Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/1a5fc70200f938f552f73dfcede1d8/fi_workdir/aih-tih-sc-693ffe-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/4fe70436d38b8d4e36879d62c15970/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/4fe70436d38b8d4e36879d62c15970/.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: 11338
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 11338
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:11338
=> 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:
AC004980.3--UPK3BL1 HAVANA gene 6366 11192 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC004980.3--UPK3BL1 HAVANA mRNA 6366 11192 . + . FI_gene_label "UPK3BL1^ENSG00000267368.1" ; ID "AC004980.3--UPK3BL1^ENST00000340457.8" ; Parent "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; ccdsid "CCDS47675.1" ; exon_id "ENSE00001683829.2" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^UPK3BL1^ENSG00000267368.1" ; gene_name UPK3BL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165036.2" ; havana_transcript "OTTHUMT00000381510.1" ; hgnc_id "HGNC:37278" ; level 2 ; orig_coord_info "chr7,102642630,102642741,-" ; protein_id "ENSP00000342938.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC004980.3--UPK3BL1^ENST00000340457.8" ; transcript_name "UPK3BL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AL121790.1--MIPOL1 HAVANA gene 5776 49225 . + . FI_gene_label "MIPOL1^ENSG00000151338.18" ; ID "AL121790.1--MIPOL1^MIPOL1^ENSG00000151338.18" ; ccdsid "CCDS9664.1" ; exon_id "ENSE00003679602.1" ; exon_number 4 ; gene_id "AL121790.1--MIPOL1^MIPOL1^ENSG00000151338.18" ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3" ; havana_transcript "OTTHUMT00000276734.1" ; hgnc_id "HGNC:21460" ; level 2 ; orig_coord_info "chr14,37247889,37247907,+" ; protein_id "ENSP00000333539.7" ; tag basic appris_principal_2 CCDS ; transcript_id "AL121790.1--MIPOL1^ENST00000327441.11" ; transcript_name "MIPOL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AL121790.1--MIPOL1 HAVANA mRNA 5776 49225 . + . FI_gene_label "MIPOL1^ENSG00000151338.18" ; ID "AL121790.1--MIPOL1^ENST00000327441.11" ; Parent "AL121790.1--MIPOL1^MIPOL1^ENSG00000151338.18" ; ccdsid "CCDS9664.1" ; exon_id "ENSE00003679602.1" ; exon_number 4 ; gene_id "AL121790.1--MIPOL1^MIPOL1^ENSG00000151338.18" ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3" ; havana_transcript "OTTHUMT00000276734.1" ; hgnc_id "HGNC:21460" ; level 2 ; orig_coord_info "chr14,37247889,37247907,+" ; protein_id "ENSP00000333539.7" ; tag basic appris_principal_2 CCDS ; transcript_id "AL121790.1--MIPOL1^ENST00000327441.11" ; transcript_name "MIPOL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ANXA2--ICE2 HAVANA gene 35015 64345 . + . FI_gene_label "ICE2^ENSG00000128915.12" ; ID "ANXA2--ICE2^ICE2^ENSG00000128915.12" ; ccdsid "CCDS10176.1" ; exon_id "ENSE00003649070.1" ; exon_number 2 ; gene_id "ANXA2--ICE2^ICE2^ENSG00000128915.12" ; gene_name ICE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132764.4" ; havana_transcript "OTTHUMT00000256136.2" ; hgnc_id "HGNC:29885" ; level 2 ; orig_coord_info "chr15,60477937,60477977,-" ; protein_id "ENSP00000261520.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANXA2--ICE2^ENST00000261520.9" ; transcript_name "ICE2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANXA2--ICE2 HAVANA mRNA 35015 64345 . + . FI_gene_label "ICE2^ENSG00000128915.12" ; ID "ANXA2--ICE2^ENST00000261520.9" ; Parent "ANXA2--ICE2^ICE2^ENSG00000128915.12" ; ccdsid "CCDS10176.1" ; exon_id "ENSE00003649070.1" ; exon_number 2 ; gene_id "ANXA2--ICE2^ICE2^ENSG00000128915.12" ; gene_name ICE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132764.4" ; havana_transcript "OTTHUMT00000256136.2" ; hgnc_id "HGNC:29885" ; level 2 ; orig_coord_info "chr15,60477937,60477977,-" ; protein_id "ENSP00000261520.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANXA2--ICE2^ENST00000261520.9" ; transcript_name "ICE2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ANXA2--ICE2 HAVANA gene 2873 31798 . + . FI_gene_label "ANXA2^ENSG00000182718.18" ; ID "ANXA2--ICE2^ANXA2^ENSG00000182718.18" ; ccdsid "CCDS32256.1" ; exon_id "ENSE00001383920.3" ; exon_number 1 ; gene_id "ANXA2--ICE2^ANXA2^ENSG00000182718.18" ; gene_name ANXA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132763.5" ; havana_transcript "OTTHUMT00000416470.1" ; hgnc_id "HGNC:537" ; level 2 ; orig_coord_info "chr15,60397871,60397913,-" ; protein_id "ENSP00000346032.3" ; tag basic CCDS ; transcript_id "ANXA2--ICE2^ENST00000332680.8" ; transcript_name "ANXA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ANXA2--ICE2 HAVANA mRNA 2873 31798 . + . FI_gene_label "ANXA2^ENSG00000182718.18" ; ID "ANXA2--ICE2^ENST00000332680.8" ; Parent "ANXA2--ICE2^ANXA2^ENSG00000182718.18" ; ccdsid "CCDS32256.1" ; exon_id "ENSE00001383920.3" ; exon_number 1 ; gene_id "ANXA2--ICE2^ANXA2^ENSG00000182718.18" ; gene_name ANXA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132763.5" ; havana_transcript "OTTHUMT00000416470.1" ; hgnc_id "HGNC:537" ; level 2 ; orig_coord_info "chr15,60397871,60397913,-" ; protein_id "ENSP00000346032.3" ; tag basic CCDS ; transcript_id "ANXA2--ICE2^ENST00000332680.8" ; transcript_name "ANXA2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BMPR1B--PDLIM5 HAVANA gene 8163 19884 . + . FI_gene_label "BMPR1B^ENSG00000138696.11" ; ID "BMPR1B--PDLIM5^BMPR1B^ENSG00000138696.11" ; ccdsid "CCDS3642.1" ; exon_id "ENSE00003894599.1" ; exon_number 2 ; gene_id "BMPR1B--PDLIM5^BMPR1B^ENSG00000138696.11" ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6" ; havana_transcript "OTTHUMT00000363051.1" ; hgnc_id "HGNC:1077" ; level 2 ; orig_coord_info "chr4,95104425,95104567,+" ; protein_id "ENSP00000264568.4" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "BMPR1B--PDLIM5^ENST00000264568.8" ; transcript_name "BMPR1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
BMPR1B--PDLIM5 HAVANA mRNA 8163 19884 . + . FI_gene_label "BMPR1B^ENSG00000138696.11" ; ID "BMPR1B--PDLIM5^ENST00000264568.8" ; Parent "BMPR1B--PDLIM5^BMPR1B^ENSG00000138696.11" ; ccdsid "CCDS3642.1" ; exon_id "ENSE00003894599.1" ; exon_number 2 ; gene_id "BMPR1B--PDLIM5^BMPR1B^ENSG00000138696.11" ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6" ; havana_transcript "OTTHUMT00000363051.1" ; hgnc_id "HGNC:1077" ; level 2 ; orig_coord_info "chr4,95104425,95104567,+" ; protein_id "ENSP00000264568.4" ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "BMPR1B--PDLIM5^ENST00000264568.8" ; transcript_name "BMPR1B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
BMPR1B--PDLIM5 HAVANA gene 26601 58161 . + . FI_gene_label "PDLIM5^ENSG00000163110.15" ; ID "BMPR1B--PDLIM5^PDLIM5^ENSG00000163110.15" ; ccdsid "CCDS3641.1" ; exon_id "ENSE00003692320.1" ; exon_number 2 ; gene_id "BMPR1B--PDLIM5^PDLIM5^ENSG00000163110.15" ; gene_name PDLIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130973.11" ; havana_transcript "OTTHUMT00000253586.2" ; hgnc_id "HGNC:17468" ; level 2 ; orig_coord_info "chr4,94455289,94455384,+" ; protein_id "ENSP00000321746.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "BMPR1B--PDLIM5^ENST00000317968.9" ; transcript_name "PDLIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
BMPR1B--PDLIM5 HAVANA mRNA 26601 58161 . + . FI_gene_label "PDLIM5^ENSG00000163110.15" ; ID "BMPR1B--PDLIM5^ENST00000317968.9" ; Parent "BMPR1B--PDLIM5^PDLIM5^ENSG00000163110.15" ; ccdsid "CCDS3641.1" ; exon_id "ENSE00003692320.1" ; exon_number 2 ; gene_id "BMPR1B--PDLIM5^PDLIM5^ENSG00000163110.15" ; gene_name PDLIM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130973.11" ; havana_transcript "OTTHUMT00000253586.2" ; hgnc_id "HGNC:17468" ; level 2 ; orig_coord_info "chr4,94455289,94455384,+" ; protein_id "ENSP00000321746.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "BMPR1B--PDLIM5^ENST00000317968.9" ; transcript_name "PDLIM5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BPTF--ABRA HAVANA gene 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--ABRA^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--ABRA^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ABRA^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding
BPTF--ABRA HAVANA mRNA 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--ABRA^ENST00000306378.11" ; Parent "BPTF--ABRA^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--ABRA^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ABRA^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BPTF--ABRA HAVANA gene 47100 50853 . + . FI_gene_label "ABRA^ENSG00000174429.4" ; ID "BPTF--ABRA^ABRA^ENSG00000174429.4" ; ccdsid "CCDS6305.1" ; exon_id "ENSE00001207130.8" ; exon_number 1 ; gene_id "BPTF--ABRA^ABRA^ENSG00000174429.4" ; gene_name ABRA ; gene_type protein_coding ; havana_gene "OTTHUMG00000164809.2" ; havana_transcript "OTTHUMT00000380416.2" ; hgnc_id "HGNC:30655" ; level 2 ; orig_coord_info "chr8,106769523,106770190,-" ; protein_id "ENSP00000311436.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BPTF--ABRA^ENST00000311955.4" ; transcript_name "ABRA-201" ; transcript_support_level 1 ; transcript_type protein_coding
BPTF--ABRA HAVANA mRNA 47100 50853 . + . FI_gene_label "ABRA^ENSG00000174429.4" ; ID "BPTF--ABRA^ENST00000311955.4" ; Parent "BPTF--ABRA^ABRA^ENSG00000174429.4" ; ccdsid "CCDS6305.1" ; exon_id "ENSE00001207130.8" ; exon_number 1 ; gene_id "BPTF--ABRA^ABRA^ENSG00000174429.4" ; gene_name ABRA ; gene_type protein_coding ; havana_gene "OTTHUMG00000164809.2" ; havana_transcript "OTTHUMT00000380416.2" ; hgnc_id "HGNC:30655" ; level 2 ; orig_coord_info "chr8,106769523,106770190,-" ; protein_id "ENSP00000311436.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BPTF--ABRA^ENST00000311955.4" ; transcript_name "ABRA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BPTF--AP003789.1 HAVANA gene 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--AP003789.1^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--AP003789.1^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--AP003789.1^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding
BPTF--AP003789.1 HAVANA mRNA 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--AP003789.1^ENST00000306378.11" ; Parent "BPTF--AP003789.1^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--AP003789.1^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--AP003789.1^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CYFIP1--GREM1 HAVANA gene 40012 42296 . + . FI_gene_label "GREM1^ENSG00000166923.12" ; ID "CYFIP1--GREM1^GREM1^ENSG00000166923.12" ; exon_id "ENSE00002539624.1" ; exon_number 2 ; gene_id "CYFIP1--GREM1^GREM1^ENSG00000166923.12" ; gene_name GREM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129319.7" ; havana_transcript "OTTHUMT00000417302.1" ; hgnc_id "HGNC:2001" ; level 2 ; orig_coord_info "chr15,32730691,32730794,+" ; protein_id "ENSP00000453387.1" ; tag non_canonical_TEC basic ; transcript_id "CYFIP1--GREM1^ENST00000560677.5" ; transcript_name "GREM1-201" ; transcript_support_level 4 ; transcript_type protein_coding
CYFIP1--GREM1 HAVANA mRNA 40012 42296 . + . FI_gene_label "GREM1^ENSG00000166923.12" ; ID "CYFIP1--GREM1^ENST00000560677.5" ; Parent "CYFIP1--GREM1^GREM1^ENSG00000166923.12" ; exon_id "ENSE00002539624.1" ; exon_number 2 ; gene_id "CYFIP1--GREM1^GREM1^ENSG00000166923.12" ; gene_name GREM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129319.7" ; havana_transcript "OTTHUMT00000417302.1" ; hgnc_id "HGNC:2001" ; level 2 ; orig_coord_info "chr15,32730691,32730794,+" ; protein_id "ENSP00000453387.1" ; tag non_canonical_TEC basic ; transcript_id "CYFIP1--GREM1^ENST00000560677.5" ; transcript_name "GREM1-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
CYFIP1--GREM1 HAVANA gene 30272 32870 . + . FI_gene_label "CYFIP1^ENSG00000273749.5" ; ID "CYFIP1--GREM1^CYFIP1^ENSG00000273749.5" ; exon_id "ENSE00002552700.1" ; exon_number 1 ; gene_id "CYFIP1--GREM1^CYFIP1^ENSG00000273749.5" ; gene_name CYFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129100.8" ; havana_transcript "OTTHUMT00000415639.2" ; hgnc_id "HGNC:13759" ; level 2 ; orig_coord_info "chr15,22875199,22875235,-" ; protein_id "ENSP00000453060.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CYFIP1--GREM1^ENST00000561263.2" ; transcript_name "CYFIP1-202" ; transcript_support_level 2 ; transcript_type protein_coding
CYFIP1--GREM1 HAVANA mRNA 30272 32870 . + . FI_gene_label "CYFIP1^ENSG00000273749.5" ; ID "CYFIP1--GREM1^ENST00000561263.2" ; Parent "CYFIP1--GREM1^CYFIP1^ENSG00000273749.5" ; exon_id "ENSE00002552700.1" ; exon_number 1 ; gene_id "CYFIP1--GREM1^CYFIP1^ENSG00000273749.5" ; gene_name CYFIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129100.8" ; havana_transcript "OTTHUMT00000415639.2" ; hgnc_id "HGNC:13759" ; level 2 ; orig_coord_info "chr15,22875199,22875235,-" ; protein_id "ENSP00000453060.1" ; tag mRNA_start_NF cds_start_NF ; transcript_id "CYFIP1--GREM1^ENST00000561263.2" ; transcript_name "CYFIP1-202" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
EP300--AC137499.1 HAVANA gene 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--AC137499.1^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--AC137499.1^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--AC137499.1^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
EP300--AC137499.1 HAVANA mRNA 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--AC137499.1^ENST00000263253.9" ; Parent "EP300--AC137499.1^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--AC137499.1^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--AC137499.1^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EP300--PABPC1P9 HAVANA gene 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--PABPC1P9^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--PABPC1P9^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--PABPC1P9^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
EP300--PABPC1P9 HAVANA mRNA 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--PABPC1P9^ENST00000263253.9" ; Parent "EP300--PABPC1P9^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--PABPC1P9^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--PABPC1P9^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EP300--SLC9B1P4 HAVANA gene 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--SLC9B1P4^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--SLC9B1P4^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--SLC9B1P4^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
EP300--SLC9B1P4 HAVANA mRNA 1001 39055 . + . FI_gene_label "EP300^ENSG00000100393.14" ; ID "EP300--SLC9B1P4^ENST00000263253.9" ; Parent "EP300--SLC9B1P4^EP300^ENSG00000100393.14" ; ccdsid "CCDS14010.1" ; exon_id "ENSE00001343011.8" ; exon_number 1 ; gene_id "EP300--SLC9B1P4^EP300^ENSG00000100393.14" ; gene_name EP300 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150937.7" ; havana_transcript "OTTHUMT00000320600.3" ; hgnc_id "HGNC:3373" ; level 2 ; orig_coord_info "chr22,41093005,41093098,+" ; protein_id "ENSP00000263253.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "EP300--SLC9B1P4^ENST00000263253.9" ; transcript_name "EP300-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXL20--LINC02089 HAVANA gene 1898 26528 . + . FI_gene_label "FBXL20^ENSG00000108306.13" ; ID "FBXL20--LINC02089^FBXL20^ENSG00000108306.13" ; ccdsid "CCDS32640.1" ; exon_id "ENSE00002727680.2" ; exon_number 1 ; gene_id "FBXL20--LINC02089^FBXL20^ENSG00000108306.13" ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9" ; havana_transcript "OTTHUMT00000444315.4" ; hgnc_id "HGNC:24679" ; level 2 ; orig_coord_info "chr17,39401361,39401402,-" ; protein_id "ENSP00000264658.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--LINC02089^ENST00000264658.11" ; transcript_name "FBXL20-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXL20--LINC02089 HAVANA mRNA 1898 26528 . + . FI_gene_label "FBXL20^ENSG00000108306.13" ; ID "FBXL20--LINC02089^ENST00000264658.11" ; Parent "FBXL20--LINC02089^FBXL20^ENSG00000108306.13" ; ccdsid "CCDS32640.1" ; exon_id "ENSE00002727680.2" ; exon_number 1 ; gene_id "FBXL20--LINC02089^FBXL20^ENSG00000108306.13" ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9" ; havana_transcript "OTTHUMT00000444315.4" ; hgnc_id "HGNC:24679" ; level 2 ; orig_coord_info "chr17,39401361,39401402,-" ; protein_id "ENSP00000264658.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--LINC02089^ENST00000264658.11" ; transcript_name "FBXL20-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXL20--LINC02876 HAVANA gene 1898 26528 . + . FI_gene_label "FBXL20^ENSG00000108306.13" ; ID "FBXL20--LINC02876^FBXL20^ENSG00000108306.13" ; ccdsid "CCDS32640.1" ; exon_id "ENSE00002727680.2" ; exon_number 1 ; gene_id "FBXL20--LINC02876^FBXL20^ENSG00000108306.13" ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9" ; havana_transcript "OTTHUMT00000444315.4" ; hgnc_id "HGNC:24679" ; level 2 ; orig_coord_info "chr17,39401361,39401402,-" ; protein_id "ENSP00000264658.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--LINC02876^ENST00000264658.11" ; transcript_name "FBXL20-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXL20--LINC02876 HAVANA mRNA 1898 26528 . + . FI_gene_label "FBXL20^ENSG00000108306.13" ; ID "FBXL20--LINC02876^ENST00000264658.11" ; Parent "FBXL20--LINC02876^FBXL20^ENSG00000108306.13" ; ccdsid "CCDS32640.1" ; exon_id "ENSE00002727680.2" ; exon_number 1 ; gene_id "FBXL20--LINC02876^FBXL20^ENSG00000108306.13" ; gene_name FBXL20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179002.9" ; havana_transcript "OTTHUMT00000444315.4" ; hgnc_id "HGNC:24679" ; level 2 ; orig_coord_info "chr17,39401361,39401402,-" ; protein_id "ENSP00000264658.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXL20--LINC02876^ENST00000264658.11" ; transcript_name "FBXL20-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LPP--TPRG1 HAVANA gene 69662 87892 . + . FI_gene_label "TPRG1^ENSG00000188001.10" ; ID "LPP--TPRG1^TPRG1^ENSG00000188001.10" ; ccdsid "CCDS3292.1" ; exon_id "ENSE00003630174.1" ; exon_number 2 ; gene_id "LPP--TPRG1^TPRG1^ENSG00000188001.10" ; gene_name TPRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156321.6" ; havana_transcript "OTTHUMT00000343931.2" ; hgnc_id "HGNC:24759" ; level 2 ; orig_coord_info "chr3,189207385,189207594,+" ; protein_id "ENSP00000341031.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LPP--TPRG1^ENST00000345063.8" ; transcript_name "TPRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
LPP--TPRG1 HAVANA mRNA 69662 87892 . + . FI_gene_label "TPRG1^ENSG00000188001.10" ; ID "LPP--TPRG1^ENST00000345063.8" ; Parent "LPP--TPRG1^TPRG1^ENSG00000188001.10" ; ccdsid "CCDS3292.1" ; exon_id "ENSE00003630174.1" ; exon_number 2 ; gene_id "LPP--TPRG1^TPRG1^ENSG00000188001.10" ; gene_name TPRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156321.6" ; havana_transcript "OTTHUMT00000343931.2" ; hgnc_id "HGNC:24759" ; level 2 ; orig_coord_info "chr3,189207385,189207594,+" ; protein_id "ENSP00000341031.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LPP--TPRG1^ENST00000345063.8" ; transcript_name "TPRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LPP--TPRG1 HAVANA gene 1648 12381 . + . FI_gene_label "LPP^ENSG00000145012.13" ; ID "LPP--TPRG1^LPP^ENSG00000145012.13" ; exon_id "ENSE00001270076.3" ; exon_number 3 ; gene_id "LPP--TPRG1^LPP^ENSG00000145012.13" ; gene_name LPP ; gene_type protein_coding ; havana_gene "OTTHUMG00000156387.5" ; havana_transcript "OTTHUMT00000344035.2" ; hgnc_id "HGNC:6679" ; level 2 ; orig_coord_info "chr3,188406121,188406313,+" ; protein_id "ENSP00000392667.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "LPP--TPRG1^ENST00000414139.5" ; transcript_name "LPP-201" ; transcript_support_level 4 ; transcript_type protein_coding
LPP--TPRG1 HAVANA mRNA 1648 12381 . + . FI_gene_label "LPP^ENSG00000145012.13" ; ID "LPP--TPRG1^ENST00000414139.5" ; Parent "LPP--TPRG1^LPP^ENSG00000145012.13" ; exon_id "ENSE00001270076.3" ; exon_number 3 ; gene_id "LPP--TPRG1^LPP^ENSG00000145012.13" ; gene_name LPP ; gene_type protein_coding ; havana_gene "OTTHUMG00000156387.5" ; havana_transcript "OTTHUMT00000344035.2" ; hgnc_id "HGNC:6679" ; level 2 ; orig_coord_info "chr3,188406121,188406313,+" ; protein_id "ENSP00000392667.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "LPP--TPRG1^ENST00000414139.5" ; transcript_name "LPP-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
MARK3--DUX4 HAVANA gene 1484 44974 . + . FI_gene_label "MARK3^ENSG00000075413.19" ; ID "MARK3--DUX4^MARK3^ENSG00000075413.19" ; ccdsid "CCDS55947.1" ; exon_id "ENSE00002452060.1" ; exon_number 1 ; gene_id "MARK3--DUX4^MARK3^ENSG00000075413.19" ; gene_name MARK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171789.5" ; havana_transcript "OTTHUMT00000415146.2" ; hgnc_id "HGNC:6897" ; level 2 ; orig_coord_info "chr14,103386030,103386080,+" ; protein_id "ENSP00000216288.7" ; tag basic CCDS ; transcript_id "MARK3--DUX4^ENST00000216288.11" ; transcript_name "MARK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
MARK3--DUX4 HAVANA mRNA 1484 44974 . + . FI_gene_label "MARK3^ENSG00000075413.19" ; ID "MARK3--DUX4^ENST00000216288.11" ; Parent "MARK3--DUX4^MARK3^ENSG00000075413.19" ; ccdsid "CCDS55947.1" ; exon_id "ENSE00002452060.1" ; exon_number 1 ; gene_id "MARK3--DUX4^MARK3^ENSG00000075413.19" ; gene_name MARK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171789.5" ; havana_transcript "OTTHUMT00000415146.2" ; hgnc_id "HGNC:6897" ; level 2 ; orig_coord_info "chr14,103386030,103386080,+" ; protein_id "ENSP00000216288.7" ; tag basic CCDS ; transcript_id "MARK3--DUX4^ENST00000216288.11" ; transcript_name "MARK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MARK3--DUX4 HAVANA gene 57980 60051 . + . FI_gene_label "DUX4^ENSG00000260596.5" ; ID "MARK3--DUX4^DUX4^ENSG00000260596.5" ; ccdsid "CCDS77990.1" ; exon_id "ENSE00002596957.1" ; exon_number 1 ; gene_id "MARK3--DUX4^DUX4^ENSG00000260596.5" ; gene_name DUX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175568.1" ; havana_transcript "OTTHUMT00000430519.1" ; hgnc_id "HGNC:50800" ; level 2 ; orig_coord_info "chr4,190173774,190175045,+" ; protein_id "ENSP00000458065.1" ; tag NMD_exception basic MANE_Select appris_principal_2 CCDS ; transcript_id "MARK3--DUX4^ENST00000565211.1" ; transcript_name "DUX4-203" ; transcript_support_level 1 ; transcript_type protein_coding
MARK3--DUX4 HAVANA mRNA 57980 60051 . + . FI_gene_label "DUX4^ENSG00000260596.5" ; ID "MARK3--DUX4^ENST00000565211.1" ; Parent "MARK3--DUX4^DUX4^ENSG00000260596.5" ; ccdsid "CCDS77990.1" ; exon_id "ENSE00002596957.1" ; exon_number 1 ; gene_id "MARK3--DUX4^DUX4^ENSG00000260596.5" ; gene_name DUX4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000175568.1" ; havana_transcript "OTTHUMT00000430519.1" ; hgnc_id "HGNC:50800" ; level 2 ; orig_coord_info "chr4,190173774,190175045,+" ; protein_id "ENSP00000458065.1" ; tag NMD_exception basic MANE_Select appris_principal_2 CCDS ; transcript_id "MARK3--DUX4^ENST00000565211.1" ; transcript_name "DUX4-203" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MARK3--DUX4L2 HAVANA gene 1484 44974 . + . FI_gene_label "MARK3^ENSG00000075413.19" ; ID "MARK3--DUX4L2^MARK3^ENSG00000075413.19" ; ccdsid "CCDS55947.1" ; exon_id "ENSE00002452060.1" ; exon_number 1 ; gene_id "MARK3--DUX4L2^MARK3^ENSG00000075413.19" ; gene_name MARK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171789.5" ; havana_transcript "OTTHUMT00000415146.2" ; hgnc_id "HGNC:6897" ; level 2 ; orig_coord_info "chr14,103386030,103386080,+" ; protein_id "ENSP00000216288.7" ; tag basic CCDS ; transcript_id "MARK3--DUX4L2^ENST00000216288.11" ; transcript_name "MARK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
MARK3--DUX4L2 HAVANA mRNA 1484 44974 . + . FI_gene_label "MARK3^ENSG00000075413.19" ; ID "MARK3--DUX4L2^ENST00000216288.11" ; Parent "MARK3--DUX4L2^MARK3^ENSG00000075413.19" ; ccdsid "CCDS55947.1" ; exon_id "ENSE00002452060.1" ; exon_number 1 ; gene_id "MARK3--DUX4L2^MARK3^ENSG00000075413.19" ; gene_name MARK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171789.5" ; havana_transcript "OTTHUMT00000415146.2" ; hgnc_id "HGNC:6897" ; level 2 ; orig_coord_info "chr14,103386030,103386080,+" ; protein_id "ENSP00000216288.7" ; tag basic CCDS ; transcript_id "MARK3--DUX4L2^ENST00000216288.11" ; transcript_name "MARK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MRTFA--ENTHD1 HAVANA gene 28239 37398 . + . FI_gene_label "ENTHD1^ENSG00000176177.10" ; ID "MRTFA--ENTHD1^ENTHD1^ENSG00000176177.10" ; ccdsid "CCDS13998.1" ; exon_id "ENSE00001290271.4" ; exon_number 2 ; gene_id "MRTFA--ENTHD1^ENTHD1^ENSG00000176177.10" ; gene_name ENTHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151098.2" ; havana_transcript "OTTHUMT00000321302.2" ; hgnc_id "HGNC:26352" ; level 2 ; orig_coord_info "chr22,39887400,39887748,-" ; protein_id "ENSP00000317431.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRTFA--ENTHD1^ENST00000325157.7" ; transcript_name "ENTHD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
MRTFA--ENTHD1 HAVANA mRNA 28239 37398 . + . FI_gene_label "ENTHD1^ENSG00000176177.10" ; ID "MRTFA--ENTHD1^ENST00000325157.7" ; Parent "MRTFA--ENTHD1^ENTHD1^ENSG00000176177.10" ; ccdsid "CCDS13998.1" ; exon_id "ENSE00001290271.4" ; exon_number 2 ; gene_id "MRTFA--ENTHD1^ENTHD1^ENSG00000176177.10" ; gene_name ENTHD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151098.2" ; havana_transcript "OTTHUMT00000321302.2" ; hgnc_id "HGNC:26352" ; level 2 ; orig_coord_info "chr22,39887400,39887748,-" ; protein_id "ENSP00000317431.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MRTFA--ENTHD1^ENST00000325157.7" ; transcript_name "ENTHD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MRTFA--ENTHD1 HAVANA gene 1001 25126 . + . FI_gene_label "MRTFA^ENSG00000196588.20" ; ID "MRTFA--ENTHD1^MRTFA^ENSG00000196588.20" ; exon_id "ENSE00003850957.1" ; exon_number 3 ; gene_id "MRTFA--ENTHD1^MRTFA^ENSG00000196588.20" ; gene_name MRTFA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151146.12" ; havana_transcript "OTTHUMT00000321522.3" ; hgnc_id "HGNC:14334" ; level 2 ; orig_coord_info "chr22,40552106,40552346,-" ; protein_id "ENSP00000347847.5" ; tag CAGE_supported_TSS non_ATG_start basic MANE_Select ; transcript_id "MRTFA--ENTHD1^ENST00000355630.10" ; transcript_name "MRTFA-201" ; transcript_support_level 1 ; transcript_type protein_coding
MRTFA--ENTHD1 HAVANA mRNA 1001 25126 . + . FI_gene_label "MRTFA^ENSG00000196588.20" ; ID "MRTFA--ENTHD1^ENST00000355630.10" ; Parent "MRTFA--ENTHD1^MRTFA^ENSG00000196588.20" ; exon_id "ENSE00003850957.1" ; exon_number 3 ; gene_id "MRTFA--ENTHD1^MRTFA^ENSG00000196588.20" ; gene_name MRTFA ; gene_type protein_coding ; havana_gene "OTTHUMG00000151146.12" ; havana_transcript "OTTHUMT00000321522.3" ; hgnc_id "HGNC:14334" ; level 2 ; orig_coord_info "chr22,40552106,40552346,-" ; protein_id "ENSP00000347847.5" ; tag CAGE_supported_TSS non_ATG_start basic MANE_Select ; transcript_id "MRTFA--ENTHD1^ENST00000355630.10" ; transcript_name "MRTFA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NF1--TSPEAR HAVANA gene 78060 95741 . + . FI_gene_label "TSPEAR^ENSG00000175894.18" ; ID "NF1--TSPEAR^TSPEAR^ENSG00000175894.18" ; ccdsid "CCDS13712.1" ; exon_id "ENSE00003826265.1" ; exon_number 1 ; gene_id "NF1--TSPEAR^TSPEAR^ENSG00000175894.18" ; gene_name TSPEAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000041215.4" ; havana_transcript "OTTHUMT00000098761.3" ; hgnc_id "HGNC:1268" ; level 2 ; orig_coord_info "chr21,44711433,44711514,-" ; protein_id "ENSP00000321987.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "NF1--TSPEAR^ENST00000323084.9" ; transcript_name "TSPEAR-201" ; transcript_support_level 1 ; transcript_type protein_coding
NF1--TSPEAR HAVANA mRNA 78060 95741 . + . FI_gene_label "TSPEAR^ENSG00000175894.18" ; ID "NF1--TSPEAR^ENST00000323084.9" ; Parent "NF1--TSPEAR^TSPEAR^ENSG00000175894.18" ; ccdsid "CCDS13712.1" ; exon_id "ENSE00003826265.1" ; exon_number 1 ; gene_id "NF1--TSPEAR^TSPEAR^ENSG00000175894.18" ; gene_name TSPEAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000041215.4" ; havana_transcript "OTTHUMT00000098761.3" ; hgnc_id "HGNC:1268" ; level 2 ; orig_coord_info "chr21,44711433,44711514,-" ; protein_id "ENSP00000321987.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "NF1--TSPEAR^ENST00000323084.9" ; transcript_name "TSPEAR-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NF1--TSPEAR HAVANA gene 1001 71265 . + . FI_gene_label "NF1^ENSG00000196712.18" ; ID "NF1--TSPEAR^NF1^ENSG00000196712.18" ; ccdsid "CCDS11264.1" ; exon_id "ENSE00003803084.1" ; exon_number 1 ; gene_id "NF1--TSPEAR^NF1^ENSG00000196712.18" ; gene_name NF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132871.10" ; havana_transcript "OTTHUMT00000256352.1" ; hgnc_id "HGNC:7765" ; level 2 ; orig_coord_info "chr17,31095310,31095369,+" ; protein_id "ENSP00000348498.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NF1--TSPEAR^ENST00000356175.7" ; transcript_name "NF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NF1--TSPEAR HAVANA mRNA 1001 71265 . + . FI_gene_label "NF1^ENSG00000196712.18" ; ID "NF1--TSPEAR^ENST00000356175.7" ; Parent "NF1--TSPEAR^NF1^ENSG00000196712.18" ; ccdsid "CCDS11264.1" ; exon_id "ENSE00003803084.1" ; exon_number 1 ; gene_id "NF1--TSPEAR^NF1^ENSG00000196712.18" ; gene_name NF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132871.10" ; havana_transcript "OTTHUMT00000256352.1" ; hgnc_id "HGNC:7765" ; level 2 ; orig_coord_info "chr17,31095310,31095369,+" ; protein_id "ENSP00000348498.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NF1--TSPEAR^ENST00000356175.7" ; transcript_name "NF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NSRP1--RUNX1 HAVANA gene 2274 19082 . + . FI_gene_label "NSRP1^ENSG00000126653.18" ; ID "NSRP1--RUNX1^NSRP1^ENSG00000126653.18" ; ccdsid "CCDS11255.1" ; exon_id "ENSE00003843705.1" ; exon_number 1 ; gene_id "NSRP1--RUNX1^NSRP1^ENSG00000126653.18" ; gene_name NSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132754.8" ; havana_transcript "OTTHUMT00000256121.3" ; hgnc_id "HGNC:25305" ; level 2 ; orig_coord_info "chr17,30116844,30116863,+" ; protein_id "ENSP00000247026.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "NSRP1--RUNX1^ENST00000247026.10" ; transcript_name "NSRP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NSRP1--RUNX1 HAVANA mRNA 2274 19082 . + . FI_gene_label "NSRP1^ENSG00000126653.18" ; ID "NSRP1--RUNX1^ENST00000247026.10" ; Parent "NSRP1--RUNX1^NSRP1^ENSG00000126653.18" ; ccdsid "CCDS11255.1" ; exon_id "ENSE00003843705.1" ; exon_number 1 ; gene_id "NSRP1--RUNX1^NSRP1^ENSG00000126653.18" ; gene_name NSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132754.8" ; havana_transcript "OTTHUMT00000256121.3" ; hgnc_id "HGNC:25305" ; level 2 ; orig_coord_info "chr17,30116844,30116863,+" ; protein_id "ENSP00000247026.5" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "NSRP1--RUNX1^ENST00000247026.10" ; transcript_name "NSRP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NSRP1--RUNX1 HAVANA gene 41688 62748 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "NSRP1--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "NSRP1--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NSRP1--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NSRP1--RUNX1 HAVANA mRNA 41688 62748 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "NSRP1--RUNX1^ENST00000300305.7" ; Parent "NSRP1--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "NSRP1--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NSRP1--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PHRF1--CDHR5 HAVANA gene 1001 17931 . + . FI_gene_label "PHRF1^ENSG00000070047.13" ; ID "PHRF1--CDHR5^PHRF1^ENSG00000070047.13" ; ccdsid "CCDS65988.1" ; exon_id "ENSE00001206357.3" ; exon_number 2 ; gene_id "PHRF1--CDHR5^PHRF1^ENSG00000070047.13" ; gene_name PHRF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165141.7" ; havana_transcript "OTTHUMT00000382133.2" ; hgnc_id "HGNC:24351" ; level 2 ; orig_coord_info "chr11,581513,581606,+" ; protein_id "ENSP00000264555.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PHRF1--CDHR5^ENST00000264555.10" ; transcript_name "PHRF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PHRF1--CDHR5 HAVANA mRNA 1001 17931 . + . FI_gene_label "PHRF1^ENSG00000070047.13" ; ID "PHRF1--CDHR5^ENST00000264555.10" ; Parent "PHRF1--CDHR5^PHRF1^ENSG00000070047.13" ; ccdsid "CCDS65988.1" ; exon_id "ENSE00001206357.3" ; exon_number 2 ; gene_id "PHRF1--CDHR5^PHRF1^ENSG00000070047.13" ; gene_name PHRF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165141.7" ; havana_transcript "OTTHUMT00000382133.2" ; hgnc_id "HGNC:24351" ; level 2 ; orig_coord_info "chr11,581513,581606,+" ; protein_id "ENSP00000264555.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PHRF1--CDHR5^ENST00000264555.10" ; transcript_name "PHRF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PHRF1--CDHR5 HAVANA gene 21841 28446 . + . FI_gene_label "CDHR5^ENSG00000099834.19" ; ID "PHRF1--CDHR5^CDHR5^ENSG00000099834.19" ; ccdsid "CCDS7708.1" ; exon_id "ENSE00002160589.1" ; exon_number 1 ; gene_id "PHRF1--CDHR5^CDHR5^ENSG00000099834.19" ; gene_name CDHR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132018.6" ; havana_transcript "OTTHUMT00000255024.3" ; hgnc_id "HGNC:7521" ; level 2 ; orig_coord_info "chr11,624818,624902,-" ; protein_id "ENSP00000345726.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "PHRF1--CDHR5^ENST00000349570.11" ; transcript_name "CDHR5-201" ; transcript_support_level 1 ; transcript_type protein_coding
PHRF1--CDHR5 HAVANA mRNA 21841 28446 . + . FI_gene_label "CDHR5^ENSG00000099834.19" ; ID "PHRF1--CDHR5^ENST00000349570.11" ; Parent "PHRF1--CDHR5^CDHR5^ENSG00000099834.19" ; ccdsid "CCDS7708.1" ; exon_id "ENSE00002160589.1" ; exon_number 1 ; gene_id "PHRF1--CDHR5^CDHR5^ENSG00000099834.19" ; gene_name CDHR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132018.6" ; havana_transcript "OTTHUMT00000255024.3" ; hgnc_id "HGNC:7521" ; level 2 ; orig_coord_info "chr11,624818,624902,-" ; protein_id "ENSP00000345726.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "PHRF1--CDHR5^ENST00000349570.11" ; transcript_name "CDHR5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PLEC--TANC2 HAVANA gene 6759 37076 . + . FI_gene_label "PLEC^ENSG00000178209.16" ; ID "PLEC--TANC2^PLEC^ENSG00000178209.16" ; ccdsid "CCDS43772.1" ; exon_id "ENSE00001244239.2" ; exon_number 1 ; gene_id "PLEC--TANC2^PLEC^ENSG00000178209.16" ; gene_name PLEC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165291.5" ; havana_transcript "OTTHUMT00000383281.1" ; hgnc_id "HGNC:9069" ; level 2 ; orig_coord_info "chr8,143950184,143950706,-" ; protein_id "ENSP00000323856.4" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEC--TANC2^ENST00000322810.8" ; transcript_name "PLEC-201" ; transcript_support_level 1 ; transcript_type protein_coding
PLEC--TANC2 HAVANA mRNA 6759 37076 . + . FI_gene_label "PLEC^ENSG00000178209.16" ; ID "PLEC--TANC2^ENST00000322810.8" ; Parent "PLEC--TANC2^PLEC^ENSG00000178209.16" ; ccdsid "CCDS43772.1" ; exon_id "ENSE00001244239.2" ; exon_number 1 ; gene_id "PLEC--TANC2^PLEC^ENSG00000178209.16" ; gene_name PLEC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165291.5" ; havana_transcript "OTTHUMT00000383281.1" ; hgnc_id "HGNC:9069" ; level 2 ; orig_coord_info "chr8,143950184,143950706,-" ; protein_id "ENSP00000323856.4" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEC--TANC2^ENST00000322810.8" ; transcript_name "PLEC-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PLEC--TANC2 HAVANA gene 40081 81368 . + . FI_gene_label "TANC2^ENSG00000170921.15" ; ID "PLEC--TANC2^TANC2^ENSG00000170921.15" ; exon_id "ENSE00002709640.1" ; exon_number 1 ; gene_id "PLEC--TANC2^TANC2^ENSG00000170921.15" ; gene_name TANC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179103.2" ; havana_transcript "OTTHUMT00000444766.1" ; hgnc_id "HGNC:30212" ; level 2 ; orig_coord_info "chr17,63009560,63009626,+" ; protein_id "ENSP00000374171.4" ; tag basic appris_alternative_2 ; transcript_id "PLEC--TANC2^ENST00000389520.8" ; transcript_name "TANC2-201" ; transcript_support_level 5 ; transcript_type protein_coding
PLEC--TANC2 HAVANA mRNA 40081 81368 . + . FI_gene_label "TANC2^ENSG00000170921.15" ; ID "PLEC--TANC2^ENST00000389520.8" ; Parent "PLEC--TANC2^TANC2^ENSG00000170921.15" ; exon_id "ENSE00002709640.1" ; exon_number 1 ; gene_id "PLEC--TANC2^TANC2^ENSG00000170921.15" ; gene_name TANC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179103.2" ; havana_transcript "OTTHUMT00000444766.1" ; hgnc_id "HGNC:30212" ; level 2 ; orig_coord_info "chr17,63009560,63009626,+" ; protein_id "ENSP00000374171.4" ; tag basic appris_alternative_2 ; transcript_id "PLEC--TANC2^ENST00000389520.8" ; transcript_name "TANC2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
POP1--ERICH5 HAVANA gene 22091 25593 . + . FI_gene_label "ERICH5^ENSG00000177459.11" ; ID "POP1--ERICH5^ERICH5^ENSG00000177459.11" ; ccdsid "CCDS34929.1" ; exon_id "ENSE00001278214.4" ; exon_number 1 ; gene_id "POP1--ERICH5^ERICH5^ENSG00000177459.11" ; gene_name ERICH5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164819.2" ; havana_transcript "OTTHUMT00000380465.2" ; hgnc_id "HGNC:26823" ; level 2 ; orig_coord_info "chr8,98064670,98064727,+" ; protein_id "ENSP00000315614.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POP1--ERICH5^ENST00000318528.8" ; transcript_name "ERICH5-201" ; transcript_support_level 1 ; transcript_type protein_coding
POP1--ERICH5 HAVANA mRNA 22091 25593 . + . FI_gene_label "ERICH5^ENSG00000177459.11" ; ID "POP1--ERICH5^ENST00000318528.8" ; Parent "POP1--ERICH5^ERICH5^ENSG00000177459.11" ; ccdsid "CCDS34929.1" ; exon_id "ENSE00001278214.4" ; exon_number 1 ; gene_id "POP1--ERICH5^ERICH5^ENSG00000177459.11" ; gene_name ERICH5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164819.2" ; havana_transcript "OTTHUMT00000380465.2" ; hgnc_id "HGNC:26823" ; level 2 ; orig_coord_info "chr8,98064670,98064727,+" ; protein_id "ENSP00000315614.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POP1--ERICH5^ENST00000318528.8" ; transcript_name "ERICH5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POP1--ERICH5 HAVANA gene 1548 17621 . + . FI_gene_label "POP1^ENSG00000104356.11" ; ID "POP1--ERICH5^POP1^ENSG00000104356.11" ; ccdsid "CCDS6277.1" ; exon_id "ENSE00001370963.2" ; exon_number 2 ; gene_id "POP1--ERICH5^POP1^ENSG00000104356.11" ; gene_name POP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164635.3" ; havana_transcript "OTTHUMT00000379471.1" ; hgnc_id "HGNC:30129" ; level 2 ; orig_coord_info "chr8,98123338,98123479,+" ; protein_id "ENSP00000339529.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "POP1--ERICH5^ENST00000349693.3" ; transcript_name "POP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
POP1--ERICH5 HAVANA mRNA 1548 17621 . + . FI_gene_label "POP1^ENSG00000104356.11" ; ID "POP1--ERICH5^ENST00000349693.3" ; Parent "POP1--ERICH5^POP1^ENSG00000104356.11" ; ccdsid "CCDS6277.1" ; exon_id "ENSE00001370963.2" ; exon_number 2 ; gene_id "POP1--ERICH5^POP1^ENSG00000104356.11" ; gene_name POP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164635.3" ; havana_transcript "OTTHUMT00000379471.1" ; hgnc_id "HGNC:30129" ; level 2 ; orig_coord_info "chr8,98123338,98123479,+" ; protein_id "ENSP00000339529.3" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "POP1--ERICH5^ENST00000349693.3" ; transcript_name "POP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RCAN1--RUNX1 HAVANA gene 37770 58830 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "RCAN1--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "RCAN1--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "RCAN1--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RCAN1--RUNX1 HAVANA mRNA 37770 58830 . + . FI_gene_label "RUNX1^ENSG00000159216.19" ; ID "RCAN1--RUNX1^ENST00000300305.7" ; Parent "RCAN1--RUNX1^RUNX1^ENSG00000159216.19" ; ccdsid "CCDS13639.1" ; exon_id "ENSE00001317351.1" ; exon_number 1 ; gene_id "RCAN1--RUNX1^RUNX1^ENSG00000159216.19" ; gene_name RUNX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086299.10" ; havana_transcript "OTTHUMT00000194231.1" ; hgnc_id "HGNC:10471" ; level 2 ; orig_coord_info "chr21,35048842,35048899,-" ; protein_id "ENSP00000300305.3" ; tag basic appris_principal_4 CCDS ; transcript_id "RCAN1--RUNX1^ENST00000300305.7" ; transcript_name "RUNX1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RCAN1--RUNX1 HAVANA gene 1001 13949 . + . FI_gene_label "RCAN1^ENSG00000159200.18" ; ID "RCAN1--RUNX1^RCAN1^ENSG00000159200.18" ; ccdsid "CCDS13637.1" ; exon_id "ENSE00001869771.2" ; exon_number 1 ; gene_id "RCAN1--RUNX1^RCAN1^ENSG00000159200.18" ; gene_name RCAN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086235.5" ; havana_transcript "OTTHUMT00000194142.2" ; hgnc_id "HGNC:3040" ; level 2 ; orig_coord_info "chr21,34614760,34615011,-" ; protein_id "ENSP00000320768.4" ; tag basic MANE_Select CCDS ; transcript_id "RCAN1--RUNX1^ENST00000313806.9" ; transcript_name "RCAN1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RCAN1--RUNX1 HAVANA mRNA 1001 13949 . + . FI_gene_label "RCAN1^ENSG00000159200.18" ; ID "RCAN1--RUNX1^ENST00000313806.9" ; Parent "RCAN1--RUNX1^RCAN1^ENSG00000159200.18" ; ccdsid "CCDS13637.1" ; exon_id "ENSE00001869771.2" ; exon_number 1 ; gene_id "RCAN1--RUNX1^RCAN1^ENSG00000159200.18" ; gene_name RCAN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086235.5" ; havana_transcript "OTTHUMT00000194142.2" ; hgnc_id "HGNC:3040" ; level 2 ; orig_coord_info "chr21,34614760,34615011,-" ; protein_id "ENSP00000320768.4" ; tag basic MANE_Select CCDS ; transcript_id "RCAN1--RUNX1^ENST00000313806.9" ; transcript_name "RCAN1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SGSM3--HLCS HAVANA gene 1004 10785 . + . FI_gene_label "SGSM3^ENSG00000100359.21" ; ID "SGSM3--HLCS^SGSM3^ENSG00000100359.21" ; ccdsid "CCDS14002.1" ; exon_id "ENSE00003487177.1" ; exon_number 2 ; gene_id "SGSM3--HLCS^SGSM3^ENSG00000100359.21" ; gene_name SGSM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151141.15" ; havana_transcript "OTTHUMT00000321504.3" ; hgnc_id "HGNC:25228" ; level 2 ; orig_coord_info "chr22,40400807,40400813,+" ; protein_id "ENSP00000248929.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SGSM3--HLCS^ENST00000248929.14" ; transcript_name "SGSM3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SGSM3--HLCS HAVANA mRNA 1004 10785 . + . FI_gene_label "SGSM3^ENSG00000100359.21" ; ID "SGSM3--HLCS^ENST00000248929.14" ; Parent "SGSM3--HLCS^SGSM3^ENSG00000100359.21" ; ccdsid "CCDS14002.1" ; exon_id "ENSE00003487177.1" ; exon_number 2 ; gene_id "SGSM3--HLCS^SGSM3^ENSG00000100359.21" ; gene_name SGSM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151141.15" ; havana_transcript "OTTHUMT00000321504.3" ; hgnc_id "HGNC:25228" ; level 2 ; orig_coord_info "chr22,40400807,40400813,+" ; protein_id "ENSP00000248929.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SGSM3--HLCS^ENST00000248929.14" ; transcript_name "SGSM3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SGSM3--HLCS HAVANA gene 13786 36084 . + . FI_gene_label "HLCS^ENSG00000159267.16" ; ID "SGSM3--HLCS^HLCS^ENSG00000159267.16" ; ccdsid "CCDS13647.1" ; exon_id "ENSE00001282204.4" ; exon_number 4 ; gene_id "SGSM3--HLCS^HLCS^ENSG00000159267.16" ; gene_name HLCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000086636.4" ; havana_transcript "OTTHUMT00000194686.2" ; hgnc_id "HGNC:4976" ; level 2 ; orig_coord_info "chr21,36938832,36938883,-" ; protein_id "ENSP00000338387.3" ; tag basic appris_principal_1 CCDS ; transcript_id "SGSM3--HLCS^ENST00000336648.8" ; transcript_name "HLCS-201" ; transcript_support_level 1 ; transcript_type protein_coding
SGSM3--HLCS HAVANA mRNA 13786 36084 . + . FI_gene_label "HLCS^ENSG00000159267.16" ; ID "SGSM3--HLCS^ENST00000336648.8" ; Parent "SGSM3--HLCS^HLCS^ENSG00000159267.16" ; ccdsid "CCDS13647.1" ; exon_id "ENSE00001282204.4" ; exon_number 4 ; gene_id "SGSM3--HLCS^HLCS^ENSG00000159267.16" ; gene_name HLCS ; gene_type protein_coding ; havana_gene "OTTHUMG00000086636.4" ; havana_transcript "OTTHUMT00000194686.2" ; hgnc_id "HGNC:4976" ; level 2 ; orig_coord_info "chr21,36938832,36938883,-" ; protein_id "ENSP00000338387.3" ; tag basic appris_principal_1 CCDS ; transcript_id "SGSM3--HLCS^ENST00000336648.8" ; transcript_name "HLCS-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC39A11--LINC00511 HAVANA gene 1020 24927 . + . FI_gene_label "SLC39A11^ENSG00000133195.11" ; ID "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11" ; ccdsid "CCDS11690.1" ; exon_id "ENSE00003519818.1" ; exon_number 2 ; gene_id "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11" ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5" ; havana_transcript "OTTHUMT00000441441.1" ; hgnc_id "HGNC:14463" ; level 2 ; orig_coord_info "chr17,73088657,73088764,-" ; protein_id "ENSP00000255559.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--LINC00511^ENST00000255559.7" ; transcript_name "SLC39A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC39A11--LINC00511 HAVANA mRNA 1020 24927 . + . FI_gene_label "SLC39A11^ENSG00000133195.11" ; ID "SLC39A11--LINC00511^ENST00000255559.7" ; Parent "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11" ; ccdsid "CCDS11690.1" ; exon_id "ENSE00003519818.1" ; exon_number 2 ; gene_id "SLC39A11--LINC00511^SLC39A11^ENSG00000133195.11" ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5" ; havana_transcript "OTTHUMT00000441441.1" ; hgnc_id "HGNC:14463" ; level 2 ; orig_coord_info "chr17,73088657,73088764,-" ; protein_id "ENSP00000255559.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--LINC00511^ENST00000255559.7" ; transcript_name "SLC39A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC39A11--SYT9 HAVANA gene 1020 24927 . + . FI_gene_label "SLC39A11^ENSG00000133195.11" ; ID "SLC39A11--SYT9^SLC39A11^ENSG00000133195.11" ; ccdsid "CCDS11690.1" ; exon_id "ENSE00003519818.1" ; exon_number 2 ; gene_id "SLC39A11--SYT9^SLC39A11^ENSG00000133195.11" ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5" ; havana_transcript "OTTHUMT00000441441.1" ; hgnc_id "HGNC:14463" ; level 2 ; orig_coord_info "chr17,73088657,73088764,-" ; protein_id "ENSP00000255559.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--SYT9^ENST00000255559.7" ; transcript_name "SLC39A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC39A11--SYT9 HAVANA mRNA 1020 24927 . + . FI_gene_label "SLC39A11^ENSG00000133195.11" ; ID "SLC39A11--SYT9^ENST00000255559.7" ; Parent "SLC39A11--SYT9^SLC39A11^ENSG00000133195.11" ; ccdsid "CCDS11690.1" ; exon_id "ENSE00003519818.1" ; exon_number 2 ; gene_id "SLC39A11--SYT9^SLC39A11^ENSG00000133195.11" ; gene_name SLC39A11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178306.5" ; havana_transcript "OTTHUMT00000441441.1" ; hgnc_id "HGNC:14463" ; level 2 ; orig_coord_info "chr17,73088657,73088764,-" ; protein_id "ENSP00000255559.3" ; tag basic appris_principal_4 CCDS ; transcript_id "SLC39A11--SYT9^ENST00000255559.7" ; transcript_name "SLC39A11-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC39A11--SYT9 HAVANA gene 29067 41944 . + . FI_gene_label "SYT9^ENSG00000170743.17" ; ID "SLC39A11--SYT9^SYT9^ENSG00000170743.17" ; ccdsid "CCDS7778.1" ; exon_id "ENSE00001291376.7" ; exon_number 1 ; gene_id "SLC39A11--SYT9^SYT9^ENSG00000170743.17" ; gene_name SYT9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165499.3" ; havana_transcript "OTTHUMT00000384483.2" ; hgnc_id "HGNC:19265" ; level 2 ; orig_coord_info "chr11,7252187,7252331,+" ; protein_id "ENSP00000324419.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC39A11--SYT9^ENST00000318881.11" ; transcript_name "SYT9-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC39A11--SYT9 HAVANA mRNA 29067 41944 . + . FI_gene_label "SYT9^ENSG00000170743.17" ; ID "SLC39A11--SYT9^ENST00000318881.11" ; Parent "SLC39A11--SYT9^SYT9^ENSG00000170743.17" ; ccdsid "CCDS7778.1" ; exon_id "ENSE00001291376.7" ; exon_number 1 ; gene_id "SLC39A11--SYT9^SYT9^ENSG00000170743.17" ; gene_name SYT9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165499.3" ; havana_transcript "OTTHUMT00000384483.2" ; hgnc_id "HGNC:19265" ; level 2 ; orig_coord_info "chr11,7252187,7252331,+" ; protein_id "ENSP00000324419.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC39A11--SYT9^ENST00000318881.11" ; transcript_name "SYT9-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TAFA5--WDR38 HAVANA gene 1040 10080 . + . FI_gene_label "TAFA5^ENSG00000219438.9" ; ID "TAFA5--WDR38^TAFA5^ENSG00000219438.9" ; exon_id "ENSE00001131477.4" ; exon_number 1 ; gene_id "TAFA5--WDR38^TAFA5^ENSG00000219438.9" ; gene_name TAFA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150308.2" ; havana_transcript "OTTHUMT00000317503.2" ; hgnc_id "HGNC:21592" ; level 2 ; orig_coord_info "chr22,48489593,48489704,+" ; protein_id "ENSP00000336812.5" ; tag mRNA_end_NF cds_end_NF ; transcript_id "TAFA5--WDR38^ENST00000336769.9" ; transcript_name "TAFA5-201" ; transcript_support_level 4 ; transcript_type protein_coding
TAFA5--WDR38 HAVANA mRNA 1040 10080 . + . FI_gene_label "TAFA5^ENSG00000219438.9" ; ID "TAFA5--WDR38^ENST00000336769.9" ; Parent "TAFA5--WDR38^TAFA5^ENSG00000219438.9" ; exon_id "ENSE00001131477.4" ; exon_number 1 ; gene_id "TAFA5--WDR38^TAFA5^ENSG00000219438.9" ; gene_name TAFA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150308.2" ; havana_transcript "OTTHUMT00000317503.2" ; hgnc_id "HGNC:21592" ; level 2 ; orig_coord_info "chr22,48489593,48489704,+" ; protein_id "ENSP00000336812.5" ; tag mRNA_end_NF cds_end_NF ; transcript_id "TAFA5--WDR38^ENST00000336769.9" ; transcript_name "TAFA5-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
TAFA5--WDR38 HAVANA gene 13124 17234 . + . FI_gene_label "WDR38^ENSG00000136918.8" ; ID "TAFA5--WDR38^WDR38^ENSG00000136918.8" ; ccdsid "CCDS43876.1" ; exon_id "ENSE00001460940.2" ; exon_number 1 ; gene_id "TAFA5--WDR38^WDR38^ENSG00000136918.8" ; gene_name WDR38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020664.1" ; havana_transcript "OTTHUMT00000054048.1" ; hgnc_id "HGNC:23745" ; level 2 ; orig_coord_info "chr9,124853532,124853600,+" ; protein_id "ENSP00000362677.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TAFA5--WDR38^ENST00000373574.2" ; transcript_name "WDR38-201" ; transcript_support_level 1 ; transcript_type protein_coding
TAFA5--WDR38 HAVANA mRNA 13124 17234 . + . FI_gene_label "WDR38^ENSG00000136918.8" ; ID "TAFA5--WDR38^ENST00000373574.2" ; Parent "TAFA5--WDR38^WDR38^ENSG00000136918.8" ; ccdsid "CCDS43876.1" ; exon_id "ENSE00001460940.2" ; exon_number 1 ; gene_id "TAFA5--WDR38^WDR38^ENSG00000136918.8" ; gene_name WDR38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020664.1" ; havana_transcript "OTTHUMT00000054048.1" ; hgnc_id "HGNC:23745" ; level 2 ; orig_coord_info "chr9,124853532,124853600,+" ; protein_id "ENSP00000362677.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TAFA5--WDR38^ENST00000373574.2" ; transcript_name "WDR38-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^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--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--LINC01347 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^ENST00000326270.13" ; Parent "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^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--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC004980.3--UPK3BL1 HAVANA gene 1001 3365 . + . FI_gene_label "AC004980.3^ENSG00000230305.2" ; ID "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; exon_id "ENSE00002500030.1" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; gene_name "AC004980.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2" ; havana_transcript "OTTHUMT00000341407.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76524515,76524698,+" ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1" ; transcript_name "AC004980.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC004980.3--UPK3BL1 HAVANA RNA 1001 3365 . + . FI_gene_label "AC004980.3^ENSG00000230305.2" ; ID "AC004980.3--UPK3BL1^ENST00000447046.1" ; Parent "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; exon_id "ENSE00002500030.1" ; exon_number 1 ; gene_id "AC004980.3--UPK3BL1^AC004980.3^ENSG00000230305.2" ; gene_name "AC004980.3" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155727.2" ; havana_transcript "OTTHUMT00000341407.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76524515,76524698,+" ; tag basic ; transcript_id "AC004980.3--UPK3BL1^ENST00000447046.1" ; transcript_name "AC004980.3-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AL121790.1--MIPOL1 HAVANA gene 1001 2738 . + . FI_gene_label "AL121790.1^ENSG00000258414.1" ; ID "AL121790.1--MIPOL1^AL121790.1^ENSG00000258414.1" ; exon_id "ENSE00002458641.1" ; exon_number 1 ; gene_id "AL121790.1--MIPOL1^AL121790.1^ENSG00000258414.1" ; gene_name "AL121790.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170995.2" ; havana_transcript "OTTHUMT00000411127.1" ; level 2 ; orig_coord_info "chr14,37564047,37564362,+" ; tag basic ; transcript_id "AL121790.1--MIPOL1^ENST00000554829.1" ; transcript_name "AL121790.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
AL121790.1--MIPOL1 HAVANA RNA 1001 2738 . + . FI_gene_label "AL121790.1^ENSG00000258414.1" ; ID "AL121790.1--MIPOL1^ENST00000554829.1" ; Parent "AL121790.1--MIPOL1^AL121790.1^ENSG00000258414.1" ; exon_id "ENSE00002458641.1" ; exon_number 1 ; gene_id "AL121790.1--MIPOL1^AL121790.1^ENSG00000258414.1" ; gene_name "AL121790.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000170995.2" ; havana_transcript "OTTHUMT00000411127.1" ; level 2 ; orig_coord_info "chr14,37564047,37564362,+" ; tag basic ; transcript_id "AL121790.1--MIPOL1^ENST00000554829.1" ; transcript_name "AL121790.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
BPTF--AP003789.1 HAVANA gene 47100 47704 . + . FI_gene_label "AP003789.1^ENSG00000275905.1" ; ID "BPTF--AP003789.1^AP003789.1^ENSG00000275905.1" ; exon_id "ENSE00003744920.1" ; exon_number 1 ; gene_id "BPTF--AP003789.1^AP003789.1^ENSG00000275905.1" ; gene_name "AP003789.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187749.1" ; havana_transcript "OTTHUMT00000475513.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,106980967,106981571,-" ; tag basic ; transcript_id "BPTF--AP003789.1^ENST00000617737.1" ; transcript_name "AP003789.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
BPTF--AP003789.1 HAVANA RNA 47100 47704 . + . FI_gene_label "AP003789.1^ENSG00000275905.1" ; ID "BPTF--AP003789.1^ENST00000617737.1" ; Parent "BPTF--AP003789.1^AP003789.1^ENSG00000275905.1" ; exon_id "ENSE00003744920.1" ; exon_number 1 ; gene_id "BPTF--AP003789.1^AP003789.1^ENSG00000275905.1" ; gene_name "AP003789.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000187749.1" ; havana_transcript "OTTHUMT00000475513.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr8,106980967,106981571,-" ; tag basic ; transcript_id "BPTF--AP003789.1^ENST00000617737.1" ; transcript_name "AP003789.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
EP300--AC137499.1 HAVANA gene 42056 42143 . + . FI_gene_label "AC137499.1^ENSG00000226160.1" ; ID "EP300--AC137499.1^AC137499.1^ENSG00000226160.1" ; exon_id "ENSE00001625751.1" ; exon_number 1 ; gene_id "EP300--AC137499.1^AC137499.1^ENSG00000226160.1" ; gene_name "AC137499.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000140366.1" ; havana_transcript "OTTHUMT00000277045.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr22,16405330,16405417,+" ; tag basic ; transcript_id "EP300--AC137499.1^ENST00000427602.1" ; transcript_name "AC137499.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
EP300--AC137499.1 HAVANA RNA 42056 42143 . + . FI_gene_label "AC137499.1^ENSG00000226160.1" ; ID "EP300--AC137499.1^ENST00000427602.1" ; Parent "EP300--AC137499.1^AC137499.1^ENSG00000226160.1" ; exon_id "ENSE00001625751.1" ; exon_number 1 ; gene_id "EP300--AC137499.1^AC137499.1^ENSG00000226160.1" ; gene_name "AC137499.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000140366.1" ; havana_transcript "OTTHUMT00000277045.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr22,16405330,16405417,+" ; tag basic ; transcript_id "EP300--AC137499.1^ENST00000427602.1" ; transcript_name "AC137499.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
EP300--PABPC1P9 HAVANA gene 42056 44144 . + . FI_gene_label "PABPC1P9^ENSG00000229658.1" ; ID "EP300--PABPC1P9^PABPC1P9^ENSG00000229658.1" ; exon_id "ENSE00001616608.1" ; exon_number 1 ; gene_id "EP300--PABPC1P9^PABPC1P9^ENSG00000229658.1" ; gene_name PABPC1P9 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000140367.3" ; havana_transcript "OTTHUMT00000277046.3" ; hgnc_id "HGNC:37991" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr22,16423943,16424108,+" ; tag pseudo_consens basic ; transcript_id "EP300--PABPC1P9^ENST00000426076.1" ; transcript_name "PABPC1P9-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EP300--PABPC1P9 HAVANA RNA 42056 44144 . + . FI_gene_label "PABPC1P9^ENSG00000229658.1" ; ID "EP300--PABPC1P9^ENST00000426076.1" ; Parent "EP300--PABPC1P9^PABPC1P9^ENSG00000229658.1" ; exon_id "ENSE00001616608.1" ; exon_number 1 ; gene_id "EP300--PABPC1P9^PABPC1P9^ENSG00000229658.1" ; gene_name PABPC1P9 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000140367.3" ; havana_transcript "OTTHUMT00000277046.3" ; hgnc_id "HGNC:37991" ; level 1 ; ont "PGO:0000005" ; orig_coord_info "chr22,16423943,16424108,+" ; tag pseudo_consens basic ; transcript_id "EP300--PABPC1P9^ENST00000426076.1" ; transcript_name "PABPC1P9-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
EP300--SLC9B1P4 HAVANA gene 42056 51120 . + . FI_gene_label "SLC9B1P4^ENSG00000227367.1" ; ID "EP300--SLC9B1P4^SLC9B1P4^ENSG00000227367.1" ; exon_id "ENSE00001666715.1" ; exon_number 1 ; gene_id "EP300--SLC9B1P4^SLC9B1P4^ENSG00000227367.1" ; gene_name SLC9B1P4 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000140399.1" ; havana_transcript "OTTHUMT00000277201.1" ; hgnc_id "HGNC:43583" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr22,16476699,16476870,-" ; tag basic ; transcript_id "EP300--SLC9B1P4^ENST00000421957.1" ; transcript_name "SLC9B1P4-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EP300--SLC9B1P4 HAVANA RNA 42056 51120 . + . FI_gene_label "SLC9B1P4^ENSG00000227367.1" ; ID "EP300--SLC9B1P4^ENST00000421957.1" ; Parent "EP300--SLC9B1P4^SLC9B1P4^ENSG00000227367.1" ; exon_id "ENSE00001666715.1" ; exon_number 1 ; gene_id "EP300--SLC9B1P4^SLC9B1P4^ENSG00000227367.1" ; gene_name SLC9B1P4 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000140399.1" ; havana_transcript "OTTHUMT00000277201.1" ; hgnc_id "HGNC:43583" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr22,16476699,16476870,-" ; tag basic ; transcript_id "EP300--SLC9B1P4^ENST00000421957.1" ; transcript_name "SLC9B1P4-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
FBXL20--LINC02089 HAVANA gene 29529 32034 . + . FI_gene_label "LINC02089^ENSG00000226364.1" ; ID "FBXL20--LINC02089^LINC02089^ENSG00000226364.1" ; exon_id "ENSE00001741493.1" ; exon_number 1 ; gene_id "FBXL20--LINC02089^LINC02089^ENSG00000226364.1" ; gene_name LINC02089 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132354.2" ; havana_transcript "OTTHUMT00000255476.2" ; hgnc_id "HGNC:52940" ; level 2 ; orig_coord_info "chr17,52862121,52862471,+" ; tag basic ; transcript_id "FBXL20--LINC02089^ENST00000412360.1" ; transcript_name "LINC02089-201" ; transcript_support_level 2 ; transcript_type lncRNA
FBXL20--LINC02089 HAVANA RNA 29529 32034 . + . FI_gene_label "LINC02089^ENSG00000226364.1" ; ID "FBXL20--LINC02089^ENST00000412360.1" ; Parent "FBXL20--LINC02089^LINC02089^ENSG00000226364.1" ; exon_id "ENSE00001741493.1" ; exon_number 1 ; gene_id "FBXL20--LINC02089^LINC02089^ENSG00000226364.1" ; gene_name LINC02089 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132354.2" ; havana_transcript "OTTHUMT00000255476.2" ; hgnc_id "HGNC:52940" ; level 2 ; orig_coord_info "chr17,52862121,52862471,+" ; tag basic ; transcript_id "FBXL20--LINC02089^ENST00000412360.1" ; transcript_name "LINC02089-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
FBXL20--LINC02876 HAVANA gene 29536 31668 . + . FI_gene_label "LINC02876^ENSG00000227011.4" ; ID "FBXL20--LINC02876^LINC02876^ENSG00000227011.4" ; exon_id "ENSE00003757840.1" ; exon_number 1 ; gene_id "FBXL20--LINC02876^LINC02876^ENSG00000227011.4" ; gene_name LINC02876 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132355.2" ; havana_transcript "OTTHUMT00000255477.1" ; hgnc_id "HGNC:42963" ; level 2 ; orig_coord_info "chr17,52985520,52985721,+" ; tag basic ; transcript_id "FBXL20--LINC02876^ENST00000623702.1" ; transcript_name "LINC02876-201" ; transcript_support_level 2 ; transcript_type lncRNA
FBXL20--LINC02876 HAVANA RNA 29536 31668 . + . FI_gene_label "LINC02876^ENSG00000227011.4" ; ID "FBXL20--LINC02876^ENST00000623702.1" ; Parent "FBXL20--LINC02876^LINC02876^ENSG00000227011.4" ; exon_id "ENSE00003757840.1" ; exon_number 1 ; gene_id "FBXL20--LINC02876^LINC02876^ENSG00000227011.4" ; gene_name LINC02876 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132355.2" ; havana_transcript "OTTHUMT00000255477.1" ; hgnc_id "HGNC:42963" ; level 2 ; orig_coord_info "chr17,52985520,52985721,+" ; tag basic ; transcript_id "FBXL20--LINC02876^ENST00000623702.1" ; transcript_name "LINC02876-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
MARK3--DUX4L2 HAVANA gene 47980 49254 . + . FI_gene_label "DUX4L2^ENSG00000280457.1" ; ID "MARK3--DUX4L2^DUX4L2^ENSG00000280457.1" ; exon_id "ENSE00002591235.3" ; exon_number 1 ; gene_id "MARK3--DUX4L2^DUX4L2^ENSG00000280457.1" ; gene_name DUX4L2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000161316.4" ; havana_transcript "OTTHUMT00000364515.3" ; hgnc_id "HGNC:37267" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr4,190091005,190092279,+" ; tag basic ; transcript_id "MARK3--DUX4L2^ENST00000561772.3" ; transcript_name "DUX4L2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
MARK3--DUX4L2 HAVANA RNA 47980 49254 . + . FI_gene_label "DUX4L2^ENSG00000280457.1" ; ID "MARK3--DUX4L2^ENST00000561772.3" ; Parent "MARK3--DUX4L2^DUX4L2^ENSG00000280457.1" ; exon_id "ENSE00002591235.3" ; exon_number 1 ; gene_id "MARK3--DUX4L2^DUX4L2^ENSG00000280457.1" ; gene_name DUX4L2 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000161316.4" ; havana_transcript "OTTHUMT00000364515.3" ; hgnc_id "HGNC:37267" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr4,190091005,190092279,+" ; tag basic ; transcript_id "MARK3--DUX4L2^ENST00000561772.3" ; transcript_name "DUX4L2-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
SLC39A11--LINC00511 HAVANA gene 37738 81945 . + . FI_gene_label "LINC00511^ENSG00000227036.8" ; ID "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8" ; exon_id "ENSE00001629418.1" ; exon_number 1 ; gene_id "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8" ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20" ; havana_transcript "OTTHUMT00000255287.2" ; hgnc_id "HGNC:43564" ; level 2 ; orig_coord_info "chr17,72592203,72592804,-" ; transcript_id "SLC39A11--LINC00511^ENST00000453722.6" ; transcript_name "LINC00511-201" ; transcript_support_level 2 ; transcript_type lncRNA
SLC39A11--LINC00511 HAVANA RNA 37738 81945 . + . FI_gene_label "LINC00511^ENSG00000227036.8" ; ID "SLC39A11--LINC00511^ENST00000453722.6" ; Parent "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8" ; exon_id "ENSE00001629418.1" ; exon_number 1 ; gene_id "SLC39A11--LINC00511^LINC00511^ENSG00000227036.8" ; gene_name LINC00511 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132227.20" ; havana_transcript "OTTHUMT00000255287.2" ; hgnc_id "HGNC:43564" ; level 2 ; orig_coord_info "chr17,72592203,72592804,-" ; transcript_id "SLC39A11--LINC00511^ENST00000453722.6" ; transcript_name "LINC00511-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--LINC01347 HAVANA RNA 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^ENST00000417964.2" ; Parent "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
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
802 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 1 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 ------------------------------
1803 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 39 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
Lets remove isoform MARK3--DUX4^ENST00000677604.1
Lets remove isoform MARK3--DUX4L2^ENST00000677604.1
2 identical isoforms removed
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed