Mercurial > repos > jjohnson > ensembl_variant_report
changeset 0:9f4ea174ce3d draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
| author | jjohnson |
|---|---|
| date | Thu, 14 Jun 2018 17:51:39 -0400 |
| parents | |
| children | a67b4de184c2 |
| files | ensembl_variant_report.py ensembl_variant_report.xml ensemblref.py test-data/GRCh38_X.2bit test-data/GRCh38_X.83.gtf test-data/GRCh38_X400k.tsv test-data/GRCh38_X400k_ANN.vcf test-data/GRCh38_X400k_EFF.vcf tool-data/twobit.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 10 files changed, 1177 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensembl_variant_report.py Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,253 @@ +#!/usr/bin/env python +""" +Report variants to Ensembl Transcripts + +FrameShift report line +# Gene Variant Position Reference Variation Prevalence Sequencing Depth Transcript AA Position AA change AA Length Stop Codon Stop Region AA Variation +TIGD6 chr5:149374879 AAG AG 1.00 13 ENSG00000164296|ENST00000296736 345 Q344 522 A-TGA-T KRWTSSRPST* + +MissSense report line +# Gene Variant Position Reference Variation Prevalence Sequencing Depth Transcript AA Position AA change AA Length Stop Codon Stop Region AA Variation +FN1 chr2:216235089 G A 1.00 7394 ENSG00000115414|ENST00000354785 2261 V2261I 2478 G-TAA TGLTRGATYN_I_IVEALKDQQR +""" +import sys +import os.path +import re +import time +import optparse +from ensemblref import EnsemblRef +from Bio.Seq import reverse_complement, translate + + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + #I/O + parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' ) + parser.add_option( '-s', '--format', dest='format', default='tabular', choices=['tabular','snpeff'], help='Tabular file with peptide_sequence column' ) + #Columns for tabular input + parser.add_option( '-C', '--chrom_column', type='int', dest='chrom_column', default=1, help='column ordinal with Ensembl transctip ID' ) + parser.add_option( '-P', '--pos_column', type='int', dest='pos_column', default=2, help='column ordinal with Ensembl transctip ID' ) + parser.add_option( '-R', '--ref_column', type='int', dest='ref_column', default=3, help='column ordinal with Ensembl transctip ID' ) + parser.add_option( '-A', '--alt_column', type='int', dest='alt_column', default=4, help='column ordinal with Ensembl transctip ID' ) + parser.add_option( '-T', '--transcript_column', type='int', dest='transcript_column', default=1, help='column ordinal with Ensembl transctip ID' ) + parser.add_option( '-F', '--dpr_column', type='int', dest='dpr_column', default=1, help='column with VCF: DPR or AD' ) + parser.add_option( '-D', '--dp_column', type='int', dest='dp_column', default=1, help='column with VCF: DP' ) + parser.add_option( '-g', '--gene_model', dest='gene_model', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.') + parser.add_option( '-2', '--twobit', dest='twobit', default=None, help='Reference genome in UCSC twobit format') + #Output file + parser.add_option( '-o', '--output', dest='output', default=None, help='The output report (else write to stdout)' ) + #filters + parser.add_option( '-d', '--min_depth', type='int', dest='min_depth', default=None, help='Minimum read depth to report' ) + parser.add_option( '-f', '--min_freq', type='float', dest='min_freq', default=None, help='Minimum variant frequency to report' ) + #peptide options + parser.add_option( '-l', '--leading_aa', type='int', dest='leading_aa', default=10, help='Number AAs before missense variant' ) + parser.add_option( '-t', '--trailing_aa', type='int', dest='trailing_aa', default=10, help='Number AAs after missense variant' ) + parser.add_option( '-r', '--readthrough', type='int', dest='readthrough', default=0, help='' ) + # + parser.add_option('--debug', dest='debug', action='store_true', default=False, help='Print debugging messages') + (options, args) = parser.parse_args() + + ##INPUTS## + if options.input != None: + try: + inputPath = os.path.abspath(options.input) + inputFile = open(inputPath, 'r') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(2) + else: + inputFile = sys.stdin + + if options.output != None: + try: + outputPath = os.path.abspath(options.output) + outputFile = open(outputPath, 'w') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(3) + else: + outputFile = sys.stdout + + def parse_tabular(): + ci = options.chrom_column - 1 + pi = options.pos_column - 1 + ri = options.ref_column - 1 + ai = options.alt_column - 1 + ti = options.transcript_column - 1 + di = options.dp_column - 1 + fi = options.dpr_column - 1 + for linenum,line in enumerate(inputFile): + if options.debug: + print >> sys.stderr, "%d: %s\n" % (linenum,line) + if line.startswith('#'): + continue + if line.strip() == '': + continue + fields = line.rstrip('\r\n').split('\t') + transcript = fields[ti] + if not transcript: + print >> sys.stderr, "%d: %s\n" % (linenum,line) + continue + chrom = fields[ci] + pos = int(fields[pi]) + ref = fields[ri] + alts = fields[ai] + dp = int(fields[di]) + dpr = [int(x) for x in fields[fi].split(',')] + for i,alt in enumerate(alts.split(',')): + freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None + yield (transcript,pos,ref,alt,dp,freq) + + def parse_snpeff_vcf(): + for linenum,line in enumerate(inputFile): + if line.startswith('##'): + if line.find('SnpEffVersion=') > 0: + SnpEffVersion = re.search('SnpEffVersion="?(\d+\.\d+)',line).groups()[0] + elif line.startswith('#CHROM'): + pass + else: + fields = line.strip('\r\n').split('\t') + if options.debug: print >> sys.stderr, "\n%s" % (fields) + (chrom, pos, id, ref, alts, qual, filter, info) = fields[0:8] + alt_list = alts.split(',') + pos = int(pos) + qual = float(qual) + dp = None + dpr = None + for info_item in info.split(';'): + if info_item.find('=') < 0: continue + (key, val) = info_item.split('=', 1) + if key == 'DP': + dp = int(val) + if key == 'DPR': + dpr = [int(x) for x in val.split(',')] + if key in ['EFF','ANN']: + for effect in val.split(','): + if options.debug: print >> sys.stderr, "\n%s" % (effect.split('|')) + if key == 'ANN': + (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|') + elif key == 'EFF': + (eff, effs) = effect.rstrip(')').split('(') + (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11] + i = alt_list.index(alt) if alt in alt_list else 0 + freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None + yield (transcript,pos,ref,alt,dp,freq) + + + #Process gene model + ens_ref = None + if options.gene_model != None: + try: + geneModelFile = os.path.abspath(options.gene_model) + twoBitFile = os.path.abspath(options.twobit) + print >> sys.stderr, "Parsing ensembl ref: %s %s" % (options.gene_model,options.twobit) + time1 = time.time() + ens_ref = EnsemblRef(geneModelFile,twoBitFile) + time2 = time.time() + print >> sys.stderr, "Parsing ensembl ref: %d seconds" % (int(time2-time1)) + except Exception, e: + print >> sys.stderr, "Parsing gene model failed: %s" % e + exit(2) + try: + parse_input = parse_tabular if options.format == 'tabular' else parse_snpeff_vcf + for tid,pos1,ref,alt,dp,freq in parse_input(): + if not tid: + continue + if options.min_depth and dp is not None and dp < options.min_depth: + continue + if options.min_freq and freq is not None and freq < options.min_freq: + continue + ## transcript_id, pos, ref, alt, dp, dpr + tx = ens_ref.get_gtf_transcript(tid) + if not tx: + continue + coding = ens_ref.transcript_is_coding(tid) + if not coding: + continue + frame_shift = len(ref) != len(alt) + cds = ens_ref.get_cds(tid) + pos0 = pos1 - 1 # zero based position + spos = pos0 if tx.gene.strand else pos0 + len(ref) - 1 + alt_seq = alt if tx.gene.strand else reverse_complement(alt) + ref_seq = ref if tx.gene.strand else reverse_complement(ref) + cds_pos = ens_ref.genome_to_cds_pos(tid, spos) + alt_cds = cds[:cds_pos] + alt_seq + cds[cds_pos+len(ref):] if cds_pos+len(ref) < len(cds) else '' + offset = 0 + if tx.gene.strand: + for i in range(min(len(ref),len(alt))): + if ref[i] == alt[i]: + offset = i + else: + break + else: + for i in range(-1,-min(len(ref),len(alt)) -1,-1): + if ref[i] == alt[i]: + offset = i + else: + break + refpep = translate(cds[:len(cds)/3*3]) + pep = translate(alt_cds[:len(alt_cds)/3*3]) + peplen = len(pep) + aa_pos = (cds_pos + offset) / 3 + if aa_pos >= len(pep): + print >> sys.stderr, "aa_pos %d >= peptide length %d : %s %d %s %s\n" % (aa_pos,len(pep),tid,pos1,ref,alt) + continue + if frame_shift: + #find stop_codons + nstops = 0 + stop_codons = [] + for i in range(aa_pos,peplen): + if refpep[i] != pep[i]: + aa_pos = i + break + for i in range(aa_pos,peplen): + if pep[i] == '*': + nstops += 1 + stop_codons.append("%s-%s%s" % (alt_cds[i*3-1],alt_cds[i*3:i*3+3],"-%s" % alt_cds[i*3+4] if len(alt_cds) > i*3 else '')) + if nstops > options.readthrough: + reported_peptide = pep[aa_pos:i+1] + reported_stop_codon = ','.join(stop_codons) + break + else: + reported_stop_codon = "%s-%s" % (alt_cds[peplen*3-4],alt_cds[peplen*3-3:peplen*3]) + reported_peptide = "%s_%s_%s" % (pep[max(aa_pos-options.leading_aa,0):aa_pos], + pep[aa_pos], + pep[aa_pos+1:min(aa_pos+1+options.trailing_aa,len(pep))]) + cs_pos = aa_pos * 3 + aa_pos = (cds_pos + offset) / 3 + ref_codon = cds[cs_pos:cs_pos+3] + ref_aa = translate(ref_codon) + alt_codon = alt_cds[cs_pos:cs_pos+3] + alt_aa = translate(alt_codon) + gene = tx.gene.names[0] + report_fields = [tx.gene.names[0], + '%s:%d %s' % (tx.gene.contig,pos1,'+' if tx.gene.strand else '-'), + ref_seq, + alt_seq, + "%1.2f" % freq if freq is not None else '', + str(dp), + "%s|%s" % (tx.gene.gene_id,tx.cdna_id), + "%d" % (aa_pos + 1), + "%s%d%s" % (ref_aa,aa_pos + 1,alt_aa), + "%d" % len(pep), + reported_stop_codon, + reported_peptide + ] + if options.debug: + report_fields.append("%d %d %d %d %s %s" % (cds_pos, offset, cs_pos,aa_pos,ref_codon,alt_codon)) + outputFile.write('\t'.join(report_fields)) + if options.debug: + print >> sys.stderr, "%s %s\n%s\n%s\n%s %s" % ( + cds[cs_pos-6:cs_pos], cds[cs_pos:cs_pos+15], + translate(cds[cs_pos-6:cs_pos+15]), + translate(alt_cds[cs_pos-6:cs_pos+15]), + alt_cds[cs_pos-6:cs_pos], alt_cds[cs_pos:cs_pos+15]) + outputFile.write('\n') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(1) + + +if __name__ == "__main__" : __main__() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensembl_variant_report.xml Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,193 @@ +<tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0"> + <requirements> + <requirement type="package" version="1.40">gtf_to_genes</requirement> + <requirement type="package" version="3.1.4">twobitreader</requirement> + <requirement type="package" version="1.62">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/ensembl_variant_report.py' + #if $ref.ref_source == 'cached': + --twobit="$ref.ref_loc.fields.path" + #else + --twobit="$ref.ref_file" + #end if + --gene_model="$gtf_file" + #if $variant.fmt == 'vcf': + --input="$variant.input_vcf" + --format=snpeff + #else + --input="$variant.input_tsv" + --pos_column=$variant.pos_column + --ref_column=$variant.ref_column + --alt_column=$variant.alt_column + --transcript_column=$variant.transcript_column + --dp_column=$variant.dp_column + --dpr_column=$variant.dpr_column + #end if + #if str($filter.min_depth) != '': + --min_depth=$filter.min_depth + #end if + #if str($filter.min_freq) != '': + --min_freq=$filter.min_freq + #end if + #if str($report.readthrough) != '': + --readthrough=$report.readthrough + #end if + #if str($report.leading_aa) != '': + --leading_aa=$report.leading_aa + #end if + #if str($report.trailing_aa) != '': + --trailing_aa=$report.trailing_aa + #end if + --output="$output" + ]]></command> + <inputs> + <conditional name="variant"> + <param name="fmt" type="select" label="Input format for variants"> + <option value="vcf">snpEff vcf</option> + <option value="tsv">tabular from snpsift extract</option> + </param> + <when value="vcf"> + <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/> + </when> + <when value="tsv"> + <param name="input_tsv" type="data" format="tabular" label="tabular file"/> + <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/> + <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/> + <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/> + <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/> + <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/> + <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/> + </when> + </conditional> + <conditional name="ref"> + <param name="ref_source" type="select" label="Source for Genomic Data"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_loc" type="select" label="Select reference 2bit file"> + <options from_data_table="twobit" /> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="twobit" label="reference 2bit file" /> + </when> + </conditional> + <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/> + <section name="filter" expanded="false" title="Filter Options"> + <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report" + help="If a value is entered, ignore variants with DP INFO field less than this value"/> + <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report" + help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/> + </section> + <section name="report" expanded="false" title="Report Options"> + <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/> + <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display" + help="Ignored for frame shifts"/> + <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display" + help="Ignored for frame shifts"/> + </section> + + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="readthrough" value="1"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="min_depth" value="100"/> + <param name="min_freq" value=".80"/> + <output name="output"> + <assert_contents> + <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" /> + <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="tsv"/> + <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="pos_column" value="2"/> + <param name="ref_column" value="3"/> + <param name="alt_column" value="4"/> + <param name="transcript_column" value="7"/> + <param name="dp_column" value="8"/> + <param name="dpr_column" value="9"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants. +Allows readthrough of stop codons, and reports the stop codons. + +Input can be a snpEff vcf file using either ANN or EFF annotations. +Alternatively, the input can be a tabular file that has columns: + + - pos + - ref + - alt + - Ensembl Transcript ID + - Read Depth (DP) + - AlleleDepth (DPR) + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt385</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensemblref.py Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,185 @@ +""" +with gtf and twobit +get_bed(transcript_id) +""" +from gtf_to_genes import gene, gene_utilities +from twobitreader import TwoBitFile +from Bio.Seq import reverse_complement, translate +import logging +logger = logging.getLogger("test") + +class EnsemblRef(object): + + def __init__(self,gtf_file,twobitfile,read_now=True): + self.gtf_file = gtf_file + self.twobitfile = twobitfile + self.twobit = TwoBitFile(self.twobitfile) + self.gene_dict = None + self.transcript_idx = None + self.name_idx = None + if read_now: + self.get_transcript_idx() + + + def get_gene_dict(self): + if self.gene_dict is None: + gene_structures = gene.t_parse_gtf('test') + self.gene_dict = gene_structures.get_genes(self.gtf_file,logger=logger) + return self.gene_dict + + + def get_transcript_idx(self): + if self.transcript_idx is None: + self.transcript_idx = gene_utilities.index_transcripts(self.get_gene_dict(),by_prot_id=False) + return self.transcript_idx + + + def get_name_idx(self): + if self.name_idx is None: + self.name_idx = dict() + for i,t in self.get_transcript_idx().items(): + for name in t.gene.names: + self.name_idx[name] = t.gene + for name in t.names: + self.name_idx[name] = t + if t.prot_id: + self.name_idx[t.prot_id] = t + return self.name_idx + + + def get_gtf_transcript(self,name): + idx = self.get_transcript_idx() + if name in idx: + return idx[name] + else: + nidx = self.get_name_idx() + if name in nidx: + return nidx[name] + return None + + + def transcript_is_coding(self,transcript_id): + tx = self.get_transcript_idx()[transcript_id] + return len(tx.start_codons) > 0 + + + def get_transcript_start_codon(self,transcript_id): + tx = self.get_transcript_idx()[transcript_id] + return tx.start_codons[0] if len(tx.start_codons) > 0 else None + + + def get_bed_line(self,transcript_id,score=0,itemRgb='0,0,0',coding=False): + tx = self.get_transcript_idx()[transcript_id] + chrom = tx.gene.contig + chromStart = tx.coding_beg if coding else tx.beg + chromEnd = tx.coding_end if coding else tx.end + name = transcript_id + strand = '+' if tx.gene.strand else '-' + thickStart = tx.coding_beg if tx.coding_beg else chromStart + thickEnd = tx.coding_end if tx.coding_end else chromEnd + exons = tx.get_coding_exons() if coding else tx.get_exons() + blockCount = len(exons) + if tx.gene.strand: + strand = '+' + blockSizes = [abs(e-s) for s,e in exons] + blockStarts = [s - chromStart for s,e in exons] + else: + strand = '-' + blockSizes = [abs(e-s) for s,e in reversed(exons)] + blockStarts = [s - chromStart for s,e in reversed(exons)] + blockSizes = ','.join([str(x) for x in blockSizes]) + blockStarts = ','.join([str(x) for x in blockStarts]) + return '%s\t%d\t%d\t%s\t%s\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) + + + def transcripts_in_range(self,chrom,startpos,endpos,strand=None): + spos = min(startpos,endpos) if endpos else startpos + epos = max(startpos,endpos) if endpos else startpos + transcripts = [] + for i,t in self.get_transcript_idx().items(): + if t.gene.contig == chrom and t.beg <= epos and spos <= t.end: + if strand and t.gene.strand != strand: + continue + transcripts.append(t) + return transcripts + + + def genes_in_range(self,chrom,startpos,endpos,strand=None,gene_types=None): + spos = min(startpos,endpos) if endpos else startpos + epos = max(startpos,endpos) if endpos else startpos + gene_dict = self.get_gene_dict() + gtypes = set(gene_types) & set(gene_dict.keys()) if gene_types else set(gene_dict.keys()) + genes = [] + for gt in gtypes: + for gene in gene_dict[gt]: + if gene.contig == chrom and gene.beg <= epos and spos <= gene.end: + if strand and gene.strand != strand: + continue + genes.append(gene) + return genes + + + def get_sequence(self,chrom,start,end): + if self.twobit: + if chrom in self.twobit: + return self.twobit[chrom][start:end] + contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom + if contig in self.twobit: + return self.twobit[contig][start:end] + return None + + + def sequence_sizes(self): + return self.twobit.sequence_sizes() + + + def get_transcript_seq(self,transcript_id,coding=False): + tx = self.get_transcript_idx()[transcript_id] + chrom = tx.gene.contig + exonbnds = tx.get_coding_exons() if coding else tx.get_exons() + if tx.gene.strand: + seqs = [self.get_sequence(chrom,s,e) for s,e in exonbnds] + else: + seqs = [reverse_complement(self.get_sequence(chrom,s,e)) for s,e in exonbnds] + return ''.join(seqs) + + + def get_cdna(self,transcript_id): + return self.get_transcript_seq(transcript_id,coding=False) + + + def get_cds(self,transcript_id): + return self.get_transcript_seq(transcript_id,coding=True) + + + def genome_to_transcript_pos(self,transcript_id,genome_pos,coding=False): + tx = self.get_transcript_idx()[transcript_id] + if not tx.beg <= genome_pos < tx.end: + return None + exonbnds = tx.get_coding_exons() if coding else tx.get_exons() + cdna_pos = 0 + if tx.gene.strand: + for s,e in exonbnds: + if s <= genome_pos < e: + cdna_pos += genome_pos - s + break + else: + cdna_pos += e - s + else: + for s,e in exonbnds: + if s <= genome_pos < e: + cdna_pos += e - genome_pos - 1 + break + else: + cdna_pos += e - s + return cdna_pos + + + def genome_to_cdna_pos(self,transcript_id,genome_pos): + return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=False) + + + def genome_to_cds_pos(self,transcript_id,genome_pos): + return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=True) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GRCh38_X.83.gtf Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,280 @@ +#!genome-build GRCh38.p5 +#!genome-version GRCh38 +#!genome-date 2013-12 +#!genome-build-accession NCBI:GCA_000001405.20 +#!genebuild-last-updated 2015-10 +X havana gene 253743 255091 . + . gene_id "ENSG00000228572"; gene_version "7"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; +X havana transcript 253743 255091 . + . gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)"; +X havana exon 253743 253846 . + . gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; exon_number "1"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; exon_id "ENSE00001702291"; exon_version "1"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)"; +X havana exon 254937 255091 . + . gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; exon_number "2"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; exon_id "ENSE00001655436"; exon_version "1"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)"; +X ensembl_havana gene 276322 303356 . + . gene_id "ENSG00000182378"; gene_version "13"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; +X havana transcript 276322 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 276322 276394 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001489430"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 291499 291654 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 291499 291654 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 293035 293218 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 293035 293218 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 299097 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001489377"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 299097 299332 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana stop_codon 299333 299335 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 276322 276394 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana three_prime_utr 299336 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)"; +X havana transcript 276324 291537 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; transcript_support_level "4 (assigned to previous version 6)"; +X havana exon 276324 276394 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00001536003"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00003657744"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00003581159"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)"; +X havana exon 290648 290792 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00001939272"; exon_version "2"; transcript_support_level "4 (assigned to previous version 6)"; +X havana exon 291499 291537 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00002190604"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)"; +X havana transcript 276353 291629 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 276353 276394 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00002160563"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 291499 291629 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00001740378"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana CDS 291499 291629 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana five_prime_utr 276353 276394 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)"; +X havana transcript 281055 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 281055 281121 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00001750899"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; protein_id "ENSP00000412018"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; protein_id "ENSP00000412018"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 281055 281121 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X ensembl_havana transcript 281192 303356 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 281192 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00001489388"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 291499 291654 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 291499 291654 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 293035 293218 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 293035 293218 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana exon 299097 303356 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00001489383"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana CDS 299097 299332 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana stop_codon 299333 299335 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana five_prime_utr 281192 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana three_prime_utr 299336 303356 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X havana transcript 281194 288787 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 281194 281256 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001719251"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; protein_id "ENSP00000400904"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 288733 288787 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001763472"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 288733 288787 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; protein_id "ENSP00000400904"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 281194 281256 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 281482 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X ensembl transcript 281462 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 281462 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002204149"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 291499 291654 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 291499 291654 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 293035 293218 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 293035 293218 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 299097 299465 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00001334714"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl CDS 299097 299332 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl stop_codon 299333 299335 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl exon 302837 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00001489403"; exon_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl five_prime_utr 281462 281684 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl three_prime_utr 299336 299465 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X ensembl three_prime_utr 302837 303353 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)"; +X havana transcript 283163 288829 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 283163 283201 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00002195046"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; protein_id "ENSP00000408558"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 288733 288829 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00002178523"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 288733 288829 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; protein_id "ENSP00000408558"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 283163 283201 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana transcript 283465 291639 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 283465 283488 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00001626975"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 291499 291639 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00001603661"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana CDS 291499 291639 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 283465 283488 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)"; +X havana transcript 283479 291629 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 283479 283520 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00001691645"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 284167 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 290648 290776 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 290648 290776 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana exon 291499 291629 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00001740378"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana CDS 291499 291629 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 283479 283520 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana five_prime_utr 284167 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)"; +X havana transcript 283734 290757 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 283734 284314 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00001621688"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana CDS 284188 284314 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana start_codon 284188 284190 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 288733 288869 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana CDS 288733 288869 . + 2 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 290648 290757 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00001690275"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana CDS 290648 290757 . + 0 gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X havana five_prime_utr 283734 284187 . + . gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)"; +X ensembl_havana gene 304529 318819 . - . gene_id "ENSG00000178605"; gene_version "13"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; +X havana transcript 304529 312463 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 311419 312463 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00001866313"; exon_version "2"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 307732 307880 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00003604694"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 307360 307512 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00003552346"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 304529 305197 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00001878585"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X ensembl_havana transcript 304750 318819 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 318439 318819 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003711516"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 318439 318787 . - 0 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana start_codon 318785 318787 . - 0 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 316914 317051 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003733507"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 316914 317051 . - 2 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 315229 315299 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003733593"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 315229 315299 . - 2 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 314890 315020 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003714129"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 314890 315020 . - 0 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 314150 314217 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "5"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003449454"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 314150 314217 . - 1 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "5"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 312766 312924 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "6"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001793174"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 312766 312924 . - 2 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "6"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 311419 311627 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001288218"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 311419 311627 . - 2 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 307732 307880 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "8"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003654058"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 307732 307880 . - 0 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "8"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 307360 307512 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003581203"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 307360 307512 . - 1 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana exon 304750 305197 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001797294"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana CDS 305077 305197 . - 1 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana stop_codon 305074 305076 . - 0 gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana five_prime_utr 318788 318819 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X ensembl_havana three_prime_utr 304750 305073 . - . gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)"; +X havana gene 320990 321851 . + . gene_id "ENSG00000226179"; gene_version "6"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; +X havana transcript 320990 321851 . + . gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X havana exon 320990 321248 . + . gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; exon_number "1"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; exon_id "ENSE00001675006"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X havana exon 321683 321851 . + . gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; exon_number "2"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; exon_id "ENSE00001778583"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)"; +X ensembl_havana gene 333963 386955 . - . gene_id "ENSG00000167393"; gene_version "17"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; +X ensembl_havana transcript 333963 386710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana exon 386368 386710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00001912068"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 386368 386691 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana start_codon 386689 386691 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana exon 361405 361590 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003653358"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 361405 361590 . - 0 gene_id "ENSG00000167393"; 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transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana exon 346174 346260 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003574906"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 346174 346260 . - 0 gene_id "ENSG00000167393"; 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havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003622978"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 338778 338896 . - 2 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "11"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana exon 338604 338710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "12"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003501875"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 338604 338710 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "12"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana exon 333963 334517 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00001844596"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana CDS 334370 334517 . - 1 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana stop_codon 334367 334369 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana five_prime_utr 386692 386710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X ensembl_havana three_prime_utr 333963 334366 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)"; +X havana transcript 334235 341711 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 341307 341711 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00001918099"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 340765 340940 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 338778 338896 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003592960"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 338604 338710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003534283"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 334235 334517 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00001489278"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana transcript 334239 347324 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 347234 347324 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001716328"; exon_version "2"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 346701 346775 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003571094"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 346174 346260 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003477290"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 345516 345672 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003641725"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 341307 341931 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001915623"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 340765 340940 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 338778 338896 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003592960"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana exon 334239 338710 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001815257"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)"; +X havana transcript 338613 345629 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana exon 345516 345629 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00001890387"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana exon 341883 341931 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003555172"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana exon 341307 341396 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003689816"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana exon 340765 340940 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana exon 338613 338896 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00001951758"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)"; +X havana transcript 340765 345626 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 345516 345626 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00001888244"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 341883 342237 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00001815626"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 341307 341396 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00003689816"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 340765 340940 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana transcript 341911 346514 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 346174 346514 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00001896157"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 345516 345672 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00003641725"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)"; +X havana exon 341911 341931 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00001911121"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)"; +X havana transcript 344896 386955 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 386368 386955 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001912680"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 362255 362332 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001847312"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 361405 361590 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003585491"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 347590 347693 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003475055"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 347234 347336 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 346701 346775 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003571094"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 346174 346260 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003477290"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana exon 344896 345672 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001950030"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)"; +X havana transcript 346637 361516 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 361405 361516 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00001916804"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 347590 347693 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00003475055"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 347234 347336 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 346637 346775 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00001851476"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana transcript 346720 347838 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 347590 347838 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00001843788"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 347234 347336 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana exon 346720 346775 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00001849084"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)"; +X havana transcript 347611 374044 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana exon 373532 374044 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00001489321"; exon_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana CDS 373532 373771 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana start_codon 373769 373771 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana exon 361405 361590 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00003653358"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana CDS 361405 361590 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana exon 347611 347693 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00001877883"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana CDS 347611 347693 . - 0 gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)"; +X havana five_prime_utr 373772 374044 . - . gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GRCh38_X400k.tsv Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,62 @@ +#CHROM POS REF ALT ANN[*].EFFECT ANN[*].GENE ANN[*].FEATUREID DP DPR ANN[*].CDS_POS ANN[*].HGVS_C ANN[*].HGVS_P ANN[*].AA_POS ANN[*].BIOTYPE +X 284201 T C missense_variant PLCXD1 ENST00000381657 693 1,598 14 n.14T>C p.Val5Ala 5 ensembl_havana +X 284201 T C missense_variant PLCXD1 ENST00000399012 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000430923 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000445062 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000429181 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000381663 693 1,598 14 n.14T>C p.Val5Ala 5 ensembl +X 284201 T C missense_variant PLCXD1 ENST00000443019 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000415337 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000447472 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 284201 T C missense_variant PLCXD1 ENST00000448477 693 1,598 14 n.14T>C p.Val5Ala 5 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000381657 21 3,10 247 n.246_247insC p.Lys83fs 83 ensembl_havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000399012 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000430923 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000445062 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000381663 21 3,10 247 n.246_247insC p.Lys83fs 83 ensembl +X 288851 G GC frameshift_variant PLCXD1 ENST00000415337 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000447472 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 288851 G GC frameshift_variant PLCXD1 ENST00000448477 21 3,10 247 n.246_247insC p.Lys83fs 83 havana +X 290695 C G missense_variant PLCXD1 ENST00000381657 910 130,681 312 n.312C>G p.Asp104Glu 104 ensembl_havana +X 290695 C G missense_variant PLCXD1 ENST00000399012 910 130,681 312 n.312C>G p.Asp104Glu 104 havana +X 290695 C G missense_variant PLCXD1 ENST00000484611 910 130,681 404 n.404C>G p.Thr135Ser 135 havana +X 290695 C G missense_variant PLCXD1 ENST00000430923 910 130,681 312 n.312C>G p.Asp104Glu 104 havana +X 290695 C G missense_variant PLCXD1 ENST00000381663 910 130,681 312 n.312C>G p.Asp104Glu 104 ensembl +X 290695 C G missense_variant PLCXD1 ENST00000415337 910 130,681 312 n.312C>G p.Asp104Glu 104 havana +X 290695 C G missense_variant PLCXD1 ENST00000447472 910 130,681 312 n.312C>G p.Asp104Glu 104 havana +X 290695 C G missense_variant PLCXD1 ENST00000448477 910 130,681 312 n.312C>G p.Asp104Glu 104 havana +X 299221 G C missense_variant PLCXD1 ENST00000381657 18 3,13 858 n.858G>C p.Glu286Asp 286 ensembl_havana +X 299221 G C missense_variant PLCXD1 ENST00000399012 18 3,13 858 n.858G>C p.Glu286Asp 286 havana +X 299221 G C missense_variant PLCXD1 ENST00000381663 18 3,13 858 n.858G>C p.Glu286Asp 286 ensembl +X 307850 G C missense_variant GTPBP6 ENST00000485332 24 7,8 1076 n.1076C>G p.Pro359Arg 359 havana +X 307850 G C missense_variant GTPBP6 ENST00000326153 24 7,8 1156 n.1156C>G p.His386Asp 386 ensembl_havana +X 311500 C CAT frameshift_variant GTPBP6 ENST00000485332 56 11,22 963 n.963_964insAT p.Gly322fs 321 havana +X 311500 C CAT frameshift_variant GTPBP6 ENST00000326153 56 11,22 1043 n.1043_1044insAT p.Asp349fs 348 ensembl_havana +X 334496 A G missense_variant PPP2R3B ENST00000477110 159 52,60 5545 n.5545T>C p.Cys1849Arg 1849 havana +X 334496 A G missense_variant PPP2R3B ENST00000479438 159 52,60 829 n.829T>C p.Cys277Arg 277 havana +X 338625 G A missense_variant PPP2R3B ENST00000390665 308 146,132 1556 n.1556C>T p.Ala519Val 519 ensembl_havana +X 338625 G A missense_variant PPP2R3B ENST00000468169 308 146,132 701 n.701C>T p.Ala234Val 234 havana +X 338627 A G missense_variant PPP2R3B ENST00000477110 301 0,271 1414 n.1414T>C p.Cys472Arg 472 havana +X 338627 A G missense_variant PPP2R3B ENST00000479438 301 0,271 784 n.784T>C p.Cys262Arg 262 havana +X 338856 A G missense_variant PPP2R3B ENST00000468169 517 15,390 470 n.470T>C p.Leu157Pro 157 havana +X 340856 CTG C frameshift_variant PPP2R3B ENST00000477110 17 0,11 1118 n.1118_1119delCA p.Ala373fs 373 havana +X 340856 CTG C frameshift_variant PPP2R3B ENST00000390665 17 0,11 1258 n.1258_1259delCA p.Gln420fs 420 ensembl_havana +X 340856 CTG C frameshift_variant PPP2R3B ENST00000479438 17 0,11 488 n.488_489delCA p.Ala163fs 163 havana +X 340856 CTG C frameshift_variant PPP2R3B ENST00000468169 17 0,11 336 n.336_337delCA p.Ser112fs 112 havana +X 340856 CTG C frameshift_variant PPP2R3B ENST00000484364 17 0,11 639 n.639_640delCA p.Ser213fs 213 havana +X 340928 C CA frameshift_variant PPP2R3B ENST00000477110 65 0,50 1047 n.1047_1048insT p.Val350fs 349 havana +X 340928 C CA frameshift_variant PPP2R3B ENST00000390665 65 0,50 1187 n.1187_1188insT p.Trp396fs 396 ensembl_havana +X 340928 C CA frameshift_variant PPP2R3B ENST00000479438 65 0,50 417 n.417_418insT p.Val140fs 139 havana +X 340928 C CA frameshift_variant PPP2R3B ENST00000468169 65 0,50 265 n.265_266insT p.Gly89fs 89 havana +X 340928 C CA frameshift_variant PPP2R3B ENST00000484364 65 0,50 568 n.568_569insT p.Gly190fs 190 havana +X 341347 A C,G missense_variant PPP2R3B ENST00000477110 48 0,20,15 995 n.995T>G p.Leu332Arg 332 havana +X 341347 A C,G missense_variant PPP2R3B ENST00000477110 48 0,20,15 995 n.995T>C p.Leu332Pro 332 havana +X 341347 A C,G missense_variant PPP2R3B ENST00000390665 48 0,20,15 1135 n.1135T>G p.Trp379Gly 379 ensembl_havana +X 341347 A C,G missense_variant PPP2R3B ENST00000390665 48 0,20,15 1135 n.1135T>C p.Trp379Arg 379 ensembl_havana +X 341347 A C,G missense_variant PPP2R3B ENST00000479438 48 0,20,15 365 n.365T>G p.Leu122Arg 122 havana +X 341347 A C,G missense_variant PPP2R3B ENST00000479438 48 0,20,15 365 n.365T>C p.Leu122Pro 122 havana +X 345580 G A missense_variant PPP2R3B ENST00000390665 6 0,4 972 n.972C>T p.Trp324Cys 324 ensembl_havana +X 345580 G A missense_variant PPP2R3B ENST00000468169 6 0,4 50 n.50C>T p.Gly17Val 17 havana +X 345580 G A missense_variant PPP2R3B ENST00000484364 6 0,4 47 n.47C>T p.Gly16Val 16 havana +X 345580 G A missense_variant PPP2R3B ENST00000477636 6 0,4 434 n.434C>T p.Gly145Val 145 havana +X 345580 G A missense_variant PPP2R3B ENST00000445792 6 0,4 1314 n.1314C>T p.Trp438Cys 438 havana
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GRCh38_X400k_ANN.vcf Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,85 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.2+htslib-1.2.1 +##samtoolsCommand=samtools mpileup -f /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa --BCF --output-tags DP,DPR,DV,DP4,INFO/DPR,SP --output /panfs/roc/galaxy/GALAXYP/files/000/144/dataset_144978.dat localbam_0.bam +##reference=file:///panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa +##contig=<ID=1,length=248956422> +##contig=<ID=2,length=242193529> +##contig=<ID=3,length=198295559> +##contig=<ID=4,length=190214555> +##contig=<ID=5,length=181538259> +##contig=<ID=6,length=170805979> +##contig=<ID=7,length=159345973> +##contig=<ID=8,length=145138636> +##contig=<ID=9,length=138394717> +##contig=<ID=10,length=133797422> +##contig=<ID=11,length=135086622> +##contig=<ID=12,length=133275309> +##contig=<ID=13,length=114364328> +##contig=<ID=14,length=107043718> +##contig=<ID=15,length=101991189> +##contig=<ID=16,length=90338345> +##contig=<ID=17,length=83257441> +##contig=<ID=18,length=80373285> +##contig=<ID=19,length=58617616> +##contig=<ID=20,length=64444167> +##contig=<ID=21,length=46709983> +##contig=<ID=22,length=50818468> +##contig=<ID=X,length=156040895> +##contig=<ID=Y,length=57227415> +##contig=<ID=MT,length=16569> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases"> +##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases"> +##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)"> +##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##bcftools_callVersion=1.3+htslib-1.3 +##bcftools_callCommand=call -m --variants-only --output-type b --threads 1 input.bcf +##bcftools_viewVersion=1.3+htslib-1.3 +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets ^Mt --output-type v --threads 1 input.bcf +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets X --output-type v --threads 1 input.vcf.gz +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --regions X:1-400000 --output-type v --threads 1 input.vcf.gz +##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -no CDS -no CHROMOSOME_LARGE_DELETION -no CODON_CHANGE -no CODON_INSERTION -no CODON_CHANGE_PLUS_CODON_INSERTION -no CODON_DELETION -no CODON_CHANGE_PLUS_CODON_DELETION -no DOWNSTREAM -no EXON -no EXON_DELETED -no GENE -no INTERGENIC -no INTERGENIC_CONSERVED -no INTRAGENIC -no INTRON -no INTRON_CONSERVED -no MICRO_RNA -no NON_SYNONYMOUS_START -no NON_SYNONYMOUS_STOP -no RARE_AMINO_ACID -no SPLICE_SITE_ACCEPTOR -no SPLICE_SITE_DONOR -no SPLICE_SITE_REGION -no SPLICE_SITE_BRANCH -no SPLICE_SITE_BRANCH_U12 -no STOP_LOST -no START_GAINED -no START_LOST -no STOP_GAINED -no SYNONYMOUS_CODING -no SYNONYMOUS_START -no SYNONYMOUS_STOP -no REGULATION -no UPSTREAM -no UTR_3_PRIME -no UTR_3_DELETED -no UTR_5_PRIME -no UTR_5_DELETED -no NEXT_PROT -stats /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148016.dat GRCh38.78 /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148008.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##SnpSiftVersion="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani" +##SnpSiftCmd="SnpSift filter -f /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148015.dat -e /panfs/roc/galaxy/GALAXYP/job_working_directory/000/126/126606/tmpTp3aAM" +##FILTER=<ID=SnpSift,Description="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani, Expression used: ( ANN[*].EFFECT has 'missense_variant' | ANN[*].EFFECT has 'frameshift_variant')"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam +X 284201 . T C 219.0 . DP=693;VDB=0.999766;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.382033;BQB=1;MQ0F=0.001443;DPR=1,598;AC=2;AN=2;DP4=1,0,425,173;MQ=17;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|2/7|n.14T>C|p.Val5Ala|528/5507|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|3/8|n.14T>C|p.Val5Ala|311/5287|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|3/4|n.14T>C|p.Val5Ala|305/555|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000429181|havana|3/4|n.14T>C|p.Val5Ala|301/469|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|2/8|n.14T>C|p.Val5Ala|258/1863|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000443019|havana|2/3|n.14T>C|p.Val5Ala|74/284|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|2/5|n.14T>C|p.Val5Ala|59/579|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|1/3|n.14T>C|p.Val5Ala|468/828|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 1/1:246,255,0:599:598:0:1,0,425,173:1,598 +X 288851 . G GC 30.4966 . DP=21;VDB=0.0115453;SGB=-0.670168;RPB=0.597928;MQB=1;BQB=0.968368;MQ0F=0;DPR=3,10;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,10,0;MQ=20;ANN=GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|3/7|n.246_247insC|p.Lys83fs|761/5507|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|4/8|n.246_247insC|p.Lys83fs|544/5287|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|4/4|n.246_247insC|p.Lys83fs|538/555|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|3/8|n.246_247insC|p.Lys83fs|491/1863|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|3/5|n.246_247insC|p.Lys83fs|292/579|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|2/3|n.246_247insC|p.Lys83fs|701/828|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 0/1:64,0,15:13:10:0:3,0,10,0:3,10 +X 290695 . C G 114.0 . DP=910;VDB=0.336517;SGB=-0.693147;RPB=0.479982;MQB=0.997299;MQSB=0.999049;BQB=0.555736;MQ0F=0.010989;DPR=130,681;AC=2;AN=2;DP4=72,58,392,289;MQ=18;ANN=G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|4/7|n.312C>G|p.Asp104Glu|826/5507|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|5/8|n.312C>G|p.Asp104Glu|609/5287|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000484611|havana|4/5|n.404C>G|p.Thr135Ser|404/540|404/-1|135/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|4/8|n.312C>G|p.Asp104Glu|556/1863|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|4/5|n.312C>G|p.Asp104Glu|357/579|312/-1|104/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|3/3|n.312C>G|p.Asp104Glu|766/828|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 1/1:141,210,0:811:681:2:72,58,392,289:130,681 +X 299221 . G C 77.0 . DP=18;VDB=0.00122481;SGB=-0.683931;RPB=0.169694;MQB=1;MQSB=1;BQB=0.560355;MQ0F=0;DPR=3,13;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,9,4;MQ=20;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|7/7|n.858G>C|p.Glu286Asp|1372/5507|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|8/8|n.858G>C|p.Glu286Asp|1155/5287|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|7/8|n.858G>C|p.Glu286Asp|1102/1863|858/-1|286/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:110,0,10:16:13:3:1,2,9,4:3,13 +X 307850 . G C 40.3947 . DP=24;VDB=0.351291;SGB=-0.651104;RPB=0.511891;MQB=1;MQSB=1;BQB=0.720273;MQ0F=0;DPR=7,8;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,6,2;MQ=20;ANN=C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|2/4|n.1076C>G|p.Pro359Arg|1076/2016|1076/-1|359/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|8/10|n.1156C>G|p.His386Asp|1188/1907|1156/-1|386/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:73,0,69:15:8:0:5,2,6,2:7,8 +X 311500 . C CAT 59.0 . DP=56;VDB=0.625112;SGB=-0.692562;RPB=0.999818;MQB=0.915545;MQSB=0.982508;BQB=0.929674;MQ0F=0;DPR=11,22;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,19,3;MQ=18;ANN=CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|1/4|n.963_964insAT|p.Gly322fs|963/2016|963/-1|321/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|7/10|n.1043_1044insAT|p.Asp349fs|1075/1907|1043/-1|348/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:92,0,40:33:22:3:11,0,19,3:11,22 +X 334496 . A G 30.4121 . DP=159;VDB=0.0384616;SGB=-0.693147;RPB=0.000107797;MQB=0.271035;MQSB=0.730753;BQB=0.124283;MQ0F=0.0880503;DPR=52,60;ICB=1;HOB=0.5;AC=1;AN=2;DP4=48,4,58,3;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.5545T>C|p.Cys1849Arg|5545/5802|5545/-1|1849/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|5/5|n.829T>C|p.Cys277Arg|829/1090|829/-1|277/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 0/1:63,0,72:113:61:2:48,4,58,3:52,60 +X 338625 . G A 74.0 . DP=308;VDB=6.22534e-11;SGB=-0.693147;RPB=0.0585974;MQB=0.956346;MQSB=0.973687;BQB=0.279044;MQ0F=0.0681818;DPR=146,132;ICB=1;HOB=0.5;AC=1;AN=2;DP4=122,24,108,24;MQ=16;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|12/13|n.1556C>T|p.Ala519Val|1575/2151|1556/-1|519/-1||,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.701C>T|p.Ala234Val|701/713|701/-1|234/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 0/1:107,0,99:278:132:1:122,24,108,24:146,132 +X 338627 . A G 190.0 . DP=301;VDB=1.9745e-09;SGB=-0.693147;MQSB=0.973119;MQ0F=0.0697674;DPR=0,271;AC=2;AN=2;DP4=0,0,229,42;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.1414T>C|p.Cys472Arg|1414/5802|1414/-1|472/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|4/5|n.784T>C|p.Cys262Arg|784/1090|784/-1|262/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:217,255,0:271:271:0:0,0,229,42:0,271 +X 338856 . A G 182.0 . DP=517;VDB=0.238596;SGB=-0.693147;RPB=0.857702;MQB=0.810962;MQSB=0.0368774;BQB=0.944745;MQ0F=0.0135397;DPR=15,390;AC=2;AN=2;DP4=7,8,244,146;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.470T>C|p.Leu157Pro|470/713|470/-1|157/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:209,255,0:405:390:6:7,8,244,146:15,390 +X 340856 . CTG C 107.0 . DP=17;VDB=3.781e-05;SGB=-0.676189;MQSB=0.8618;MQ0F=0;DPR=0,11;AC=2;AN=2;DP4=0,0,6,5;MQ=18;ANN=C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1118_1119delCA|p.Ala373fs|1119/5802|1118/-1|373/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1258_1259delCA|p.Gln420fs|1278/2151|1258/-1|420/-1||,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.488_489delCA|p.Ala163fs|489/1090|488/-1|163/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.336_337delCA|p.Ser112fs|337/713|336/-1|112/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.639_640delCA|p.Ser213fs|640/732|639/-1|213/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:134,33,0:11:11:0:0,0,6,5:0,11 +X 340928 . C CA 181.0 . DP=65;VDB=2.0017e-11;SGB=-0.693147;MQSB=0.996914;MQ0F=0;DPR=0,50;AC=2;AN=2;DP4=0,0,21,29;MQ=19;ANN=CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1047_1048insT|p.Val350fs|1047/5802|1047/-1|349/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1187_1188insT|p.Trp396fs|1206/2151|1187/-1|396/-1||,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.417_418insT|p.Val140fs|417/1090|417/-1|139/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.265_266insT|p.Gly89fs|265/713|265/-1|89/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.568_569insT|p.Gly190fs|568/732|568/-1|190/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:208,151,0:50:50:0:0,0,21,29:0,50 +X 341347 . A C,G 170.0 . DP=48;VDB=0.802018;SGB=-0.693136;MQSB=0.969233;MQ0F=0;DPR=0,20,15;AC=2;AN=2;DP4=0,0,20,15;MQ=19;ANN=C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>G|p.Leu332Arg|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>C|p.Leu332Pro|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>G|p.Trp379Gly|1154/2151|1135/-1|379/-1||,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>C|p.Trp379Arg|1154/2151|1135/-1|379/-1||,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>G|p.Leu122Arg|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>C|p.Leu122Pro|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:197,105,0:35:35:0:0,0,20,15:0,20,15 +X 345580 . G A 41.8455 . DP=6;VDB=0.910845;SGB=-0.556411;MQSB=1;MQ0F=0;DPR=0,4;AC=2;AN=2;DP4=0,0,3,1;MQ=20;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|7/13|n.972C>T|p.Trp324Cys|991/2151|972/-1|324/-1||WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|1/5|n.50C>T|p.Gly17Val|50/713|50/-1|17/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|1/4|n.47C>T|p.Gly16Val|47/732|47/-1|16/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477636|havana|2/3|n.434C>T|p.Gly145Val|434/519|434/-1|145/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000445792|havana|8/8|n.1314C>T|p.Trp438Cys|1314/1998|1314/-1|438/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME GT:PL:DP:DV:SP:DP4:DPR 1/1:69,12,0:4:4:0:0,0,3,1:0,4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GRCh38_X400k_EFF.vcf Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,85 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.2+htslib-1.2.1 +##samtoolsCommand=samtools mpileup -f /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa --BCF --output-tags DP,DPR,DV,DP4,INFO/DPR,SP --output /panfs/roc/galaxy/GALAXYP/files/000/144/dataset_144978.dat localbam_0.bam +##reference=file:///panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa +##contig=<ID=1,length=248956422> +##contig=<ID=2,length=242193529> +##contig=<ID=3,length=198295559> +##contig=<ID=4,length=190214555> +##contig=<ID=5,length=181538259> +##contig=<ID=6,length=170805979> +##contig=<ID=7,length=159345973> +##contig=<ID=8,length=145138636> +##contig=<ID=9,length=138394717> +##contig=<ID=10,length=133797422> +##contig=<ID=11,length=135086622> +##contig=<ID=12,length=133275309> +##contig=<ID=13,length=114364328> +##contig=<ID=14,length=107043718> +##contig=<ID=15,length=101991189> +##contig=<ID=16,length=90338345> +##contig=<ID=17,length=83257441> +##contig=<ID=18,length=80373285> +##contig=<ID=19,length=58617616> +##contig=<ID=20,length=64444167> +##contig=<ID=21,length=46709983> +##contig=<ID=22,length=50818468> +##contig=<ID=X,length=156040895> +##contig=<ID=Y,length=57227415> +##contig=<ID=MT,length=16569> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases"> +##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases"> +##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)"> +##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##bcftools_callVersion=1.3+htslib-1.3 +##bcftools_callCommand=call -m --variants-only --output-type b --threads 1 input.bcf +##bcftools_viewVersion=1.3+htslib-1.3 +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets ^Mt --output-type v --threads 1 input.bcf +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets X --output-type v --threads 1 input.vcf.gz +##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --regions X:1-400000 --output-type v --threads 1 input.vcf.gz +##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -classic -formatEff -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -no CDS -no CHROMOSOME_LARGE_DELETION -no CODON_CHANGE -no CODON_INSERTION -no CODON_CHANGE_PLUS_CODON_INSERTION -no CODON_DELETION -no CODON_CHANGE_PLUS_CODON_DELETION -no DOWNSTREAM -no EXON -no EXON_DELETED -no GENE -no INTERGENIC -no INTERGENIC_CONSERVED -no INTRAGENIC -no INTRON -no INTRON_CONSERVED -no MICRO_RNA -no NON_SYNONYMOUS_START -no NON_SYNONYMOUS_STOP -no RARE_AMINO_ACID -no SPLICE_SITE_ACCEPTOR -no SPLICE_SITE_DONOR -no SPLICE_SITE_REGION -no SPLICE_SITE_BRANCH -no SPLICE_SITE_BRANCH_U12 -no STOP_LOST -no START_GAINED -no START_LOST -no STOP_GAINED -no SYNONYMOUS_CODING -no SYNONYMOUS_START -no SYNONYMOUS_STOP -no REGULATION -no UPSTREAM -no UTR_3_PRIME -no UTR_3_DELETED -no UTR_5_PRIME -no UTR_5_DELETED -no NEXT_PROT -stats /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148027.dat GRCh38.78 /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148008.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##SnpSiftVersion="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani" +##SnpSiftCmd="SnpSift filter -f /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148026.dat -e /panfs/roc/galaxy/GALAXYP/job_working_directory/000/126/126614/tmpzEvowV" +##FILTER=<ID=SnpSift,Description="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani, Expression used: ( EFF[*].EFFECT has 'NON_SYNONYMOUS_CODING' | EFF[*].EFFECT has 'FRAME_SHIFT')"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam +X 284201 . T C 219.0 . DP=693;VDB=0.999766;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.382033;BQB=1;MQ0F=0.001443;DPR=1,598;AC=2;AN=2;DP4=1,0,425,173;MQ=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|ensembl_havana||ENST00000381657|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000399012|3|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000430923|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000445062|3|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000429181|3|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|ensembl||ENST00000381663|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000443019|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000415337|2|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000447472|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000448477|1|C|WARNING_TRANSCRIPT_INCOMPLETE) GT:PL:DP:DV:SP:DP4:DPR 1/1:246,255,0:599:598:0:1,0,425,173:1,598 +X 288851 . G GC 30.4966 . DP=21;VDB=0.0115453;SGB=-0.670168;RPB=0.597928;MQB=1;BQB=0.968368;MQ0F=0;DPR=3,10;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,10,0;MQ=20;EFF=FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|ensembl_havana||ENST00000381657|3|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000399012|4|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000430923|3|GC|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000445062|4|GC|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|ensembl||ENST00000381663|3|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000415337|3|GC|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000447472|3|GC|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000448477|2|GC|WARNING_TRANSCRIPT_INCOMPLETE) GT:PL:DP:DV:SP:DP4:DPR 0/1:64,0,15:13:10:0:3,0,10,0:3,10 +X 290695 . C G 114.0 . DP=910;VDB=0.336517;SGB=-0.693147;RPB=0.479982;MQB=0.997299;MQSB=0.999049;BQB=0.555736;MQ0F=0.010989;DPR=130,681;AC=2;AN=2;DP4=72,58,392,289;MQ=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|ensembl_havana||ENST00000381657|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000399012|5|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aGc|T135S||PLCXD1|havana||ENST00000484611|4|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000430923|4|G|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|ensembl||ENST00000381663|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000415337|4|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000447472|4|G|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000448477|3|G|WARNING_TRANSCRIPT_INCOMPLETE) GT:PL:DP:DV:SP:DP4:DPR 1/1:141,210,0:811:681:2:72,58,392,289:130,681 +X 299221 . G C 77.0 . DP=18;VDB=0.00122481;SGB=-0.683931;RPB=0.169694;MQB=1;MQSB=1;BQB=0.560355;MQ0F=0;DPR=3,13;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,9,4;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|ensembl_havana||ENST00000381657|7|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|havana||ENST00000399012|8|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|ensembl||ENST00000381663|7|C) GT:PL:DP:DV:SP:DP4:DPR 0/1:110,0,10:16:13:3:1,2,9,4:3,13 +X 307850 . G C 40.3947 . DP=24;VDB=0.351291;SGB=-0.651104;RPB=0.511891;MQB=1;MQSB=1;BQB=0.720273;MQ0F=0;DPR=7,8;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,6,2;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P359R||GTPBP6|havana||ENST00000485332|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H386D||GTPBP6|ensembl_havana||ENST00000326153|8|C) GT:PL:DP:DV:SP:DP4:DPR 0/1:73,0,69:15:8:0:5,2,6,2:7,8 +X 311500 . C CAT 59.0 . DP=56;VDB=0.625112;SGB=-0.692562;RPB=0.999818;MQB=0.915545;MQSB=0.982508;BQB=0.929674;MQ0F=0;DPR=11,22;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,19,3;MQ=18;EFF=FRAME_SHIFT(HIGH||cgt/cgtAT|R321R?||GTPBP6|havana||ENST00000485332|1|CAT|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||gtg/gtATg|V348V?||GTPBP6|ensembl_havana||ENST00000326153|7|CAT) GT:PL:DP:DV:SP:DP4:DPR 0/1:92,0,40:33:22:3:11,0,19,3:11,22 +X 334496 . A G 30.4121 . DP=159;VDB=0.0384616;SGB=-0.693147;RPB=0.000107797;MQB=0.271035;MQSB=0.730753;BQB=0.124283;MQ0F=0.0880503;DPR=52,60;ICB=1;HOB=0.5;AC=1;AN=2;DP4=48,4,58,3;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1849R||PPP2R3B|havana||ENST00000477110|8|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C277R||PPP2R3B|havana||ENST00000479438|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 0/1:63,0,72:113:61:2:48,4,58,3:52,60 +X 338625 . G A 74.0 . DP=308;VDB=6.22534e-11;SGB=-0.693147;RPB=0.0585974;MQB=0.956346;MQSB=0.973687;BQB=0.279044;MQ0F=0.0681818;DPR=146,132;ICB=1;HOB=0.5;AC=1;AN=2;DP4=122,24,108,24;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A519V||PPP2R3B|ensembl_havana||ENST00000390665|12|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A234V||PPP2R3B|havana||ENST00000468169|5|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 0/1:107,0,99:278:132:1:122,24,108,24:146,132 +X 338627 . A G 190.0 . DP=301;VDB=1.9745e-09;SGB=-0.693147;MQSB=0.973119;MQ0F=0.0697674;DPR=0,271;AC=2;AN=2;DP4=0,0,229,42;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C472R||PPP2R3B|havana||ENST00000477110|8|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C262R||PPP2R3B|havana||ENST00000479438|4|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 1/1:217,255,0:271:271:0:0,0,229,42:0,271 +X 338856 . A G 182.0 . DP=517;VDB=0.238596;SGB=-0.693147;RPB=0.857702;MQB=0.810962;MQSB=0.0368774;BQB=0.944745;MQ0F=0.0135397;DPR=15,390;AC=2;AN=2;DP4=7,8,244,146;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L157P||PPP2R3B|havana||ENST00000468169|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 1/1:209,255,0:405:390:6:7,8,244,146:15,390 +X 340856 . CTG C 107.0 . DP=17;VDB=3.781e-05;SGB=-0.676189;MQSB=0.8618;MQ0F=0;DPR=0,11;AC=2;AN=2;DP4=0,0,6,5;MQ=18;EFF=FRAME_SHIFT(HIGH||gca/|A373||PPP2R3B|havana||ENST00000477110|6|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||cag/|Q420||PPP2R3B|ensembl_havana||ENST00000390665|10|C),FRAME_SHIFT(HIGH||gca/|A163||PPP2R3B|havana||ENST00000479438|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||agcagt/|SS112||PPP2R3B|havana||ENST00000468169|4|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||agcagt/|SS213||PPP2R3B|havana||ENST00000484364|4|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 1/1:134,33,0:11:11:0:0,0,6,5:0,11 +X 340928 . C CA 181.0 . DP=65;VDB=2.0017e-11;SGB=-0.693147;MQSB=0.996914;MQ0F=0;DPR=0,50;AC=2;AN=2;DP4=0,0,21,29;MQ=19;EFF=FRAME_SHIFT(HIGH||ctg/ctgT|L349L?||PPP2R3B|havana||ENST00000477110|6|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||tgg/tgTg|W396C?||PPP2R3B|ensembl_havana||ENST00000390665|10|CA),FRAME_SHIFT(HIGH||ctg/ctgT|L139L?||PPP2R3B|havana||ENST00000479438|2|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||ggt/gTgt|G89V?||PPP2R3B|havana||ENST00000468169|4|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||ggt/gTgt|G190V?||PPP2R3B|havana||ENST00000484364|4|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 1/1:208,151,0:50:50:0:0,0,21,29:0,50 +X 341347 . A C,G 170.0 . DP=48;VDB=0.802018;SGB=-0.693136;MQSB=0.969233;MQ0F=0;DPR=0,20,15;AC=2;AN=2;DP4=0,0,20,15;MQ=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L332R||PPP2R3B|havana||ENST00000477110|5|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L332P||PPP2R3B|havana||ENST00000477110|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W379G||PPP2R3B|ensembl_havana||ENST00000390665|9|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W379R||PPP2R3B|ensembl_havana||ENST00000390665|9|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L122R||PPP2R3B|havana||ENST00000479438|1|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L122P||PPP2R3B|havana||ENST00000479438|1|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) GT:PL:DP:DV:SP:DP4:DPR 1/1:197,105,0:35:35:0:0,0,20,15:0,20,15 +X 345580 . G A 41.8455 . DP=6;VDB=0.910845;SGB=-0.556411;MQSB=1;MQ0F=0;DPR=0,4;AC=2;AN=2;DP4=0,0,3,1;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W324C||PPP2R3B|ensembl_havana||ENST00000390665|7|A|WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G17V||PPP2R3B|havana||ENST00000468169|1|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G16V||PPP2R3B|havana||ENST00000484364|1|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G145V||PPP2R3B|havana||ENST00000477636|2|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W438C||PPP2R3B|havana||ENST00000445792|8|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME) GT:PL:DP:DV:SP:DP4:DPR 1/1:69,12,0:4:4:0:0,0,3,1:0,4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/twobit.loc.sample Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that is used by some +#tools. The twobit.loc file has this format (white space characters +#are TAB characters): +# +#<Build> <FullPathToFile> +# +#So, for example, if you had droPer1 twobit files stored in +#/depot/data2/galaxy/droPer1/, then the twobit.loc entry +#would look like this: +# +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +# +#and your /depot/data2/galaxy/droPer1/ directory would +#contain all of your twobit files (e.g.): +# +#-rw-rw-r-- 1 nate galaxy 48972650 2007-05-04 11:27 droPer1.2bit +#...etc... +# +#Your twobit.loc file should include an entry per line for each twobit +#file you have stored. For example: +# +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#...etc...
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the 2bit format --> + <table name="twobit" comment_char="#" allow_duplicate_entries="False"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table> +</tables>