Template:Event2

2025-07-29T12:21:57Z

Pusher: Pushed from VastDB.

<includeonly>__NOTOC__{{#vardefine:id|{{#cleanTag:{{{1}}}|at|pre}}}}{{#vardefine:genome|{{#cleanTag:{{{1}}}|pre}}}}{{BioDB_oldid|{{#var:id|}}|{{#var:genome|}}}}{{#vardefine:sub|{{#rmatch:{{#var:id}}|(\D+\d{4})|$1}}}}<nowiki />{{DISPLAYTITLE:{{#var:id|}}}}{{#CustomMsg:Help:Event.ini|ini}}<nowiki /><span id="molid" data-molid="{{{1}}}"></span><nowiki />
''{{TypeEvent|{{PAGENAME}}}}''<nowiki />{{BioDB_event|{{#var:id|}}|{{#var:genome|}}}}<nowiki />
{{BioDB_event_metrics|{{#var:id}}}}<nowiki />
<div class="tablebox event-assembly">
<div class="row"><div class="label small-6 large-4 columns">Gene</div><div class="content small-6 large-8 columns">{{#ifeq:{{#var:gene_id|}}||NA|[{{SERVER}}/gene/{{#var:gene_id|}}@{{#var:genome|}} {{#var:gene_id|}}]
}}{{#ifeq:{{#var:gene_name|}}||| {{!}} ''{{#var:gene_name|}}'' }}</div></div>
<div class="row"><div class="label small-6 large-4 columns">Description</div><div class="content small-6 large-8 columns">{{#if:{{#var:description|}}|{{#var:description|}}|NA}}</div></div>
<div class="row"><div class="label small-6 large-4 columns">Coordinates</div>
<div class="content small-6 large-8 columns">
<div class="block">
<div class="head"><span class='genome-nor'>{{#var:chro_c|}}:{{#var:start_c|}}-{{#var:end_c|}}:{{#var:strand_c|}}</span>{{HelpLinkedPage2|type=helpicon|msg=event-coords|output=data-tooltip}}<span class="unfold up"></span></div>
<div class="body">
<div class="rowin"><div class="labelin">Coord C1 exon</div><div class="contentin">{{#var:co_c1|}}</div></div>
<div class="rowin"><div class="labelin">Coord A exon</div><div class="contentin">{{#var:co_a|}}</div></div>
<div class="rowin"><div class="labelin">Coord C2 exon</div><div class="contentin">{{#var:co_c2|}}</div></div>
</div>
</div>

</div>
</div>
<div class="row"><div class="label small-6 large-4 columns">Length</div><div class="content small-6 large=8 columns">{{#var:length_n|}} bp{{HelpLinkedPage2|type=helpicon|msg=event-length|output=data-tooltip}}</div></div>
<div class="row"><div class="label small-6 large-4 columns">Sequences</div>
<div class="content small-6 large-8 columns">
<div class="block">
<div class="head"><span>Splice sites</span>{{HelpLinkedPage2|type=helpicon|msg=event-splice|output=data-tooltip}}<span class="unfold up"></span></div>
<div class="body">
{{Score_SS|{{#var:id|}}|{{#var:genome|}}}}
</div>
</div>
<div class="block">
<div class="head"><span>Exon sequences</span>{{HelpLinkedPage2|type=helpicon|msg=event-exon|output=data-tooltip}}<span class="unfold down"></span></div>
<div class="body folded">
<div class="rowin"><div class="labelin">Seq C1 exon</div>{{#var:seq_c1|}}</div>
<div class="rowin"><div class="labelin">Seq A exon</div>{{#var:seq_a|}}</div>
<div class="rowin"><div class="labelin">Seq C2 exon</div>{{#var:seq_c2|}}</div>
</div>
</div>
</div>
</div>
<div class="row"><div class="label small-6 large-4 columns">VastDB Features</div>{{BioDB_mappability|{{#var:id|}}|{{#var:genome|}}}}
<div class="content small-6 large-8 columns">
<div class="block">
<div class="head"><span>Vast-tools module Information</span>{{HelpLinkedPage2|type=helpicon|msg=event-vastdbfeatures|output=data-tooltip}}<span class="unfold down"></span></div>
<div class="body folded">
<div class="rowin"><div class="labelin">Secondary ID</div><div class="contentin">{{#var:oldid|}}</div>{{HelpLinkedPage2|type=helpicon|msg=event-internal|output=data-tooltip}}</div>
<div class="rowin"><div class="labelin">Average complexity</div><div class="contentin">{{#var:complex|}}</div>{{HelpLinkedPage2|type=helpicon|msg=event-complexity|output=data-tooltip}}</div>
<div class="rowin"><div class="labelin">Mappability confidence:</div><div class="contentin">{{#ifeq:{{#var:minc|}}||NA|{{#var:minc|}}%={{#var:mexc1|}}={{#var:mexc2|}}%}}</div>{{HelpLinkedPage2|type=helpicon|msg=event-mappability|output=data-tooltip}}</div>
</div>
</div>
</div>
</div>
<div class="row"><div class="label small-6 large-4 columns">Protein Impact</div>{{BioDB_protimpact|{{#var:id|}}|{{#var:genome|}}}}
{{BioDB_protdisorder|{{#var:id|}}|{{#var:genome|}}}}
<div class="content small-6 large-8 columns">
<div class="">{{#var:protimpact|No protein impact description available}}{{HelpLinkedPage2|type=helpicon|msg=event-impact|output=data-tooltip}}
{{PDBshow|{{#var:id|}}}}</div>
<div class="block">
<div class="head"><span>Features</span>
<span class="unfold up"></span></div>
<div class="body">
<div class="rowin"><div class="labelin">Disorder rate (Iupred):</div><div class="contentin">  <span class="colorc1">C1</span>={{#var:c1dis|NA}} <span class="colora">A</span>={{#var:adis|NA}} <span class="colorc2">C2</span>={{#var:c2dis|NA}}</div>
</div>{{HelpLinkedPage2|type=helpicon|msg=event-disorder|output=data-tooltip}}
<div class="rowin"><div class="labelin">Domain overlap (PFAM):</div><div class="contentin">{{HelpLinkedPage2|type=helpicon|msg=event-pfam|output=data-tooltip}}
<div class="block">{{BioDB_pfam|{{#var:id|}}|{{#var:genome|}}}}
<div class="body">
<div class="rowin"><div class="labelin colorc1">C1:</div><div class="contentin">{{#var:c1pfam|NA}}</div></div>
<div class="rowin"><div class="labelin colora">A:</div><div class="contentin">{{#var:apfam|NA}}</div></div>
<div class="rowin"><div class="labelin colorc2">C2:</div><div class="contentin">{{#var:c2pfam|NA}}</div></div>
</div>
</div>
</div></div>
<div class="rowin">{{#vardefine:isoid|{{#replace:{{#var:id}}|/|_}}}}
{{BioDB protein isoforms|{{#var:id}}|{{#var:genome}}|Incl_main}}
<div class="labelin">Main Inclusion Isoform:</div><div class="contentin isoforms">{{#var:isoformid}}</div>
</div>
<div class="rowin">
<div class="contentin domainimg">{{#ifeq:{{#vastDBFileExists:domain_plots/{{#var:genome}}/{{#var:sub}}/{{#var:isoid}}-INC.png}}|1|{{ExternalImgURL|{{SERVER}}/domain_plots/{{#var:genome}}/{{#var:sub}}/{{#var:isoid}}-INC.png|{{#var:isoid}}-INC}}}}</div>
</div>
<div class="rowin">
{{BioDB protein isoforms|{{#var:id}}|{{#var:genome}}|Excl_main}}
<div class="labelin">Main Skipping Isoform:</div><div class="contentin isoforms">{{#var:isoformid}}</div>
</div>
<div class="rowin">
<div class="contentin domainimg">{{#ifeq:{{#vastDBFileExists:domain_plots/{{#var:genome}}/{{#var:sub}}/{{#var:isoid}}-EXC.png}}|1|{{ExternalImgURL|{{SERVER}}/domain_plots/{{#var:genome}}/{{#var:sub}}/{{#var:isoid}}-EXC.png|{{#var:isoid}}-EXC}}}}</div>
</div>
<div class="rowin">
{{BioDB protein isoforms|{{#var:id}}|{{#var:genome}}|Incl_other}}
<div class="labelin">Other Inclusion Isoforms:</div><div class="contentin isoforms">{{#var:isoformid}}</div>
</div>
<div class="rowin">
{{BioDB protein isoforms|{{#var:id}}|{{#var:genome}}|Excl_other}}
<div class="labelin">Other Skipping Isoforms:</div><div class="contentin isoforms">{{#var:isoformid}}</div>
</div></div></div></div></div>
<div class="row"><div class="label small-6 large-4 columns">Associated events</div><div class="content small-6 large-8 columns">{{Associated2|{{#var:id|}}|{{#var:genome|}}}}{{HelpLinkedPage2|type=helpicon|msg=event-associated|output=data-tooltip}}</div>
</div>{{Event Other Assemblies|{{#var:id|}}|{{#var:genome|}}}}
<div class="row"><div class="label small-6 large-4">Conservation</div><div class="content small-6 large-8 columns">{{HelpLinkedPage2|type=helpicon|msg=event-conservation|output=data-tooltip}}{{ConservationFull2|{{#var:id|}}|{{#var:genome|}}}}</div>
</div>{{BioDB primer|{{#var:id|}}|{{#var:genome|}}}}
<div class="row"><div class="label small-6 large-4 columns">Primers PCR</div>
<div class="content small-6 large-8 columns">
<div class="block">
<div class="head"><span>Suggestions for RT-PCR validation</span>{{HelpLinkedPage2|type=helpicon|msg=event-primers|output=data-tooltip}}<span class="unfold down"></span></div>
<div class="body folded">
<div class="rowin"><div class="labelin">F: </div>{{#ifeq:{{#var:primerf|}}||<div class="contentin">No suggested primer sequences</div>|<div class="contentin bioseq">{{#var:primerf|}}</div>}}</div>
<div class="rowin"><div class="labelin">R: </div>{{#ifeq:{{#var:primerr|}}||<div class="contentin">No suggested primer sequences</div>|<div class="contentin bioseq">{{#var:primerr|}}</div>}}</div>
<div class="rowin"><div class="labelin">Band lengths: </div><div class="contentin">{{#ifeq:{{#var:pskipping|}}|||{{#var:pskipping|}}-{{#var:pinclusion|}}}}</div></div>
</div>
</div>
</div>
</div>
<div class="row">
<div class="label small-6 large-4 columns">Functional annotations<div class="submitfunction">[[EventFunction|(Submit an annotation)]]</div></div>
<div class="content small-6 large-8 columns">{{AnnotatedFunction|{{#var:id|}}|{{#var:genome|}}}}</div>
</div>
</div>
<br />
====GENOMIC CONTEXT====
<div class="content large-12">
<div style="float:right">{{HelpLinkedPage2|type=helpicon|msg=event-browser|output=data-tooltip}}</div>
</div>
<div class="browser-container genome-nor">
{{#embedUCSC:chrom={{#var:chro_c|}}|start={{#var:start_c|}}|end={{#var:end_c|}}|genome_id={{#var:genome|}}}}</div>
====INCLUSION PATTERN====
<div class="tissuevalue-list sample-chart">{{HelpLinkedPage2|type=helpicon|msg=event-tissuevalue|output=data-tooltip}}</div>{{#printCharts:}}
<hr>
{{#specialImages:{{#var:id|}}|{{#var:genome|}}|AS_TCGA,AS_GTEX,AS_ASD_UCLA,AS_EARLY_DEV,AS_SCHEIFFELE,AS_NEU_DIF,AS_MYOBLAST,AS_SPERMATOG,AS_REPROGR_CARSTENS,AS_VICKY,AS_HEMATO_PREC,AS_PANCREAS,AS_ABIOTIC,AS_BIOTIC,AS_LIGHT,AS_SPL_FACTORS,AS_NEURAL_DIVERSITY,AS_NEUROGENESIS,AS_NEURONAL_ACT,AS_REGULATION_RBP_BRAIN,AS_REGULATION_RBP_SL2|The Cancer Genome Atlas (TCGA),Genotype-Tissue Expression Project (GTEx),Autistic and control brains,Pre-implantation embryo development,Ribosome-engaged transcriptomes of neuronal types,Neural differentiation time course,Muscular differentiation time course,Spermatogenesis cell types,Reprogramming of fibroblasts to iPSCs,Naive to Primed (Vicky),Hematopoietic precursors and cell types,Pancreas cell types,Abiotic stress,Biotic stress,Light response,Splicing factor regulation,Neural diversity,Neurogenesis,Neuronal activity,Splicing factor regulation (brain),Splicing factor regulation (SL2)|{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-tcga|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-gtex|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-asducla|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-earlydev|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-scheiffele|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-neudif|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-myoblast|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-spermatogenesis|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-reprogr_carstens|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-vicky|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-hemato|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-pancreas|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-abiotic|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-biotic|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-light|output=data-tooltip}},{{HelpLinkedPage2|type=helpicon|msg=event-specialpsi-spl_factors|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-neural_diversity|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-neurogenesis|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-neuronal_act|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-regulation_rbp_brain|output=data-tooltip}},{{HelpLinkedPage|type=helpicon|msg=event-specialpsi-regulation_rbp_sl2|output=data-tooltip}}
}}

{{Event Links|{{#var:genome}}|{{#var:gene_id}}|{{#var:gene_name}}}}
{{PDBdiv|{{#var:genome|}}}}[[Category:Events]][[Category:Events in Genome:{{#var:genome|}}]]<nowiki /></includeonly>

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Template:Event2