{% if not standalone %}{% extends "base.html" %}{% endif -%}

Name Checker

{% set active_page = "name-checker" %} {% set page_title = "Name Checker" %} {% block content %}
{% if not standalone %}
Please insert the mutation name using the HGVS format:
<accession number>.<version number>(<gene symbol>):<sequence type>.<variant description>

Example: AB026906.1:c.274G>T


Help
{% endif %} {% if visualisation %}

Overview of the raw variants:

{% for i in visualisation %}

Raw variant {{ loop.index }}: {{ i[0] }}

{{ i[1] }}
{{ i[2] }}
{% endfor %} {% endif %} {% if browserLink %}

View original variant in UCSC Genome Browser

{% endif %}
{% if description %}

Name checker results:

{% for m in messages %}

{{ m.description }}

{% endfor %}

{{ summary }}

{% if parse_error %}

Details of the parse error:

{{ parse_error[0] }}
{{ parse_error[1] }}

The "^" indicates the position where the error occurred.

{% endif %} {% if genomicDescription %} {% if genomicDNA %}

Genomic description:

{% else %}

Description relative to transcription start:
(Not for use in LSDBs in case of protein-coding transcripts).

{% endif %}

{{ genomicDescription }}

{% endif %} {% if chromDescription %}

Alternative chromosomal position:

{{ chromDescription }}

{% endif %} {% if descriptions %}

Affected transcripts:

{% for i in descriptions %} {% if i.endswith('?') %} {{ i }} {% else %} {{ i }} {% endif %}
{% endfor %}

{% endif %} {% if protDescriptions %}

Affected proteins:

{% for i in protDescriptions %} {{ i }}
{% endfor %}

{% endif %} {% if transcriptInfo %}

Detailed information about the selected transcript:

{% if oldProtein %}

Reference protein:

        {%- for i in oldProtein -%}
          {{- i|safe -}}
{%- endfor -%}

Protein predicted from variant coding sequence:

{% if newProtein %}
            {%- for i in newProtein -%}
              {{- i|safe -}}
{%- endfor -%}
{% else %}

No change: Predicted protein (not shown) equals reference protein.

{% endif %} {% if altStart %}

Alternative protein using start codon {{ altStart }}

{% if altProtein %}
              {%- for i in altProtein -%}
                {{- i|safe -}}
{%- endfor -%}
{% else %}

No change: Predicted protein (not shown) equals reference protein.

{% endif %} {% endif %} {% endif %}

Exon information:

{% for i in exonInfo %} {% for j in i %} {% endfor %} {% endfor %}
Number Start (g.) Stop (g.) Start {{ '(c.)' if transcriptCoding else '(n.)' }} Stop {{ '(c.)' if transcriptCoding else '(n.)' }}
{{ loop.index }}{{ j }}
{% if transcriptCoding %}

CDS information:

g. c.
Start {{ cdsStart_g }} {{ cdsStart_c }}
Stop {{ cdsStop_g }} {{ cdsStop_c }}
{% endif %}
{% endif %} {% if restrictionSites %}

Effects on Restriction sites:

{% for i in restrictionSites %} {% endfor %}
Raw variant Created Deleted
{{ loop.index }} {% for j in i[0] %} {{ j }}{{ ',' if not loop.last }} {% endfor %} {% for j in i[1] %} {{ j }}{{ ',' if not loop.last }} {% endfor %}
{% endif %} {% if legends %}

Legend:

{% for i in legends %} {% for j in i %} {% endfor %} {% endfor %}
Name ID Locus tag Product Link method
{{ j if j else '' }}
{% endif %} {% if reference_filename and not standalone %}

Links:

Download this reference sequence file: {{ reference_filename }}

{% endif %} {% if extractedDescription %}

Experimental services:

Genomic description: {{ extractedDescription }}

Protein description: {{ extractedProtein }}

{% endif %} {% endif %} {% endblock content %}