Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/769f8aa83b47436208d94ea1f27306/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/6cf3394e920e3972991caa8d47282e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/6cf3394e920e3972991caa8d47282e/.command.run
==> STAGING COMPLETE (3 inputs)
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file
------------------------------------------------------------------------------
| Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 |
| https://github.com/NBISweden/AGAT |
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
------------------------------------------------------------------------------
------ Start parsing ------
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
* locus_tag
* gene_id
=> merge_loci option deactivated
=> Machine information:
This script is being run by perl v5.32.1
Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
Operating system being used: linux
=> Accessing Ontology
No ontology accessible from the gff file header!
We use the SOFA ontology distributed with AGAT:
/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
4 root terms, and 2596 total terms, and 1516 leaf terms
Filtering ontology:
We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 8990
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 8990
=> 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:8990
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 2 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
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:
ADNP--KATNBL1 HAVANA gene 18483 36498 . + . FI_gene_label "KATNBL1^ENSG00000134152.11" ; ID "ADNP--KATNBL1^KATNBL1^ENSG00000134152.11" ; ccdsid "CCDS10034.1" ; exon_id "ENSE00003793181.1" ; exon_number 2 ; gene_id "ADNP--KATNBL1^KATNBL1^ENSG00000134152.11" ; gene_name KATNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129368.4" ; havana_transcript "OTTHUMT00000251520.2" ; hgnc_id "HGNC:26199" ; level 2 ; orig_coord_info "chr15,34163560,34163676,-" ; protein_id "ENSP00000256544.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADNP--KATNBL1^ENST00000256544.8" ; transcript_name "KATNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADNP--KATNBL1 HAVANA mRNA 18483 36498 . + . FI_gene_label "KATNBL1^ENSG00000134152.11" ; ID "ADNP--KATNBL1^ENST00000256544.8" ; Parent "ADNP--KATNBL1^KATNBL1^ENSG00000134152.11" ; ccdsid "CCDS10034.1" ; exon_id "ENSE00003793181.1" ; exon_number 2 ; gene_id "ADNP--KATNBL1^KATNBL1^ENSG00000134152.11" ; gene_name KATNBL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129368.4" ; havana_transcript "OTTHUMT00000251520.2" ; hgnc_id "HGNC:26199" ; level 2 ; orig_coord_info "chr15,34163560,34163676,-" ; protein_id "ENSP00000256544.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADNP--KATNBL1^ENST00000256544.8" ; transcript_name "KATNBL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADNP--KATNBL1 HAVANA gene 4831 14049 . + . FI_gene_label "ADNP^ENSG00000101126.18" ; ID "ADNP--KATNBL1^ADNP^ENSG00000101126.18" ; ccdsid "CCDS13433.1" ; exon_id "ENSE00001455633.1" ; exon_number 2 ; gene_id "ADNP--KATNBL1^ADNP^ENSG00000101126.18" ; gene_name ADNP ; gene_type protein_coding ; havana_gene "OTTHUMG00000032737.28" ; havana_transcript "OTTHUMT00000258382.4" ; hgnc_id "HGNC:15766" ; level 2 ; orig_coord_info "chr20,50903889,50903996,-" ; protein_id "ENSP00000342905.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ADNP--KATNBL1^ENST00000349014.8" ; transcript_name "ADNP-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADNP--KATNBL1 HAVANA mRNA 4831 14049 . + . FI_gene_label "ADNP^ENSG00000101126.18" ; ID "ADNP--KATNBL1^ENST00000349014.8" ; Parent "ADNP--KATNBL1^ADNP^ENSG00000101126.18" ; ccdsid "CCDS13433.1" ; exon_id "ENSE00001455633.1" ; exon_number 2 ; gene_id "ADNP--KATNBL1^ADNP^ENSG00000101126.18" ; gene_name ADNP ; gene_type protein_coding ; havana_gene "OTTHUMG00000032737.28" ; havana_transcript "OTTHUMT00000258382.4" ; hgnc_id "HGNC:15766" ; level 2 ; orig_coord_info "chr20,50903889,50903996,-" ; protein_id "ENSP00000342905.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ADNP--KATNBL1^ENST00000349014.8" ; transcript_name "ADNP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARAP1--FCHSD2 HAVANA gene 35404 59694 . + . FI_gene_label "FCHSD2^ENSG00000137478.15" ; ID "ARAP1--FCHSD2^FCHSD2^ENSG00000137478.15" ; exon_id "ENSE00003654343.1" ; exon_number 3 ; gene_id "ARAP1--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 "ARAP1--FCHSD2^ENST00000311172.11" ; transcript_name "FCHSD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARAP1--FCHSD2 HAVANA mRNA 35404 59694 . + . FI_gene_label "FCHSD2^ENSG00000137478.15" ; ID "ARAP1--FCHSD2^ENST00000311172.11" ; Parent "ARAP1--FCHSD2^FCHSD2^ENSG00000137478.15" ; exon_id "ENSE00003654343.1" ; exon_number 3 ; gene_id "ARAP1--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 "ARAP1--FCHSD2^ENST00000311172.11" ; transcript_name "FCHSD2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARAP1--FCHSD2 HAVANA gene 6443 32125 . + . FI_gene_label "ARAP1^ENSG00000186635.15" ; ID "ARAP1--FCHSD2^ARAP1^ENSG00000186635.15" ; ccdsid "CCDS8217.2" ; exon_id "ENSE00003639727.1" ; exon_number 3 ; gene_id "ARAP1--FCHSD2^ARAP1^ENSG00000186635.15" ; gene_name ARAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157102.4" ; havana_transcript "OTTHUMT00000347430.2" ; hgnc_id "HGNC:16925" ; level 2 ; orig_coord_info "chr11,72713176,72713187,-" ; protein_id "ENSP00000335506.8" ; tag basic CCDS ; transcript_id "ARAP1--FCHSD2^ENST00000334211.12" ; transcript_name "ARAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARAP1--FCHSD2 HAVANA mRNA 6443 32125 . + . FI_gene_label "ARAP1^ENSG00000186635.15" ; ID "ARAP1--FCHSD2^ENST00000334211.12" ; Parent "ARAP1--FCHSD2^ARAP1^ENSG00000186635.15" ; ccdsid "CCDS8217.2" ; exon_id "ENSE00003639727.1" ; exon_number 3 ; gene_id "ARAP1--FCHSD2^ARAP1^ENSG00000186635.15" ; gene_name ARAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157102.4" ; havana_transcript "OTTHUMT00000347430.2" ; hgnc_id "HGNC:16925" ; level 2 ; orig_coord_info "chr11,72713176,72713187,-" ; protein_id "ENSP00000335506.8" ; tag basic CCDS ; transcript_id "ARAP1--FCHSD2^ENST00000334211.12" ; transcript_name "ARAP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AVEN--NFATC2 HAVANA gene 7136 15737 . + . FI_gene_label "AVEN^ENSG00000169857.9" ; ID "AVEN--NFATC2^AVEN^ENSG00000169857.9" ; ccdsid "CCDS10030.1" ; exon_id "ENSE00001235829.5" ; exon_number 1 ; gene_id "AVEN--NFATC2^AVEN^ENSG00000169857.9" ; gene_name AVEN ; gene_type protein_coding ; havana_gene "OTTHUMG00000129371.3" ; havana_transcript "OTTHUMT00000251523.3" ; hgnc_id "HGNC:13509" ; level 2 ; orig_coord_info "chr15,34038780,34039046,-" ; protein_id "ENSP00000306822.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AVEN--NFATC2^ENST00000306730.8" ; transcript_name "AVEN-201" ; transcript_support_level 1 ; transcript_type protein_coding
AVEN--NFATC2 HAVANA mRNA 7136 15737 . + . FI_gene_label "AVEN^ENSG00000169857.9" ; ID "AVEN--NFATC2^ENST00000306730.8" ; Parent "AVEN--NFATC2^AVEN^ENSG00000169857.9" ; ccdsid "CCDS10030.1" ; exon_id "ENSE00001235829.5" ; exon_number 1 ; gene_id "AVEN--NFATC2^AVEN^ENSG00000169857.9" ; gene_name AVEN ; gene_type protein_coding ; havana_gene "OTTHUMG00000129371.3" ; havana_transcript "OTTHUMT00000251523.3" ; hgnc_id "HGNC:13509" ; level 2 ; orig_coord_info "chr15,34038780,34039046,-" ; protein_id "ENSP00000306822.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AVEN--NFATC2^ENST00000306730.8" ; transcript_name "AVEN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AVEN--NFATC2 HAVANA gene 22542 39940 . + . FI_gene_label "NFATC2^ENSG00000101096.20" ; ID "AVEN--NFATC2^NFATC2^ENSG00000101096.20" ; ccdsid "CCDS33488.1" ; exon_id "ENSE00001455518.1" ; exon_number 1 ; gene_id "AVEN--NFATC2^NFATC2^ENSG00000101096.20" ; gene_name NFATC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032747.4" ; havana_transcript "OTTHUMT00000079729.3" ; hgnc_id "HGNC:7776" ; level 2 ; orig_coord_info "chr20,51542370,51542499,-" ; protein_id "ENSP00000360619.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "AVEN--NFATC2^ENST00000371564.8" ; transcript_name "NFATC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
AVEN--NFATC2 HAVANA mRNA 22542 39940 . + . FI_gene_label "NFATC2^ENSG00000101096.20" ; ID "AVEN--NFATC2^ENST00000371564.8" ; Parent "AVEN--NFATC2^NFATC2^ENSG00000101096.20" ; ccdsid "CCDS33488.1" ; exon_id "ENSE00001455518.1" ; exon_number 1 ; gene_id "AVEN--NFATC2^NFATC2^ENSG00000101096.20" ; gene_name NFATC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032747.4" ; havana_transcript "OTTHUMT00000079729.3" ; hgnc_id "HGNC:7776" ; level 2 ; orig_coord_info "chr20,51542370,51542499,-" ; protein_id "ENSP00000360619.3" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "AVEN--NFATC2^ENST00000371564.8" ; transcript_name "NFATC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CASZ1--UBE4B HAVANA gene 33468 68036 . + . FI_gene_label "UBE4B^ENSG00000130939.20" ; ID "CASZ1--UBE4B^UBE4B^ENSG00000130939.20" ; ccdsid "CCDS110.1" ; exon_id "ENSE00001928381.1" ; exon_number 1 ; gene_id "CASZ1--UBE4B^UBE4B^ENSG00000130939.20" ; gene_name UBE4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000001797.4" ; havana_transcript "OTTHUMT00000005017.1" ; hgnc_id "HGNC:12500" ; level 2 ; orig_coord_info "chr1,10033671,10033694,+" ; protein_id "ENSP00000253251.8" ; tag basic appris_principal_1 CCDS ; transcript_id "CASZ1--UBE4B^ENST00000253251.12" ; transcript_name "UBE4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CASZ1--UBE4B HAVANA mRNA 33468 68036 . + . FI_gene_label "UBE4B^ENSG00000130939.20" ; ID "CASZ1--UBE4B^ENST00000253251.12" ; Parent "CASZ1--UBE4B^UBE4B^ENSG00000130939.20" ; ccdsid "CCDS110.1" ; exon_id "ENSE00001928381.1" ; exon_number 1 ; gene_id "CASZ1--UBE4B^UBE4B^ENSG00000130939.20" ; gene_name UBE4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000001797.4" ; havana_transcript "OTTHUMT00000005017.1" ; hgnc_id "HGNC:12500" ; level 2 ; orig_coord_info "chr1,10033671,10033694,+" ; protein_id "ENSP00000253251.8" ; tag basic appris_principal_1 CCDS ; transcript_id "CASZ1--UBE4B^ENST00000253251.12" ; transcript_name "UBE4B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CASZ1--UBE4B HAVANA gene 1001 21524 . + . FI_gene_label "CASZ1^ENSG00000130940.15" ; ID "CASZ1--UBE4B^CASZ1^ENSG00000130940.15" ; ccdsid "CCDS120.2" ; exon_id "ENSE00003613107.1" ; exon_number 4 ; gene_id "CASZ1--UBE4B^CASZ1^ENSG00000130940.15" ; gene_name CASZ1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002035.6" ; havana_transcript "OTTHUMT00000005671.2" ; hgnc_id "HGNC:26002" ; level 2 ; orig_coord_info "chr1,10693874,10693889,-" ; protein_id "ENSP00000339445.5" ; tag basic CCDS ; transcript_id "CASZ1--UBE4B^ENST00000344008.5" ; transcript_name "CASZ1-201" ; transcript_support_level 2 ; transcript_type protein_coding
CASZ1--UBE4B HAVANA mRNA 1001 21524 . + . FI_gene_label "CASZ1^ENSG00000130940.15" ; ID "CASZ1--UBE4B^ENST00000344008.5" ; Parent "CASZ1--UBE4B^CASZ1^ENSG00000130940.15" ; ccdsid "CCDS120.2" ; exon_id "ENSE00003613107.1" ; exon_number 4 ; gene_id "CASZ1--UBE4B^CASZ1^ENSG00000130940.15" ; gene_name CASZ1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002035.6" ; havana_transcript "OTTHUMT00000005671.2" ; hgnc_id "HGNC:26002" ; level 2 ; orig_coord_info "chr1,10693874,10693889,-" ; protein_id "ENSP00000339445.5" ; tag basic CCDS ; transcript_id "CASZ1--UBE4B^ENST00000344008.5" ; transcript_name "CASZ1-201" ; 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:
FAM135A--AL080275.1 HAVANA gene 5056 32431 . + . FI_gene_label "FAM135A^ENSG00000082269.17" ; ID "FAM135A--AL080275.1^FAM135A^ENSG00000082269.17" ; exon_id "ENSE00001709616.1" ; exon_number 2 ; gene_id "FAM135A--AL080275.1^FAM135A^ENSG00000082269.17" ; gene_name FAM135A ; gene_type protein_coding ; havana_gene "OTTHUMG00000014991.4" ; havana_transcript "OTTHUMT00000360646.1" ; hgnc_id "HGNC:21084" ; level 2 ; orig_coord_info "chr6,70428343,70428419,+" ; protein_id "ENSP00000194672.7" ; transcript_id "FAM135A--AL080275.1^ENST00000194672.11" ; transcript_name "FAM135A-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
FAM135A--AL080275.1 HAVANA mRNA 5056 32431 . + . FI_gene_label "FAM135A^ENSG00000082269.17" ; ID "FAM135A--AL080275.1^ENST00000194672.11" ; Parent "FAM135A--AL080275.1^FAM135A^ENSG00000082269.17" ; exon_id "ENSE00001709616.1" ; exon_number 2 ; gene_id "FAM135A--AL080275.1^FAM135A^ENSG00000082269.17" ; gene_name FAM135A ; gene_type protein_coding ; havana_gene "OTTHUMG00000014991.4" ; havana_transcript "OTTHUMT00000360646.1" ; hgnc_id "HGNC:21084" ; level 2 ; orig_coord_info "chr6,70428343,70428419,+" ; protein_id "ENSP00000194672.7" ; transcript_id "FAM135A--AL080275.1^ENST00000194672.11" ; transcript_name "FAM135A-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FAM135A--AL365226.1 HAVANA gene 5056 32431 . + . FI_gene_label "FAM135A^ENSG00000082269.17" ; ID "FAM135A--AL365226.1^FAM135A^ENSG00000082269.17" ; exon_id "ENSE00001709616.1" ; exon_number 2 ; gene_id "FAM135A--AL365226.1^FAM135A^ENSG00000082269.17" ; gene_name FAM135A ; gene_type protein_coding ; havana_gene "OTTHUMG00000014991.4" ; havana_transcript "OTTHUMT00000360646.1" ; hgnc_id "HGNC:21084" ; level 2 ; orig_coord_info "chr6,70428343,70428419,+" ; protein_id "ENSP00000194672.7" ; transcript_id "FAM135A--AL365226.1^ENST00000194672.11" ; transcript_name "FAM135A-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
FAM135A--AL365226.1 HAVANA mRNA 5056 32431 . + . FI_gene_label "FAM135A^ENSG00000082269.17" ; ID "FAM135A--AL365226.1^ENST00000194672.11" ; Parent "FAM135A--AL365226.1^FAM135A^ENSG00000082269.17" ; exon_id "ENSE00001709616.1" ; exon_number 2 ; gene_id "FAM135A--AL365226.1^FAM135A^ENSG00000082269.17" ; gene_name FAM135A ; gene_type protein_coding ; havana_gene "OTTHUMG00000014991.4" ; havana_transcript "OTTHUMT00000360646.1" ; hgnc_id "HGNC:21084" ; level 2 ; orig_coord_info "chr6,70428343,70428419,+" ; protein_id "ENSP00000194672.7" ; transcript_id "FAM135A--AL365226.1^ENST00000194672.11" ; transcript_name "FAM135A-201" ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1 HAVANA mRNA 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^ENST00000276326.9" ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAPK6--TRPM7 HAVANA gene 3412 18928 . + . FI_gene_label "MAPK6^ENSG00000069956.13" ; ID "MAPK6--TRPM7^MAPK6^ENSG00000069956.13" ; ccdsid "CCDS10147.1" ; exon_id "ENSE00000942191.1" ; exon_number 2 ; gene_id "MAPK6--TRPM7^MAPK6^ENSG00000069956.13" ; gene_name MAPK6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131891.4" ; havana_transcript "OTTHUMT00000254841.4" ; hgnc_id "HGNC:6879" ; level 2 ; orig_coord_info "chr15,52046461,52047015,+" ; protein_id "ENSP00000261845.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAPK6--TRPM7^ENST00000261845.7" ; transcript_name "MAPK6-201" ; transcript_support_level 1 ; transcript_type protein_coding
MAPK6--TRPM7 HAVANA mRNA 3412 18928 . + . FI_gene_label "MAPK6^ENSG00000069956.13" ; ID "MAPK6--TRPM7^ENST00000261845.7" ; Parent "MAPK6--TRPM7^MAPK6^ENSG00000069956.13" ; ccdsid "CCDS10147.1" ; exon_id "ENSE00000942191.1" ; exon_number 2 ; gene_id "MAPK6--TRPM7^MAPK6^ENSG00000069956.13" ; gene_name MAPK6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131891.4" ; havana_transcript "OTTHUMT00000254841.4" ; hgnc_id "HGNC:6879" ; level 2 ; orig_coord_info "chr15,52046461,52047015,+" ; protein_id "ENSP00000261845.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAPK6--TRPM7^ENST00000261845.7" ; transcript_name "MAPK6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MAPK6--TRPM7 HAVANA gene 34582 44338 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "MAPK6--TRPM7^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "MAPK6--TRPM7^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MAPK6--TRPM7^ENST00000560638.1" ; transcript_name "TRPM7-204" ; transcript_support_level 1 ; transcript_type protein_coding
MAPK6--TRPM7 HAVANA mRNA 34582 44338 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "MAPK6--TRPM7^ENST00000560638.1" ; Parent "MAPK6--TRPM7^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "MAPK6--TRPM7^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "MAPK6--TRPM7^ENST00000560638.1" ; transcript_name "TRPM7-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PIP5K1B--TJP2 HAVANA gene 1001 30751 . + . FI_gene_label "PIP5K1B^ENSG00000107242.20" ; ID "PIP5K1B--TJP2^PIP5K1B^ENSG00000107242.20" ; ccdsid "CCDS6624.1" ; exon_id "ENSE00003756251.1" ; exon_number 4 ; gene_id "PIP5K1B--TJP2^PIP5K1B^ENSG00000107242.20" ; gene_name PIP5K1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019976.6" ; havana_transcript "OTTHUMT00000052561.3" ; hgnc_id "HGNC:8995" ; level 2 ; orig_coord_info "chr9,68822615,68822683,+" ; protein_id "ENSP00000265382.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PIP5K1B--TJP2^ENST00000265382.8" ; transcript_name "PIP5K1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
PIP5K1B--TJP2 HAVANA mRNA 1001 30751 . + . FI_gene_label "PIP5K1B^ENSG00000107242.20" ; ID "PIP5K1B--TJP2^ENST00000265382.8" ; Parent "PIP5K1B--TJP2^PIP5K1B^ENSG00000107242.20" ; ccdsid "CCDS6624.1" ; exon_id "ENSE00003756251.1" ; exon_number 4 ; gene_id "PIP5K1B--TJP2^PIP5K1B^ENSG00000107242.20" ; gene_name PIP5K1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019976.6" ; havana_transcript "OTTHUMT00000052561.3" ; hgnc_id "HGNC:8995" ; level 2 ; orig_coord_info "chr9,68822615,68822683,+" ; protein_id "ENSP00000265382.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PIP5K1B--TJP2^ENST00000265382.8" ; transcript_name "PIP5K1B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PIP5K1B--TJP2 HAVANA gene 38958 72091 . + . FI_gene_label "TJP2^ENSG00000119139.21" ; ID "PIP5K1B--TJP2^TJP2^ENSG00000119139.21" ; ccdsid "CCDS6628.1" ; exon_id "ENSE00001473273.3" ; exon_number 1 ; gene_id "PIP5K1B--TJP2^TJP2^ENSG00000119139.21" ; gene_name TJP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019978.17" ; havana_transcript "OTTHUMT00000253612.2" ; hgnc_id "HGNC:11828" ; level 2 ; orig_coord_info "chr9,69174373,69174432,+" ; protein_id "ENSP00000345893.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "PIP5K1B--TJP2^ENST00000348208.9" ; transcript_name "TJP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PIP5K1B--TJP2 HAVANA mRNA 38958 72091 . + . FI_gene_label "TJP2^ENSG00000119139.21" ; ID "PIP5K1B--TJP2^ENST00000348208.9" ; Parent "PIP5K1B--TJP2^TJP2^ENSG00000119139.21" ; ccdsid "CCDS6628.1" ; exon_id "ENSE00001473273.3" ; exon_number 1 ; gene_id "PIP5K1B--TJP2^TJP2^ENSG00000119139.21" ; gene_name TJP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019978.17" ; havana_transcript "OTTHUMT00000253612.2" ; hgnc_id "HGNC:11828" ; level 2 ; orig_coord_info "chr9,69174373,69174432,+" ; protein_id "ENSP00000345893.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "PIP5K1B--TJP2^ENST00000348208.9" ; transcript_name "TJP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRELID3A--AFG3L2 HAVANA gene 13163 33135 . + . FI_gene_label "AFG3L2^ENSG00000141385.10" ; ID "PRELID3A--AFG3L2^AFG3L2^ENSG00000141385.10" ; ccdsid "CCDS11859.1" ; exon_id "ENSE00001255364.6" ; exon_number 1 ; gene_id "PRELID3A--AFG3L2^AFG3L2^ENSG00000141385.10" ; gene_name AFG3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131695.4" ; havana_transcript "OTTHUMT00000254603.3" ; hgnc_id "HGNC:315" ; level 2 ; orig_coord_info "chr18,12376969,12377082,-" ; protein_id "ENSP00000269143.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRELID3A--AFG3L2^ENST00000269143.8" ; transcript_name "AFG3L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRELID3A--AFG3L2 HAVANA mRNA 13163 33135 . + . FI_gene_label "AFG3L2^ENSG00000141385.10" ; ID "PRELID3A--AFG3L2^ENST00000269143.8" ; Parent "PRELID3A--AFG3L2^AFG3L2^ENSG00000141385.10" ; ccdsid "CCDS11859.1" ; exon_id "ENSE00001255364.6" ; exon_number 1 ; gene_id "PRELID3A--AFG3L2^AFG3L2^ENSG00000141385.10" ; gene_name AFG3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131695.4" ; havana_transcript "OTTHUMT00000254603.3" ; hgnc_id "HGNC:315" ; level 2 ; orig_coord_info "chr18,12376969,12377082,-" ; protein_id "ENSP00000269143.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRELID3A--AFG3L2^ENST00000269143.8" ; transcript_name "AFG3L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRELID3A--AFG3L2 HAVANA gene 1001 10159 . + . FI_gene_label "PRELID3A^ENSG00000141391.14" ; ID "PRELID3A--AFG3L2^PRELID3A^ENSG00000141391.14" ; ccdsid "CCDS11860.1" ; exon_id "ENSE00003628463.1" ; exon_number 1 ; gene_id "PRELID3A--AFG3L2^PRELID3A^ENSG00000141391.14" ; gene_name PRELID3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000131694.5" ; havana_transcript "OTTHUMT00000254602.2" ; hgnc_id "HGNC:24639" ; level 2 ; orig_coord_info "chr18,12407976,12408007,+" ; protein_id "ENSP00000338988.3" ; tag basic appris_principal_1 CCDS ; transcript_id "PRELID3A--AFG3L2^ENST00000336990.8" ; transcript_name "PRELID3A-201" ; transcript_support_level 2 ; transcript_type protein_coding
PRELID3A--AFG3L2 HAVANA mRNA 1001 10159 . + . FI_gene_label "PRELID3A^ENSG00000141391.14" ; ID "PRELID3A--AFG3L2^ENST00000336990.8" ; Parent "PRELID3A--AFG3L2^PRELID3A^ENSG00000141391.14" ; ccdsid "CCDS11860.1" ; exon_id "ENSE00003628463.1" ; exon_number 1 ; gene_id "PRELID3A--AFG3L2^PRELID3A^ENSG00000141391.14" ; gene_name PRELID3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000131694.5" ; havana_transcript "OTTHUMT00000254602.2" ; hgnc_id "HGNC:24639" ; level 2 ; orig_coord_info "chr18,12407976,12408007,+" ; protein_id "ENSP00000338988.3" ; tag basic appris_principal_1 CCDS ; transcript_id "PRELID3A--AFG3L2^ENST00000336990.8" ; transcript_name "PRELID3A-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 1328 8540 . + . FI_gene_label "PRSS27^ENSG00000172382.10" ; ID "PRSS27--TPSB2^ENST00000302641.8" ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; ccdsid "CCDS10476.1" ; exon_id "ENSE00001215985.4" ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10" ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3" ; havana_transcript "OTTHUMT00000250908.2" ; hgnc_id "HGNC:15475" ; level 2 ; orig_coord_info "chr16,2720115,2720160,-" ; protein_id "ENSP00000306390.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8" ; transcript_name "PRSS27-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PRSS27--TPSB2 HAVANA gene 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2 HAVANA mRNA 11544 13392 . + . FI_gene_label "TPSB2^ENSG00000197253.13" ; ID "PRSS27--TPSB2^ENST00000606293.5" ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; exon_id "ENSE00003747406.1" ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13" ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4" ; havana_transcript "OTTHUMT00000342363.2" ; hgnc_id "HGNC:14120" ; level 2 ; orig_coord_info "chr16,1229891,1229951,-" ; protein_id "ENSP00000482743.1" ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5" ; transcript_name "TPSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^ENST00000356698.9" ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTPRK--RSPO3 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
PTPRK--RSPO3 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^ENST00000368207.7" ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RAI1--DRC3 ENSEMBL gene 20922 38489 . + . FI_gene_label "DRC3^ENSG00000171962.18" ; ID "RAI1--DRC3^DRC3^ENSG00000171962.18" ; exon_id "ENSE00003662203.1" ; exon_number 3 ; gene_id "RAI1--DRC3^DRC3^ENSG00000171962.18" ; gene_name DRC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059355.9" ; hgnc_id "HGNC:25384" ; level 3 ; orig_coord_info "chr17,17977599,17977758,+" ; protein_id "ENSP00000326870.8" ; tag basic appris_principal_2 ; transcript_id "RAI1--DRC3^ENST00000313838.12" ; transcript_name "DRC3-201" ; transcript_support_level 5 ; transcript_type protein_coding
RAI1--DRC3 ENSEMBL mRNA 20922 38489 . + . FI_gene_label "DRC3^ENSG00000171962.18" ; ID "RAI1--DRC3^ENST00000313838.12" ; Parent "RAI1--DRC3^DRC3^ENSG00000171962.18" ; exon_id "ENSE00003662203.1" ; exon_number 3 ; gene_id "RAI1--DRC3^DRC3^ENSG00000171962.18" ; gene_name DRC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059355.9" ; hgnc_id "HGNC:25384" ; level 3 ; orig_coord_info "chr17,17977599,17977758,+" ; protein_id "ENSP00000326870.8" ; tag basic appris_principal_2 ; transcript_id "RAI1--DRC3^ENST00000313838.12" ; transcript_name "DRC3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RAI1--DRC3 HAVANA gene 1001 17921 . + . FI_gene_label "RAI1^ENSG00000108557.19" ; ID "RAI1--DRC3^RAI1^ENSG00000108557.19" ; ccdsid "CCDS11188.1" ; exon_id "ENSE00001291642.2" ; exon_number 3 ; gene_id "RAI1--DRC3^RAI1^ENSG00000108557.19" ; gene_name RAI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059314.4" ; havana_transcript "OTTHUMT00000131775.2" ; hgnc_id "HGNC:9834" ; level 2 ; orig_coord_info "chr17,17792949,17798513,+" ; protein_id "ENSP00000323074.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAI1--DRC3^ENST00000353383.6" ; transcript_name "RAI1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RAI1--DRC3 HAVANA mRNA 1001 17921 . + . FI_gene_label "RAI1^ENSG00000108557.19" ; ID "RAI1--DRC3^ENST00000353383.6" ; Parent "RAI1--DRC3^RAI1^ENSG00000108557.19" ; ccdsid "CCDS11188.1" ; exon_id "ENSE00001291642.2" ; exon_number 3 ; gene_id "RAI1--DRC3^RAI1^ENSG00000108557.19" ; gene_name RAI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059314.4" ; havana_transcript "OTTHUMT00000131775.2" ; hgnc_id "HGNC:9834" ; level 2 ; orig_coord_info "chr17,17792949,17798513,+" ; protein_id "ENSP00000323074.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAI1--DRC3^ENST00000353383.6" ; transcript_name "RAI1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ROCK1--AFG3L2 HAVANA gene 41772 61744 . + . FI_gene_label "AFG3L2^ENSG00000141385.10" ; ID "ROCK1--AFG3L2^AFG3L2^ENSG00000141385.10" ; ccdsid "CCDS11859.1" ; exon_id "ENSE00001255364.6" ; exon_number 1 ; gene_id "ROCK1--AFG3L2^AFG3L2^ENSG00000141385.10" ; gene_name AFG3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131695.4" ; havana_transcript "OTTHUMT00000254603.3" ; hgnc_id "HGNC:315" ; level 2 ; orig_coord_info "chr18,12376969,12377082,-" ; protein_id "ENSP00000269143.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ROCK1--AFG3L2^ENST00000269143.8" ; transcript_name "AFG3L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ROCK1--AFG3L2 HAVANA mRNA 41772 61744 . + . FI_gene_label "AFG3L2^ENSG00000141385.10" ; ID "ROCK1--AFG3L2^ENST00000269143.8" ; Parent "ROCK1--AFG3L2^AFG3L2^ENSG00000141385.10" ; ccdsid "CCDS11859.1" ; exon_id "ENSE00001255364.6" ; exon_number 1 ; gene_id "ROCK1--AFG3L2^AFG3L2^ENSG00000141385.10" ; gene_name AFG3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131695.4" ; havana_transcript "OTTHUMT00000254603.3" ; hgnc_id "HGNC:315" ; level 2 ; orig_coord_info "chr18,12376969,12377082,-" ; protein_id "ENSP00000269143.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ROCK1--AFG3L2^ENST00000269143.8" ; transcript_name "AFG3L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ROCK1--AFG3L2 HAVANA gene 1001 38771 . + . FI_gene_label "ROCK1^ENSG00000067900.8" ; ID "ROCK1--AFG3L2^ROCK1^ENSG00000067900.8" ; ccdsid "CCDS11870.2" ; exon_id "ENSE00001540250.2" ; exon_number 1 ; gene_id "ROCK1--AFG3L2^ROCK1^ENSG00000067900.8" ; gene_name ROCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131723.5" ; havana_transcript "OTTHUMT00000254641.3" ; hgnc_id "HGNC:10251" ; level 2 ; orig_coord_info "chr18,21110818,21110910,-" ; protein_id "ENSP00000382697.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ROCK1--AFG3L2^ENST00000399799.3" ; transcript_name "ROCK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ROCK1--AFG3L2 HAVANA mRNA 1001 38771 . + . FI_gene_label "ROCK1^ENSG00000067900.8" ; ID "ROCK1--AFG3L2^ENST00000399799.3" ; Parent "ROCK1--AFG3L2^ROCK1^ENSG00000067900.8" ; ccdsid "CCDS11870.2" ; exon_id "ENSE00001540250.2" ; exon_number 1 ; gene_id "ROCK1--AFG3L2^ROCK1^ENSG00000067900.8" ; gene_name ROCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131723.5" ; havana_transcript "OTTHUMT00000254641.3" ; hgnc_id "HGNC:10251" ; level 2 ; orig_coord_info "chr18,21110818,21110910,-" ; protein_id "ENSP00000382697.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ROCK1--AFG3L2^ENST00000399799.3" ; transcript_name "ROCK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SAE1--AC011495.1 HAVANA gene 3541 19880 . + . FI_gene_label "SAE1^ENSG00000142230.13" ; ID "SAE1--AC011495.1^SAE1^ENSG00000142230.13" ; ccdsid "CCDS12696.1" ; exon_id "ENSE00003031595.2" ; exon_number 1 ; gene_id "SAE1--AC011495.1^SAE1^ENSG00000142230.13" ; gene_name SAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183464.5" ; havana_transcript "OTTHUMT00000466775.2" ; hgnc_id "HGNC:30660" ; level 2 ; orig_coord_info "chr19,47130931,47131028,+" ; protein_id "ENSP00000270225.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAE1--AC011495.1^ENST00000270225.12" ; transcript_name "SAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SAE1--AC011495.1 HAVANA mRNA 3541 19880 . + . FI_gene_label "SAE1^ENSG00000142230.13" ; ID "SAE1--AC011495.1^ENST00000270225.12" ; Parent "SAE1--AC011495.1^SAE1^ENSG00000142230.13" ; ccdsid "CCDS12696.1" ; exon_id "ENSE00003031595.2" ; exon_number 1 ; gene_id "SAE1--AC011495.1^SAE1^ENSG00000142230.13" ; gene_name SAE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183464.5" ; havana_transcript "OTTHUMT00000466775.2" ; hgnc_id "HGNC:30660" ; level 2 ; orig_coord_info "chr19,47130931,47131028,+" ; protein_id "ENSP00000270225.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SAE1--AC011495.1^ENST00000270225.12" ; transcript_name "SAE1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SF3B3--COG4 HAVANA gene 1026 35771 . + . FI_gene_label "SF3B3^ENSG00000189091.13" ; ID "SF3B3--COG4^SF3B3^ENSG00000189091.13" ; ccdsid "CCDS10894.1" ; exon_id "ENSE00001298396.3" ; exon_number 2 ; gene_id "SF3B3--COG4^SF3B3^ENSG00000189091.13" ; gene_name SF3B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137582.8" ; havana_transcript "OTTHUMT00000268972.3" ; hgnc_id "HGNC:10770" ; level 2 ; orig_coord_info "chr16,70526657,70526726,+" ; protein_id "ENSP00000305790.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SF3B3--COG4^ENST00000302516.10" ; transcript_name "SF3B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SF3B3--COG4 HAVANA mRNA 1026 35771 . + . FI_gene_label "SF3B3^ENSG00000189091.13" ; ID "SF3B3--COG4^ENST00000302516.10" ; Parent "SF3B3--COG4^SF3B3^ENSG00000189091.13" ; ccdsid "CCDS10894.1" ; exon_id "ENSE00001298396.3" ; exon_number 2 ; gene_id "SF3B3--COG4^SF3B3^ENSG00000189091.13" ; gene_name SF3B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137582.8" ; havana_transcript "OTTHUMT00000268972.3" ; hgnc_id "HGNC:10770" ; level 2 ; orig_coord_info "chr16,70526657,70526726,+" ; protein_id "ENSP00000305790.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SF3B3--COG4^ENST00000302516.10" ; transcript_name "SF3B3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SF3B3--COG4 HAVANA gene 38780 57464 . + . FI_gene_label "COG4^ENSG00000103051.20" ; ID "SF3B3--COG4^COG4^ENSG00000103051.20" ; ccdsid "CCDS10892.2" ; exon_id "ENSE00001284953.3" ; exon_number 1 ; gene_id "SF3B3--COG4^COG4^ENSG00000103051.20" ; gene_name COG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128515.11" ; havana_transcript "OTTHUMT00000250326.4" ; hgnc_id "HGNC:18620" ; level 2 ; orig_coord_info "chr16,70523373,70523543,-" ; protein_id "ENSP00000315775.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SF3B3--COG4^ENST00000323786.10" ; transcript_name "COG4-201" ; transcript_support_level 1 ; transcript_type protein_coding
SF3B3--COG4 HAVANA mRNA 38780 57464 . + . FI_gene_label "COG4^ENSG00000103051.20" ; ID "SF3B3--COG4^ENST00000323786.10" ; Parent "SF3B3--COG4^COG4^ENSG00000103051.20" ; ccdsid "CCDS10892.2" ; exon_id "ENSE00001284953.3" ; exon_number 1 ; gene_id "SF3B3--COG4^COG4^ENSG00000103051.20" ; gene_name COG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128515.11" ; havana_transcript "OTTHUMT00000250326.4" ; hgnc_id "HGNC:18620" ; level 2 ; orig_coord_info "chr16,70523373,70523543,-" ; protein_id "ENSP00000315775.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SF3B3--COG4^ENST00000323786.10" ; transcript_name "COG4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SIN3A--CORO2B HAVANA gene 40525 54738 . + . FI_gene_label "CORO2B^ENSG00000103647.13" ; ID "SIN3A--CORO2B^CORO2B^ENSG00000103647.13" ; ccdsid "CCDS10229.2" ; exon_id "ENSE00001405057.5" ; exon_number 1 ; gene_id "SIN3A--CORO2B^CORO2B^ENSG00000103647.13" ; gene_name CORO2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133288.6" ; havana_transcript "OTTHUMT00000504477.2" ; hgnc_id "HGNC:2256" ; level 2 ; orig_coord_info "chr15,68579263,68579277,+" ; protein_id "ENSP00000261861.6" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "SIN3A--CORO2B^ENST00000261861.10" ; transcript_name "CORO2B-201" ; transcript_support_level 1 ; transcript_type protein_coding
SIN3A--CORO2B HAVANA mRNA 40525 54738 . + . FI_gene_label "CORO2B^ENSG00000103647.13" ; ID "SIN3A--CORO2B^ENST00000261861.10" ; Parent "SIN3A--CORO2B^CORO2B^ENSG00000103647.13" ; ccdsid "CCDS10229.2" ; exon_id "ENSE00001405057.5" ; exon_number 1 ; gene_id "SIN3A--CORO2B^CORO2B^ENSG00000103647.13" ; gene_name CORO2B ; gene_type protein_coding ; havana_gene "OTTHUMG00000133288.6" ; havana_transcript "OTTHUMT00000504477.2" ; hgnc_id "HGNC:2256" ; level 2 ; orig_coord_info "chr15,68579263,68579277,+" ; protein_id "ENSP00000261861.6" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "SIN3A--CORO2B^ENST00000261861.10" ; transcript_name "CORO2B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SIN3A--CORO2B HAVANA gene 1060 35970 . + . FI_gene_label "SIN3A^ENSG00000169375.16" ; ID "SIN3A--CORO2B^SIN3A^ENSG00000169375.16" ; ccdsid "CCDS10279.1" ; exon_id "ENSE00001326532.2" ; exon_number 2 ; gene_id "SIN3A--CORO2B^SIN3A^ENSG00000169375.16" ; gene_name SIN3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000142834.5" ; havana_transcript "OTTHUMT00000286470.1" ; hgnc_id "HGNC:19353" ; level 2 ; orig_coord_info "chr15,75430187,75430375,-" ; protein_id "ENSP00000353622.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SIN3A--CORO2B^ENST00000360439.8" ; transcript_name "SIN3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
SIN3A--CORO2B HAVANA mRNA 1060 35970 . + . FI_gene_label "SIN3A^ENSG00000169375.16" ; ID "SIN3A--CORO2B^ENST00000360439.8" ; Parent "SIN3A--CORO2B^SIN3A^ENSG00000169375.16" ; ccdsid "CCDS10279.1" ; exon_id "ENSE00001326532.2" ; exon_number 2 ; gene_id "SIN3A--CORO2B^SIN3A^ENSG00000169375.16" ; gene_name SIN3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000142834.5" ; havana_transcript "OTTHUMT00000286470.1" ; hgnc_id "HGNC:19353" ; level 2 ; orig_coord_info "chr15,75430187,75430375,-" ; protein_id "ENSP00000353622.4" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SIN3A--CORO2B^ENST00000360439.8" ; transcript_name "SIN3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPIRE1--GREB1L HAVANA gene 31238 70188 . + . FI_gene_label "GREB1L^ENSG00000141449.15" ; ID "SPIRE1--GREB1L^GREB1L^ENSG00000141449.15" ; exon_id "ENSE00003694289.1" ; exon_number 3 ; gene_id "SPIRE1--GREB1L^GREB1L^ENSG00000141449.15" ; gene_name GREB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000178892.3" ; havana_transcript "OTTHUMT00000443781.2" ; hgnc_id "HGNC:31042" ; level 2 ; orig_coord_info "chr18,21383519,21383675,+" ; protein_id "ENSP00000269218.6" ; tag basic ; transcript_id "SPIRE1--GREB1L^ENST00000269218.10" ; transcript_name "GREB1L-201" ; transcript_support_level 5 ; transcript_type protein_coding
SPIRE1--GREB1L HAVANA mRNA 31238 70188 . + . FI_gene_label "GREB1L^ENSG00000141449.15" ; ID "SPIRE1--GREB1L^ENST00000269218.10" ; Parent "SPIRE1--GREB1L^GREB1L^ENSG00000141449.15" ; exon_id "ENSE00003694289.1" ; exon_number 3 ; gene_id "SPIRE1--GREB1L^GREB1L^ENSG00000141449.15" ; gene_name GREB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000178892.3" ; havana_transcript "OTTHUMT00000443781.2" ; hgnc_id "HGNC:31042" ; level 2 ; orig_coord_info "chr18,21383519,21383675,+" ; protein_id "ENSP00000269218.6" ; tag basic ; transcript_id "SPIRE1--GREB1L^ENST00000269218.10" ; transcript_name "GREB1L-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
SPIRE1--GREB1L HAVANA gene 2403 25129 . + . FI_gene_label "SPIRE1^ENSG00000134278.15" ; ID "SPIRE1--GREB1L^SPIRE1^ENSG00000134278.15" ; exon_id "ENSE00003595447.1" ; exon_number 2 ; gene_id "SPIRE1--GREB1L^SPIRE1^ENSG00000134278.15" ; gene_name SPIRE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153940.4" ; havana_transcript "OTTHUMT00000333113.2" ; hgnc_id "HGNC:30622" ; level 2 ; orig_coord_info "chr18,12635062,12635073,-" ; protein_id "ENSP00000309661.5" ; tag basic ; transcript_id "SPIRE1--GREB1L^ENST00000309836.9" ; transcript_name "SPIRE1-201" ; transcript_support_level 2 ; transcript_type protein_coding
SPIRE1--GREB1L HAVANA mRNA 2403 25129 . + . FI_gene_label "SPIRE1^ENSG00000134278.15" ; ID "SPIRE1--GREB1L^ENST00000309836.9" ; Parent "SPIRE1--GREB1L^SPIRE1^ENSG00000134278.15" ; exon_id "ENSE00003595447.1" ; exon_number 2 ; gene_id "SPIRE1--GREB1L^SPIRE1^ENSG00000134278.15" ; gene_name SPIRE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153940.4" ; havana_transcript "OTTHUMT00000333113.2" ; hgnc_id "HGNC:30622" ; level 2 ; orig_coord_info "chr18,12635062,12635073,-" ; protein_id "ENSP00000309661.5" ; tag basic ; transcript_id "SPIRE1--GREB1L^ENST00000309836.9" ; transcript_name "SPIRE1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
SPRED1--ATP10A HAVANA gene 1001 16750 . + . FI_gene_label "SPRED1^ENSG00000166068.13" ; ID "SPRED1--ATP10A^SPRED1^ENSG00000166068.13" ; ccdsid "CCDS32193.1" ; exon_id "ENSE00002554709.2" ; exon_number 1 ; gene_id "SPRED1--ATP10A^SPRED1^ENSG00000166068.13" ; gene_name SPRED1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172377.4" ; havana_transcript "OTTHUMT00000418217.2" ; hgnc_id "HGNC:20249" ; level 2 ; orig_coord_info "chr15,38253186,38253217,+" ; protein_id "ENSP00000299084.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPRED1--ATP10A^ENST00000299084.9" ; transcript_name "SPRED1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPRED1--ATP10A HAVANA mRNA 1001 16750 . + . FI_gene_label "SPRED1^ENSG00000166068.13" ; ID "SPRED1--ATP10A^ENST00000299084.9" ; Parent "SPRED1--ATP10A^SPRED1^ENSG00000166068.13" ; ccdsid "CCDS32193.1" ; exon_id "ENSE00002554709.2" ; exon_number 1 ; gene_id "SPRED1--ATP10A^SPRED1^ENSG00000166068.13" ; gene_name SPRED1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172377.4" ; havana_transcript "OTTHUMT00000418217.2" ; hgnc_id "HGNC:20249" ; level 2 ; orig_coord_info "chr15,38253186,38253217,+" ; protein_id "ENSP00000299084.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPRED1--ATP10A^ENST00000299084.9" ; transcript_name "SPRED1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SPRED1--ATP10A HAVANA gene 20921 63242 . + . FI_gene_label "ATP10A^ENSG00000206190.12" ; ID "SPRED1--ATP10A^ATP10A^ENSG00000206190.12" ; ccdsid "CCDS32178.1" ; exon_id "ENSE00001494352.1" ; exon_number 2 ; gene_id "SPRED1--ATP10A^ATP10A^ENSG00000206190.12" ; gene_name ATP10A ; gene_type protein_coding ; havana_gene "OTTHUMG00000171703.5" ; havana_transcript "OTTHUMT00000414831.2" ; hgnc_id "HGNC:13542" ; level 2 ; orig_coord_info "chr15,25862648,25863096,-" ; protein_id "ENSP00000349325.6" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SPRED1--ATP10A^ENST00000356865.11" ; transcript_name "ATP10A-201" ; transcript_support_level 1 ; transcript_type protein_coding
SPRED1--ATP10A HAVANA mRNA 20921 63242 . + . FI_gene_label "ATP10A^ENSG00000206190.12" ; ID "SPRED1--ATP10A^ENST00000356865.11" ; Parent "SPRED1--ATP10A^ATP10A^ENSG00000206190.12" ; ccdsid "CCDS32178.1" ; exon_id "ENSE00001494352.1" ; exon_number 2 ; gene_id "SPRED1--ATP10A^ATP10A^ENSG00000206190.12" ; gene_name ATP10A ; gene_type protein_coding ; havana_gene "OTTHUMG00000171703.5" ; havana_transcript "OTTHUMT00000414831.2" ; hgnc_id "HGNC:13542" ; level 2 ; orig_coord_info "chr15,25862648,25863096,-" ; protein_id "ENSP00000349325.6" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "SPRED1--ATP10A^ENST00000356865.11" ; transcript_name "ATP10A-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:
TAF4--UBE2Q2 HAVANA gene 1001 23695 . + . FI_gene_label "TAF4^ENSG00000130699.18" ; ID "TAF4--UBE2Q2^TAF4^ENSG00000130699.18" ; ccdsid "CCDS33500.1" ; exon_id "ENSE00001379037.1" ; exon_number 1 ; gene_id "TAF4--UBE2Q2^TAF4^ENSG00000130699.18" ; gene_name TAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032893.9" ; havana_transcript "OTTHUMT00000079968.2" ; hgnc_id "HGNC:11537" ; level 2 ; orig_coord_info "chr20,62064451,62065810,-" ; protein_id "ENSP00000252996.3" ; tag basic appris_principal_1 CCDS ; transcript_id "TAF4--UBE2Q2^ENST00000252996.8" ; transcript_name "TAF4-201" ; transcript_support_level 1 ; transcript_type protein_coding
TAF4--UBE2Q2 HAVANA mRNA 1001 23695 . + . FI_gene_label "TAF4^ENSG00000130699.18" ; ID "TAF4--UBE2Q2^ENST00000252996.8" ; Parent "TAF4--UBE2Q2^TAF4^ENSG00000130699.18" ; ccdsid "CCDS33500.1" ; exon_id "ENSE00001379037.1" ; exon_number 1 ; gene_id "TAF4--UBE2Q2^TAF4^ENSG00000130699.18" ; gene_name TAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032893.9" ; havana_transcript "OTTHUMT00000079968.2" ; hgnc_id "HGNC:11537" ; level 2 ; orig_coord_info "chr20,62064451,62065810,-" ; protein_id "ENSP00000252996.3" ; tag basic appris_principal_1 CCDS ; transcript_id "TAF4--UBE2Q2^ENST00000252996.8" ; transcript_name "TAF4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TAF4--UBE2Q2 HAVANA gene 28196 43418 . + . FI_gene_label "UBE2Q2^ENSG00000140367.12" ; ID "TAF4--UBE2Q2^UBE2Q2^ENSG00000140367.12" ; ccdsid "CCDS10286.1" ; exon_id "ENSE00001836297.2" ; exon_number 1 ; gene_id "TAF4--UBE2Q2^UBE2Q2^ENSG00000140367.12" ; gene_name UBE2Q2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142839.3" ; havana_transcript "OTTHUMT00000286475.2" ; hgnc_id "HGNC:19248" ; level 2 ; orig_coord_info "chr15,75843667,75843846,+" ; protein_id "ENSP00000267938.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TAF4--UBE2Q2^ENST00000267938.9" ; transcript_name "UBE2Q2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TAF4--UBE2Q2 HAVANA mRNA 28196 43418 . + . FI_gene_label "UBE2Q2^ENSG00000140367.12" ; ID "TAF4--UBE2Q2^ENST00000267938.9" ; Parent "TAF4--UBE2Q2^UBE2Q2^ENSG00000140367.12" ; ccdsid "CCDS10286.1" ; exon_id "ENSE00001836297.2" ; exon_number 1 ; gene_id "TAF4--UBE2Q2^UBE2Q2^ENSG00000140367.12" ; gene_name UBE2Q2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000142839.3" ; havana_transcript "OTTHUMT00000286475.2" ; hgnc_id "HGNC:19248" ; level 2 ; orig_coord_info "chr15,75843667,75843846,+" ; protein_id "ENSP00000267938.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TAF4--UBE2Q2^ENST00000267938.9" ; transcript_name "UBE2Q2-201" ; 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:
TMEM87B--MERTK HAVANA gene 1001 23704 . + . FI_gene_label "TMEM87B^ENSG00000153214.11" ; ID "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; ccdsid "CCDS33275.1" ; exon_id "ENSE00001009506.5" ; exon_number 1 ; gene_id "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; gene_name TMEM87B ; gene_type protein_coding ; havana_gene "OTTHUMG00000153266.6" ; havana_transcript "OTTHUMT00000330500.2" ; hgnc_id "HGNC:25913" ; level 2 ; orig_coord_info "chr2,112055592,112055756,+" ; protein_id "ENSP00000283206.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000283206.9" ; transcript_name "TMEM87B-201" ; transcript_support_level 2 ; transcript_type protein_coding
TMEM87B--MERTK HAVANA mRNA 1001 23704 . + . FI_gene_label "TMEM87B^ENSG00000153214.11" ; ID "TMEM87B--MERTK^ENST00000283206.9" ; Parent "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; ccdsid "CCDS33275.1" ; exon_id "ENSE00001009506.5" ; exon_number 1 ; gene_id "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; gene_name TMEM87B ; gene_type protein_coding ; havana_gene "OTTHUMG00000153266.6" ; havana_transcript "OTTHUMT00000330500.2" ; hgnc_id "HGNC:25913" ; level 2 ; orig_coord_info "chr2,112055592,112055756,+" ; protein_id "ENSP00000283206.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000283206.9" ; transcript_name "TMEM87B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TMEM87B--MERTK HAVANA gene 26709 55872 . + . FI_gene_label "MERTK^ENSG00000153208.17" ; ID "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; ccdsid "CCDS2094.1" ; exon_id "ENSE00001254759.8" ; exon_number 1 ; gene_id "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; gene_name MERTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131278.5" ; havana_transcript "OTTHUMT00000254046.3" ; hgnc_id "HGNC:7027" ; level 2 ; orig_coord_info "chr2,111898736,111898796,+" ; protein_id "ENSP00000295408.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000295408.9" ; transcript_name "MERTK-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM87B--MERTK HAVANA mRNA 26709 55872 . + . FI_gene_label "MERTK^ENSG00000153208.17" ; ID "TMEM87B--MERTK^ENST00000295408.9" ; Parent "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; ccdsid "CCDS2094.1" ; exon_id "ENSE00001254759.8" ; exon_number 1 ; gene_id "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; gene_name MERTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131278.5" ; havana_transcript "OTTHUMT00000254046.3" ; hgnc_id "HGNC:7027" ; level 2 ; orig_coord_info "chr2,111898736,111898796,+" ; protein_id "ENSP00000295408.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000295408.9" ; transcript_name "MERTK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRPM7--MAPK6 HAVANA gene 52109 67625 . + . FI_gene_label "MAPK6^ENSG00000069956.13" ; ID "TRPM7--MAPK6^MAPK6^ENSG00000069956.13" ; ccdsid "CCDS10147.1" ; exon_id "ENSE00000942191.1" ; exon_number 2 ; gene_id "TRPM7--MAPK6^MAPK6^ENSG00000069956.13" ; gene_name MAPK6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131891.4" ; havana_transcript "OTTHUMT00000254841.4" ; hgnc_id "HGNC:6879" ; level 2 ; orig_coord_info "chr15,52046461,52047015,+" ; protein_id "ENSP00000261845.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPM7--MAPK6^ENST00000261845.7" ; transcript_name "MAPK6-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRPM7--MAPK6 HAVANA mRNA 52109 67625 . + . FI_gene_label "MAPK6^ENSG00000069956.13" ; ID "TRPM7--MAPK6^ENST00000261845.7" ; Parent "TRPM7--MAPK6^MAPK6^ENSG00000069956.13" ; ccdsid "CCDS10147.1" ; exon_id "ENSE00000942191.1" ; exon_number 2 ; gene_id "TRPM7--MAPK6^MAPK6^ENSG00000069956.13" ; gene_name MAPK6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131891.4" ; havana_transcript "OTTHUMT00000254841.4" ; hgnc_id "HGNC:6879" ; level 2 ; orig_coord_info "chr15,52046461,52047015,+" ; protein_id "ENSP00000261845.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPM7--MAPK6^ENST00000261845.7" ; transcript_name "MAPK6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRPM7--MAPK6 HAVANA gene 13654 23410 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "TRPM7--MAPK6^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "TRPM7--MAPK6^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TRPM7--MAPK6^ENST00000560638.1" ; transcript_name "TRPM7-204" ; transcript_support_level 1 ; transcript_type protein_coding
TRPM7--MAPK6 HAVANA mRNA 13654 23410 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "TRPM7--MAPK6^ENST00000560638.1" ; Parent "TRPM7--MAPK6^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "TRPM7--MAPK6^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TRPM7--MAPK6^ENST00000560638.1" ; transcript_name "TRPM7-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRPM7--TMOD3 HAVANA gene 49723 69857 . + . FI_gene_label "TMOD3^ENSG00000138594.14" ; ID "TRPM7--TMOD3^TMOD3^ENSG00000138594.14" ; ccdsid "CCDS10145.1" ; exon_id "ENSE00001170748.1" ; exon_number 2 ; gene_id "TRPM7--TMOD3^TMOD3^ENSG00000138594.14" ; gene_name TMOD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131803.8" ; havana_transcript "OTTHUMT00000254740.5" ; hgnc_id "HGNC:11873" ; level 2 ; orig_coord_info "chr15,51862885,51863010,+" ; protein_id "ENSP00000308753.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPM7--TMOD3^ENST00000308580.12" ; transcript_name "TMOD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TRPM7--TMOD3 HAVANA mRNA 49723 69857 . + . FI_gene_label "TMOD3^ENSG00000138594.14" ; ID "TRPM7--TMOD3^ENST00000308580.12" ; Parent "TRPM7--TMOD3^TMOD3^ENSG00000138594.14" ; ccdsid "CCDS10145.1" ; exon_id "ENSE00001170748.1" ; exon_number 2 ; gene_id "TRPM7--TMOD3^TMOD3^ENSG00000138594.14" ; gene_name TMOD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131803.8" ; havana_transcript "OTTHUMT00000254740.5" ; hgnc_id "HGNC:11873" ; level 2 ; orig_coord_info "chr15,51862885,51863010,+" ; protein_id "ENSP00000308753.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TRPM7--TMOD3^ENST00000308580.12" ; transcript_name "TMOD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRPM7--TMOD3 HAVANA gene 13654 23410 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "TRPM7--TMOD3^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "TRPM7--TMOD3^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TRPM7--TMOD3^ENST00000560638.1" ; transcript_name "TRPM7-204" ; transcript_support_level 1 ; transcript_type protein_coding
TRPM7--TMOD3 HAVANA mRNA 13654 23410 . + . FI_gene_label "TRPM7^ENSG00000092439.16" ; ID "TRPM7--TMOD3^ENST00000560638.1" ; Parent "TRPM7--TMOD3^TRPM7^ENSG00000092439.16" ; exon_id "ENSE00002541088.1" ; exon_number 1 ; gene_id "TRPM7--TMOD3^TRPM7^ENSG00000092439.16" ; gene_name TRPM7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172449.3" ; havana_transcript "OTTHUMT00000418611.1" ; hgnc_id "HGNC:17994" ; level 2 ; orig_coord_info "chr15,50624166,50624216,-" ; protein_id "ENSP00000452873.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "TRPM7--TMOD3^ENST00000560638.1" ; transcript_name "TRPM7-204" ; 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:
VAPB--AURKA HAVANA gene 20960 32133 . + . FI_gene_label "AURKA^ENSG00000087586.18" ; ID "VAPB--AURKA^AURKA^ENSG00000087586.18" ; ccdsid "CCDS13451.1" ; exon_id "ENSE00000845695.3" ; exon_number 3 ; gene_id "VAPB--AURKA^AURKA^ENSG00000087586.18" ; gene_name AURKA ; gene_type protein_coding ; havana_gene "OTTHUMG00000032796.7" ; havana_transcript "OTTHUMT00000079807.2" ; hgnc_id "HGNC:11393" ; level 2 ; orig_coord_info "chr20,56388156,56388197,-" ; protein_id "ENSP00000321591.6" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "VAPB--AURKA^ENST00000312783.10" ; transcript_name "AURKA-201" ; transcript_support_level 1 ; transcript_type protein_coding
VAPB--AURKA HAVANA mRNA 20960 32133 . + . FI_gene_label "AURKA^ENSG00000087586.18" ; ID "VAPB--AURKA^ENST00000312783.10" ; Parent "VAPB--AURKA^AURKA^ENSG00000087586.18" ; ccdsid "CCDS13451.1" ; exon_id "ENSE00000845695.3" ; exon_number 3 ; gene_id "VAPB--AURKA^AURKA^ENSG00000087586.18" ; gene_name AURKA ; gene_type protein_coding ; havana_gene "OTTHUMG00000032796.7" ; havana_transcript "OTTHUMT00000079807.2" ; hgnc_id "HGNC:11393" ; level 2 ; orig_coord_info "chr20,56388156,56388197,-" ; protein_id "ENSP00000321591.6" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "VAPB--AURKA^ENST00000312783.10" ; transcript_name "AURKA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VAPB--AURKA HAVANA gene 1085 12368 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "VAPB--AURKA^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "VAPB--AURKA^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "VAPB--AURKA^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
VAPB--AURKA HAVANA mRNA 1085 12368 . + . FI_gene_label "VAPB^ENSG00000124164.16" ; ID "VAPB--AURKA^ENST00000395802.7" ; Parent "VAPB--AURKA^VAPB^ENSG00000124164.16" ; ccdsid "CCDS56198.1" ; exon_id "ENSE00001373311.6" ; exon_number 1 ; gene_id "VAPB--AURKA^VAPB^ENSG00000124164.16" ; gene_name VAPB ; gene_type protein_coding ; havana_gene "OTTHUMG00000032840.4" ; havana_transcript "OTTHUMT00000267817.1" ; hgnc_id "HGNC:12649" ; level 2 ; orig_coord_info "chr20,58389460,58389517,+" ; protein_id "ENSP00000379147.3" ; tag basic CCDS ; transcript_id "VAPB--AURKA^ENST00000395802.7" ; transcript_name "VAPB-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VWA8--ZNF346 HAVANA gene 1001 27826 . + . FI_gene_label "VWA8^ENSG00000102763.18" ; ID "VWA8--ZNF346^VWA8^ENSG00000102763.18" ; ccdsid "CCDS31963.1" ; exon_id "ENSE00001842780.1" ; exon_number 1 ; gene_id "VWA8--ZNF346^VWA8^ENSG00000102763.18" ; gene_name VWA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016799.6" ; havana_transcript "OTTHUMT00000044689.1" ; hgnc_id "HGNC:29071" ; level 2 ; orig_coord_info "chr13,41960853,41961015,-" ; protein_id "ENSP00000281496.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "VWA8--ZNF346^ENST00000281496.6" ; transcript_name "VWA8-201" ; transcript_support_level 1 ; transcript_type protein_coding
VWA8--ZNF346 HAVANA mRNA 1001 27826 . + . FI_gene_label "VWA8^ENSG00000102763.18" ; ID "VWA8--ZNF346^ENST00000281496.6" ; Parent "VWA8--ZNF346^VWA8^ENSG00000102763.18" ; ccdsid "CCDS31963.1" ; exon_id "ENSE00001842780.1" ; exon_number 1 ; gene_id "VWA8--ZNF346^VWA8^ENSG00000102763.18" ; gene_name VWA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016799.6" ; havana_transcript "OTTHUMT00000044689.1" ; hgnc_id "HGNC:29071" ; level 2 ; orig_coord_info "chr13,41960853,41961015,-" ; protein_id "ENSP00000281496.6" ; tag basic appris_alternative_2 CCDS ; transcript_id "VWA8--ZNF346^ENST00000281496.6" ; transcript_name "VWA8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
VWA8--ZNF346 HAVANA gene 53850 64521 . + . FI_gene_label "ZNF346^ENSG00000113761.12" ; ID "VWA8--ZNF346^ZNF346^ENSG00000113761.12" ; ccdsid "CCDS4409.1" ; exon_id "ENSE00001412343.2" ; exon_number 1 ; gene_id "VWA8--ZNF346^ZNF346^ENSG00000113761.12" ; gene_name ZNF346 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130848.3" ; havana_transcript "OTTHUMT00000253415.3" ; hgnc_id "HGNC:16403" ; level 2 ; orig_coord_info "chr5,177022739,177022913,+" ; protein_id "ENSP00000350869.3" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "VWA8--ZNF346^ENST00000358149.8" ; transcript_name "ZNF346-201" ; transcript_support_level 1 ; transcript_type protein_coding
VWA8--ZNF346 HAVANA mRNA 53850 64521 . + . FI_gene_label "ZNF346^ENSG00000113761.12" ; ID "VWA8--ZNF346^ENST00000358149.8" ; Parent "VWA8--ZNF346^ZNF346^ENSG00000113761.12" ; ccdsid "CCDS4409.1" ; exon_id "ENSE00001412343.2" ; exon_number 1 ; gene_id "VWA8--ZNF346^ZNF346^ENSG00000113761.12" ; gene_name ZNF346 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130848.3" ; havana_transcript "OTTHUMT00000253415.3" ; hgnc_id "HGNC:16403" ; level 2 ; orig_coord_info "chr5,177022739,177022913,+" ; protein_id "ENSP00000350869.3" ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "VWA8--ZNF346^ENST00000358149.8" ; transcript_name "ZNF346-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WSB2--NOS1 HAVANA gene 2252 11537 . + . FI_gene_label "WSB2^ENSG00000176871.9" ; ID "WSB2--NOS1^WSB2^ENSG00000176871.9" ; ccdsid "CCDS9186.1" ; exon_id "ENSE00002241893.2" ; exon_number 1 ; gene_id "WSB2--NOS1^WSB2^ENSG00000176871.9" ; gene_name WSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168885.5" ; havana_transcript "OTTHUMT00000401515.1" ; hgnc_id "HGNC:19222" ; level 2 ; orig_coord_info "chr12,118061036,118061048,-" ; protein_id "ENSP00000319474.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WSB2--NOS1^ENST00000315436.8" ; transcript_name "WSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
WSB2--NOS1 HAVANA mRNA 2252 11537 . + . FI_gene_label "WSB2^ENSG00000176871.9" ; ID "WSB2--NOS1^ENST00000315436.8" ; Parent "WSB2--NOS1^WSB2^ENSG00000176871.9" ; ccdsid "CCDS9186.1" ; exon_id "ENSE00002241893.2" ; exon_number 1 ; gene_id "WSB2--NOS1^WSB2^ENSG00000176871.9" ; gene_name WSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168885.5" ; havana_transcript "OTTHUMT00000401515.1" ; hgnc_id "HGNC:19222" ; level 2 ; orig_coord_info "chr12,118061036,118061048,-" ; protein_id "ENSP00000319474.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "WSB2--NOS1^ENST00000315436.8" ; transcript_name "WSB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WSB2--NOS1 HAVANA gene 16184 57242 . + . FI_gene_label "NOS1^ENSG00000089250.19" ; ID "WSB2--NOS1^NOS1^ENSG00000089250.19" ; ccdsid "CCDS41842.1" ; exon_id "ENSE00000835093.5" ; exon_number 2 ; gene_id "WSB2--NOS1^NOS1^ENSG00000089250.19" ; gene_name NOS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137376.4" ; havana_transcript "OTTHUMT00000268052.2" ; hgnc_id "HGNC:7872" ; level 2 ; orig_coord_info "chr12,117330345,117331069,-" ; protein_id "ENSP00000320758.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WSB2--NOS1^ENST00000317775.11" ; transcript_name "NOS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
WSB2--NOS1 HAVANA mRNA 16184 57242 . + . FI_gene_label "NOS1^ENSG00000089250.19" ; ID "WSB2--NOS1^ENST00000317775.11" ; Parent "WSB2--NOS1^NOS1^ENSG00000089250.19" ; ccdsid "CCDS41842.1" ; exon_id "ENSE00000835093.5" ; exon_number 2 ; gene_id "WSB2--NOS1^NOS1^ENSG00000089250.19" ; gene_name NOS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137376.4" ; havana_transcript "OTTHUMT00000268052.2" ; hgnc_id "HGNC:7872" ; level 2 ; orig_coord_info "chr12,117330345,117331069,-" ; protein_id "ENSP00000320758.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WSB2--NOS1^ENST00000317775.11" ; transcript_name "NOS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
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:
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:
FAM135A--AL080275.1 HAVANA gene 35435 39699 . + . FI_gene_label "AL080275.1^ENSG00000287300.1" ; ID "FAM135A--AL080275.1^AL080275.1^ENSG00000287300.1" ; exon_id "ENSE00003871771.1" ; exon_number 1 ; gene_id "FAM135A--AL080275.1^AL080275.1^ENSG00000287300.1" ; gene_name "AL080275.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195367.1" ; havana_transcript "OTTHUMT00000526641.1" ; level 2 ; orig_coord_info "chr6,70351643,70351802,-" ; tag basic TAGENE ; transcript_id "FAM135A--AL080275.1^ENST00000662517.1" ; transcript_name "AL080275.1-201" ; transcript_type lncRNA
FAM135A--AL080275.1 HAVANA RNA 35435 39699 . + . FI_gene_label "AL080275.1^ENSG00000287300.1" ; ID "FAM135A--AL080275.1^ENST00000662517.1" ; Parent "FAM135A--AL080275.1^AL080275.1^ENSG00000287300.1" ; exon_id "ENSE00003871771.1" ; exon_number 1 ; gene_id "FAM135A--AL080275.1^AL080275.1^ENSG00000287300.1" ; gene_name "AL080275.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195367.1" ; havana_transcript "OTTHUMT00000526641.1" ; level 2 ; orig_coord_info "chr6,70351643,70351802,-" ; tag basic TAGENE ; transcript_id "FAM135A--AL080275.1^ENST00000662517.1" ; transcript_name "AL080275.1-201" ; transcript_type lncRNA
L1 and L2 created:
FAM135A--AL365226.1 HAVANA gene 35437 37023 . + . FI_gene_label "AL365226.1^ENSG00000237643.2" ; ID "FAM135A--AL365226.1^AL365226.1^ENSG00000237643.2" ; exon_id "ENSE00001659472.2" ; exon_number 1 ; gene_id "FAM135A--AL365226.1^AL365226.1^ENSG00000237643.2" ; gene_name "AL365226.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014989.4" ; havana_transcript "OTTHUMT00000041135.2" ; level 2 ; orig_coord_info "chr6,70394883,70395043,+" ; tag TAGENE ; transcript_id "FAM135A--AL365226.1^ENST00000418403.2" ; transcript_name "AL365226.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
FAM135A--AL365226.1 HAVANA RNA 35437 37023 . + . FI_gene_label "AL365226.1^ENSG00000237643.2" ; ID "FAM135A--AL365226.1^ENST00000418403.2" ; Parent "FAM135A--AL365226.1^AL365226.1^ENSG00000237643.2" ; exon_id "ENSE00001659472.2" ; exon_number 1 ; gene_id "FAM135A--AL365226.1^AL365226.1^ENSG00000237643.2" ; gene_name "AL365226.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000014989.4" ; havana_transcript "OTTHUMT00000041135.2" ; level 2 ; orig_coord_info "chr6,70394883,70395043,+" ; tag TAGENE ; transcript_id "FAM135A--AL365226.1^ENST00000418403.2" ; transcript_name "AL365226.1-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1 HAVANA RNA 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^ENST00000624936.2" ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
SAE1--AC011495.1 HAVANA gene 22881 23464 . + . FI_gene_label "AC011495.1^ENSG00000243829.1" ; ID "SAE1--AC011495.1^AC011495.1^ENSG00000243829.1" ; exon_id "ENSE00001816650.1" ; exon_number 1 ; gene_id "SAE1--AC011495.1^AC011495.1^ENSG00000243829.1" ; gene_name "AC011495.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158217.1" ; havana_transcript "OTTHUMT00000350414.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr19,49719498,49720081,-" ; tag pseudo_consens basic ; transcript_id "SAE1--AC011495.1^ENST00000498085.1" ; transcript_name "AC011495.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
SAE1--AC011495.1 HAVANA RNA 22881 23464 . + . FI_gene_label "AC011495.1^ENSG00000243829.1" ; ID "SAE1--AC011495.1^ENST00000498085.1" ; Parent "SAE1--AC011495.1^AC011495.1^ENSG00000243829.1" ; exon_id "ENSE00001816650.1" ; exon_number 1 ; gene_id "SAE1--AC011495.1^AC011495.1^ENSG00000243829.1" ; gene_name "AC011495.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158217.1" ; havana_transcript "OTTHUMT00000350414.1" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr19,49719498,49720081,-" ; tag pseudo_consens basic ; transcript_id "SAE1--AC011495.1^ENST00000498085.1" ; transcript_name "AC011495.1-201" ; transcript_support_level NA ; transcript_type processed_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
592 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 ------------------------------
1115 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 47 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