FBN3--IGH@-ext^ENST00000270509.6" ; Parent "FBN3--IGH@-ext^FBN3^ENSG00000142449.13" ; ccdsid "CCDS12196.1" ; exon_id "ENSE00002311286.1" ; exon_number 1 ; gene_id "FBN3--IGH@-ext^FBN3^ENSG00000142449.13" ; gene_name FBN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182462.7" ; havana_transcript "OTTHUMT00000461469.1" ; hgnc_id "HGNC:18794" ; level 2 ; orig_coord_info "chr19,8147314,8147480,-" ; protein_id "ENSP00000270509.2" ; tag alternative_5_UTR basic CCDS ; transcript_id "FBN3--IGH@-ext^ENST00000270509.6" ; transcript_name "FBN3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUCY1B2--NKAIN2 HAVANA mRNA 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^ENST00000368416.5" ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LINC00381--NKAIN2 HAVANA gene 10218 17864 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
LINC00381--NKAIN2 HAVANA mRNA 10218 17864 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "LINC00381--NKAIN2^ENST00000368416.5" ; Parent "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; 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:
PMS2P6--CCDC146 HAVANA gene 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146 HAVANA mRNA 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^ENST00000285871.5" ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC136431.1--PKD1P5 HAVANA gene 9015 30646 . + . FI_gene_label "PKD1P5^ENSG00000254681.6" ; ID "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6" ; exon_id "ENSE00002185250.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6" ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2" ; havana_transcript "OTTHUMT00000388923.1" ; hgnc_id "HGNC:30069" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,18401584,18401940,-" ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5" ; transcript_name "PKD1P5-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AC136431.1--PKD1P5 HAVANA RNA 9015 30646 . + . FI_gene_label "PKD1P5^ENSG00000254681.6" ; ID "AC136431.1--PKD1P5^ENST00000532415.5" ; Parent "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6" ; exon_id "ENSE00002185250.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6" ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2" ; havana_transcript "OTTHUMT00000388923.1" ; hgnc_id "HGNC:30069" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr16,18401584,18401940,-" ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5" ; transcript_name "PKD1P5-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
AC136431.1--PKD1P5 HAVANA gene 1001 6014 . + . FI_gene_label "AC136431.1^ENSG00000260126.2" ; ID "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2" ; exon_id "ENSE00003856180.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2" ; gene_name "AC136431.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2" ; havana_transcript "OTTHUMT00000436080.2" ; level 2 ; orig_coord_info "chr16,16499533,16499619,+" ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2" ; transcript_name "AC136431.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC136431.1--PKD1P5 HAVANA RNA 1001 6014 . + . FI_gene_label "AC136431.1^ENSG00000260126.2" ; ID "AC136431.1--PKD1P5^ENST00000567465.2" ; Parent "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2" ; exon_id "ENSE00003856180.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2" ; gene_name "AC136431.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2" ; havana_transcript "OTTHUMT00000436080.2" ; level 2 ; orig_coord_info "chr16,16499533,16499619,+" ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2" ; transcript_name "AC136431.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
COX6CP1--COX6C HAVANA gene 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
COX6CP1--COX6C HAVANA RNA 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^ENST00000564972.1" ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
ERC1--AC087341.1 HAVANA gene 44808 47379 . + . FI_gene_label "AC087341.1^ENSG00000253407.2" ; ID "ERC1--AC087341.1^AC087341.1^ENSG00000253407.2" ; exon_id "ENSE00002099505.2" ; exon_number 1 ; gene_id "ERC1--AC087341.1^AC087341.1^ENSG00000253407.2" ; gene_name "AC087341.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164759.2" ; havana_transcript "OTTHUMT00000380085.2" ; level 2 ; orig_coord_info "chr8,131144834,131144948,-" ; tag basic TAGENE ; transcript_id "ERC1--AC087341.1^ENST00000521490.2" ; transcript_name "AC087341.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
ERC1--AC087341.1 HAVANA RNA 44808 47379 . + . FI_gene_label "AC087341.1^ENSG00000253407.2" ; ID "ERC1--AC087341.1^ENST00000521490.2" ; Parent "ERC1--AC087341.1^AC087341.1^ENSG00000253407.2" ; exon_id "ENSE00002099505.2" ; exon_number 1 ; gene_id "ERC1--AC087341.1^AC087341.1^ENSG00000253407.2" ; gene_name "AC087341.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000164759.2" ; havana_transcript "OTTHUMT00000380085.2" ; level 2 ; orig_coord_info "chr8,131144834,131144948,-" ; tag basic TAGENE ; transcript_id "ERC1--AC087341.1^ENST00000521490.2" ; transcript_name "AC087341.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
FBN3--IGH@-ext SuperLocus-ext gene 54211 1345551 . + . FI_gene_label "IGH@-ext^IGH.g@-ext" ; ID "FBN3--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_id "FBN3--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_name "IGH@-ext" ; orig_coord_info "chr14,105583731,106875071,-" ; transcript_id "FBN3--IGH@-ext^IGH.t@-ext"
FBN3--IGH@-ext SuperLocus-ext RNA 54211 1345551 . + . FI_gene_label "IGH@-ext^IGH.g@-ext" ; ID "FBN3--IGH@-ext^IGH.t@-ext" ; Parent "FBN3--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_id "FBN3--IGH@-ext^IGH@-ext^IGH.g@-ext" ; gene_name "IGH@-ext" ; orig_coord_info "chr14,105583731,106875071,-" ; transcript_id "FBN3--IGH@-ext^IGH.t@-ext"
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
GUCY1B2--NKAIN2 HAVANA RNA 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^ENST00000389600.6" ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
LINC00381--NKAIN2 HAVANA gene 1016 4365 . + . FI_gene_label "LINC00381^ENSG00000226240.2" ; ID "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; exon_id "ENSE00001743371.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2" ; havana_transcript "OTTHUMT00000045275.1" ; hgnc_id "HGNC:42708" ; level 2 ; orig_coord_info "chr13,74419173,74419228,+" ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1" ; transcript_name "LINC00381-201" ; transcript_support_level 5 ; transcript_type lncRNA
LINC00381--NKAIN2 HAVANA RNA 1016 4365 . + . FI_gene_label "LINC00381^ENSG00000226240.2" ; ID "LINC00381--NKAIN2^ENST00000423629.1" ; Parent "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; exon_id "ENSE00001743371.1" ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2" ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2" ; havana_transcript "OTTHUMT00000045275.1" ; hgnc_id "HGNC:42708" ; level 2 ; orig_coord_info "chr13,74419173,74419228,+" ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1" ; transcript_name "LINC00381-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
PMS2P6--CCDC146 HAVANA gene 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146 HAVANA RNA 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^ENST00000333674.5" ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; transcript_support_level NA ; transcript_type 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
222 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 ------------------------------
389 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 1 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 1 second) ------
GFF3 file parsed