<?xml version='1.0' encoding="ISO-8859-1" ?>
<pml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="pml.xsd" >


        <!-- Note: date in ISO 8601 format -->
        <contributor name="Heikki Lehväslaiho" date="2005-05-06">
                <annotation name="meta" value="sample HGVbase entry v3" />
                <annotation name="comment" value="latest schema fixes db_xref placement problem" />
        </contributor>

        <!-- Full submitter information is kept in a separate XML file in HGVbase -->
	<source uid="SUB000000001" 
                id="SUB000000001" 
                name="Anthony J Brookes" 
                laboratory="Center for Genomics Research"
                institution="Karolinska Institute"
                address="Theorelsväg 3, 171 77 Stockholm, Sweden"
                tel="+46 8 728 6630"
                fax="+46 8 331547"
                email="Anthony.Brookes@cgb.ki.se"
                />

	<distributor uid="HGVbase" name="HGVbase" db="HGVbase" />

        <!-- location of the gene structure is not included in the HGVbase entry -->
        <genomic_gene_structure id="GID000004227" gene_symbol="IRS4" >
                <annotation name="name" value="Insulin receptor substrate 4" />
                <annotation name="otherMotifsChanged" value="Unknown" />
                <annotation name="protSeqChanged" value="Yes" />
                <annotation name="region" value="I-Ex:CDS+" />
                <annotation name="spliceSiteChanged" value="Unknown" />
                <annotation name="type" value="Functional Gene" />
        </genomic_gene_structure>


        <!-- Variation centered section -->
	<genomic_polymorphism id="GEN000002654"
        	flank_up="AGCGAGCCTGTGGCCCACTCCAGGC"
	        flank_down="GGAAGACTGCACCTGCCCAGAGGGC"
                >
        	<source uid="SUB000000001" />

                <annotation name="curationStatus" value="MRA" />
                <annotation name="status" value="Proven" />
                <annotation name="type" value="Generic" />

		<genomic_allele id="GEN000002654.ALE000000001"  sequence="GA" />
		<genomic_allele id="GEN000002654.ALE000000002"  sequence="AT" />

		<reference_genomic_location id="10"  start="120395" end="120396" strand="0">
			<reference_genomic_landmark id="AL035425.13" molecule="DNA" >
				<db_xref db="EMBL" uid="AL035425.13" field="version" />
			</reference_genomic_landmark>
		</reference_genomic_location>
		<reference_genomic_location  id="11" start="1310" end="1311" strand="0" >
			<reference_genomic_landmark id="AF007567.1" molecule="RNA" >
				<db_xref db="EMBL" uid="AF007567.1" field="version" />
			</reference_genomic_landmark>
		</reference_genomic_location>

                <!-- links variant to one transcript -->
                <genic_polymorphism original_residue="" changed_residue="">
                        <genomic_gene_structure id="GID000004227" />
                        <transcription_change   original_residue="GA"
                                                changed_residue="AT" 
                                                original_codon="CGA"
                                                changed_codon="CAT">
                                 <translation_change original_residue="R" changed_residue="H"/>
                        </transcription_change>
                </genic_polymorphism>
        	<db_xref db="dbSNP" uid="rs1800993" field="rsID"/>

                <!-- additional genomic features -->
                <annotation name="externalFeatures" value="LINE"  unit="repeat"/>
                <annotation name="externalFeatures" value="L1ME4a"  unit="repeat"/>
                <annotation name="comment" value="Low heterozygosity observed. STS & polymorphism developed from public database sequence" />

                <!-- bibliographic reference -->
                <journal_article volume="41" first_page="969" last_page="974" date="1998">
                  <person role="author" surname="Almind" first_name="K" et_al="true" />
                  <journal name="Diabetologia"/>   
                  <db_xref role="identifier" db="Pubmed" uid="9726601" field="pmid"/>
                  <source id="SUB000000001" name="Anthony J Brookes" />
                  <bibref_subject>
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Adult" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Alleles" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Amino Acid Sequence" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Amino Acids/genetics*" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Codon" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Cohort Studies" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Diabetes Mellitus, Non-Insulin-Dependent/genetics*" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Female" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Gene Frequency" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Glucose Tolerance Test" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Human" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Insulin Resistance/genetics*" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Male" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Middle Age" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Mutation*" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Phosphoproteins/genetics*" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Phosphoproteins/chemistry" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Polymorphism, Single-Stranded Conformational" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="Support, Non-U.S. Govt" />
                     <subject_descriptor role="subject_heading" vocabulary_name="MeSH" term="X Chromosome" />
                     <subject_descriptor role="keyword"  vocabulary_name="HGVbase" term="Literature" />
                  </bibref_subject>
                </journal_article>
  
	</genomic_polymorphism>




<!--

	<db_xref db="Pubmed" uid="9726601" field="pmid"/>

-->

        <!-- Assay centered section -->
        <panel id="POP000000227" ethnicity="Danish Caucasian" count_unit="chromosome" size="267" />

        <polymorphism_assay id ="1000" >
                <genomic_polymorphism  id="GEN000002654" >
                        <genomic_allele id="GEN000002654.ALE000000001">
                                <genomic_allele_population_frequency value="0.06">
                                        <panel id="POP000000227" />
                                </genomic_allele_population_frequency>
                        </genomic_allele>
                </genomic_polymorphism>
                <genomic_polymorphism  id="GEN000002654" >
                        <genomic_allele id="GEN000002654.ALE000000002">
                                <genomic_allele_population_frequency value="0.94">
                                        <panel id="POP000000227" />
                                </genomic_allele_population_frequency>
                        </genomic_allele>
                </genomic_polymorphism>
        </polymorphism_assay>

</pml>