From ebaf0956c24c7adb11c6ea082518bd3e2a005454 Mon Sep 17 00:00:00 2001 From: Sana Shah <54493565+sanashah007@users.noreply.github.com> Date: Thu, 22 Aug 2024 12:23:33 -0700 Subject: [PATCH] fix: move mapk1.gtf to large dir --- .../tools/walkers/conversion/GtfToBed.java | 3 +- .../conversion/ConversionTestUtils.java | 6 +- src/test/resources/large/gtfToBed/mapk1.gtf | 3 + .../tools/walkers/gtfToBed/mapk1.gtf | 71 ------------------- 4 files changed, 5 insertions(+), 78 deletions(-) create mode 100644 src/test/resources/large/gtfToBed/mapk1.gtf delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/gtfToBed/mapk1.gtf diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java index 9116615215f..23e0b833375 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java @@ -190,7 +190,7 @@ private void updateGeneEnd(GencodeGtfFeature gtfFeature) { // get the end value of the gene int geneEnd = featureInfoMap.get(gtfFeature.getGeneId()).getEnd(); - // if the transcript start is greater than the gene start + // if the transcript end is greater than the gene end if (gtfFeature.getEnd() > geneEnd) { // set the gene end to be the transcript end geneEnd = gtfFeature.getEnd(); @@ -211,7 +211,6 @@ public Object onTraversalSuccess() { // get dictionary SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary(); - // create linked hash map to store sorted values of idToInfo LinkedHashMap karyotypeIdToInfo = getSortedMap(sequenceDictionary); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java index d13e6ff75e7..7084fe2700d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java @@ -13,7 +13,7 @@ public static String getDecoySampleGtf(){ } public static String getMapk1Gtf(){ - return getTestDataDir()+"/mapk1.gtf"; + return GATKBaseTest.largeFileTestDir + "/gtfToBed/mapk1.gtf"; } public static String getManyTranscriptsGtf(){ @@ -24,10 +24,6 @@ public static String getReferenceDict(){ return getTestDataDir()+"/reference.dict"; } -// public static String getReferenceDict(){ -// return GATKBaseTest.publicTestDir + "large/Homo_sapiens_assembly38.dict"; -// } - public static String getDecoySamplesGeneBed(){ return getTestDataDir() + "/decoySampleGene.bed"; } diff --git a/src/test/resources/large/gtfToBed/mapk1.gtf b/src/test/resources/large/gtfToBed/mapk1.gtf new file mode 100644 index 00000000000..a4f2a512e17 --- /dev/null +++ b/src/test/resources/large/gtfToBed/mapk1.gtf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:34bb02952d42ce6f737630754bf89ad8b28384c60d240a626b33c9e8307d32a3 +size 32274 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/gtfToBed/mapk1.gtf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/gtfToBed/mapk1.gtf deleted file mode 100644 index 1bf44c8164a..00000000000 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/gtfToBed/mapk1.gtf +++ /dev/null @@ -1,71 +0,0 @@ -##description: evidence-based annotation of the human genome (GRCh38), version 38 (Ensembl 104) -##provider: GENCODE -##contact: gencode-help@ebi.ac.uk -##format: gtf -##date: 2021-03-12 -chr22 HAVANA gene 21759657 21867680 . - . gene_id "ENSG00000100030.15"; gene_type "protein_coding"; gene_name "MAPK1"; level 1; hgnc_id "HGNC:6871"; havana_gene "OTTHUMG00000030508.2"; -chr22 HAVANA transcript 21759657 21867645 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21867322 21867645 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 1; exon_id "ENSE00001838512.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21867322 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 1; exon_id "ENSE00001838512.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA start_codon 21867438 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 1; exon_id "ENSE00001838512.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21807664 21807846 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 2; exon_id "ENSE00000879359.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21807664 21807846 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 2; exon_id "ENSE00000879359.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21805850 21806039 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 3; exon_id "ENSE00000879358.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21805850 21806039 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 3; exon_id "ENSE00000879358.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21799012 21799128 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 4; exon_id "ENSE00000879357.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21799012 21799128 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 4; exon_id "ENSE00000879357.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21788694 21788808 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 5; exon_id "ENSE00001650159.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21788694 21788808 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 5; exon_id "ENSE00001650159.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21788257 21788388 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 6; exon_id "ENSE00000651102.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21788257 21788388 . - 2 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 6; exon_id "ENSE00000651102.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21772873 21772982 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 7; exon_id "ENSE00000651101.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21772873 21772982 . - 2 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 7; exon_id "ENSE00000651101.1"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21769195 21769320 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 8; exon_id "ENSE00001135958.3"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA CDS 21769207 21769320 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 8; exon_id "ENSE00001135958.3"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA stop_codon 21769204 21769206 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 8; exon_id "ENSE00001135958.3"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA exon 21759657 21764240 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 9; exon_id "ENSE00001857706.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA UTR 21867441 21867645 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 1; exon_id "ENSE00001838512.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA UTR 21769195 21769206 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 8; exon_id "ENSE00001135958.3"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA UTR 21759657 21764240 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000215832.11"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-201"; exon_number 9; exon_id "ENSE00001857706.2"; level 1; protein_id "ENSP00000215832.7"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000075396.2"; -chr22 HAVANA transcript 21763984 21769428 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000491588.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "processed_transcript"; transcript_name "MAPK1-203"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6871"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268187.1"; -chr22 HAVANA exon 21769195 21769428 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000491588.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "processed_transcript"; transcript_name "MAPK1-203"; exon_number 1; exon_id "ENSE00001883497.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6871"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268187.1"; -chr22 HAVANA exon 21763984 21764240 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000491588.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "processed_transcript"; transcript_name "MAPK1-203"; exon_number 2; exon_id "ENSE00001885512.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6871"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268187.1"; -chr22 HAVANA transcript 21769040 21867680 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21867322 21867680 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 1; exon_id "ENSE00001135965.5"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21867322 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 1; exon_id "ENSE00001135965.5"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA start_codon 21867438 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 1; exon_id "ENSE00001135965.5"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21807664 21807846 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 2; exon_id "ENSE00000879359.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21807664 21807846 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 2; exon_id "ENSE00000879359.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21805850 21806039 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 3; exon_id "ENSE00000879358.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21805850 21806039 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 3; exon_id "ENSE00000879358.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21799012 21799128 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 4; exon_id "ENSE00000879357.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21799012 21799128 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 4; exon_id "ENSE00000879357.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21788694 21788808 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 5; exon_id "ENSE00001650159.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21788694 21788808 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 5; exon_id "ENSE00001650159.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21788257 21788388 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 6; exon_id "ENSE00000651102.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21788257 21788388 . - 2 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 6; exon_id "ENSE00000651102.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21772873 21772982 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 7; exon_id "ENSE00000651101.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21772873 21772982 . - 2 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 7; exon_id "ENSE00000651101.1"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA exon 21769040 21769320 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 8; exon_id "ENSE00001535106.3"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA CDS 21769207 21769320 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 8; exon_id "ENSE00001535106.3"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA stop_codon 21769204 21769206 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 8; exon_id "ENSE00001535106.3"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA UTR 21867441 21867680 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 1; exon_id "ENSE00001135965.5"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 HAVANA UTR 21769040 21769206 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000398822.7"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-202"; exon_number 8; exon_id "ENSE00001535106.3"; level 2; protein_id "ENSP00000381803.3"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS13795.1"; havana_gene "OTTHUMG00000030508.2"; havana_transcript "OTTHUMT00000268186.1"; -chr22 ENSEMBL transcript 21769204 21867440 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21867322 21867440 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 1; exon_id "ENSE00002235201.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21867322 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 1; exon_id "ENSE00002235201.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL start_codon 21867438 21867440 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 1; exon_id "ENSE00002235201.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21807664 21807846 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 2; exon_id "ENSE00000879359.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21807664 21807846 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 2; exon_id "ENSE00000879359.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21805850 21806039 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 3; exon_id "ENSE00000879358.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21805850 21806039 . - 1 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 3; exon_id "ENSE00000879358.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21799012 21799128 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 4; exon_id "ENSE00000879357.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21799012 21799128 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 4; exon_id "ENSE00000879357.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21788694 21788808 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 5; exon_id "ENSE00001650159.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21788694 21788808 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 5; exon_id "ENSE00001650159.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21772873 21772982 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 6; exon_id "ENSE00000651101.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21772873 21772982 . - 2 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 6; exon_id "ENSE00000651101.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL exon 21769204 21769320 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 7; exon_id "ENSE00002248625.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL CDS 21769207 21769320 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 7; exon_id "ENSE00002248625.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL stop_codon 21769204 21769206 . - 0 gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 7; exon_id "ENSE00002248625.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2"; -chr22 ENSEMBL UTR 21769204 21769206 . - . gene_id "ENSG00000100030.15"; transcript_id "ENST00000544786.1"; gene_type "protein_coding"; gene_name "MAPK1"; transcript_type "protein_coding"; transcript_name "MAPK1-204"; exon_number 7; exon_id "ENSE00002248625.1"; level 3; protein_id "ENSP00000440842.1"; transcript_support_level "1"; hgnc_id "HGNC:6871"; tag "basic"; havana_gene "OTTHUMG00000030508.2";