branch-1-6/t/data/mutations.old.xml

   1
   2 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G&gt;A" trivname="E2K">
   3     <DNA number="1" start="4" end="4" length="1" isMutation="1">
   4         <label>point</label>
   5         <label>transition</label>
   6         <proof>computed</proof>
   7         <upFlank>gaagattcagccaagctcaaggatg</upFlank>
   8         <allele_ori>g</allele_ori>
   9         <allele_mut>a</allele_mut>
  10         <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
  11         <restriction_changes>-BccI</restriction_changes>
  12     </DNA>
  13     <RNA number="1" start="4" end="4" length="1" isMutation="1">
  14         <label>missense</label>
  15         <proof>experimental</proof>
  16         <upFlank>gaagattcagccaagctcaaggatg</upFlank>
  17         <allele_ori>g</allele_ori>
  18         <allele_mut>a</allele_mut>
  19         <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
  20         <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
  21         <restriction_changes>-BccI</restriction_changes>
  22         <region>coding</region>
  23     </RNA>
  24     <AA number="1" start="2" end="2" length="1" isMutation="1">
  25         <label>substitution</label>
  26         <label>conservative</label>
  27         <proof>computed</proof>
  28         <allele_ori>E</allele_ori>
  29         <allele_mut>K</allele_mut>
  30     </AA>
  31 </seqDiff>
  32
  33 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+14T&gt;A" trivname="L5X">
  34     <DNA number="1" start="14" end="14" length="1" isMutation="1">
  35         <label>point</label>
  36         <label>transversion</label>
  37         <proof>computed</proof>
  38         <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
  39         <allele_ori>t</allele_ori>
  40         <allele_mut>a</allele_mut>
  41         <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
  42     </DNA>
  43     <RNA number="1" start="14" end="14" length="1" isMutation="1">
  44         <label>nonsense</label>
  45         <proof>experimental</proof>
  46         <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
  47         <allele_ori>t</allele_ori>
  48         <allele_mut>a</allele_mut>
  49         <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
  50         <codon codon_ori="tta" codon_mut="taa" codon_pos="2"></codon>
  51         <region>coding</region>
  52     </RNA>
  53     <AA number="1" start="5" end="5" length="1" isMutation="1">
  54         <label>truncation</label>
  55         <proof>computed</proof>
  56         <allele_ori>L</allele_ori>
  57         <allele_mut>*</allele_mut>
  58     </AA>
  59 </seqDiff>
  60
  61 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G&gt;A" trivname="E2K">
  62     <DNA number="1" start="4" end="4" length="1" isMutation="1">
  63         <label>point</label>
  64         <label>transition</label>
  65         <proof>computed</proof>
  66         <upFlank>gaagattcagccaagctcaaggatg</upFlank>
  67         <allele_ori>g</allele_ori>
  68         <allele_mut>a</allele_mut>
  69         <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
  70         <restriction_changes>-BccI</restriction_changes>
  71     </DNA>
  72     <RNA number="1" start="4" end="4" length="1" isMutation="1">
  73         <label>missense</label>
  74         <proof>experimental</proof>
  75         <upFlank>gaagattcagccaagctcaaggatg</upFlank>
  76         <allele_ori>g</allele_ori>
  77         <allele_mut>a</allele_mut>
  78         <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
  79         <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
  80         <restriction_changes>-BccI</restriction_changes>
  81         <region>coding</region>
  82     </RNA>
  83     <AA number="1" start="2" end="2" length="1" isMutation="1">
  84         <label>substitution</label>
  85         <label>conservative</label>
  86         <proof>computed</proof>
  87         <allele_ori>E</allele_ori>
  88         <allele_mut>K</allele_mut>
  89     </AA>
  90 </seqDiff>
  91
  92 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100delATCCAG" trivname="I34del-2">
  93     <DNA number="1" start="100" end="105" length="6" isMutation="1">
  94         <label>deletion</label>
  95         <proof>computed</proof>
  96         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
  97         <allele_ori>atccag</allele_ori>
  98         <allele_mut></allele_mut>
  99         <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
 100         <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
 101     </DNA>
 102     <RNA number="1" start="100" end="105" length="6" isMutation="1">
 103         <label>inframe</label>
 104         <label>deletion</label>
 105         <proof>experimental</proof>
 106         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
 107         <allele_ori>atccag</allele_ori>
 108         <allele_mut></allele_mut>
 109         <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
 110         <codon codon_ori="atc" codon_pos="1"></codon>
 111         <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
 112         <region>coding</region>
 113     </RNA>
 114     <AA number="1" start="34" end="35" length="2" isMutation="1">
 115         <label>deletion</label>
 116         <proof>computed</proof>
 117         <allele_ori>IQ</allele_ori>
 118         <allele_mut></allele_mut>
 119     </AA>
 120 </seqDiff>
 121
 122 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101delT" trivname="I34delX172">
 123     <DNA number="1" start="101" end="101" length="1" isMutation="1">
 124         <label>deletion</label>
 125         <proof>computed</proof>
 126         <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
 127         <allele_ori>t</allele_ori>
 128         <allele_mut></allele_mut>
 129         <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
 130         <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
 131     </DNA>
 132     <RNA number="1" start="101" end="101" length="1" isMutation="1">
 133         <label>frameshift</label>
 134         <label>deletion</label>
 135         <proof>experimental</proof>
 136         <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
 137         <allele_ori>t</allele_ori>
 138         <allele_mut></allele_mut>
 139         <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
 140         <codon codon_ori="atc" codon_pos="2"></codon>
 141         <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
 142         <region>coding</region>
 143     </RNA>
 144     <AA number="1" start="34" end="34" length="1" isMutation="1">
 145         <label>out-of-frame translation</label>
 146         <label>truncation</label>
 147         <proof>computed</proof>
 148         <allele_ori>I</allele_ori>
 149         <allele_mut>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*</allele_mut>
 150     </AA>
 151 </seqDiff>
 152
 153 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101insGGGCCC" trivname="I34ins+2">
 154     <DNA number="1" start="101" end="101" length="0" isMutation="1">
 155         <label>insertion</label>
 156         <proof>computed</proof>
 157         <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
 158         <allele_ori></allele_ori>
 159         <allele_mut>gggccc</allele_mut>
 160         <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
 161         <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
 162     </DNA>
 163     <RNA number="1" start="101" end="101" length="0" isMutation="1">
 164         <label>inframe</label>
 165         <label>insertion</label>
 166         <proof>experimental</proof>
 167         <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
 168         <allele_ori></allele_ori>
 169         <allele_mut>gggccc</allele_mut>
 170         <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
 171         <codon codon_ori="atc" codon_pos="2"></codon>
 172         <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
 173         <region>coding</region>
 174     </RNA>
 175     <AA number="1" start="34" end="34" length="1" isMutation="1">
 176         <label>insertion</label>
 177         <label>complex</label>
 178         <proof>computed</proof>
 179         <allele_ori>I</allele_ori>
 180         <allele_mut>RAL</allele_mut>
 181     </AA>
 182 </seqDiff>
 183
 184 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100insG" trivname="I34ins81X">
 185     <DNA number="1" start="100" end="100" length="0" isMutation="1">
 186         <label>insertion</label>
 187         <proof>computed</proof>
 188         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
 189         <allele_ori></allele_ori>
 190         <allele_mut>g</allele_mut>
 191         <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
 192         <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
 193     </DNA>
 194     <RNA number="1" start="100" end="100" length="0" isMutation="1">
 195         <label>frameshift</label>
 196         <label>insertion</label>
 197         <proof>experimental</proof>
 198         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
 199         <allele_ori></allele_ori>
 200         <allele_mut>g</allele_mut>
 201         <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
 202         <codon codon_ori="atc" codon_pos="1"></codon>
 203         <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
 204         <region>coding</region>
 205     </RNA>
 206     <AA number="1" start="34" end="34" length="1" isMutation="1">
 207         <label>out-of-frame translation</label>
 208         <label>truncation</label>
 209         <proof>computed</proof>
 210         <allele_ori>I</allele_ori>
 211         <allele_mut>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
 212     </AA>
 213 </seqDiff>
 214
 215 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100AT&gt;GGGCCC" trivname="I34ins82X">
 216     <DNA number="1" start="100" end="101" length="2" isMutation="1">
 217         <label>complex</label>
 218         <proof>computed</proof>
 219         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
 220         <allele_ori>at</allele_ori>
 221         <allele_mut>gggccc</allele_mut>
 222         <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
 223         <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
 224     </DNA>
 225     <RNA number="1" start="100" end="101" length="2" isMutation="1">
 226         <label>frameshift</label>
 227         <label>complex</label>
 228         <proof>experimental</proof>
 229         <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
 230         <allele_ori>at</allele_ori>
 231         <allele_mut>gggccc</allele_mut>
 232         <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
 233         <codon codon_ori="atc" codon_pos="1"></codon>
 234         <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
 235         <region>coding</region>
 236     </RNA>
 237     <AA number="1" start="34" end="34" length="1" isMutation="1">
 238         <label>out-of-frame translation</label>
 239         <label>truncation</label>
 240         <proof>computed</proof>
 241         <allele_ori>I</allele_ori>
 242         <allele_mut>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
 243     </AA>
 244 </seqDiff>
 245
 246 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.-1G&gt;A">
 247     <DNA number="1" start="-1" end="-1" length="1" isMutation="1">
 248         <label>point</label>
 249         <label>transition</label>
 250         <proof>computed</proof>
 251         <upFlank>ggtggaagattcagccaagctcaag</upFlank>
 252         <allele_ori>g</allele_ori>
 253         <allele_mut>a</allele_mut>
 254         <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
 255         <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
 256     </DNA>
 257     <RNA number="1" start="-1" end="-1" length="1" isMutation="1">
 258         <label>unknown</label>
 259         <proof>experimental</proof>
 260         <upFlank>ggtggaagattcagccaagctcaag</upFlank>
 261         <allele_ori>g</allele_ori>
 262         <allele_mut>a</allele_mut>
 263         <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
 264         <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
 265         <region>5'UTR</region>
 266     </RNA>
 267 </seqDiff>
 268
 269 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+2766T&gt;C">
 270     <DNA number="1" start="2766" end="2766" length="1" isMutation="1">
 271         <label>point</label>
 272         <label>transition</label>
 273         <proof>computed</proof>
 274         <upFlank>tctatttccacacccagtgaagcat</upFlank>
 275         <allele_ori>t</allele_ori>
 276         <allele_mut>c</allele_mut>
 277         <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
 278         <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
 279     </DNA>
 280     <RNA number="1" start="2766" end="2766" length="1" isMutation="1">
 281         <label>unknown</label>
 282         <proof>experimental</proof>
 283         <upFlank>tctatttccacacccagtgaagcat</upFlank>
 284         <allele_ori>t</allele_ori>
 285         <allele_mut>c</allele_mut>
 286         <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
 287         <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
 288         <region>3'UTR</region>
 289     </RNA>
 290 </seqDiff>
 291
 292 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+12165A&gt;G">
 293     <DNA number="1" start="12165" end="12165" length="1" isMutation="1">
 294         <label>point</label>
 295         <label>transition</label>
 296         <proof>experimental</proof>
 297         <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
 298         <allele_ori>a</allele_ori>
 299         <allele_mut>g</allele_mut>
 300         <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
 301         <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
 302         <region dist="1027">3'UTR</region>
 303     </DNA>
 304     <RNA number="1" start="2428" end="2428" length="1" isMutation="1">
 305         <label>unknown</label>
 306         <proof>computed</proof>
 307         <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
 308         <allele_ori>a</allele_ori>
 309         <allele_mut>g</allele_mut>
 310         <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
 311         <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
 312         <region dist="-1">3'UTR</region>
 313     </RNA>
 314 </seqDiff>
 315
 316 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+4G&gt;T" trivname="V2F">
 317     <DNA number="1" start="4" end="4" length="1" isMutation="1">
 318         <label>point</label>
 319         <label>transversion</label>
 320         <proof>computed</proof>
 321         <upFlank>gcagcactgcagagatttcatcatg</upFlank>
 322         <allele_ori>g</allele_ori>
 323         <allele_mut>t</allele_mut>
 324         <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
 325         <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
 326         <region value="1" dist="4">exon</region>
 327     </DNA>
 328     <RNA number="1" start="4" end="4" length="1" isMutation="1">
 329         <label>missense</label>
 330         <proof>experimental</proof>
 331         <upFlank>gcagcactgcagagatttcatcatg</upFlank>
 332         <allele_ori>g</allele_ori>
 333         <allele_mut>t</allele_mut>
 334         <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
 335         <codon codon_ori="gtc" codon_mut="ttc" codon_pos="1"></codon>
 336         <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
 337         <region>coding</region>
 338     </RNA>
 339     <AA number="1" start="2" end="2" length="1" isMutation="1">
 340         <label>substitution</label>
 341         <label>nonconservative</label>
 342         <proof>computed</proof>
 343         <allele_ori>V</allele_ori>
 344         <allele_mut>F</allele_mut>
 345     </AA>
 346 </seqDiff>
 347
 348 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+1168G&gt;T" trivname="D34Y">
 349     <DNA number="1" start="1168" end="1168" length="1" isMutation="1">
 350         <label>point</label>
 351         <label>transversion</label>
 352         <proof>computed</proof>
 353         <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
 354         <allele_ori>g</allele_ori>
 355         <allele_mut>t</allele_mut>
 356         <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
 357         <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
 358         <region value="1" dist="-29">exon</region>
 359     </DNA>
 360     <RNA number="1" start="100" end="100" length="1" isMutation="1">
 361         <label>missense</label>
 362         <proof>experimental</proof>
 363         <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
 364         <allele_ori>g</allele_ori>
 365         <allele_mut>t</allele_mut>
 366         <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
 367         <codon codon_ori="gac" codon_mut="tac" codon_pos="1"></codon>
 368         <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
 369         <region>coding</region>
 370     </RNA>
 371     <AA number="1" start="34" end="34" length="1" isMutation="1">
 372         <label>substitution</label>
 373         <label>nonconservative</label>
 374         <proof>computed</proof>
 375         <allele_ori>D</allele_ori>
 376         <allele_mut>Y</allele_mut>
 377     </AA>
 378 </seqDiff>
 379
 380 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.-4C&gt;G">
 381     <DNA number="1" start="-4" end="-4" length="1" isMutation="1">
 382         <label>point</label>
 383         <label>transversion</label>
 384         <proof>computed</proof>
 385         <upFlank>ggcaggggcagcactgcagagattt</upFlank>
 386         <allele_ori>c</allele_ori>
 387         <allele_mut>g</allele_mut>
 388         <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
 389         <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
 390         <region dist="-4">5'UTR</region>
 391     </DNA>
 392     <RNA number="1" start="-4" end="-4" length="1" isMutation="1">
 393         <label>unknown</label>
 394         <proof>experimental</proof>
 395         <upFlank>ggcaggggcagcactgcagagattt</upFlank>
 396         <allele_ori>c</allele_ori>
 397         <allele_mut>g</allele_mut>
 398         <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
 399         <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
 400         <region dist="31">5'UTR</region>
 401     </RNA>
 402 </seqDiff>