t/data/LittleChrY.dbsnp.xml

   1 <?xml version="1.0"?>
   2 <ExchangeSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   3 xmlns="http://www.ncbi.nlm.nih.gov/SNP/docsum"
   4 xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/SNP/docsum
   5 http://www.ncbi.nlm.nih.gov/SNP/docsum/docsum_eutil_ver1.0a.xsd">
   6
   7
   8
   9
  10 <Rs>
  11   <Rs_organism>Homo sapiens</Rs_organism>
  12   <Rs_taxId>9606</Rs_taxId>
  13   <Rs_rsId>12345</Rs_rsId>
  14   <Rs_snpClass value="snp"/>
  15   <Rs_snpType value="notwithdrawn"/>
  16   <Rs_molType value="cDNA"/>
  17   <Rs_het>
  18     <Rs_het_type value="est"/>
  19     <Rs_het_value>0</Rs_het_value>
  20     <Rs_het_stdError>0</Rs_het_stdError>
  21   </Rs_het>
  22   <Rs_validation></Rs_validation>
  23   <Rs_create>
  24     <Rs_create_build>52</Rs_create_build>
  25     <Rs_create_date>2000-09-19 17:02</Rs_create_date>
  26   </Rs_create>
  27   <Rs_update>
  28     <Rs_update_build>120</Rs_update_build>
  29     <Rs_update_date>2004-10-04 13:37</Rs_update_date>
  30   </Rs_update>
  31   <Rs_sequence>
  32     <Rs_sequence_exemplarSs>14616</Rs_sequence_exemplarSs>
  33
  34 <Rs_sequence_seq5>GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA
  35 GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT</Rs_sequence_seq5>
  36     <Rs_sequence_observed>C/T</Rs_sequence_observed>
  37
  38 <Rs_sequence_seq3>GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT
  39 AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT</Rs_sequence_seq3>
  40   </Rs_sequence>
  41   <Rs_ss>
  42     <Ss>
  43       <Ss_ssId>14616</Ss_ssId>
  44       <Ss_handle>CGAP-GAI</Ss_handle>
  45       <Ss_batchId>607</Ss_batchId>
  46       <Ss_locSnpId>59089</Ss_locSnpId>
  47       <Ss_subSnpClass value="snp"/>
  48       <Ss_orient value="forward"/>
  49       <Ss_strand value="bottom"/>
  50       <Ss_molType value="cDNA"/>
  51       <Ss_buildId>52</Ss_buildId>
  52       <Ss_methodClass value="computed"/>
  53
  54 <Ss_linkoutUrl>http://lpgws.nci.nih.gov:82/perl/gettrace.pl?type=7&amp;trace=</Ss_linkoutUrl>
  55       <Ss_sequence>
  56
  57 <Ss_sequence_seq5>GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA
  58 GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT</Ss_sequence_seq5>
  59         <Ss_sequence_observed>C/T</Ss_sequence_observed>
  60
  61 <Ss_sequence_seq3>GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT
  62 AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT</Ss_sequence_seq3>
  63       </Ss_sequence>
  64     </Ss>
  65     <Ss>
  66       <Ss_ssId>1539216</Ss_ssId>
  67       <Ss_handle>LEE</Ss_handle>
  68       <Ss_batchId>3129</Ss_batchId>
  69       <Ss_locSnpId>750160</Ss_locSnpId>
  70       <Ss_subSnpClass value="snp"/>
  71       <Ss_orient value="reverse"/>
  72       <Ss_strand value="top"/>
  73       <Ss_molType value="cDNA"/>
  74       <Ss_buildId>92</Ss_buildId>
  75       <Ss_methodClass value="computed"/>
  76
  77 <Ss_linkoutUrl>http://www.bioinformatics.ucla.edu/snp/snp/snp_report.php3?db_ver
  78 sion=db_april_00&amp;allele_id=</Ss_linkoutUrl>
  79       <Ss_sequence>
  80
  81 <Ss_sequence_seq5>ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC</Ss_sequence_seq5>
  82         <Ss_sequence_observed>A/G</Ss_sequence_observed>
  83
  84 <Ss_sequence_seq3>ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC</Ss_sequence_seq3>
  85       </Ss_sequence>
  86     </Ss>
  87     <Ss>
  88       <Ss_ssId>4398532</Ss_ssId>
  89       <Ss_handle>LEE</Ss_handle>
  90       <Ss_batchId>5288</Ss_batchId>
  91       <Ss_locSnpId>ge750160</Ss_locSnpId>
  92       <Ss_subSnpClass value="snp"/>
  93       <Ss_orient value="reverse"/>
  94       <Ss_strand value="top"/>
  95       <Ss_molType value="cDNA"/>
  96       <Ss_buildId>106</Ss_buildId>
  97       <Ss_methodClass value="unknown"/>
  98       <Ss_linkoutUrl> </Ss_linkoutUrl>
  99       <Ss_sequence>
 100
 101 <Ss_sequence_seq5>ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC</Ss_sequence_seq5>
 102         <Ss_sequence_observed>A/G</Ss_sequence_observed>
 103
 104 <Ss_sequence_seq3>ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC</Ss_sequence_seq3>
 105       </Ss_sequence>
 106     </Ss>
 107     <Ss>
 108       <Ss_ssId>4426703</Ss_ssId>
 109       <Ss_handle>LEE</Ss_handle>
 110       <Ss_batchId>5293</Ss_batchId>
 111       <Ss_locSnpId>e750160</Ss_locSnpId>
 112       <Ss_subSnpClass value="snp"/>
 113       <Ss_orient value="reverse"/>
 114       <Ss_strand value="top"/>
 115       <Ss_molType value="cDNA"/>
 116       <Ss_buildId>106</Ss_buildId>
 117       <Ss_methodClass value="computed"/>
 118       <Ss_linkoutUrl> </Ss_linkoutUrl>
 119       <Ss_sequence>
 120
 121 <Ss_sequence_seq5>ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC</Ss_sequence_seq5>
 122         <Ss_sequence_observed>A/G</Ss_sequence_observed>
 123
 124 <Ss_sequence_seq3>ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC</Ss_sequence_seq3>
 125       </Ss_sequence>
 126     </Ss>
 127     <Ss>
 128       <Ss_ssId>16250752</Ss_ssId>
 129       <Ss_handle>CGAP-GAI</Ss_handle>
 130       <Ss_batchId>8532</Ss_batchId>
 131       <Ss_locSnpId>1500705</Ss_locSnpId>
 132       <Ss_subSnpClass value="snp"/>
 133       <Ss_orient value="forward"/>
 134       <Ss_strand value="bottom"/>
 135       <Ss_molType value="cDNA"/>
 136       <Ss_buildId>120</Ss_buildId>
 137       <Ss_methodClass value="computed"/>
 138
 139 <Ss_linkoutUrl>http://lpgws.nci.nih.gov/perl/gettrace.pl?type=7&amp;trace=</Ss_linkoutUrl>
 140       <Ss_sequence>
 141
 142 <Ss_sequence_seq5>GTCGTGGATGCAGCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT</Ss_sequence_seq5>
 143         <Ss_sequence_observed>C/T</Ss_sequence_observed>
 144
 145 <Ss_sequence_seq3>GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGT</Ss_sequence_seq3>
 146       </Ss_sequence>
 147     </Ss>
 148   </Rs_ss>
 149   <Rs_assembly>
 150     <Assembly>
 151       <Assembly_dbSnpBuild>125</Assembly_dbSnpBuild>
 152       <Assembly_genomeBuild>34_3</Assembly_genomeBuild>
 153       <Assembly_groupLabel>reference</Assembly_groupLabel>
 154       <Assembly_component>
 155         <Component>
 156           <Component_componentType value="contig"/>
 157           <Component_ctgId>960600311</Component_ctgId>
 158           <Component_accession>NT_011520.9</Component_accession>
 159           <Component_name>Hs22_11677_34</Component_name>
 160           <Component_chromosome>22</Component_chromosome>
 161           <Component_start>18933985</Component_start>
 162           <Component_end>42112197</Component_end>
 163           <Component_orientation value="fwd"/>
 164           <Component_gi>29807292</Component_gi>
 165           <Component_groupTerm>ref_haplotype</Component_groupTerm>
 166           <Component_contigLabel>reference</Component_contigLabel>
 167           <Component_mapLoc>
 168             <MapLoc>
 169               <MapLoc_asnFrom>5246027</MapLoc_asnFrom>
 170               <MapLoc_asnTo>5246027</MapLoc_asnTo>
 171               <MapLoc_locType value="exact"/>
 172               <MapLoc_alnQuality>0.913983</MapLoc_alnQuality>
 173               <MapLoc_orient value="reverse"/>
 174               <MapLoc_physMapStr>24180013</MapLoc_physMapStr>
 175               <MapLoc_physMapInt>24180012</MapLoc_physMapInt>
 176               <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 177               <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 178
 179 <MapLoc_leftContigNeighborPos>5246026</MapLoc_leftContigNeighborPos>
 180
 181 <MapLoc_rightContigNeighborPos>5246028</MapLoc_rightContigNeighborPos>
 182               <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 183               <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 184               <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 185             </MapLoc>
 186           </Component_mapLoc>
 187         </Component>
 188       </Assembly_component>
 189       <Assembly_snpStat>
 190         <Assembly_snpStat_mapWeight value="unique-in-contig"/>
 191         <Assembly_snpStat_chromCount>1</Assembly_snpStat_chromCount>
 192
 193 <Assembly_snpStat_placedContigCount>1</Assembly_snpStat_placedContigCount>
 194
 195 <Assembly_snpStat_unplacedContigCount>0</Assembly_snpStat_unplacedContigCount>
 196         <Assembly_snpStat_seqlocCount>1</Assembly_snpStat_seqlocCount>
 197         <Assembly_snpStat_hapCount>1</Assembly_snpStat_hapCount>
 198       </Assembly_snpStat>
 199     </Assembly>
 200     <Assembly>
 201       <Assembly_dbSnpBuild>125</Assembly_dbSnpBuild>
 202       <Assembly_genomeBuild>35_1</Assembly_genomeBuild>
 203       <Assembly_groupLabel>Celera</Assembly_groupLabel>
 204       <Assembly_current value="true"/>
 205       <Assembly_component>
 206         <Component>
 207           <Component_componentType value="contig"/>
 208           <Component_ctgId>960600397</Component_ctgId>
 209           <Component_accession>NT_086921.1</Component_accession>
 210           <Component_name>Hs22_86581_35</Component_name>
 211           <Component_chromosome>22</Component_chromosome>
 212           <Component_start>18936537</Component_start>
 213           <Component_end>48069707</Component_end>
 214           <Component_orientation value="fwd"/>
 215           <Component_gi>51477137</Component_gi>
 216           <Component_groupTerm>alt_assembly_2</Component_groupTerm>
 217           <Component_contigLabel>Celera</Component_contigLabel>
 218           <Component_mapLoc>
 219             <MapLoc>
 220               <MapLoc_asnFrom>3888702</MapLoc_asnFrom>
 221               <MapLoc_asnTo>3888702</MapLoc_asnTo>
 222               <MapLoc_locType value="exact"/>
 223               <MapLoc_alnQuality>0.919897</MapLoc_alnQuality>
 224               <MapLoc_orient value="reverse"/>
 225               <MapLoc_physMapStr>22825240</MapLoc_physMapStr>
 226               <MapLoc_physMapInt>22825239</MapLoc_physMapInt>
 227               <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 228               <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 229
 230 <MapLoc_leftContigNeighborPos>3888701</MapLoc_leftContigNeighborPos>
 231
 232 <MapLoc_rightContigNeighborPos>3888703</MapLoc_rightContigNeighborPos>
 233               <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 234               <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 235               <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 236               <MapLoc_fxnSet>
 237                 <FxnSet>
 238                   <FxnSet_geneId>1415</FxnSet_geneId>
 239                   <FxnSet_symbol>CRYBB2</FxnSet_symbol>
 240                   <FxnSet_mrnaAcc>NM_000496</FxnSet_mrnaAcc>
 241                   <FxnSet_mrnaVer>1</FxnSet_mrnaVer>
 242                   <FxnSet_protAcc>NP_000487</FxnSet_protAcc>
 243                   <FxnSet_protVer>1</FxnSet_protVer>
 244                   <FxnSet_fxnClass value="intron"/>
 245                 </FxnSet>
 246               </MapLoc_fxnSet>
 247             </MapLoc>
 248           </Component_mapLoc>
 249         </Component>
 250       </Assembly_component>
 251       <Assembly_snpStat>
 252         <Assembly_snpStat_mapWeight value="unique-in-contig"/>
 253         <Assembly_snpStat_chromCount>1</Assembly_snpStat_chromCount>
 254
 255 <Assembly_snpStat_placedContigCount>1</Assembly_snpStat_placedContigCount>
 256
 257 <Assembly_snpStat_unplacedContigCount>0</Assembly_snpStat_unplacedContigCount>
 258         <Assembly_snpStat_seqlocCount>1</Assembly_snpStat_seqlocCount>
 259         <Assembly_snpStat_hapCount>0</Assembly_snpStat_hapCount>
 260       </Assembly_snpStat>
 261     </Assembly>
 262     <Assembly>
 263       <Assembly_dbSnpBuild>125</Assembly_dbSnpBuild>
 264       <Assembly_genomeBuild>35_1</Assembly_genomeBuild>
 265       <Assembly_groupLabel>reference</Assembly_groupLabel>
 266       <Assembly_current value="true"/>
 267       <Assembly_component>
 268         <Component>
 269           <Component_componentType value="contig"/>
 270           <Component_ctgId>960600396</Component_ctgId>
 271           <Component_accession>NT_011520.10</Component_accession>
 272           <Component_name>Hs22_11677_35</Component_name>
 273           <Component_chromosome>22</Component_chromosome>
 274           <Component_start>18933985</Component_start>
 275           <Component_end>42210286</Component_end>
 276           <Component_orientation value="fwd"/>
 277           <Component_gi>51476066</Component_gi>
 278           <Component_groupTerm>ref_haplotype</Component_groupTerm>
 279           <Component_contigLabel>reference</Component_contigLabel>
 280           <Component_mapLoc>
 281             <MapLoc>
 282               <MapLoc_asnFrom>5246027</MapLoc_asnFrom>
 283               <MapLoc_asnTo>5246027</MapLoc_asnTo>
 284               <MapLoc_locType value="exact"/>
 285               <MapLoc_alnQuality>0.919897</MapLoc_alnQuality>
 286               <MapLoc_orient value="reverse"/>
 287               <MapLoc_physMapStr>24180013</MapLoc_physMapStr>
 288               <MapLoc_physMapInt>24180012</MapLoc_physMapInt>
 289               <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 290               <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 291
 292 <MapLoc_leftContigNeighborPos>5246026</MapLoc_leftContigNeighborPos>
 293
 294 <MapLoc_rightContigNeighborPos>5246028</MapLoc_rightContigNeighborPos>
 295               <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 296               <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 297               <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 298               <MapLoc_fxnSet>
 299                 <FxnSet>
 300                   <FxnSet_geneId>1416</FxnSet_geneId>
 301                   <FxnSet_symbol>CRYBB2P1</FxnSet_symbol>
 302                   <FxnSet_fxnClass value="locus-region"/>
 303                 </FxnSet>
 304               </MapLoc_fxnSet>
 305             </MapLoc>
 306           </Component_mapLoc>
 307         </Component>
 308       </Assembly_component>
 309       <Assembly_snpStat>
 310         <Assembly_snpStat_mapWeight value="unique-in-contig"/>
 311         <Assembly_snpStat_chromCount>1</Assembly_snpStat_chromCount>
 312
 313 <Assembly_snpStat_placedContigCount>1</Assembly_snpStat_placedContigCount>
 314
 315 <Assembly_snpStat_unplacedContigCount>0</Assembly_snpStat_unplacedContigCount>
 316         <Assembly_snpStat_seqlocCount>1</Assembly_snpStat_seqlocCount>
 317         <Assembly_snpStat_hapCount>1</Assembly_snpStat_hapCount>
 318       </Assembly_snpStat>
 319     </Assembly>
 320   </Rs_assembly>
 321   <Rs_primarySequence>
 322     <PrimarySequence>
 323       <PrimarySequence_dbSnpBuild>125</PrimarySequence_dbSnpBuild>
 324       <PrimarySequence_gi>3171883</PrimarySequence_gi>
 325       <PrimarySequence_source value="blastmb"/>
 326       <PrimarySequence_mapLoc>
 327         <MapLoc>
 328           <MapLoc_asnFrom>24363</MapLoc_asnFrom>
 329           <MapLoc_asnTo>24363</MapLoc_asnTo>
 330           <MapLoc_locType value="exact"/>
 331           <MapLoc_alnQuality>0.913983</MapLoc_alnQuality>
 332           <MapLoc_orient value="reverse"/>
 333           <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 334           <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 335           <MapLoc_leftContigNeighborPos>24362</MapLoc_leftContigNeighborPos>
 336           <MapLoc_rightContigNeighborPos>24364</MapLoc_rightContigNeighborPos>
 337           <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 338           <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 339           <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 340         </MapLoc>
 341       </PrimarySequence_mapLoc>
 342     </PrimarySequence>
 343     <PrimarySequence>
 344       <PrimarySequence_dbSnpBuild>125</PrimarySequence_dbSnpBuild>
 345       <PrimarySequence_gi>9863690</PrimarySequence_gi>
 346       <PrimarySequence_source value="blastmb"/>
 347       <PrimarySequence_mapLoc>
 348         <MapLoc>
 349           <MapLoc_asnFrom>52075</MapLoc_asnFrom>
 350           <MapLoc_asnTo>52075</MapLoc_asnTo>
 351           <MapLoc_locType value="exact"/>
 352           <MapLoc_alnQuality>0.913983</MapLoc_alnQuality>
 353           <MapLoc_orient value="forward"/>
 354           <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 355           <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 356           <MapLoc_leftContigNeighborPos>52074</MapLoc_leftContigNeighborPos>
 357           <MapLoc_rightContigNeighborPos>52076</MapLoc_rightContigNeighborPos>
 358           <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 359           <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 360           <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 361         </MapLoc>
 362       </PrimarySequence_mapLoc>
 363     </PrimarySequence>
 364     <PrimarySequence>
 365       <PrimarySequence_dbSnpBuild>125</PrimarySequence_dbSnpBuild>
 366       <PrimarySequence_gi>51511751</PrimarySequence_gi>
 367       <PrimarySequence_source value="blastmb"/>
 368       <PrimarySequence_mapLoc>
 369         <MapLoc>
 370           <MapLoc_asnFrom>24180012</MapLoc_asnFrom>
 371           <MapLoc_asnTo>24180012</MapLoc_asnTo>
 372           <MapLoc_locType value="exact"/>
 373           <MapLoc_alnQuality>0.913983</MapLoc_alnQuality>
 374           <MapLoc_orient value="reverse"/>
 375           <MapLoc_leftFlankNeighborPos>99</MapLoc_leftFlankNeighborPos>
 376           <MapLoc_rightFlankNeighborPos>101</MapLoc_rightFlankNeighborPos>
 377           <MapLoc_leftContigNeighborPos>24180011</MapLoc_leftContigNeighborPos>
 378
 379 <MapLoc_rightContigNeighborPos>24180013</MapLoc_rightContigNeighborPos>
 380           <MapLoc_numberOfMismatches>3</MapLoc_numberOfMismatches>
 381           <MapLoc_numberOfDeletions>0</MapLoc_numberOfDeletions>
 382           <MapLoc_numberOfInsertions>1</MapLoc_numberOfInsertions>
 383         </MapLoc>
 384       </PrimarySequence_mapLoc>
 385     </PrimarySequence>
 386   </Rs_primarySequence>
 387   <Rs_rsLinkout>
 388     <RsLinkout>
 389       <RsLinkout_resourceId>1</RsLinkout_resourceId>
 390       <RsLinkout_linkValue>12345</RsLinkout_linkValue>
 391     </RsLinkout>
 392   </Rs_rsLinkout>
 393 </Rs>
 394
 395
 396
 397
 398 </ExchangeSet>