From 028316a65deaf0c44489c722709bc256db1149e7 Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 11:07:16 -0400 Subject: [PATCH 01/15] First cut. Runs but found an issue. --- scripts/mutect2_wdl/mutect2.wdl | 243 +++++++++--------- .../mafOutput/MafOutputRenderer.java | 82 +++--- .../funcotator/FuncotatorIntegrationTest.java | 24 ++ 3 files changed, 193 insertions(+), 156 deletions(-) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index b342c7a249a..c1699b8a36f 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -42,6 +42,9 @@ ## sequencing_center, sequence_source: metadata for Oncotator ## filter_oncotator_maf: Whether the MAF generated by oncotator should have the filtered variants removed. Default: true ## realignment_index_bundle: resource for FilterAlignmentArtifacts, which runs if and only if it is specified. Generated by BwaMemIndexImageCreator. +## funco_reference_version: "hg19" for hg19 or b37. "hg38" for hg38. Default: "hg19" +## funco_transcript_selection_list: +## TODO: Finish docs! ## ## Outputs : ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam @@ -102,12 +105,12 @@ workflow Mutect2 { # funcotator inputs Boolean? run_funcotator Boolean run_funcotator_or_default = select_first([run_funcotator, false]) - String? reference_version - String? data_sources_tar_gz - String? transcript_selection_mode - Array[String]? transcript_selection_list - Array[String]? annotation_defaults - Array[String]? annotation_overrides + String? funco_reference_version + String? funco_data_sources_tar_gz + String? funco_transcript_selection_mode + File? funco_transcript_selection_list + Array[String]? funco_annotation_defaults + Array[String]? funco_annotation_overrides File? gatk_override @@ -348,24 +351,24 @@ workflow Mutect2 { if (run_funcotator_or_default) { File funcotate_vcf_input = select_first([FilterAlignmentArtifacts.filtered_vcf, FilterByOrientationBias.filtered_vcf, Filter.filtered_vcf]) File funcotate_vcf_input_index = select_first([FilterAlignmentArtifacts.filtered_vcf_index, FilterByOrientationBias.filtered_vcf_index, Filter.filtered_vcf_index]) - call Funcotate { + call FuncotateMaf { input: - m2_vcf = funcotate_vcf_input, - m2_vcf_index = funcotate_vcf_input_index, + input_vcf = funcotate_vcf_input, + input_vcf_idx = funcotate_vcf_input_index, ref_fasta = ref_fasta, - ref_fai = ref_fai, + ref_fasta_index = ref_fai, ref_dict = ref_dict, - reference_version = select_first([reference_version, "NO_REFERENCE_VERSION_GIVEN"]), - output_name = funcotated_name, - compress = compress, - data_sources_tar_gz = data_sources_tar_gz, - transcript_selection_mode = transcript_selection_mode, - transcript_selection_list = transcript_selection_list, - annotation_defaults = annotation_defaults, - annotation_overrides = annotation_overrides, + reference_version = select_first([funco_reference_version, "hg19"]), + data_sources_tar_gz = funco_data_sources_tar_gz, + transcript_selection_mode = funco_transcript_selection_mode, + transcript_selection_list = funco_transcript_selection_list, + annotation_defaults = funco_annotation_defaults, + annotation_overrides = funco_annotation_overrides, gatk_docker = gatk_docker, gatk_override = gatk_override, - filter_funcotations = filter_funcotations_or_default + filter_funcotations = filter_funcotations_or_default, + sequencing_center = sequencing_center, + sequence_source = sequence_source } } @@ -375,10 +378,8 @@ workflow Mutect2 { File filtered_vcf = select_first([FilterAlignmentArtifacts.filtered_vcf, FilterByOrientationBias.filtered_vcf, Filter.filtered_vcf]) File filtered_vcf_index = select_first([FilterAlignmentArtifacts.filtered_vcf_index, FilterByOrientationBias.filtered_vcf_index, Filter.filtered_vcf_index]) File? contamination_table = CalculateContamination.contamination_table - File? oncotated_m2_maf = oncotate_m2.oncotated_m2_maf - File? funcotated_vcf = Funcotate.funcotated_vcf - File? funcotated_vcf_index = Funcotate.funcotated_vcf_index + File? funcotated_maf = FuncotateMaf.funcotated_output File? preadapter_detail_metrics = CollectSequencingArtifactMetrics.pre_adapter_metrics File? bamout = MergeBamOuts.merged_bam_out File? bamout_index = MergeBamOuts.merged_bam_out_index @@ -975,98 +976,106 @@ task SumFloats { } } -task Funcotate { - # inputs - File ref_fasta - File ref_fai - File ref_dict - File m2_vcf - File m2_vcf_index - String reference_version - String output_name - Boolean compress - String output_vcf = output_name + if compress then ".vcf.gz" else ".vcf" - String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx" - - File? data_sources_tar_gz - String? transcript_selection_mode - Array[String]? transcript_selection_list - Array[String]? annotation_defaults - Array[String]? annotation_overrides - Boolean filter_funcotations - - # ============== - # Process input args: - String transcript_selection_arg = if defined(transcript_selection_list) then " --transcript-list " else "" - String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" - String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" - String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else "" - # ============== - - # runtime - - String gatk_docker - File? gatk_override - Int? mem - Int? preemptible_attempts - Int? disk_space_gb - Int? cpu - - Boolean use_ssd = false - - # You may have to change the following two parameter values depending on the task requirements - Int default_ram_mb = 3000 - # WARNING: In the workflow, you should calculate the disk space as an input to this task (disk_space_gb). Please see [TODO: Link from Jose] for examples. - Int default_disk_space_gb = 100 - - # Mem is in units of GB but our command and memory runtime values are in MB - Int machine_mem = if defined(mem) then mem *1000 else default_ram_mb - Int command_mem = machine_mem - 1000 - - command <<< - set -e - export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override} - - DATA_SOURCES_TAR_GZ=${data_sources_tar_gz} - if [[ ! -e $DATA_SOURCES_TAR_GZ ]] ; then - # We have to download the data sources: - echo "Data sources gzip does not exist: $DATA_SOURCES_TAR_GZ" - echo "Downloading default data sources..." - wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.0.20180105.tar.gz - tar -zxf funcotator_dataSources.v1.0.20180105.tar.gz - DATA_SOURCES_FOLDER=funcotator_dataSources.v1.0.20180105 - else - # Extract the tar.gz: - mkdir datasources_dir - tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1 - DATA_SOURCES_FOLDER="$PWD/datasources_dir" - fi - - gatk --java-options "-Xmx${command_mem}m" Funcotator \ - --data-sources-path $DATA_SOURCES_FOLDER \ - --ref-version ${reference_version} \ - -R ${ref_fasta} \ - -V ${m2_vcf} \ - -O ${output_vcf} \ - ${"--transcript-selection-mode " + transcript_selection_mode} \ - ${transcript_selection_arg}${default="" sep=" --transcript-list " transcript_selection_list} \ - ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ - ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ - ${filter_funcotations_args} - >>> - - runtime { - docker: gatk_docker - bootDiskSizeGb: 12 - memory: machine_mem + " MB" - disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" - preemptible: select_first([preemptible_attempts, 3]) - cpu: select_first([cpu, 1]) - } - - output { - File funcotated_vcf = "${output_vcf}" - File funcotated_vcf_index = "${output_vcf_index}" - } -} - +task FuncotateMaf { + # inputs + File ref_fasta + File ref_fasta_index + File ref_dict + File input_vcf + File input_vcf_idx + String reference_version + String output_format = "MAF" + String? sequencing_center + String? sequence_source + + File? data_sources_tar_gz + String? transcript_selection_mode + File? transcript_selection_list + Array[String]? annotation_defaults + Array[String]? annotation_overrides + Boolean filter_funcotations + File? interval_list + + String? extra_args + + # ============== + # Process input args: + String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" + String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" + String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else "" + String interval_list_arg = if defined(interval_list) then " -L " else "" + String extra_args_arg = select_first([extra_args, ""]) + String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated" + # ============== + + # runtime + + String gatk_docker + File? gatk_override + Int? mem + Int? preemptible_attempts + Int? disk_space_gb + Int? cpu + + Boolean use_ssd = false + + # This should be updated when a new version of the data sources is released + # TODO: Make this dynamically chosen in the command. + String default_datasources_version = "funcotator_dataSources.v1.3.20180531" + + # You may have to change the following two parameter values depending on the task requirements + Int default_ram_mb = 3000 + # WARNING: In the workflow, you should calculate the disk space as an input to this task (disk_space_gb). + Int default_disk_space_gb = 100 + + # Mem is in units of GB but our command and memory runtime values are in MB + Int machine_mem = if defined(mem) then mem *1000 else default_ram_mb + Int command_mem = machine_mem - 1000 + + command <<< + set -e + export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override} + + DATA_SOURCES_TAR_GZ=${data_sources_tar_gz} + if [[ ! -e $DATA_SOURCES_TAR_GZ ]] ; then + # We have to download the data sources: + echo "Data sources gzip does not exist: $DATA_SOURCES_TAR_GZ" + echo "Downloading default data sources..." + wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/${default_datasources_version}.tar.gz + tar -zxf ${default_datasources_version}.tar.gz + DATA_SOURCES_FOLDER=${default_datasources_version} + else + # Extract the tar.gz: + mkdir datasources_dir + tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1 + DATA_SOURCES_FOLDER="$PWD/datasources_dir" + fi + + gatk --java-options "-Xmx${command_mem}m" Funcotator \ + --data-sources-path $DATA_SOURCES_FOLDER \ + --ref-version ${reference_version} \ + --output-file-format ${output_format} \ + -R ${ref_fasta} \ + -V ${input_vcf} \ + -O ${final_output_filename} \ + ${interval_list_arg} ${default="" interval_list} \ + ${"--transcript-selection-mode " + transcript_selection_mode} \ + ${"--transcript-list " + transcript_selection_list} \ + ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ + ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ + ${filter_funcotations_args} \ + ${extra_args_arg} + >>> + + runtime { + docker: gatk_docker + memory: machine_mem + " MB" + disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" + preemptible: select_first([preemptible_attempts, 3]) + cpu: select_first([cpu, 1]) + } + + output { + File funcotated_output = "${final_output_filename}" + } + } \ No newline at end of file diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java index 654dd79f4c8..07827b55265 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java @@ -248,45 +248,12 @@ public void write(final VariantContext variant, final FuncotationMap txToFuncota for (final String txId : txToFuncotationMap.getTranscriptList()) { final List funcotations = txToFuncotationMap.get(txId); - - // Create our output maps: - final LinkedHashMap outputMap = new LinkedHashMap<>(defaultMap); - final LinkedHashMap extraFieldOutputMap = new LinkedHashMap<>(); - - // Get our funcotations for this allele and add them to the output maps: - for (final Funcotation funcotation : funcotations) { - if (funcotation.getAltAllele().equals(altAllele)) { - // Add all the fields from the other funcotations into the extra field output: - for (final String field : funcotation.getFieldNames()) { - setField(extraFieldOutputMap, field, funcotation.getField(field)); - } - } - } - - // Now add in our annotation overrides so they can be aliased correctly with the outputFieldNameMap: - extraFieldOutputMap.putAll(overrideAnnotations); - - // Go through all output fields and see if any of the names in the value list are in our extraFieldOutputMap. - // For any that match, we remove them from our extraFieldOutputMap and add them to the outputMap with the - // correct key. - for (final Map.Entry> entry : outputFieldNameMap.entrySet()) { - for (final String fieldName : entry.getValue()) { - if (extraFieldOutputMap.containsKey(fieldName)) { - outputMap.put(entry.getKey(), extraFieldOutputMap.remove(fieldName)); - break; - } - } - } - - // Merge our output maps together: - outputMap.putAll(extraFieldOutputMap); - - // Now translate fields to the field names that MAF likes: - final LinkedHashMap mafCompliantOutputMap = replaceFuncotationValuesWithMafCompliantValues(outputMap); + final LinkedHashMap mafCompliantOutputMap = createMafCompliantOutputMap(altAllele, funcotations); // Write our header if we have to: if (!hasWrittenHeader) { - writeHeader(mafCompliantOutputMap); + // Please note that we are implicitly using the ordering of a LinkedHashMap under the hood. + writeHeader(new ArrayList<>(mafCompliantOutputMap.keySet())); } // Write the output (with manual annotations at the end): @@ -299,6 +266,43 @@ public void write(final VariantContext variant, final FuncotationMap txToFuncota } } + private LinkedHashMap createMafCompliantOutputMap(final Allele altAllele, final List funcotations) { + // Create our output maps: + final LinkedHashMap outputMap = new LinkedHashMap<>(defaultMap); + final LinkedHashMap extraFieldOutputMap = new LinkedHashMap<>(); + + // Get our funcotations for this allele and add them to the output maps: + for (final Funcotation funcotation : funcotations) { + if (funcotation.getAltAllele().equals(altAllele)) { + // Add all the fields from the other funcotations into the extra field output: + for (final String field : funcotation.getFieldNames()) { + setField(extraFieldOutputMap, field, funcotation.getField(field)); + } + } + } + + // Now add in our annotation overrides so they can be aliased correctly with the outputFieldNameMap: + extraFieldOutputMap.putAll(overrideAnnotations); + + // Go through all output fields and see if any of the names in the value list are in our extraFieldOutputMap. + // For any that match, we remove them from our extraFieldOutputMap and add them to the outputMap with the + // correct key. + for (final Map.Entry> entry : outputFieldNameMap.entrySet()) { + for (final String fieldName : entry.getValue()) { + if (extraFieldOutputMap.containsKey(fieldName)) { + outputMap.put(entry.getKey(), extraFieldOutputMap.remove(fieldName)); + break; + } + } + } + + // Merge our output maps together: + outputMap.putAll(extraFieldOutputMap); + + // Now translate fields to the field names that MAF likes: + return replaceFuncotationValuesWithMafCompliantValues(outputMap); + } + //================================================================================================================== // Instance Methods: @@ -501,9 +505,9 @@ private void writeString(final String s) { /** * Write the header to the output file. - * @param outputMap A populated output map from which to derive the header columns. + * @param outputFields Ordered list of the header columns. These will be written as presented. */ - protected void writeHeader(final LinkedHashMap outputMap) { + protected void writeHeader(final List outputFields) { // Write out version: writeLine(MafOutputRendererConstants.COMMENT_STRING + "version " + VERSION); writeLine(MafOutputRendererConstants.COMMENT_STRING + MafOutputRendererConstants.COMMENT_STRING); @@ -537,7 +541,7 @@ protected void writeHeader(final LinkedHashMap outputMap) { writeLine(""); // Write the column headers for our output set and our manual annotations: - printWriter.write( outputMap.keySet().stream().collect(Collectors.joining(MafOutputRendererConstants.FIELD_DELIMITER)) ); + printWriter.write( outputFields.stream().collect(Collectors.joining(MafOutputRendererConstants.FIELD_DELIMITER)) ); writeLine(MafOutputRendererConstants.FIELD_DELIMITER + manualAnnotations.keySet().stream().collect(Collectors.joining(MafOutputRendererConstants.FIELD_DELIMITER))); // Make sure we keep track of the fact that we've now written the header: diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index 057aeae7d89..378b1c60384 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -73,6 +73,7 @@ public class FuncotatorIntegrationTest extends CommandLineProgramTest { private static final String MAF_TEST_CONFIG = toolsTestDir + "funcotator" + File.separator + "maf.config"; private static final String XSV_CLINVAR_COL_TEST_VCF = toolsTestDir + "funcotator" + File.separator + "clinvar_hg19_column_test.vcf"; private static final String DS_XSV_CLINVAR_COL_TEST = largeFileTestDir + "funcotator" + File.separator + "small_ds_clinvar_hg19" + File.separator; + private static final String EMPTY_VCF = publicTestDir + File.separator + "empty.vcf"; private static String hg38Chr3Ref; private static String b37Chr3Ref; @@ -1053,5 +1054,28 @@ public void testSequenceDictionaryCheck() { runCommandLine(arguments); } + + @Test + public void testNoVariantsProduceMaf() { + // Make sure that a MAF is actually produced (not a blank file). Testing https://github.com/broadinstitute/gatk/issues/4937 + final FuncotatorArgumentDefinitions.OutputFormatType outputFormatType = FuncotatorArgumentDefinitions.OutputFormatType.MAF; + final File outputFile = getOutputFile(outputFormatType); + + final ArgumentsBuilder arguments = new ArgumentsBuilder(); + + arguments.addVCF(new File(EMPTY_VCF)); + arguments.addOutput(outputFile); + arguments.addReference(new File(b37Chr3Ref)); + arguments.addArgument(FuncotatorArgumentDefinitions.DATA_SOURCES_PATH_LONG_NAME, DS_PIK3CA_DIR); + arguments.addArgument(FuncotatorArgumentDefinitions.REFERENCE_VERSION_LONG_NAME, FuncotatorTestConstants.REFERENCE_VERSION_HG19); + arguments.addArgument(FuncotatorArgumentDefinitions.OUTPUT_FORMAT_LONG_NAME, outputFormatType.toString()); + arguments.addBooleanArgument(FuncotatorArgumentDefinitions.ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME, true); + arguments.addArgument(FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_LONG_NAME, TranscriptSelectionMode.CANONICAL.toString()); + + runCommandLine(arguments); + + final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), null); + Assert.assertEquals(maf.getRecords().size(), 0); + } } From 65793a61cbeca17f27c51f8f97f3d9d9cddca3ee Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 11:17:55 -0400 Subject: [PATCH 02/15] Fixes #4937 --- .../tools/funcotator/mafOutput/MafOutputRenderer.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java index 07827b55265..4b076c18e9d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java @@ -220,6 +220,10 @@ public MafOutputRenderer(final Path outputFilePath, @Override public void close() { + if (!hasWrittenHeader) { + final LinkedHashMap mafCompliantOutputMap = createMafCompliantOutputMap(Allele.create("AT"), Collections.emptyList()); + writeHeader(new ArrayList<>(mafCompliantOutputMap.keySet())); + } if ( printWriter != null ) { printWriter.flush(); printWriter.close(); From c4922ff208d0ba931a5016dd3468543a86b04d0c Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 12:14:21 -0400 Subject: [PATCH 03/15] Updates for turning on Funcotator in the M2 autotesting of WDL. --- scripts/m2_cromwell_tests/test_m2_wdl_multi.json | 2 +- .../hellbender/tools/funcotator/FuncotatorIntegrationTest.java | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json index 023aa21492b..656c41191d2 100644 --- a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json +++ b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json @@ -9,7 +9,7 @@ "Mutect2_Multi.scatter_count": 2, "Mutect2_Multi.run_orientation_bias_filter": true, "Mutect2_Multi.run_oncotator": true, - "Mutect2_Multi.run_funcotator": false, + "Mutect2_Multi.run_funcotator": true, "Mutect2_Multi.preemptible_attempts": 2, "Mutect2_Multi.artifact_modes": ["G/T", "C/T"], "Mutect2_Multi.compress_vcfs": false, diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index 378b1c60384..441fade1eb7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -1076,6 +1076,7 @@ public void testNoVariantsProduceMaf() { final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), null); Assert.assertEquals(maf.getRecords().size(), 0); + // TODO: Check for the custom Maf fields } } From 6295f6ac8b066193c2e3492dba544655e7857f6c Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 14:22:36 -0400 Subject: [PATCH 04/15] Wiring up the WDL test. --- scripts/m2_cromwell_tests/run_m2_wdl.sh | 9 +++++++ .../m2_cromwell_tests/test_m2_wdl_multi.json | 2 ++ scripts/mutect2_wdl/mutect2.wdl | 2 +- scripts/mutect2_wdl/mutect2_multi_sample.wdl | 27 ++++++++++--------- 4 files changed, 26 insertions(+), 14 deletions(-) diff --git a/scripts/m2_cromwell_tests/run_m2_wdl.sh b/scripts/m2_cromwell_tests/run_m2_wdl.sh index ab25f52ecb0..faea6a5e0bf 100644 --- a/scripts/m2_cromwell_tests/run_m2_wdl.sh +++ b/scripts/m2_cromwell_tests/run_m2_wdl.sh @@ -7,6 +7,15 @@ cd "$script_path" WORKING_DIR=/home/travis/build/broadinstitute set -e + +echo "Creating tar.gz for Funcotator datasources ==========" +pushd . +FUNCOTATOR_TEST_DS_DIR=${WORKING_DIR}/gatk/src/test/resources/large/funcotator/ +cd ${FUNCOTATOR_TEST_DS_DIR} +# First parameter must match Mutect2_Multi.funco_data_sources_tar_gz test_m2_wdl_multi.json +tar zcvf ${WORKING_DIR}/small_ds_pik3ca.tar.gz small_ds_pik3ca/* +popd + echo "Building docker image for M2 WDL tests (skipping unit tests)..." #cd $WORKING_DIR/gatk/scripts/docker/ diff --git a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json index 656c41191d2..00d664f85cf 100644 --- a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json +++ b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json @@ -6,6 +6,8 @@ "Mutect2_Multi.ref_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", "Mutect2_Multi.ref_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", "Mutect2_Multi.pair_list": "/home/travis/build/broadinstitute/gatk/scripts/m2_cromwell_tests/pair_list", + "Mutect2_Multi.funco_data_sources_tar_gz": "/home/travis/build/broadinstitute/small_ds_pik3ca.tar.gz", + "Mutect2_Multi.funco_reference_version": "hg19", "Mutect2_Multi.scatter_count": 2, "Mutect2_Multi.run_orientation_bias_filter": true, "Mutect2_Multi.run_oncotator": true, diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index c1699b8a36f..994b70c7152 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -106,7 +106,7 @@ workflow Mutect2 { Boolean? run_funcotator Boolean run_funcotator_or_default = select_first([run_funcotator, false]) String? funco_reference_version - String? funco_data_sources_tar_gz + File? funco_data_sources_tar_gz String? funco_transcript_selection_mode File? funco_transcript_selection_list Array[String]? funco_annotation_defaults diff --git a/scripts/mutect2_wdl/mutect2_multi_sample.wdl b/scripts/mutect2_wdl/mutect2_multi_sample.wdl index 86b94ea3242..1f0b4fd0258 100644 --- a/scripts/mutect2_wdl/mutect2_multi_sample.wdl +++ b/scripts/mutect2_wdl/mutect2_multi_sample.wdl @@ -51,19 +51,19 @@ workflow Mutect2_Multi { # funcotator inputs Boolean? run_funcotator - String? reference_version - String? data_sources_tar_gz - String? transcript_selection_mode - Array[String]? transcript_selection_list - Array[String]? annotation_defaults - Array[String]? annotation_overrides + String? funco_reference_version + File? funco_data_sources_tar_gz + String? funco_transcript_selection_mode + File? funco_transcript_selection_list + Array[String]? funco_annotation_defaults + Array[String]? funco_annotation_overrides - File? gatk_override # runtime String gatk_docker String? oncotator_docker Int? preemptible_attempts + File? gatk_override scatter( row in pairs ) { # If the condition is true, variables inside the 'if' block retain their values outside the block. @@ -101,12 +101,13 @@ workflow Mutect2_Multi { sequence_source = sequence_source, default_config_file = default_config_file, run_funcotator = run_funcotator, - reference_version = reference_version, - data_sources_tar_gz = data_sources_tar_gz, - transcript_selection_mode = transcript_selection_mode, - transcript_selection_list = transcript_selection_list, - annotation_defaults = annotation_defaults, - annotation_overrides = annotation_overrides, + funco_reference_version = funco_reference_version, + funco_data_sources_tar_gz = funco_data_sources_tar_gz, + funco_transcript_selection_mode = funco_transcript_selection_mode, + funco_transcript_selection_list = funco_transcript_selection_list, + funco_annotation_defaults = funco_annotation_defaults, + funco_annotation_overrides = funco_annotation_overrides, + make_bamout = make_bamout, compress_vcfs = compress_vcfs, gatk_override = gatk_override, From f8a980bad32bfc8a370e83476e6efd1f6bb34a97 Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 15:18:05 -0400 Subject: [PATCH 05/15] Adding a little more to the integration test to make sure that MAF outputs have a header that includes custom fields. --- .../funcotator/mafOutput/CustomMafFuncotationCreator.java | 2 +- .../tools/funcotator/FuncotatorIntegrationTest.java | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java index 7db5c147964..2c67d847411 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java @@ -27,7 +27,7 @@ */ public class CustomMafFuncotationCreator { - final static List COUNT_FIELD_NAMES = Arrays.asList( + final public static List COUNT_FIELD_NAMES = Arrays.asList( MafOutputRendererConstants.FieldName_t_alt_count, MafOutputRendererConstants.FieldName_t_ref_count, MafOutputRendererConstants.FieldName_n_alt_count, diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index 441fade1eb7..5bfa9fb93a2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -16,6 +16,7 @@ import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection; import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation; import org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory; +import org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator; import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer; import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants; import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer; @@ -1076,7 +1077,10 @@ public void testNoVariantsProduceMaf() { final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), null); Assert.assertEquals(maf.getRecords().size(), 0); - // TODO: Check for the custom Maf fields + + // Double-check that the custom MAF fields are present. + Assert.assertTrue(CustomMafFuncotationCreator.COUNT_FIELD_NAMES.stream() + .allMatch(f -> maf.getAnnotations().contains(f))); } } From 6f63b777d9bc9dc19e83fa460bf285da09758a95 Mon Sep 17 00:00:00 2001 From: lichtens Date: Fri, 22 Jun 2018 15:27:20 -0400 Subject: [PATCH 06/15] Doc updates. --- scripts/mutect2_wdl/mutect2.wdl | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 994b70c7152..06cd1dea5f4 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -42,10 +42,18 @@ ## sequencing_center, sequence_source: metadata for Oncotator ## filter_oncotator_maf: Whether the MAF generated by oncotator should have the filtered variants removed. Default: true ## realignment_index_bundle: resource for FilterAlignmentArtifacts, which runs if and only if it is specified. Generated by BwaMemIndexImageCreator. +## +## Funcotator parameters (see Funcotator help for more details). ## funco_reference_version: "hg19" for hg19 or b37. "hg38" for hg38. Default: "hg19" -## funco_transcript_selection_list: -## TODO: Finish docs! +## funco_transcript_selection_list: Transcripts (one GENCODE ID per line) to give priority during selection process. +## funco_transcript_selection_mode: How to select transcripts in Funcotator. ALL, CANONICAL, or BEST_EFFECT +## funco_data_sources_tar_gz: Funcotator datasources tar gz file. Bucket location is recommended when running on the cloud. +## funco_annotation_defaults: Default values for annotations, when values are unspecified. Specified as :. For example: "Center:Broad" +## funco_annotation_overrides: Values for annotations, even when values are unspecified. Specified as :. For example: "Center:Broad" ## + +## TODO: Merge with mutect2_nio.wdl + ## Outputs : ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam ## file of reassembled reads if requested From 33dcbad2507a53275fde216fac44a0bfa2f2bd65 Mon Sep 17 00:00:00 2001 From: lichtens Date: Tue, 26 Jun 2018 09:52:44 -0400 Subject: [PATCH 07/15] Doc updates. --- scripts/mutect2_wdl/mutect2.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 06cd1dea5f4..3660f12ec59 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -1077,6 +1077,7 @@ task FuncotateMaf { runtime { docker: gatk_docker + bootDiskSizeGb: 12 memory: machine_mem + " MB" disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" preemptible: select_first([preemptible_attempts, 3]) From 129a968d9a61de8de0018d4861d6452a96d7bf95 Mon Sep 17 00:00:00 2001 From: lichtens Date: Wed, 27 Jun 2018 09:39:20 -0400 Subject: [PATCH 08/15] - Fixes #4952 --- .../gencode/GencodeFuncotationFactory.java | 40 +- .../GencodeFuncotationFactoryUnitTest.java | 80 ++++ .../gencode.v19.CNTN4.annotation.gtf | 445 ++++++++++++++++++ .../gencode.v19.CNTN4.pc_transcripts.dict | 12 + .../gencode.v19.CNTN4.pc_transcripts.fasta | 22 + ...gencode.v19.CNTN4.pc_transcripts.fasta.fai | 11 + 6 files changed, 596 insertions(+), 14 deletions(-) create mode 100755 src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.annotation.gtf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.dict create mode 100755 src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta.fai diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java index 4c90029d65a..14fe72d426e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java @@ -264,11 +264,18 @@ protected List createDefaultFuncotationsOnVariant( final VariantCon return funcotationList; } - private List createAndFilterGencodeFuncotationsByTranscript(final VariantContext variant, final ReferenceContext referenceContext, final Allele altAllele, final GencodeGtfGeneFeature feature) { - // By this point we know the feature type is correct, so we cast it: - final List gencodeFuncotationList = createFuncotationsHelper(variant, altAllele, feature, referenceContext); + private List createAndFilterGencodeFuncotationsByTranscripts(final VariantContext variant, final ReferenceContext referenceContext, final Allele altAllele, final List gencodeGtfGeneFeatures) { + + // If the variant overlaps more than one gene, we need to create a flat list of the transcripts in all genes. + final List gencodeFuncotationList = gencodeGtfGeneFeatures.stream() + .map(f -> createFuncotationsHelper(variant, altAllele, f, referenceContext)) + .flatMap(List::stream).collect(Collectors.toList()); + + // Sort and filter the transcript list sortAndFilterInPlace(gencodeFuncotationList); + // Grab the best choice in the case of transcript selection modes other than ALL. The selection will be the first + // transcript in the list. if ((this.transcriptSelectionMode != TranscriptSelectionMode.ALL) && (gencodeFuncotationList.size() > 0)) { return Collections.singletonList(gencodeFuncotationList.get(0)); } @@ -304,27 +311,32 @@ private void populateOtherTranscriptsMapForFuncotation(final List createFuncotationsOnVariant(final VariantContext variant, final ReferenceContext referenceContext, final List featureList) { + @Override + protected List createFuncotationsOnVariant(final VariantContext variant, final ReferenceContext referenceContext, final List geneFeatureList) { final List outputFuncotations = new ArrayList<>(); // If we have features we need to annotate, go through them and create annotations: - if ( featureList.size() > 0 ) { + if ( geneFeatureList.size() > 0 ) { for ( final Allele altAllele : variant.getAlternateAlleles() ) { - for ( final Feature feature : featureList ) { - if ( (feature != null) ) { - // By this point we know the feature type is correct, so we cast it: - final List gencodeFuncotationList = createAndFilterGencodeFuncotationsByTranscript(variant, referenceContext, altAllele, (GencodeGtfGeneFeature) feature); + // At this point we know the feature list is composed of GTF Gene Features + final List gencodeGtfGeneFeatures = geneFeatureList.stream() + .filter(g -> g != null) + .map(g -> (GencodeGtfGeneFeature) g) + .collect(Collectors.toList()); - // Add the filtered funcotations here: - outputFuncotations.addAll(gencodeFuncotationList); - } - } + // By this point we know the feature type is correct, so we cast it: + final List gencodeFuncotationList = createAndFilterGencodeFuncotationsByTranscripts(variant, referenceContext, altAllele, gencodeGtfGeneFeatures); + + // Add the filtered funcotations here: + outputFuncotations.addAll(gencodeFuncotationList); } } else { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java index e5525336094..ddea846fd66 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java @@ -9,6 +9,7 @@ import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureReader; import htsjdk.tribble.annotation.Strand; +import htsjdk.tribble.readers.LineIterator; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; @@ -29,7 +30,9 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.io.BufferedInputStream; import java.io.File; +import java.io.FileInputStream; import java.io.IOException; import java.util.*; import java.util.stream.Collectors; @@ -39,6 +42,9 @@ * Created by jonn on 9/1/17. */ public class GencodeFuncotationFactoryUnitTest extends GATKBaseTest { + // Gencode v19 + private static final String CNTN4_GENCODE_ANNOTATIONS_FILE_NAME = toolsTestDir + "funcotator/gencode.v19.CNTN4.annotation.gtf"; + private static final String CNTN4_GENCODE_TRANSCRIPT_FASTA_FILE = toolsTestDir + "funcotator/gencode.v19.CNTN4.pc_transcripts.fasta"; //================================================================================================================== // Multi-Test Static Variables: @@ -1513,4 +1519,78 @@ public void testSortingOfUserRequestedTranscripts(final List Assert.assertEquals(gencodeFuncotations.get(0).getAnnotationTranscript(), gtFirstTranscript, " Failed on " + transcriptSelectionMode.toString()); } } + + + /** + * This test (of {@link GencodeFuncotationFactory#createFuncotationsOnVariant}) makes sure that if multiple gene features are detected, there is still only one transcript returned + * when in the BEST_EFFECT or CANONICAL selection mode. And tests that ALL has multiple transcripts returned. + * The selected test data will ensure that ALL returns more than one transcript. + * @throws IOException + */ + @Test + public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOException { + final GencodeGtfCodec gencodeGtfCodec = new GencodeGtfCodec(); + Assert.assertTrue(gencodeGtfCodec.canDecode(CNTN4_GENCODE_ANNOTATIONS_FILE_NAME)); + + final List gencodeFeatures = new ArrayList<>(); + + // Note the "chr" here to make this work. + final SimpleInterval variantInterval = new SimpleInterval("chr3", 2944600, 2944600); + final ReferenceContext referenceContext = new ReferenceContext(refDataSourceHg19Ch3, variantInterval); + final VariantContext vc = new VariantContextBuilder() + .alleles(Arrays.asList(Allele.create("A", true), Allele.create("AT", false))) + .chr(variantInterval.getContig()).start(variantInterval.getStart()).stop(variantInterval.getEnd()) + .make(); + + try (BufferedInputStream bufferedInputStream = + new BufferedInputStream( + new FileInputStream(CNTN4_GENCODE_ANNOTATIONS_FILE_NAME) + ) + ) { + // Get the line iterator: + final LineIterator lineIterator = gencodeGtfCodec.makeSourceFromStream(bufferedInputStream); + + // Get the header (required for the read to work correctly): + gencodeGtfCodec.readHeader(lineIterator); + + while (lineIterator.hasNext()) { + gencodeFeatures.add(gencodeGtfCodec.decode(lineIterator)); + } + Assert.assertTrue(gencodeFeatures.size() > 1); + } + + try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory( + IOUtils.getPath(CNTN4_GENCODE_TRANSCRIPT_FASTA_FILE), + "VERSION", + GencodeFuncotationFactory.DEFAULT_NAME, + TranscriptSelectionMode.CANONICAL, + Collections.emptySet(), + new LinkedHashMap<>(), true)) { + final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); + Assert.assertEquals(gencodeFuncotations.size(), 1); + } + + try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory( + IOUtils.getPath(CNTN4_GENCODE_TRANSCRIPT_FASTA_FILE), + "VERSION", + GencodeFuncotationFactory.DEFAULT_NAME, + TranscriptSelectionMode.BEST_EFFECT, + Collections.emptySet(), + new LinkedHashMap<>(), true)) { + final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); + Assert.assertEquals(gencodeFuncotations.size(), 1); + } + + try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory( + IOUtils.getPath(CNTN4_GENCODE_TRANSCRIPT_FASTA_FILE), + "VERSION", + GencodeFuncotationFactory.DEFAULT_NAME, + TranscriptSelectionMode.ALL, + Collections.emptySet(), + new LinkedHashMap<>(), true)) { + final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); + Assert.assertTrue(gencodeFuncotations.size() > 1); + } + + } } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.annotation.gtf b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.annotation.gtf new file mode 100755 index 00000000000..00f292d398b --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.annotation.gtf @@ -0,0 +1,445 @@ +##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74) +##provider: GENCODE +##contact: gencode@sanger.ac.uk +##format: gtf +##date: 2013-12-06 +chr3 HAVANA gene 2140497 3099645 . + . gene_id "ENSG00000144619.10"; transcript_id "ENSG00000144619.10"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4"; level 1; havana_gene "OTTHUMG00000119031.9"; +chr3 HAVANA transcript 2140497 2787371 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA exon 2140497 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 1; exon_id "ENSE00001762594.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA exon 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 2; exon_id "ENSE00001528800.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA exon 2787206 2787371 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 5; exon_id "ENSE00001634536.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA CDS 2787206 2787371 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; exon_number 5; exon_id "ENSE00001634536.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA UTR 2140497 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA UTR 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000422330.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-004"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337401.2"; +chr3 HAVANA transcript 2140550 3084662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2140550 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 1; exon_id "ENSE00001742756.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2140958 2141333 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 2; exon_id "ENSE00001601880.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 3; exon_id "ENSE00001528800.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 5; exon_id "ENSE00003595035.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 5; exon_id "ENSE00003595035.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 6; exon_id "ENSE00003558658.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2787206 2787381 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 6; exon_id "ENSE00003558658.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 7; exon_id "ENSE00003530275.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2861170 2861265 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 7; exon_id "ENSE00003530275.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 8; exon_id "ENSE00003683442.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2908436 2908633 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 8; exon_id "ENSE00003683442.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 9; exon_id "ENSE00003564209.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA CDS 2928724 2928767 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 9; exon_id "ENSE00003564209.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA stop_codon 2928768 2928770 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 9; exon_id "ENSE00003564209.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 10; exon_id "ENSE00003594764.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 11; exon_id "ENSE00003611164.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 12; exon_id "ENSE00003690093.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 13; exon_id "ENSE00003634587.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 14; exon_id "ENSE00003495004.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3072542 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 15; exon_id "ENSE00001741935.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 16; exon_id "ENSE00003648372.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 17; exon_id "ENSE00003615222.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 18; exon_id "ENSE00003525538.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 19; exon_id "ENSE00003609673.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 20; exon_id "ENSE00003514183.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA exon 3084661 3084662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; exon_number 21; exon_id "ENSE00001758800.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2140550 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2140958 2141333 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2928768 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3072542 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA UTR 3084661 3084662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427741.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "CNTN4-003"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337400.1"; +chr3 HAVANA transcript 2140572 2778007 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2140572 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 1; exon_id "ENSE00001784079.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2142242 2142323 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 2; exon_id "ENSE00001626659.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2304030 2304114 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 3; exon_id "ENSE00001701778.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 4; exon_id "ENSE00001528800.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 5; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 5; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 5; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA exon 2777899 2778007 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 6; exon_id "ENSE00001624904.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA CDS 2777899 2778007 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; exon_number 6; exon_id "ENSE00001624904.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA UTR 2140572 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA UTR 2142242 2142323 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA UTR 2304030 2304114 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA UTR 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000455083.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-005"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337402.2"; +chr3 HAVANA transcript 2140610 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2140610 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 1; exon_id "ENSE00001707604.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2142242 2142323 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 2; exon_id "ENSE00001626659.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 3; exon_id "ENSE00001528800.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 4; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 5; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 5; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 6; exon_id "ENSE00003558658.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2787206 2787381 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 6; exon_id "ENSE00003558658.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 7; exon_id "ENSE00003530275.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2861170 2861265 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 7; exon_id "ENSE00003530275.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 8; exon_id "ENSE00003683442.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2908436 2908633 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 8; exon_id "ENSE00003683442.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 9; exon_id "ENSE00003649288.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2924829 2924931 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 9; exon_id "ENSE00003649288.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 10; exon_id "ENSE00003663088.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2928724 2928908 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 10; exon_id "ENSE00003663088.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 11; exon_id "ENSE00003474195.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2942369 2942505 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 11; exon_id "ENSE00003474195.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 12; exon_id "ENSE00003544489.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 12; exon_id "ENSE00003544489.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 13; exon_id "ENSE00003694230.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 13; exon_id "ENSE00003694230.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 14; exon_id "ENSE00003655493.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 14; exon_id "ENSE00003655493.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 15; exon_id "ENSE00003681466.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 15; exon_id "ENSE00003681466.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 16; exon_id "ENSE00003529385.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 16; exon_id "ENSE00003529385.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 17; exon_id "ENSE00003677554.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 17; exon_id "ENSE00003677554.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 18; exon_id "ENSE00003490499.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 18; exon_id "ENSE00003490499.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 19; exon_id "ENSE00003544849.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 19; exon_id "ENSE00003544849.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 20; exon_id "ENSE00003666648.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 20; exon_id "ENSE00003666648.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 21; exon_id "ENSE00003502342.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 21; exon_id "ENSE00003502342.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 22; exon_id "ENSE00003595816.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 22; exon_id "ENSE00003595816.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 23; exon_id "ENSE00003694585.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 23; exon_id "ENSE00003694585.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 24; exon_id "ENSE00003553752.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 24; exon_id "ENSE00003553752.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA exon 3097804 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 25; exon_id "ENSE00003503077.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 25; exon_id "ENSE00003503077.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; exon_number 25; exon_id "ENSE00003503077.1"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA UTR 2140610 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA UTR 2142242 2142323 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA UTR 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA UTR 3097902 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000418658.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-009"; level 2; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337405.2"; +chr3 HAVANA transcript 2140612 2141457 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000490876.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "CNTN4-007"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337404.1"; +chr3 HAVANA exon 2140612 2140662 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000490876.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "CNTN4-007"; exon_number 1; exon_id "ENSE00001810091.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337404.1"; +chr3 HAVANA exon 2140958 2141457 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000490876.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "CNTN4-007"; exon_number 2; exon_id "ENSE00001876945.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337404.1"; +chr3 HAVANA transcript 2280513 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2280513 2280752 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 1; exon_id "ENSE00001441377.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 2; exon_id "ENSE00001528800.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 3; exon_id "ENSE00003620663.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 5; exon_id "ENSE00003558658.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2787206 2787381 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 5; exon_id "ENSE00003558658.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 6; exon_id "ENSE00003530275.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2861170 2861265 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 6; exon_id "ENSE00003530275.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 7; exon_id "ENSE00003683442.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2908436 2908633 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 7; exon_id "ENSE00003683442.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 8; exon_id "ENSE00003649288.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2924829 2924931 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 8; exon_id "ENSE00003649288.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 9; exon_id "ENSE00003663088.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2928724 2928908 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 9; exon_id "ENSE00003663088.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 10; exon_id "ENSE00003474195.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2942369 2942505 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 10; exon_id "ENSE00003474195.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 11; exon_id "ENSE00003544489.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 11; exon_id "ENSE00003544489.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 12; exon_id "ENSE00003694230.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 12; exon_id "ENSE00003694230.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 13; exon_id "ENSE00003655493.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 13; exon_id "ENSE00003655493.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 14; exon_id "ENSE00003681466.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 14; exon_id "ENSE00003681466.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 15; exon_id "ENSE00003529385.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 15; exon_id "ENSE00003529385.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 16; exon_id "ENSE00003677554.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 16; exon_id "ENSE00003677554.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 17; exon_id "ENSE00003490499.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 17; exon_id "ENSE00003490499.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 18; exon_id "ENSE00003544849.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 18; exon_id "ENSE00003544849.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 19; exon_id "ENSE00003666648.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 19; exon_id "ENSE00003666648.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 20; exon_id "ENSE00003502342.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 20; exon_id "ENSE00003502342.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 21; exon_id "ENSE00003595816.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 21; exon_id "ENSE00003595816.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 22; exon_id "ENSE00003694585.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 22; exon_id "ENSE00003694585.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 23; exon_id "ENSE00003553752.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 23; exon_id "ENSE00003553752.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA exon 3097804 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 24; exon_id "ENSE00003503077.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 24; exon_id "ENSE00003503077.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; exon_number 24; exon_id "ENSE00003503077.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA UTR 2280513 2280752 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA UTR 2380862 2380917 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA UTR 3097902 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397461.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239236.2"; +chr3 HAVANA transcript 2553034 3030697 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2553034 2553381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 1; exon_id "ENSE00001694342.2"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 2; exon_id "ENSE00003644400.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 3; exon_id "ENSE00003546944.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 4; exon_id "ENSE00003509920.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 5; exon_id "ENSE00003670352.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 6; exon_id "ENSE00003509889.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 7; exon_id "ENSE00003506678.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 8; exon_id "ENSE00003625912.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 9; exon_id "ENSE00003594764.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 10; exon_id "ENSE00003611164.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 11; exon_id "ENSE00003690093.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA exon 3030029 3030697 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000438282.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-006"; exon_number 12; exon_id "ENSE00001801709.1"; level 2; tag "alternative_5_UTR"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337403.3"; +chr3 HAVANA transcript 2553273 3079360 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2553273 2553381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 1; exon_id "ENSE00001683142.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 2; exon_id "ENSE00003644400.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 3; exon_id "ENSE00003546944.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 4; exon_id "ENSE00003509920.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 5; exon_id "ENSE00003670352.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 6; exon_id "ENSE00003509889.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 7; exon_id "ENSE00003506678.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 8; exon_id "ENSE00003625912.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 9; exon_id "ENSE00003594764.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 10; exon_id "ENSE00003611164.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 11; exon_id "ENSE00003690093.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 12; exon_id "ENSE00003634587.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 13; exon_id "ENSE00003495004.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 14; exon_id "ENSE00003510685.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 15; exon_id "ENSE00003648372.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA exon 3078863 3079360 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000430505.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-010"; exon_number 16; exon_id "ENSE00001681409.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337406.5"; +chr3 HAVANA transcript 2553354 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA exon 2553354 2553381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 1; exon_id "ENSE00001677707.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA exon 2613100 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 2; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 2; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 2; exon_id "ENSE00003620663.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA exon 2671210 2671263 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 3; exon_id "ENSE00001792206.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA CDS 2671210 2671263 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 3; exon_id "ENSE00001792206.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 4; exon_id "ENSE00003595035.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 5; exon_id "ENSE00003494744.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA CDS 2787206 2787381 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; exon_number 5; exon_id "ENSE00003494744.1"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA UTR 2553354 2553381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 HAVANA UTR 2613100 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000434053.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-011"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337449.6"; +chr3 ENSEMBL transcript 2613025 3099645 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2613025 2613242 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 1; exon_id "ENSE00001788467.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2613188 2613242 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 1; exon_id "ENSE00001788467.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL start_codon 2613188 2613190 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 1; exon_id "ENSE00001788467.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2777899 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 2; exon_id "ENSE00003595035.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2777899 2778025 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 2; exon_id "ENSE00003595035.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2787206 2787381 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 3; exon_id "ENSE00003558658.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2787206 2787381 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 3; exon_id "ENSE00003558658.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2861170 2861265 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 4; exon_id "ENSE00003530275.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2861170 2861265 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 4; exon_id "ENSE00003530275.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 5; exon_id "ENSE00003683442.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2908436 2908633 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 5; exon_id "ENSE00003683442.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 6; exon_id "ENSE00003649288.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2924829 2924931 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 6; exon_id "ENSE00003649288.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 7; exon_id "ENSE00003663088.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2928724 2928908 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 7; exon_id "ENSE00003663088.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 8; exon_id "ENSE00003474195.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2942369 2942505 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 8; exon_id "ENSE00003474195.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 9; exon_id "ENSE00003544489.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 9; exon_id "ENSE00003544489.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 10; exon_id "ENSE00003694230.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 10; exon_id "ENSE00003694230.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 11; exon_id "ENSE00003655493.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 11; exon_id "ENSE00003655493.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 12; exon_id "ENSE00003681466.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 12; exon_id "ENSE00003681466.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 13; exon_id "ENSE00003529385.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 13; exon_id "ENSE00003529385.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 14; exon_id "ENSE00003677554.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 14; exon_id "ENSE00003677554.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 15; exon_id "ENSE00003490499.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 15; exon_id "ENSE00003490499.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 16; exon_id "ENSE00003544849.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 16; exon_id "ENSE00003544849.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 17; exon_id "ENSE00003666648.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 17; exon_id "ENSE00003666648.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 18; exon_id "ENSE00003502342.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 18; exon_id "ENSE00003502342.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 19; exon_id "ENSE00003595816.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 19; exon_id "ENSE00003595816.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 20; exon_id "ENSE00003694585.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 20; exon_id "ENSE00003694585.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 21; exon_id "ENSE00003553752.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 21; exon_id "ENSE00003553752.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3097804 3099645 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 22; exon_id "ENSE00001419282.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 22; exon_id "ENSE00001419282.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; exon_number 22; exon_id "ENSE00001419282.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 2613025 2613187 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 3097902 3099645 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000427331.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-202"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS43041.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 HAVANA transcript 2777557 2787311 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000480113.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-012"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337450.1"; +chr3 HAVANA exon 2777557 2778025 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000480113.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-012"; exon_number 1; exon_id "ENSE00001862393.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337450.1"; +chr3 HAVANA exon 2787206 2787311 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000480113.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-012"; exon_number 2; exon_id "ENSE00001914221.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337450.1"; +chr3 ENSEMBL transcript 2908102 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2908102 2908185 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 1; exon_id "ENSE00002274305.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 2; exon_id "ENSE00003509889.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 3; exon_id "ENSE00003551068.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2924834 2924931 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 3; exon_id "ENSE00003551068.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL start_codon 2924834 2924836 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 3; exon_id "ENSE00003551068.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 4; exon_id "ENSE00003663088.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2928724 2928908 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 4; exon_id "ENSE00003663088.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 5; exon_id "ENSE00003474195.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2942369 2942505 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 5; exon_id "ENSE00003474195.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 6; exon_id "ENSE00003544489.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 6; exon_id "ENSE00003544489.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 7; exon_id "ENSE00003694230.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 7; exon_id "ENSE00003694230.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 8; exon_id "ENSE00003655493.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 8; exon_id "ENSE00003655493.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 9; exon_id "ENSE00003681466.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 9; exon_id "ENSE00003681466.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 10; exon_id "ENSE00003529385.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 10; exon_id "ENSE00003529385.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 11; exon_id "ENSE00003677554.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 11; exon_id "ENSE00003677554.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 12; exon_id "ENSE00003490499.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 12; exon_id "ENSE00003490499.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 13; exon_id "ENSE00003544849.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 13; exon_id "ENSE00003544849.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 14; exon_id "ENSE00003666648.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 14; exon_id "ENSE00003666648.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 15; exon_id "ENSE00003502342.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 15; exon_id "ENSE00003502342.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 16; exon_id "ENSE00003595816.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 16; exon_id "ENSE00003595816.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 17; exon_id "ENSE00003694585.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 17; exon_id "ENSE00003694585.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 18; exon_id "ENSE00003553752.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 18; exon_id "ENSE00003553752.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3097804 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 19; exon_id "ENSE00001528738.2"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 19; exon_id "ENSE00001528738.2"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; exon_number 19; exon_id "ENSE00001528738.2"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 2908102 2908185 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 2924829 2924833 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 3097902 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000358480.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000119031.9"; +chr3 HAVANA transcript 2908104 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473058.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-013"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337451.1"; +chr3 HAVANA exon 2908104 2908185 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473058.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-013"; exon_number 1; exon_id "ENSE00001920912.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337451.1"; +chr3 HAVANA exon 2908436 2908633 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473058.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-013"; exon_number 2; exon_id "ENSE00003509889.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337451.1"; +chr3 HAVANA exon 2924829 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473058.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-013"; exon_number 3; exon_id "ENSE00003506678.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337451.1"; +chr3 HAVANA exon 2928724 2928908 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473058.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-013"; exon_number 4; exon_id "ENSE00003625912.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337451.1"; +chr3 HAVANA transcript 2924423 2928779 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473173.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-014"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337452.1"; +chr3 HAVANA exon 2924423 2924931 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473173.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-014"; exon_number 1; exon_id "ENSE00001926274.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337452.1"; +chr3 HAVANA exon 2928724 2928779 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473173.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-014"; exon_number 2; exon_id "ENSE00001929016.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337452.1"; +chr3 HAVANA transcript 2933899 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 2933899 2933944 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 1; exon_id "ENSE00001528739.2"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 2942369 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 2; exon_id "ENSE00003478415.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 2942413 2942505 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 2; exon_id "ENSE00003478415.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA start_codon 2942413 2942415 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 2; exon_id "ENSE00003478415.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 3; exon_id "ENSE00003544489.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 3; exon_id "ENSE00003544489.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 4; exon_id "ENSE00003694230.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 4; exon_id "ENSE00003694230.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 5; exon_id "ENSE00003655493.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 5; exon_id "ENSE00003655493.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 6; exon_id "ENSE00003681466.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 6; exon_id "ENSE00003681466.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 7; exon_id "ENSE00003529385.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 7; exon_id "ENSE00003529385.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 8; exon_id "ENSE00003677554.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 8; exon_id "ENSE00003677554.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 9; exon_id "ENSE00003490499.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 9; exon_id "ENSE00003490499.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 10; exon_id "ENSE00003544849.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 10; exon_id "ENSE00003544849.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 11; exon_id "ENSE00003666648.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 11; exon_id "ENSE00003666648.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 12; exon_id "ENSE00003502342.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 12; exon_id "ENSE00003502342.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 13; exon_id "ENSE00003595816.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 13; exon_id "ENSE00003595816.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 14; exon_id "ENSE00003694585.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 14; exon_id "ENSE00003694585.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 15; exon_id "ENSE00003553752.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 15; exon_id "ENSE00003553752.1"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA exon 3097804 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 16; exon_id "ENSE00001528738.2"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 16; exon_id "ENSE00001528738.2"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; exon_number 16; exon_id "ENSE00001528738.2"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA UTR 2933899 2933944 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA UTR 2942369 2942412 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 HAVANA UTR 3097902 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000397459.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-002"; level 2; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000239237.2"; +chr3 ENSEMBL transcript 2942366 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2942366 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 1; exon_id "ENSE00002318066.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2942413 2942505 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 1; exon_id "ENSE00002318066.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL start_codon 2942413 2942415 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 1; exon_id "ENSE00002318066.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 2; exon_id "ENSE00003544489.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 2; exon_id "ENSE00003544489.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 3; exon_id "ENSE00003694230.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 3; exon_id "ENSE00003694230.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 4; exon_id "ENSE00003655493.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3030029 3030156 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 4; exon_id "ENSE00003655493.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3067786 3067961 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 5; exon_id "ENSE00003681466.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3067786 3067961 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 5; exon_id "ENSE00003681466.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3072539 3072659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 6; exon_id "ENSE00003529385.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3072539 3072659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 6; exon_id "ENSE00003529385.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3076316 3076474 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 7; exon_id "ENSE00003677554.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3076316 3076474 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 7; exon_id "ENSE00003677554.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3078863 3079012 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 8; exon_id "ENSE00003490499.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3078863 3079012 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 8; exon_id "ENSE00003490499.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3080617 3080687 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 9; exon_id "ENSE00003544849.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3080617 3080687 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 9; exon_id "ENSE00003544849.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3081721 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 10; exon_id "ENSE00003666648.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3081721 3081955 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 10; exon_id "ENSE00003666648.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 11; exon_id "ENSE00003502342.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3083994 3084106 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 11; exon_id "ENSE00003502342.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 12; exon_id "ENSE00003595816.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3084661 3084847 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 12; exon_id "ENSE00003595816.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 13; exon_id "ENSE00003694585.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3085276 3085388 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 13; exon_id "ENSE00003694585.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 14; exon_id "ENSE00003553752.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3095491 3095659 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 14; exon_id "ENSE00003553752.1"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL exon 3097804 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 15; exon_id "ENSE00001528738.2"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL CDS 3097804 3097901 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 15; exon_id "ENSE00001528738.2"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL stop_codon 3097902 3097904 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; exon_number 15; exon_id "ENSE00001528738.2"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 2942366 2942412 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 ENSEMBL UTR 3097902 3098039 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000448906.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CNTN4-203"; level 3; tag "basic"; tag "CCDS"; ccdsid "CCDS2558.1"; havana_gene "OTTHUMG00000119031.9"; +chr3 HAVANA transcript 2942395 2969315 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA exon 2942395 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 1; exon_id "ENSE00001846877.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA CDS 2942395 2942505 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 1; exon_id "ENSE00001846877.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 2; exon_id "ENSE00003544489.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA CDS 2944560 2944689 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 2; exon_id "ENSE00003544489.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 3; exon_id "ENSE00003694230.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA CDS 2967313 2967463 . + 2 gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 3; exon_id "ENSE00003694230.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA exon 2968982 2969315 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 4; exon_id "ENSE00001885658.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA CDS 2968982 2969018 . + 1 gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 4; exon_id "ENSE00001885658.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA stop_codon 2969019 2969021 . + 0 gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; exon_number 4; exon_id "ENSE00001885658.1"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA UTR 2969019 2969315 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000473845.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "protein_coding"; transcript_status "PUTATIVE"; transcript_name "CNTN4-015"; level 1; tag "mRNA_start_NF"; tag "cds_start_NF"; tag "exp_conf"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337472.2"; +chr3 HAVANA transcript 2942398 3040828 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA exon 2942398 2942505 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; exon_number 1; exon_id "ENSE00001886639.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA exon 2944560 2944689 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; exon_number 2; exon_id "ENSE00003611164.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA exon 2967313 2967463 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; exon_number 3; exon_id "ENSE00003690093.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA exon 3030029 3030156 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; exon_number 4; exon_id "ENSE00003634587.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA exon 3040732 3040828 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000475817.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "CNTN4-017"; exon_number 5; exon_id "ENSE00001861750.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337471.1"; +chr3 HAVANA transcript 3081308 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3081308 3081955 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 1; exon_id "ENSE00001880444.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3083994 3084106 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 2; exon_id "ENSE00003514183.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3084661 3084847 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 3; exon_id "ENSE00003681457.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3085276 3085388 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 4; exon_id "ENSE00003486548.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3095491 3095659 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 5; exon_id "ENSE00003667179.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA exon 3097804 3099637 . + . gene_id "ENSG00000144619.10"; transcript_id "ENST00000484686.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CNTN4"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "CNTN4-016"; exon_number 6; exon_id "ENSE00003485292.1"; level 2; havana_gene "OTTHUMG00000119031.9"; havana_transcript "OTTHUMT00000337454.1"; +chr3 HAVANA gene 2152093 2185925 . - . gene_id "ENSG00000227588.2"; transcript_id "ENSG00000227588.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "CNTN4-AS2"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "CNTN4-AS2"; level 1; havana_gene "OTTHUMG00000156185.2"; +chr3 HAVANA transcript 2152093 2185925 . - . gene_id "ENSG00000227588.2"; transcript_id "ENST00000447256.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "CNTN4-AS2"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "CNTN4-AS2-001"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000156185.2"; havana_transcript "OTTHUMT00000343338.2"; +chr3 HAVANA exon 2185814 2185925 . - . gene_id "ENSG00000227588.2"; transcript_id "ENST00000447256.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "CNTN4-AS2"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "CNTN4-AS2-001"; exon_number 1; exon_id "ENSE00001592168.2"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000156185.2"; havana_transcript "OTTHUMT00000343338.2"; +chr3 HAVANA exon 2174045 2174134 . - . gene_id "ENSG00000227588.2"; transcript_id "ENST00000447256.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "CNTN4-AS2"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "CNTN4-AS2-001"; exon_number 2; exon_id "ENSE00001602338.2"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000156185.2"; havana_transcript "OTTHUMT00000343338.2"; +chr3 HAVANA exon 2152093 2152316 . - . gene_id "ENSG00000227588.2"; transcript_id "ENST00000447256.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "CNTN4-AS2"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "CNTN4-AS2-001"; exon_number 3; exon_id "ENSE00001664369.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000156185.2"; havana_transcript "OTTHUMT00000343338.2"; +chr3 HAVANA gene 3080717 3102829 . - . gene_id "ENSG00000237990.2"; transcript_id "ENSG00000237990.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "NOVEL"; transcript_name "CNTN4-AS1"; level 2; havana_gene "OTTHUMG00000154875.3"; +chr3 HAVANA transcript 3080717 3102829 . - . gene_id "ENSG00000237990.2"; transcript_id "ENST00000442749.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CNTN4-AS1-001"; level 2; tag "basic"; havana_gene "OTTHUMG00000154875.3"; havana_transcript "OTTHUMT00000337448.3"; +chr3 HAVANA exon 3102751 3102829 . - . gene_id "ENSG00000237990.2"; transcript_id "ENST00000442749.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CNTN4-AS1-001"; exon_number 1; exon_id "ENSE00001798518.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000154875.3"; havana_transcript "OTTHUMT00000337448.3"; +chr3 HAVANA exon 3084597 3084697 . - . gene_id "ENSG00000237990.2"; transcript_id "ENST00000442749.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CNTN4-AS1-001"; exon_number 2; exon_id "ENSE00001657739.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000154875.3"; havana_transcript "OTTHUMT00000337448.3"; +chr3 HAVANA exon 3082729 3082838 . - . gene_id "ENSG00000237990.2"; transcript_id "ENST00000442749.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CNTN4-AS1-001"; exon_number 3; exon_id "ENSE00001803308.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000154875.3"; havana_transcript "OTTHUMT00000337448.3"; +chr3 HAVANA exon 3080717 3082066 . - . gene_id "ENSG00000237990.2"; transcript_id "ENST00000442749.2"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CNTN4-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CNTN4-AS1-001"; exon_number 4; exon_id "ENSE00001747179.2"; level 2; tag "basic"; havana_gene "OTTHUMG00000154875.3"; havana_transcript "OTTHUMT00000337448.3"; diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.dict b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.dict new file mode 100644 index 00000000000..b7667444e68 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.dict @@ -0,0 +1,12 @@ +@HD VN:1.5 +@SQ SN:ENST00000422330.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337401.2|CNTN4-004|CNTN4|658|UTR5:1-310|CDS:311-658| LN:658 M5:6c0429f1665fae2ff13236cd08494f00 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000427741.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337400.1|CNTN4-003|CNTN4|3040|UTR5:1-633|CDS:634-1332|UTR3:1333-3040| LN:3040 M5:aae23b0d76c55fe9aee00034ff2461b0 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000455083.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337402.2|CNTN4-005|CNTN4|566|UTR5:1-402|CDS:403-566| LN:566 M5:3dd124e4b79f9d14e5fd0fa1d270efd7 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000418658.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337405.2|CNTN4-009|CNTN4|5093|UTR5:1-279|CDS:280-3360|UTR3:3361-5093| LN:5093 M5:92027ee4fef7213ef86b51cc95afe11a UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000397461.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239236.2|CNTN4-001|CNTN4|5198|UTR5:1-384|CDS:385-3465|UTR3:3466-5198| LN:5198 M5:859c718b2179be9589fb8a96f64f68fa UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000434053.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337449.6|CNTN4-011|CNTN4|528|UTR5:1-116|CDS:117-528| LN:528 M5:55f6937dbe2f937f4475c252f3fd399e UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000427331.1|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-202|CNTN4|4985|UTR5:1-163|CDS:164-3244|UTR3:3245-4985| LN:4985 M5:bf31cc63aaf747e143442300eb9dd4b5 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000358480.3|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-201|CNTN4|2846|UTR5:1-287|CDS:288-2711|UTR3:2712-2846| LN:2846 M5:08dac99f1fee8753a5286e4fd275dc50 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000397459.2|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239237.2|CNTN4-002|CNTN4|2322|UTR5:1-90|CDS:91-2187|UTR3:2188-2322| LN:2322 M5:89c7a1ed253e226824750a889ae1ab0f UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000448906.2|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-203|CNTN4|2279|UTR5:1-47|CDS:48-2144|UTR3:2145-2279| LN:2279 M5:c43f528423eaa129e9c9f00876a738cf UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta +@SQ SN:ENST00000473845.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337472.2|CNTN4-015|CNTN4|726|CDS:1-432|UTR3:433-726| LN:726 M5:eb0381c47655b23574b90f884a232e98 UR:file:/home/lichtens/IdeaProjects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta new file mode 100755 index 00000000000..1f4d5a5cdff --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta @@ -0,0 +1,22 @@ +>ENST00000422330.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337401.2|CNTN4-004|CNTN4|658|UTR5:1-310|CDS:311-658| +AGCCGCCGCGAGCGCCGGGAGGGAGGGCAGCGCCGCGCCAGACGGAGCCCGGGGTTCGACGCCAGGATTGGCTGCAAGTAGGGAGCTTTCGCCGCCGCCCCGGGCCCCTCGGACTGTGCCGGCGCCGCACCCGAGGCTCTCGCCAGCCCGGCGCCCCGGTGCTGAGGAATCATTGACATAGAGTAACTCCACAGCATGTGTCTTCAAGAGCTTCCCTAAAAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTT +>ENST00000427741.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337400.1|CNTN4-003|CNTN4|3040|UTR5:1-633|CDS:634-1332|UTR3:1333-3040| +GTTCGACGCCAGGATTGGCTGCAAGTAGGGAGCTTTCGCCGCCGCCCCGGGCCCCTCGGACTGTGCCGGCGCCGCACCCGAGGCTCTCGCCAGCCCGGCGCCCCGGTGCTGAGCCGGAAAATAAGTTTGTTGCGCTGCGAGGCAGCCACAAAACAAGGAACCGAGAGCCCGGAATGCTGCGGGAAGCCTTCAAGTCAGCTCCTCCGACTGGTTCGGGCTACTGCCCCCTCTCCGTGCGCCCTGGCCTCTGGCGCCGGGTTCCCGGCGGGGCTTTTCTTCTGACAGCCCAGTCACAGCCCGCAGCAGAGGGACGCGAACCTGGGGAGTGGAGGGACCTGGGACTAAAGGAACAGGAGCCCGTAGCCGTGGTGGAAGGAGCCGCGTGGAGACGGAGGCTGATGTCTGTGGCGCCCGCTGGGTGCCGGGCTGGCTGCTGAGCGCTGAGGCTGCGGCGGCGAGCGACAGGCCAGGTGCCTGCTCTTAGGGAAGGAATCATTGACATAGAGTAACTCCACAGCATGTGTCTTCAAGAGCTTCCCTAAAAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTTCAGTTTGCTTATCTTGACAACTTTAAAACAAGAACAAGAAGCACTGTGTCTGTCCGTCGAGGTCAAGGAATGGTGCTACTGTGTGGCCCGCCACCCCATTCTGGAGAGCTGAGTTATGCCTGGATCTTCAATGAATACCCTTCCTATCAGGATAATCGCCGCTTTGTTTCTCAAGAGACTGGGAATCTGTATATTGCCAAAGTAGAAAAATCAGATGTTGGGAATTATACCTGTGTGGTTACCAATACCGTGACAAACCACAAGGTCCTGGGGCCACCTACACCACTAATATTGAGAAATGATGTCCAGTACCAACTATTATCTGGCGAAGAGCTGATGGAAAGCCAATAGCAAGGAAAGCCAGAAGACACAAGTCAAATGGAATTCTTGAGATCCCTAATTTTCAGCAGGAGGATGCTGGTTTATATGAATGTGTAGCTGAAAATTCCAGAGGGAAAAATGTAGCAAGGGGACAGCTAACTTTCTATGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGT +>ENST00000455083.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337402.2|CNTN4-005|CNTN4|566|UTR5:1-402|CDS:403-566| +AAGTAGGGAGCTTTCGCCGCCGCCCCGGGCCCCTCGGACTGTGCCGGCGCCGCACCCGAGGCTCTCGCCAGCCCGGCGCCCCGGTGCTGAGTGGGTGAAAAAGAACAGTGTGTCATGAAGACAGGCACCTGGAGGTGATTTGGGTGGCATTCATGAGAAAATTCACGTTACCCACTTCGCTAACTGATGAAACACTGCCAGAGCCCACTTGGACTGTTTCGCAACTTTACTTAAGGGAATAAAAGCTCTCATGCTGAGGAATCATTGACATAGAGTAACTCCACAGCATGTGTCTTCAAGAGCTTCCCTAAAAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAA +>ENST00000418658.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337405.2|CNTN4-009|CNTN4|5093|UTR5:1-279|CDS:280-3360|UTR3:3361-5093| +CTGTGCCGGCGCCGCACCCGAGGCTCTCGCCAGCCCGGCGCCCCGGTGCTGAGTGGGTGAAAAAGAACAGTGTGTCATGAAGACAGGCACCTGGAGGTGATTTGGGTGGCATTCATGAGAAAATTCACGTTACCCGAATCATTGACATAGAGTAACTCCACAGCATGTGTCTTCAAGAGCTTCCCTAAAAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTTCAGTTTGCTTATCTTGACAACTTTAAAACAAGAACAAGAAGCACTGTGTCTGTCCGTCGAGGTCAAGGAATGGTGCTACTGTGTGGCCCGCCACCCCATTCTGGAGAGCTGAGTTATGCCTGGATCTTCAATGAATACCCTTCCTATCAGGATAATCGCCGCTTTGTTTCTCAAGAGACTGGGAATCTGTATATTGCCAAAGTAGAAAAATCAGATGTTGGGAATTATACCTGTGTGGTTACCAATACCGTGACAAACCACAAGGTCCTGGGGCCACCTACACCACTAATATTGAGAAATGATGGAGTGATGGGTGAATATGAGCCCAAAATAGAAGTGCAGTTCCCAGAAACAGTTCCGACTGCAAAAGGAGCAACGGTGAAGCTGGAATGCTTTGCTTTAGGAAATCCAGTACCAACTATTATCTGGCGAAGAGCTGATGGAAAGCCAATAGCAAGGAAAGCCAGAAGACACAAGTCAAATGGAATTCTTGAGATCCCTAATTTTCAGCAGGAGGATGCTGGTTTATATGAATGTGTAGCTGAAAATTCCAGAGGGAAAAATGTAGCAAGGGGACAGCTAACTTTCTATGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTTAGGAATGGCATTATACAGTACTTCCTCAAAGCAAATCTAGCTTTGTCTGAAGTTTCTTTGGAAACTCTGCAATGCACTGAAGACATCTGTAATATGATGTTACCAAAGCAGTTTACATATGTCCTTATATGCATATTTTTTATTATATATTTAGTGTTTTATAGAATTTTTTAAAGTTAACATATAATGTAGATATTAATTTTTTCCTCGGCTGTAAAATGCTATGGGCAACACAATCATGCAATTATAATTTGAAAATATTTCCTTTAAAGACAGAGTTTGAAACTCATCTTGGTAAATAAATTGCAAATTACTCGTACAGTTTTACAAGGATCTCATGGCAGAACAGCGGAAGACTTGGTCCGTAACTCAAGGCTGTTGTATGCAAACTACTCTTCTAGTGGTTAATGCACTTGACATGTACAGTATGTTTCCCATGCCGTTGTGATTTTGACATGTACAGTATGTTTTCATGCCGTTGTGAATTTTGTTGTTCAACCCAACTTGAGATGGTTTCAGGAATGGCTGCAATCTCAAAAGCTCAATGTACTGCCCAAGAGGCACCTTGTGCAATATTCCCATCCCTGAATTTAGCATTGTACAGGAAGATTTTCTTTTCACTCAACTGAGTTAGCATTGTCTTTGTGGTAGCATTATCTTAGACATTAAATTTGAAGTAACATATATCCTGTAGTAACATAGACCCAAAGTTACTATAGTCAACCAAGTCTTTCAAAGGATAAAAGATCATTTTATTATCTTTAACTGTATCTATTTTGAATGTAAATTTAAAAAAAGTAATTCTCTGTCAATGGATTCGTAATTTCTTTACAAAATTTCTTATATATAATATGTGTATCTCTGTAATAATAGAGCCCTTCTTTTGAATCAAAATTACATATGGACTTTGGAAGATTGCTCCTATTTCAACAAATAGTTGCTGCAAGAATTTTTAATATGACTCTATAAAAGCTCTTTAGTACAATTGTATGGTTTCTTGATGATTCTGTTTTGCAATAGGTAGCCTAGTTGCTTTATATGCTTTACCTTCTAGGTCTTAAAATCACACATTGGAAAATGACAATATCAACAAAACTGTATTCTTATGAAAAGAACTATTTGTTACAATGAGAAAGGTTTTGTGAGTAAACCCTACTGGACAGTGACATAAAAGGCAATGGAATTTTCTATAAACATTTTCTCATGTAAACATGCTGCCACCTTTTCTTCTTTCTCAGAGAACTCAAATTTGCTATAGTTTGTCATTTTTGCTTACAAATAATATAACTTTTCAACCTTCTAGTTATATTTATCCAATAAAGTCATAATCGGGATTCCATTTGTGTAAAAACTAGGGTGGTAACCGGAAAAAAATATTGTCAGTATTTCAAGCTGTGTTCCTTTCTTAGTTTGATATGGTTACTTCTATGTTGAAATAAAATTTAAAATCACATGCAAAAAAAAAATCAGCAAAATAATAAAATGAACGAAAAAAAATGACACCCAGGGAGTTCCCAACCCCAGTGTAAATGATATTTACCAGTGATCTAGCATATGTAATCTTTTTTAAAGGTATTGTTAATAAATATTCTGTCATT +>ENST00000397461.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239236.2|CNTN4-001|CNTN4|5198|UTR5:1-384|CDS:385-3465|UTR3:3466-5198| +GCCATTCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCGCCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCACCGTGCCCGGCCTGGCTCTGTTTTTATTAGAAAAATTCTCAATCGTCGTCTTTTAAGAATCATTGACATAGAGTAACTCCACAGCATGTGTCTTCAAGAGCTTCCCTAAAAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTTCAGTTTGCTTATCTTGACAACTTTAAAACAAGAACAAGAAGCACTGTGTCTGTCCGTCGAGGTCAAGGAATGGTGCTACTGTGTGGCCCGCCACCCCATTCTGGAGAGCTGAGTTATGCCTGGATCTTCAATGAATACCCTTCCTATCAGGATAATCGCCGCTTTGTTTCTCAAGAGACTGGGAATCTGTATATTGCCAAAGTAGAAAAATCAGATGTTGGGAATTATACCTGTGTGGTTACCAATACCGTGACAAACCACAAGGTCCTGGGGCCACCTACACCACTAATATTGAGAAATGATGGAGTGATGGGTGAATATGAGCCCAAAATAGAAGTGCAGTTCCCAGAAACAGTTCCGACTGCAAAAGGAGCAACGGTGAAGCTGGAATGCTTTGCTTTAGGAAATCCAGTACCAACTATTATCTGGCGAAGAGCTGATGGAAAGCCAATAGCAAGGAAAGCCAGAAGACACAAGTCAAATGGAATTCTTGAGATCCCTAATTTTCAGCAGGAGGATGCTGGTTTATATGAATGTGTAGCTGAAAATTCCAGAGGGAAAAATGTAGCAAGGGGACAGCTAACTTTCTATGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTTAGGAATGGCATTATACAGTACTTCCTCAAAGCAAATCTAGCTTTGTCTGAAGTTTCTTTGGAAACTCTGCAATGCACTGAAGACATCTGTAATATGATGTTACCAAAGCAGTTTACATATGTCCTTATATGCATATTTTTTATTATATATTTAGTGTTTTATAGAATTTTTTAAAGTTAACATATAATGTAGATATTAATTTTTTCCTCGGCTGTAAAATGCTATGGGCAACACAATCATGCAATTATAATTTGAAAATATTTCCTTTAAAGACAGAGTTTGAAACTCATCTTGGTAAATAAATTGCAAATTACTCGTACAGTTTTACAAGGATCTCATGGCAGAACAGCGGAAGACTTGGTCCGTAACTCAAGGCTGTTGTATGCAAACTACTCTTCTAGTGGTTAATGCACTTGACATGTACAGTATGTTTCCCATGCCGTTGTGATTTTGACATGTACAGTATGTTTTCATGCCGTTGTGAATTTTGTTGTTCAACCCAACTTGAGATGGTTTCAGGAATGGCTGCAATCTCAAAAGCTCAATGTACTGCCCAAGAGGCACCTTGTGCAATATTCCCATCCCTGAATTTAGCATTGTACAGGAAGATTTTCTTTTCACTCAACTGAGTTAGCATTGTCTTTGTGGTAGCATTATCTTAGACATTAAATTTGAAGTAACATATATCCTGTAGTAACATAGACCCAAAGTTACTATAGTCAACCAAGTCTTTCAAAGGATAAAAGATCATTTTATTATCTTTAACTGTATCTATTTTGAATGTAAATTTAAAAAAAGTAATTCTCTGTCAATGGATTCGTAATTTCTTTACAAAATTTCTTATATATAATATGTGTATCTCTGTAATAATAGAGCCCTTCTTTTGAATCAAAATTACATATGGACTTTGGAAGATTGCTCCTATTTCAACAAATAGTTGCTGCAAGAATTTTTAATATGACTCTATAAAAGCTCTTTAGTACAATTGTATGGTTTCTTGATGATTCTGTTTTGCAATAGGTAGCCTAGTTGCTTTATATGCTTTACCTTCTAGGTCTTAAAATCACACATTGGAAAATGACAATATCAACAAAACTGTATTCTTATGAAAAGAACTATTTGTTACAATGAGAAAGGTTTTGTGAGTAAACCCTACTGGACAGTGACATAAAAGGCAATGGAATTTTCTATAAACATTTTCTCATGTAAACATGCTGCCACCTTTTCTTCTTTCTCAGAGAACTCAAATTTGCTATAGTTTGTCATTTTTGCTTACAAATAATATAACTTTTCAACCTTCTAGTTATATTTATCCAATAAAGTCATAATCGGGATTCCATTTGTGTAAAAACTAGGGTGGTAACCGGAAAAAAATATTGTCAGTATTTCAAGCTGTGTTCCTTTCTTAGTTTGATATGGTTACTTCTATGTTGAAATAAAATTTAAAATCACATGCAAAAAAAAAATCAGCAAAATAATAAAATGAACGAAAAAAAATGACACCCAGGGAGTTCCCAACCCCAGTGTAAATGATATTTACCAGTGATCTAGCATATGTAATCTTTTTTAAAGGTATTGTTAATAAATATTCTGTCATT +>ENST00000434053.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337449.6|CNTN4-011|CNTN4|528|UTR5:1-116|CDS:117-528| +GAAACTGGGACATTTTACTTTACAGTCTATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGGTTCACAGACTGACTTCTGGTCCTTGCTGGGGGTGCTGCCAGCCTTGGAGGCTGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTTCAGTTTGCTT +>ENST00000427331.1|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-202|CNTN4|4985|UTR5:1-163|CDS:164-3244|UTR3:3245-4985| +AGTAAAGATAAACTTGCAGAGACCACAAGGAGAAATATTCCCAAATCTCATTGTAATGTCTCTTCTTTCCCACAGATTAAAGGTTATACAAAACTTAAAAGAAGCAGCAATTCTATTCGCTTGTTATTGGACTTGAAACTCCCTTTGACCTCGGAAACTGAAGATGAGGTTGCCATGGGAACTGCTGGTACTGCAATCATTCATTTTGTGCCTTGCAGATGATTCCACACTGCATGGCCCGATTTTTATTCAAGAACCAAGTCCTGTAATGTTCCCTTTGGATTCTGAGGAGAAAAAAGTGAAGCTCAATTGTGAAGTTAAAGGAAATCCAAAACCTCATATCAGGTGGAAGTTAAATGGAACAGATGTTGACACTGGTATGGATTTCCGCTACAGTGTTGTTGAAGGGAGCTTGTTGATCAATAACCCCAATAAAACCCAAGATGCTGGAACGTACCAGTGCACAGCGACAAACTCGTTTGGAACAATTGTTAGCAGAGAAGCAAAGCTTCAGTTTGCTTATCTTGACAACTTTAAAACAAGAACAAGAAGCACTGTGTCTGTCCGTCGAGGTCAAGGAATGGTGCTACTGTGTGGCCCGCCACCCCATTCTGGAGAGCTGAGTTATGCCTGGATCTTCAATGAATACCCTTCCTATCAGGATAATCGCCGCTTTGTTTCTCAAGAGACTGGGAATCTGTATATTGCCAAAGTAGAAAAATCAGATGTTGGGAATTATACCTGTGTGGTTACCAATACCGTGACAAACCACAAGGTCCTGGGGCCACCTACACCACTAATATTGAGAAATGATGGAGTGATGGGTGAATATGAGCCCAAAATAGAAGTGCAGTTCCCAGAAACAGTTCCGACTGCAAAAGGAGCAACGGTGAAGCTGGAATGCTTTGCTTTAGGAAATCCAGTACCAACTATTATCTGGCGAAGAGCTGATGGAAAGCCAATAGCAAGGAAAGCCAGAAGACACAAGTCAAATGGAATTCTTGAGATCCCTAATTTTCAGCAGGAGGATGCTGGTTTATATGAATGTGTAGCTGAAAATTCCAGAGGGAAAAATGTAGCAAGGGGACAGCTAACTTTCTATGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTTAGGAATGGCATTATACAGTACTTCCTCAAAGCAAATCTAGCTTTGTCTGAAGTTTCTTTGGAAACTCTGCAATGCACTGAAGACATCTGTAATATGATGTTACCAAAGCAGTTTACATATGTCCTTATATGCATATTTTTTATTATATATTTAGTGTTTTATAGAATTTTTTAAAGTTAACATATAATGTAGATATTAATTTTTTCCTCGGCTGTAAAATGCTATGGGCAACACAATCATGCAATTATAATTTGAAAATATTTCCTTTAAAGACAGAGTTTGAAACTCATCTTGGTAAATAAATTGCAAATTACTCGTACAGTTTTACAAGGATCTCATGGCAGAACAGCGGAAGACTTGGTCCGTAACTCAAGGCTGTTGTATGCAAACTACTCTTCTAGTGGTTAATGCACTTGACATGTACAGTATGTTTCCCATGCCGTTGTGATTTTGACATGTACAGTATGTTTTCATGCCGTTGTGAATTTTGTTGTTCAACCCAACTTGAGATGGTTTCAGGAATGGCTGCAATCTCAAAAGCTCAATGTACTGCCCAAGAGGCACCTTGTGCAATATTCCCATCCCTGAATTTAGCATTGTACAGGAAGATTTTCTTTTCACTCAACTGAGTTAGCATTGTCTTTGTGGTAGCATTATCTTAGACATTAAATTTGAAGTAACATATATCCTGTAGTAACATAGACCCAAAGTTACTATAGTCAACCAAGTCTTTCAAAGGATAAAAGATCATTTTATTATCTTTAACTGTATCTATTTTGAATGTAAATTTAAAAAAAGTAATTCTCTGTCAATGGATTCGTAATTTCTTTACAAAATTTCTTATATATAATATGTGTATCTCTGTAATAATAGAGCCCTTCTTTTGAATCAAAATTACATATGGACTTTGGAAGATTGCTCCTATTTCAACAAATAGTTGCTGCAAGAATTTTTAATATGACTCTATAAAAGCTCTTTAGTACAATTGTATGGTTTCTTGATGATTCTGTTTTGCAATAGGTAGCCTAGTTGCTTTATATGCTTTACCTTCTAGGTCTTAAAATCACACATTGGAAAATGACAATATCAACAAAACTGTATTCTTATGAAAAGAACTATTTGTTACAATGAGAAAGGTTTTGTGAGTAAACCCTACTGGACAGTGACATAAAAGGCAATGGAATTTTCTATAAACATTTTCTCATGTAAACATGCTGCCACCTTTTCTTCTTTCTCAGAGAACTCAAATTTGCTATAGTTTGTCATTTTTGCTTACAAATAATATAACTTTTCAACCTTCTAGTTATATTTATCCAATAAAGTCATAATCGGGATTCCATTTGTGTAAAAACTAGGGTGGTAACCGGAAAAAAATATTGTCAGTATTTCAAGCTGTGTTCCTTTCTTAGTTTGATATGGTTACTTCTATGTTGAAATAAAATTTAAAATCACATGCAAAAAAAAAATCAGCAAAATAATAAAATGAACGAAAAAAAATGACACCCAGGGAGTTCCCAACCCCAGTGTAAATGATATTTACCAGTGATCTAGCATATGTAATCTTTTTTAAAGGTATTGTTAATAAATATTCTGTCATTTGTAAAGA +>ENST00000358480.3|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-201|CNTN4|2846|UTR5:1-287|CDS:288-2711|UTR3:2712-2846| +AATTTGAGCATTACTCAATACATGTTACATAGTGCCTGACACCTGATTAGCAAACTATAAATGCTTAGCCCTTGACTTAAAGAGAGCTGAGTTATGCCTGGATCTTCAATGAATACCCTTCCTATCAGGATAATCGCCGCTTTGTTTCTCAAGAGACTGGGAATCTGTATATTGCCAAAGTAGAAAAATCAGATGTTGGGAATTATACCTGTGTGGTTACCAATACCGTGACAAACCACAAGGTCCTGGGGCCACCTACACCACTAATATTGAGAAATGATGGAGTGATGGGTGAATATGAGCCCAAAATAGAAGTGCAGTTCCCAGAAACAGTTCCGACTGCAAAAGGAGCAACGGTGAAGCTGGAATGCTTTGCTTTAGGAAATCCAGTACCAACTATTATCTGGCGAAGAGCTGATGGAAAGCCAATAGCAAGGAAAGCCAGAAGACACAAGTCAAATGGAATTCTTGAGATCCCTAATTTTCAGCAGGAGGATGCTGGTTTATATGAATGTGTAGCTGAAAATTCCAGAGGGAAAAATGTAGCAAGGGGACAGCTAACTTTCTATGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTT +>ENST00000397459.2|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239237.2|CNTN4-002|CNTN4|2322|UTR5:1-90|CDS:91-2187|UTR3:2188-2322| +GTTCTATGTTCCCAGTGGGAACATACCAGATGGAGGCTTTGATTTGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTT +>ENST00000448906.2|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-203|CNTN4|2279|UTR5:1-47|CDS:48-2144|UTR3:2145-2279| +TAGCTCAACCTAATTGGATTCAAAAAATAAATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGAATTACCATTTCTGAAGATGGAAACCTCAGAATCATCAACGTTACTAAATCAGACGCTGGGAGTTATACCTGTATAGCCACTAACCATTTTGGAACTGCTAGCAGTACTGGAAACTTGGTAGTGAAAGATCCAACAAGGGTAATGGTACCCCCTTCCAGTATGGATGTCACTGTTGGAGAGAGTATTGTTTTACCGTGCCAGGTAACGCATGATCACTCGCTAGACATCGTGTTTACTTGGTCATTTAATGGACACCTGATAGACTTTGACAGAGATGGGGACCACTTTGAAAGAGTTGGAGGGCAGGATTCAGCTGGTGATTTGATGATCCGAAACATCCAACTGAAGCATGCTGGGAAATATGTCTGCATGGTCCAAACAAGTGTGGACAGGCTATCTGCTGCTGCAGACCTGATTGTAAGAGGTCCTCCAGGTCCCCCAGAGGCTGTGACAATAGACGAAATCACAGATACCACTGCTCAGCTCTCCTGGAGACCCGGGCCTGACAACCACAGCCCCATCACCATGTATGTCATTCAAGCCAGGACTCCATTCTCCGTGGGCTGGCAAGCAGTCAGTACAGTCCCAGAACTCATTGATGGGAAGACATTCACAGCGACCGTGGTGGGTTTGAACCCTTGGGTTGAATATGAATTCCGCACAGTTGCAGCCAACGTGATTGGGATTGGGGAGCCCAGCCGCCCCTCAGAGAAACGGAGAACAGAAGAAGCTCTCCCCGAAGTCACACCAGCGAATGTCAGTGGTGGCGGAGGCAGCAAATCTGAACTGGTTATAACCTGGGAGACGGTCCCTGAGGAATTACAGAATGGTCGAGGCTTTGGTTATGTGGTGGCCTTCCGGCCCTACGGTAAAATGATCTGGATGCTGACAGTGCTGGCCTCAGCTGATGCCTCTAGATACGTGTTCAGGAATGAGAGCGTGCACCCCTTCTCTCCCTTTGAGGTTAAAGTAGGTGTCTTCAACAACAAAGGAGAAGGCCCTTTCAGTCCCACCACGGTGGTGTATTCTGCAGAAGAAGAACCCACCAAACCACCAGCCAGTATCTTTGCCAGAAGTCTTTCTGCCACAGATATTGAAGTTTTCTGGGCCTCCCCACTGGAGAAGAATAGAGGACGAATACAAGGTTATGAGGTTAAATATTGGAGACATGAAGACAAAGAAGAAAATGCTAGAAAAATACGAACAGTTGGAAATCAGACATCAACAAAAATCACGAACTTAAAAGGCAGTGTGCTGTATCACTTAGCTGTCAAGGCATATAATTCTGCTGGGACAGGCCCCTCTAGTGCAACAGTCAATGTGACAACCCGAAAGCCACCACCAAGTCAACCCCCCGGAAACATCATATGGAATTCATCAGACTCCAAAATTATCCTGAATTGGGATCAAGTGAAGGCCCTGGATAATGAGTCGGAAGTAAAAGGATACAAAGTCTTGTACAGATGGAACAGACAAAGCAGCACATCTGTCATTGAAACAAATAAAACATCGGTGGAGCTTTCTTTGCCTTTCGATGAAGATTATATAATAGAAATTAAGCCATTCAGCGACGGAGGAGATGGCAGCAGCAGTGAACAAATTCGAATTCCAAAGATATCAAATGCCTACGCGAGAGGATCTGGGGCTTCCACTTCGAATGCATGTACGCTGTCAGCCATCAGTACAATAATGATTTCCCTCACAGCTAGGTCCAGTTTATGACAAAAGTTATCTGAAGGACTTGCTGTTTATAATATAAGCAACATTTAGCTAGTTGTTTTGAAGACACCCAGTACTAAGTAATATTGTTGTTCAAGTACATCTTATTACTGGAATAAAAATGTTTTTTGCTTCTTT +>ENST00000473845.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337472.2|CNTN4-015|CNTN4|726|CDS:1-432|UTR3:433-726| +AATGATATTCACGTGGCCATGGAAGAAAATGTCTTTTGGGAATGTAAAGCAAATGGAAGGCCTAAGCCTACATACAAGTGGCTAAAAAATGGCGAACCTCTGCTAACTCGGGATAGAATTCAAATTGAGCAAGGAACACTCAACATAACAATAGTGAACCTCTCAGATGCTGGCATGTATCAGTGTTTGGCAGAGAATAAACATGGAGTTATCTTTTCCAACGCAGAGCTTAGTGTTATAGCTGTAGGTCCAGATTTTTCAAGAACACTCTTGAAAAGAGTAACTCTTGTCAAAGTGGGAGGTGAAGTTGTCATTGAGTGTAAGCCAAAAGCGTCTCCAAAACCTGTTTACACCTGGAAGAAAGGAAGGGATATATTAAAAGAAAATGAAAGTGTACATCAGGGGTTTGGTAGTGGCTCTGCTCCTCTCTAAGGCCAGCCTGGTGGACCAAGATGCTCTGGACGTTGCCATTGCAGAAGGAAAAGAGCCAAACATGCATGGGTTCTTAAAGCCTCTACTTAGAAGTGCAACACTTGCACTTTCACTCACATTTCATTGGCCAAAACAGGTCACATGTTCCTGCAACTCAGCAGGGAAATATAATCTTGCTATGTGCCTGGAAGAAAAGAGACAACCTAATATTTTGAACAGTATTAATGACTGCTTACAACTGCTACAGCTTAACCATTGTTACAAGCTAATTAAATTACCTTTGGGGAAATAGTA diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta.fai new file mode 100644 index 00000000000..9be86629b2c --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/gencode.v19.CNTN4.pc_transcripts.fasta.fai @@ -0,0 +1,11 @@ +ENST00000422330.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337401.2|CNTN4-004|CNTN4|658|UTR5:1-310|CDS:311-658| 658 124 658 659 +ENST00000427741.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337400.1|CNTN4-003|CNTN4|3040|UTR5:1-633|CDS:634-1332|UTR3:1333-3040| 3040 924 3040 3041 +ENST00000455083.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337402.2|CNTN4-005|CNTN4|566|UTR5:1-402|CDS:403-566| 566 4089 566 567 +ENST00000418658.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337405.2|CNTN4-009|CNTN4|5093|UTR5:1-279|CDS:280-3360|UTR3:3361-5093| 5093 4797 5093 5094 +ENST00000397461.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239236.2|CNTN4-001|CNTN4|5198|UTR5:1-384|CDS:385-3465|UTR3:3466-5198| 5198 10032 5198 5199 +ENST00000434053.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337449.6|CNTN4-011|CNTN4|528|UTR5:1-116|CDS:117-528| 528 15355 528 529 +ENST00000427331.1|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-202|CNTN4|4985|UTR5:1-163|CDS:164-3244|UTR3:3245-4985| 4985 16006 4985 4986 +ENST00000358480.3|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-201|CNTN4|2846|UTR5:1-287|CDS:288-2711|UTR3:2712-2846| 2846 21114 2846 2847 +ENST00000397459.2|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000239237.2|CNTN4-002|CNTN4|2322|UTR5:1-90|CDS:91-2187|UTR3:2188-2322| 2322 24100 2322 2323 +ENST00000448906.2|ENSG00000144619.10|OTTHUMG00000119031.9|-|CNTN4-203|CNTN4|2279|UTR5:1-47|CDS:48-2144|UTR3:2145-2279| 2279 26543 2279 2280 +ENST00000473845.1|ENSG00000144619.10|OTTHUMG00000119031.9|OTTHUMT00000337472.2|CNTN4-015|CNTN4|726|CDS:1-432|UTR3:433-726| 726 28947 726 727 From dab2f3d6283a801e00fb82e00381be140bf85b09 Mon Sep 17 00:00:00 2001 From: lichtens Date: Wed, 27 Jun 2018 13:18:59 -0400 Subject: [PATCH 09/15] Non-NIO WDL works in FireCloud. NIO, not so much. --- scripts/mutect2_wdl/mutect2.wdl | 5 +- scripts/mutect2_wdl/mutect2_nio.wdl | 248 ++++++++++-------- .../GencodeFuncotationFactoryUnitTest.java | 5 +- 3 files changed, 138 insertions(+), 120 deletions(-) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 3660f12ec59..8a5885835ef 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -51,9 +51,6 @@ ## funco_annotation_defaults: Default values for annotations, when values are unspecified. Specified as :. For example: "Center:Broad" ## funco_annotation_overrides: Values for annotations, even when values are unspecified. Specified as :. For example: "Center:Broad" ## - -## TODO: Merge with mutect2_nio.wdl - ## Outputs : ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam ## file of reassembled reads if requested @@ -1077,7 +1074,7 @@ task FuncotateMaf { runtime { docker: gatk_docker - bootDiskSizeGb: 12 + bootDiskSizeGb: 20 memory: machine_mem + " MB" disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" preemptible: select_first([preemptible_attempts, 3]) diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl index 06096ca312f..1f6c9dfbd60 100755 --- a/scripts/mutect2_wdl/mutect2_nio.wdl +++ b/scripts/mutect2_wdl/mutect2_nio.wdl @@ -47,6 +47,14 @@ ## filter_oncotator_maf: Whether the MAF generated by oncotator should have the filtered variants removed. Default: true ## realignment_index_bundle: resource for FilterAlignmentArtifacts, which runs if and only if it is specified. Generated by BwaMemIndexImageCreator. ## +## Funcotator parameters (see Funcotator help for more details). +## funco_reference_version: "hg19" for hg19 or b37. "hg38" for hg38. Default: "hg19" +## funco_transcript_selection_list: Transcripts (one GENCODE ID per line) to give priority during selection process. +## funco_transcript_selection_mode: How to select transcripts in Funcotator. ALL, CANONICAL, or BEST_EFFECT +## funco_data_sources_tar_gz: Funcotator datasources tar gz file. Bucket location is recommended when running on the cloud. +## funco_annotation_defaults: Default values for annotations, when values are unspecified. Specified as :. For example: "Center:Broad" +## funco_annotation_overrides: Values for annotations, even when values are unspecified. Specified as :. For example: "Center:Broad" +## ## Outputs : ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam ## file of reassembled reads if requested @@ -102,12 +110,12 @@ workflow Mutect2 { # funcotator inputs Boolean? run_funcotator Boolean run_funcotator_or_default = select_first([run_funcotator, false]) - String? reference_version - String? data_sources_tar_gz - String? transcript_selection_mode - Array[String]? transcript_selection_list - Array[String]? annotation_defaults - Array[String]? annotation_overrides + String? funco_reference_version + File? funco_data_sources_tar_gz + String? funco_transcript_selection_mode + File? funco_transcript_selection_list + Array[String]? funco_annotation_defaults + Array[String]? funco_annotation_overrides File? gatk_override @@ -115,9 +123,11 @@ workflow Mutect2 { String gatk_docker String basic_bash_docker = "ubuntu:16.04" String? oncotator_docker - String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.8.0"]) + String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.9.0"]) Boolean? filter_oncotator_maf Boolean filter_oncotator_maf_or_default = select_first([filter_oncotator_maf, true]) + Boolean? filter_funcotations + Boolean filter_funcotations_or_default = select_first([filter_funcotations, true]) String? oncotator_extra_args Int? preemptible_attempts @@ -329,23 +339,24 @@ workflow Mutect2 { } if (run_funcotator_or_default) { - File funcotate_vcf_input = select_first([FilterByOrientationBias.filtered_vcf, Filter.filtered_vcf]) - File funcotate_vcf_input_index = select_first([FilterAlignmentArtifacts.filtered_vcf, FilterByOrientationBias.filtered_vcf_index, Filter.filtered_vcf_index]) - call Funcotate { + File funcotate_vcf_input = select_first([FilterAlignmentArtifacts.filtered_vcf, FilterByOrientationBias.filtered_vcf, Filter.filtered_vcf]) + File funcotate_vcf_input_index = select_first([FilterAlignmentArtifacts.filtered_vcf_index, FilterByOrientationBias.filtered_vcf_index, Filter.filtered_vcf_index]) + call FuncotateMaf { input: - m2_vcf = funcotate_vcf_input, - m2_vcf_index = funcotate_vcf_input_index, + input_vcf = funcotate_vcf_input, + input_vcf_idx = funcotate_vcf_input_index, ref_fasta = ref_fasta, - reference_version = select_first([reference_version, "NO_REFERENCE_VERSION_GIVEN"]), - output_name = funcotated_name, - compress = compress, - data_sources_tar_gz = data_sources_tar_gz, - transcript_selection_mode = transcript_selection_mode, - transcript_selection_list = transcript_selection_list, - annotation_defaults = annotation_defaults, - annotation_overrides = annotation_overrides, + reference_version = select_first([funco_reference_version, "hg19"]), + data_sources_tar_gz = funco_data_sources_tar_gz, + transcript_selection_mode = funco_transcript_selection_mode, + transcript_selection_list = funco_transcript_selection_list, + annotation_defaults = funco_annotation_defaults, + annotation_overrides = funco_annotation_overrides, gatk_docker = gatk_docker, - gatk_override = gatk_override + gatk_override = gatk_override, + filter_funcotations = filter_funcotations_or_default, + sequencing_center = sequencing_center, + sequence_source = sequence_source } } @@ -357,8 +368,7 @@ workflow Mutect2 { File? contamination_table = CalculateContamination.contamination_table File? oncotated_m2_maf = oncotate_m2.oncotated_m2_maf - File? funcotated_vcf = Funcotate.funcotated_vcf - File? funcotated_vcf_index = Funcotate.funcotated_vcf_index + File? funcotated_maf = FuncotateMaf.funcotated_output File? preadapter_detail_metrics = CollectSequencingArtifactMetrics.pre_adapter_metrics File? bamout = MergeBamOuts.merged_bam_out File? bamout_index = MergeBamOuts.merged_bam_out_index @@ -940,93 +950,105 @@ task SumFloats { } } -task Funcotate { - # inputs - String ref_fasta - String m2_vcf - String m2_vcf_index - String reference_version - String output_name - Boolean compress - String output_vcf = output_name + if compress then ".vcf.gz" else ".vcf" - String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx" - - File? data_sources_tar_gz - String? transcript_selection_mode - Array[String]? transcript_selection_list - Array[String]? annotation_defaults - Array[String]? annotation_overrides - - # ============== - # Process input args: - String transcript_selection_arg = if defined(transcript_selection_list) then " --transcript-list " else "" - String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" - String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" - # ============== - - # runtime - - String gatk_docker - File? gatk_override - Int? mem - Int? preemptible_attempts - Int? disk_space_gb - Int? cpu - - Boolean use_ssd = false - - # You may have to change the following two parameter values depending on the task requirements - Int default_ram_mb = 3000 - # WARNING: In the workflow, you should calculate the disk space as an input to this task (disk_space_gb). Please see [TODO: Link from Jose] for examples. - Int default_disk_space_gb = 100 - - # Mem is in units of GB but our command and memory runtime values are in MB - Int machine_mem = if defined(mem) then mem *1000 else default_ram_mb - Int command_mem = machine_mem - 1000 - - command <<< - set -e - export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override} - - DATA_SOURCES_TAR_GZ=${data_sources_tar_gz} - if [[ ! -e $DATA_SOURCES_TAR_GZ ]] ; then - # We have to download the data sources: - echo "Data sources gzip does not exist: $DATA_SOURCES_TAR_GZ" - echo "Downloading default data sources..." - wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.0.20180105.tar.gz - tar -zxf funcotator_dataSources.v1.0.20180105.tar.gz - DATA_SOURCES_FOLDER=funcotator_dataSources.v1.0.20180105 - else - # Extract the tar.gz: - mkdir datasources_dir - tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1 - DATA_SOURCES_FOLDER="$PWD/datasources_dir" - fi - - gatk --java-options "-Xmx${command_mem}m" Funcotator \ - --data-sources-path $DATA_SOURCES_FOLDER \ - --ref-version ${reference_version} \ - -R ${ref_fasta} \ - -V ${m2_vcf} \ - -O ${output_vcf} \ - ${"--transcript-selection-mode " + transcript_selection_mode} \ - ${transcript_selection_arg}${default="" sep=" --transcript-list " transcript_selection_list} \ - ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ - ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} - >>> - - runtime { - docker: gatk_docker - bootDiskSizeGb: 12 - memory: machine_mem + " MB" - disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" - preemptible: select_first([preemptible_attempts, 3]) - cpu: select_first([cpu, 1]) - } - - output { - File funcotated_vcf = "${output_vcf}" - File funcotated_vcf_index = "${output_vcf_index}" - } -} - +task FuncotateMaf { + # inputs + String ref_fasta + String input_vcf + String input_vcf_idx + String reference_version + String output_format = "MAF" + String? sequencing_center + String? sequence_source + + File? data_sources_tar_gz + String? transcript_selection_mode + File? transcript_selection_list + Array[String]? annotation_defaults + Array[String]? annotation_overrides + Boolean filter_funcotations + File? interval_list + + String? extra_args + + # ============== + # Process input args: + String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" + String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" + String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else "" + String interval_list_arg = if defined(interval_list) then " -L " else "" + String extra_args_arg = select_first([extra_args, ""]) + String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated" + # ============== + + # runtime + + String gatk_docker + File? gatk_override + Int? mem + Int? preemptible_attempts + Int? disk_space_gb + Int? cpu + + Boolean use_ssd = false + + # This should be updated when a new version of the data sources is released + # TODO: Make this dynamically chosen in the command. + String default_datasources_version = "funcotator_dataSources.v1.3.20180531" + + # You may have to change the following two parameter values depending on the task requirements + Int default_ram_mb = 3000 + # WARNING: In the workflow, you should calculate the disk space as an input to this task (disk_space_gb). + Int default_disk_space_gb = 100 + + # Mem is in units of GB but our command and memory runtime values are in MB + Int machine_mem = if defined(mem) then mem *1000 else default_ram_mb + Int command_mem = machine_mem - 1000 + + command <<< + set -e + export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override} + + DATA_SOURCES_TAR_GZ=${data_sources_tar_gz} + if [[ ! -e $DATA_SOURCES_TAR_GZ ]] ; then + # We have to download the data sources: + echo "Data sources gzip does not exist: $DATA_SOURCES_TAR_GZ" + echo "Downloading default data sources..." + wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/${default_datasources_version}.tar.gz + tar -zxf ${default_datasources_version}.tar.gz + DATA_SOURCES_FOLDER=${default_datasources_version} + else + # Extract the tar.gz: + mkdir datasources_dir + tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1 + DATA_SOURCES_FOLDER="$PWD/datasources_dir" + fi + + gatk --java-options "-Xmx${command_mem}m" Funcotator \ + --data-sources-path $DATA_SOURCES_FOLDER \ + --ref-version ${reference_version} \ + --output-file-format ${output_format} \ + -R ${ref_fasta} \ + -V ${input_vcf} \ + -O ${final_output_filename} \ + ${interval_list_arg} ${default="" interval_list} \ + ${"--transcript-selection-mode " + transcript_selection_mode} \ + ${"--transcript-list " + transcript_selection_list} \ + ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ + ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ + ${filter_funcotations_args} \ + ${extra_args_arg} + >>> + + runtime { + docker: gatk_docker + bootDiskSizeGb: 20 + memory: machine_mem + " MB" + disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD" + preemptible: select_first([preemptible_attempts, 3]) + cpu: select_first([cpu, 1]) + } + + output { + File funcotated_output = "${final_output_filename}" + } + } \ No newline at end of file diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java index ddea846fd66..36a7e527217 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java @@ -1507,7 +1507,7 @@ public Object[][] provideSortingOfUserRequestedTranscripts() { } /** - * Also, tests some basic sorting. + * Also, tests some basic sorting independent of the user defined list. */ @Test(dataProvider = "provideSortingOfUserRequestedTranscripts") public void testSortingOfUserRequestedTranscripts(final List gencodeFuncotations, final Set userRequestedTranscripts, final String gtFirstTranscript) { @@ -1538,7 +1538,7 @@ public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOExceptio final SimpleInterval variantInterval = new SimpleInterval("chr3", 2944600, 2944600); final ReferenceContext referenceContext = new ReferenceContext(refDataSourceHg19Ch3, variantInterval); final VariantContext vc = new VariantContextBuilder() - .alleles(Arrays.asList(Allele.create("A", true), Allele.create("AT", false))) + .alleles(Arrays.asList(Allele.create("T", true), Allele.create("AT", false))) .chr(variantInterval.getContig()).start(variantInterval.getStart()).stop(variantInterval.getEnd()) .make(); @@ -1591,6 +1591,5 @@ public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOExceptio final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); Assert.assertTrue(gencodeFuncotations.size() > 1); } - } } From 18b9e91692cf7e7536d08828db01a7d3164c6141 Mon Sep 17 00:00:00 2001 From: lichtens Date: Mon, 2 Jul 2018 13:41:14 -0400 Subject: [PATCH 10/15] Getting extra funcotator args into the WDL. --- scripts/mutect2_wdl/mutect2.wdl | 4 +++- scripts/mutect2_wdl/mutect2_nio.wdl | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 8a5885835ef..b37390496d4 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -129,6 +129,7 @@ workflow Mutect2 { Boolean? filter_funcotations Boolean filter_funcotations_or_default = select_first([filter_funcotations, true]) String? oncotator_extra_args + String? funcotator_extra_args Int? preemptible_attempts @@ -373,7 +374,8 @@ workflow Mutect2 { gatk_override = gatk_override, filter_funcotations = filter_funcotations_or_default, sequencing_center = sequencing_center, - sequence_source = sequence_source + sequence_source = sequence_source, + extra_args = funcotator_extra_args } } diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl index 1f6c9dfbd60..91a58684560 100755 --- a/scripts/mutect2_wdl/mutect2_nio.wdl +++ b/scripts/mutect2_wdl/mutect2_nio.wdl @@ -129,6 +129,7 @@ workflow Mutect2 { Boolean? filter_funcotations Boolean filter_funcotations_or_default = select_first([filter_funcotations, true]) String? oncotator_extra_args + String? funcotator_extra_args Int? preemptible_attempts @@ -356,7 +357,8 @@ workflow Mutect2 { gatk_override = gatk_override, filter_funcotations = filter_funcotations_or_default, sequencing_center = sequencing_center, - sequence_source = sequence_source + sequence_source = sequence_source, + extra_args = funcotator_extra_args } } From 5fa68f9c38bb808037b5629431df8e494d03ef2d Mon Sep 17 00:00:00 2001 From: lichtens Date: Tue, 3 Jul 2018 09:09:43 -0400 Subject: [PATCH 11/15] Adding more args into Funcotator M2 WDL. --- scripts/mutect2_wdl/mutect2.wdl | 8 ++++++++ scripts/mutect2_wdl/mutect2_nio.wdl | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index b37390496d4..89da813166f 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -366,6 +366,8 @@ workflow Mutect2 { ref_dict = ref_dict, reference_version = select_first([funco_reference_version, "hg19"]), data_sources_tar_gz = funco_data_sources_tar_gz, + case_id = M2.tumor_sample[0], + control_id = M2.normal_sample[0], transcript_selection_mode = funco_transcript_selection_mode, transcript_selection_list = funco_transcript_selection_list, annotation_defaults = funco_annotation_defaults, @@ -994,6 +996,8 @@ task FuncotateMaf { String output_format = "MAF" String? sequencing_center String? sequence_source + String case_id + String? control_id File? data_sources_tar_gz String? transcript_selection_mode @@ -1068,6 +1072,10 @@ task FuncotateMaf { ${interval_list_arg} ${default="" interval_list} \ ${"--transcript-selection-mode " + transcript_selection_mode} \ ${"--transcript-list " + transcript_selection_list} \ + --annotation-default normal_barcode:${control_id} \ + --annotation-default tumor_barcode:${case_id} \ + --annotation-default Center:${default="Unknown" sequencing_center} \ + --annotation-default source:${default="Unknown" sequence_source} \ ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ ${filter_funcotations_args} \ diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl index 91a58684560..21d1983a029 100755 --- a/scripts/mutect2_wdl/mutect2_nio.wdl +++ b/scripts/mutect2_wdl/mutect2_nio.wdl @@ -349,6 +349,8 @@ workflow Mutect2 { ref_fasta = ref_fasta, reference_version = select_first([funco_reference_version, "hg19"]), data_sources_tar_gz = funco_data_sources_tar_gz, + case_id = M2.tumor_sample[0], + control_id = M2.normal_sample[0], transcript_selection_mode = funco_transcript_selection_mode, transcript_selection_list = funco_transcript_selection_list, annotation_defaults = funco_annotation_defaults, @@ -961,6 +963,8 @@ task FuncotateMaf { String output_format = "MAF" String? sequencing_center String? sequence_source + String case_id + String? control_id File? data_sources_tar_gz String? transcript_selection_mode @@ -1035,6 +1039,10 @@ task FuncotateMaf { ${interval_list_arg} ${default="" interval_list} \ ${"--transcript-selection-mode " + transcript_selection_mode} \ ${"--transcript-list " + transcript_selection_list} \ + --annotation-default normal_barcode:${control_id} \ + --annotation-default tumor_barcode:${case_id} \ + --annotation-default Center:${default="Unknown" sequencing_center} \ + --annotation-default source:${default="Unknown" sequence_source} \ ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ ${filter_funcotations_args} \ From 9a4fa40a0600654b714bca5e5db2659cf14bd844 Mon Sep 17 00:00:00 2001 From: lichtens Date: Tue, 3 Jul 2018 09:47:22 -0400 Subject: [PATCH 12/15] Addressing rebase issues. --- .../tools/funcotator/FuncotatorIntegrationTest.java | 1 - .../gencode/GencodeFuncotationFactoryUnitTest.java | 6 +++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index 5bfa9fb93a2..fa141b14336 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -1070,7 +1070,6 @@ public void testNoVariantsProduceMaf() { arguments.addArgument(FuncotatorArgumentDefinitions.DATA_SOURCES_PATH_LONG_NAME, DS_PIK3CA_DIR); arguments.addArgument(FuncotatorArgumentDefinitions.REFERENCE_VERSION_LONG_NAME, FuncotatorTestConstants.REFERENCE_VERSION_HG19); arguments.addArgument(FuncotatorArgumentDefinitions.OUTPUT_FORMAT_LONG_NAME, outputFormatType.toString()); - arguments.addBooleanArgument(FuncotatorArgumentDefinitions.ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME, true); arguments.addArgument(FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_LONG_NAME, TranscriptSelectionMode.CANONICAL.toString()); runCommandLine(arguments); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java index 36a7e527217..86e02345f82 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java @@ -1565,7 +1565,7 @@ public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOExceptio GencodeFuncotationFactory.DEFAULT_NAME, TranscriptSelectionMode.CANONICAL, Collections.emptySet(), - new LinkedHashMap<>(), true)) { + new LinkedHashMap<>())) { final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); Assert.assertEquals(gencodeFuncotations.size(), 1); } @@ -1576,7 +1576,7 @@ public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOExceptio GencodeFuncotationFactory.DEFAULT_NAME, TranscriptSelectionMode.BEST_EFFECT, Collections.emptySet(), - new LinkedHashMap<>(), true)) { + new LinkedHashMap<>())) { final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); Assert.assertEquals(gencodeFuncotations.size(), 1); } @@ -1587,7 +1587,7 @@ public void testMultipleGeneFeaturesOnlyProduceOneTranscript() throws IOExceptio GencodeFuncotationFactory.DEFAULT_NAME, TranscriptSelectionMode.ALL, Collections.emptySet(), - new LinkedHashMap<>(), true)) { + new LinkedHashMap<>())) { final List gencodeFuncotations = funcotationFactory.createFuncotationsOnVariant(vc, referenceContext, gencodeFeatures); Assert.assertTrue(gencodeFuncotations.size() > 1); } From 200212315889b399d8944fbfb840a16b1025658f Mon Sep 17 00:00:00 2001 From: lichtens Date: Tue, 3 Jul 2018 12:12:18 -0400 Subject: [PATCH 13/15] Addressing funcotator size estimation. --- scripts/mutect2_wdl/mutect2.wdl | 2 ++ scripts/mutect2_wdl/mutect2_nio.wdl | 2 ++ 2 files changed, 4 insertions(+) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 89da813166f..be9ca3cedc4 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -144,6 +144,7 @@ workflow Mutect2 { # If no tar is provided, the task downloads one from broads ftp server Int onco_tar_size = if defined(onco_ds_tar_gz) then ceil(size(onco_ds_tar_gz, "GB") * 3) else 100 + Int funco_tar_size = if defined(funco_data_sources_tar_gz) then ceil(size(funco_data_sources_tar_gz, "GB") * 3) else 100 Int gatk_override_size = if defined(gatk_override) then ceil(size(gatk_override, "GB")) else 0 # This is added to every task as padding, should increase if systematically you need more disk for every call @@ -377,6 +378,7 @@ workflow Mutect2 { filter_funcotations = filter_funcotations_or_default, sequencing_center = sequencing_center, sequence_source = sequence_source, + disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + onco_tar_size + disk_pad, extra_args = funcotator_extra_args } } diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl index 21d1983a029..f6f929af9ba 100755 --- a/scripts/mutect2_wdl/mutect2_nio.wdl +++ b/scripts/mutect2_wdl/mutect2_nio.wdl @@ -144,6 +144,7 @@ workflow Mutect2 { # If no tar is provided, the task downloads one from broads ftp server Int onco_tar_size = if defined(onco_ds_tar_gz) then ceil(size(onco_ds_tar_gz, "GB") * 3) else 100 + Int funco_tar_size = if defined(funco_data_sources_tar_gz) then ceil(size(funco_data_sources_tar_gz, "GB") * 3) else 100 Int gatk_override_size = if defined(gatk_override) then ceil(size(gatk_override, "GB")) else 0 # This is added to every task as padding, should increase if systematically you need more disk for every call @@ -360,6 +361,7 @@ workflow Mutect2 { filter_funcotations = filter_funcotations_or_default, sequencing_center = sequencing_center, sequence_source = sequence_source, + disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + onco_tar_size + disk_pad, extra_args = funcotator_extra_args } } From d4c5ef5c65adc678e63891d0d60ca82dac4f64a9 Mon Sep 17 00:00:00 2001 From: lichtens Date: Tue, 3 Jul 2018 13:55:13 -0400 Subject: [PATCH 14/15] Fixed broken test. --- .../hellbender/tools/funcotator/FuncotatorIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index fa141b14336..df2c5174713 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -1071,7 +1071,7 @@ public void testNoVariantsProduceMaf() { arguments.addArgument(FuncotatorArgumentDefinitions.REFERENCE_VERSION_LONG_NAME, FuncotatorTestConstants.REFERENCE_VERSION_HG19); arguments.addArgument(FuncotatorArgumentDefinitions.OUTPUT_FORMAT_LONG_NAME, outputFormatType.toString()); arguments.addArgument(FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_LONG_NAME, TranscriptSelectionMode.CANONICAL.toString()); - + arguments.addBooleanArgument(StandardArgumentDefinitions.DISABLE_SEQUENCE_DICT_VALIDATION_NAME, true); runCommandLine(arguments); final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), null); From 9df8d607b9593b78f09719771ac204c6e9a95c85 Mon Sep 17 00:00:00 2001 From: lichtens Date: Mon, 16 Jul 2018 09:44:59 -0400 Subject: [PATCH 15/15] Answering PRs. --- scripts/mutect2_wdl/mutect2.wdl | 9 +++------ scripts/mutect2_wdl/mutect2_nio.wdl | 11 ++++------- .../mafOutput/CustomMafFuncotationCreator.java | 2 +- .../tools/funcotator/mafOutput/MafOutputRenderer.java | 6 ++++-- 4 files changed, 12 insertions(+), 16 deletions(-) diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index be9ca3cedc4..10b40c03edd 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -1016,8 +1016,6 @@ task FuncotateMaf { String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else "" - String interval_list_arg = if defined(interval_list) then " -L " else "" - String extra_args_arg = select_first([extra_args, ""]) String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated" # ============== @@ -1033,8 +1031,7 @@ task FuncotateMaf { Boolean use_ssd = false # This should be updated when a new version of the data sources is released - # TODO: Make this dynamically chosen in the command. - String default_datasources_version = "funcotator_dataSources.v1.3.20180531" + String default_datasources_version = "funcotator_dataSources.v1.4.20180615" # You may have to change the following two parameter values depending on the task requirements Int default_ram_mb = 3000 @@ -1071,7 +1068,7 @@ task FuncotateMaf { -R ${ref_fasta} \ -V ${input_vcf} \ -O ${final_output_filename} \ - ${interval_list_arg} ${default="" interval_list} \ + ${"-L " + interval_list} \ ${"--transcript-selection-mode " + transcript_selection_mode} \ ${"--transcript-list " + transcript_selection_list} \ --annotation-default normal_barcode:${control_id} \ @@ -1081,7 +1078,7 @@ task FuncotateMaf { ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ ${filter_funcotations_args} \ - ${extra_args_arg} + ${extra_args} >>> runtime { diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl index f6f929af9ba..b65d4fba276 100755 --- a/scripts/mutect2_wdl/mutect2_nio.wdl +++ b/scripts/mutect2_wdl/mutect2_nio.wdl @@ -361,7 +361,7 @@ workflow Mutect2 { filter_funcotations = filter_funcotations_or_default, sequencing_center = sequencing_center, sequence_source = sequence_source, - disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + onco_tar_size + disk_pad, + disk_space_gb = ceil(size(funcotate_vcf_input, "GB") * large_input_to_output_multiplier) + funco_tar_size + disk_pad, extra_args = funcotator_extra_args } } @@ -983,8 +983,6 @@ task FuncotateMaf { String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else "" String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else "" String filter_funcotations_args = if (filter_funcotations) then " --remove-filtered-variants " else "" - String interval_list_arg = if defined(interval_list) then " -L " else "" - String extra_args_arg = select_first([extra_args, ""]) String final_output_filename = basename(input_vcf, ".vcf") + ".maf.annotated" # ============== @@ -1000,8 +998,7 @@ task FuncotateMaf { Boolean use_ssd = false # This should be updated when a new version of the data sources is released - # TODO: Make this dynamically chosen in the command. - String default_datasources_version = "funcotator_dataSources.v1.3.20180531" + String default_datasources_version = "funcotator_dataSources.v1.4.20180615" # You may have to change the following two parameter values depending on the task requirements Int default_ram_mb = 3000 @@ -1038,7 +1035,7 @@ task FuncotateMaf { -R ${ref_fasta} \ -V ${input_vcf} \ -O ${final_output_filename} \ - ${interval_list_arg} ${default="" interval_list} \ + ${"-L " + interval_list} \ ${"--transcript-selection-mode " + transcript_selection_mode} \ ${"--transcript-list " + transcript_selection_list} \ --annotation-default normal_barcode:${control_id} \ @@ -1048,7 +1045,7 @@ task FuncotateMaf { ${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \ ${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \ ${filter_funcotations_args} \ - ${extra_args_arg} + ${extra_args} >>> runtime { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java index 2c67d847411..ee2d15f44a7 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/CustomMafFuncotationCreator.java @@ -27,7 +27,7 @@ */ public class CustomMafFuncotationCreator { - final public static List COUNT_FIELD_NAMES = Arrays.asList( + public final static List COUNT_FIELD_NAMES = Arrays.asList( MafOutputRendererConstants.FieldName_t_alt_count, MafOutputRendererConstants.FieldName_t_ref_count, MafOutputRendererConstants.FieldName_n_alt_count, diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java index 4b076c18e9d..7f46a0e3221 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRenderer.java @@ -221,8 +221,10 @@ public MafOutputRenderer(final Path outputFilePath, @Override public void close() { if (!hasWrittenHeader) { - final LinkedHashMap mafCompliantOutputMap = createMafCompliantOutputMap(Allele.create("AT"), Collections.emptyList()); - writeHeader(new ArrayList<>(mafCompliantOutputMap.keySet())); + // The alt allele can be anything here. We just need to write the header, not any actual funcotations. + final String dummyAltAllele = "AT"; + final LinkedHashMap dummyMafCompliantOutputMap = createMafCompliantOutputMap(Allele.create(dummyAltAllele), Collections.emptyList()); + writeHeader(new ArrayList<>(dummyMafCompliantOutputMap.keySet())); } if ( printWriter != null ) { printWriter.flush();