Difference between revisions of "Task 7: Research SNPs"

From Bioinformatikpedia
Line 67: Line 67:
   
 
{| class="colBasic2"
  
{| class="colBasic2"
−
! codon change || position in codon || aa change || codon number
 +
! accession number || codon change || aa change || codon codon number
 
|-
  
|-
−
| G -> C || 3 || Arg -> Ser || 6
 +
|CM032270 || AGGc-AGC || Arg-Ser || 6
 
|-
  
|-
−
| T -> G || 2 || Leu -> Trp || 46
 +
|CM091838 || TTG-TGG || Leu-Trp || 46
 
|-
  
|-
−
| || || ||
 +
|CM994469 || cGTG-ATG || Val-Met || 53
 
|-
  
|-
−
| || || ||
 +
|CM994470 || cGTG-ATG || Val-Met || 59
 
|-
  
|-
−
| || || ||
 +
|HM971246 || CATg-CAC || His-His || 63
 
|-
  
|-
−
| || || ||
 +
|CM960827 || tCAT-GAT || His-Asp || 63
 
|-
  
|-
−
| || || ||
 +
|CM990718 || gAGT-TGT || Ser-Cys || 65
 
|-
  
|-
−
| || || ||
 +
|CM033969 || tCGC-TGC || Arg-Cys || 66
 
|-
  
|-
−
| || || ||
 +
|CM020721 || cCGA-TGA || Arg-Term || 71
  +
|-
−  
  +
|CM990719 || aGGG-CGG || Gly-Arg || 93
−  
  +
|-
  +
|CM990720 || ATT-ACT || Ile-Thr || 105
  +
|-
  +
|CM990721 || CAAg-CAC || Gln-His || 127
  +
|-
  +
|CM091839 || aGAC-AAC || Asp-Asn || 129
  +
|-
  +
|CM091840 || TACg-TAG || Tyr-Term || 138
  +
|-
  +
|CM004810 || gGAG-CAG || Glu-Gln || 168
  +
|-
  +
|CM004106 || gGAG-TAG || Glu-Term || 168
  +
|-
  +
|CM004107 || TGG-TAG || Trp-Term || 169
  +
|-
  +
|CM015326 || GCC-GTC || Ala-Val || 176
  +
|-
  +
||CM081301 || CTG-CCG || Leu-Pro || 183
  +
|-
  +
|CM034097 || CGG-CAG || Arg-Gln || 224
  +
|-
  +
|CM101181 || cCAG-TAG || Gln-Term || 233
  +
|-
  +
|CM024530 || tGTA-TTA || Val-Leu || 272
  +
|-
  +
|CM994771 || aGAG-AAG || Glu-Lys || 277
  +
|-
  +
|CM960828 || TGC-TAC || Cys-Tyr || 282
  +
|-
  +
|CM004391 || TGC-TCC || Cys-Ser || 282
  +
|-
  +
|CM032271 || CAG-CCG || Gln-Pro || 283
  +
|-
  +
|HM030028 || GTG-GCG || Val-Ala || 295
  +
|-
  +
|CM990722 || AGG-ATG || Arg-Met || 330
 
|}
  
|}
  +
   
 
== dbSNP ==
  
== dbSNP ==

Revision as of 20:58, 23 June 2013

Lab journal Task 7

<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; width: 60%; }

.colBasic2 th,td { padding: 3px; border: 1px solid black; }

.colBasic2 td { text-align:left; }

/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff

maria's style blue: #adceff grey: #efefef

  • /

.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}

[edit] </css>

HGMD (The Human Gene Mutation Database)

The results for the HFE gene contain the following types of mutations:

mutation type definition number
missense, nonsense mutation that leads to a change of amino acid or a stop codon 28
splicing mutation that affects mRNA splicing 3
regulatory substitiution causing abnormal regulation 1
small deletion micro deletion (<= 20 bp) 4
small insertion micro insertions (<= 20 bp) 1
small indel micro indels (<= 20 bp) 0
gross deletion delition > 20 bp 2
gross insertions/duplications insertion > 20bp 0
complex rearrangments rearrangements of stretches of the DNA sequence 1
repeat variations differences in repeat length 0
  • total in public 40
  • non public 49
missense, nonsens mutations for HFE
accession number codon change aa change codon codon number
CM032270 AGGc-AGC Arg-Ser 6
CM091838 TTG-TGG Leu-Trp 46
CM994469 cGTG-ATG Val-Met 53
CM994470 cGTG-ATG Val-Met 59
HM971246 CATg-CAC His-His 63
CM960827 tCAT-GAT His-Asp 63
CM990718 gAGT-TGT Ser-Cys 65
CM033969 tCGC-TGC Arg-Cys 66
CM020721 cCGA-TGA Arg-Term 71
CM990719 aGGG-CGG Gly-Arg 93
CM990720 ATT-ACT Ile-Thr 105
CM990721 CAAg-CAC Gln-His 127
CM091839 aGAC-AAC Asp-Asn 129
CM091840 TACg-TAG Tyr-Term 138
CM004810 gGAG-CAG Glu-Gln 168
CM004106 gGAG-TAG Glu-Term 168
CM004107 TGG-TAG Trp-Term 169
CM015326 GCC-GTC Ala-Val 176
CM081301 CTG-CCG Leu-Pro 183
CM034097 CGG-CAG Arg-Gln 224
CM101181 cCAG-TAG Gln-Term 233
CM024530 tGTA-TTA Val-Leu 272
CM994771 aGAG-AAG Glu-Lys 277
CM960828 TGC-TAC Cys-Tyr 282
CM004391 TGC-TCC Cys-Ser 282
CM032271 CAG-CCG Gln-Pro 283
HM030028 GTG-GCG Val-Ala 295
CM990722 AGG-ATG Arg-Met 330


dbSNP

Results

synonymous SNPS in coding region of isoform 1 human and transcript variant 1

cluster ID MAF SNP allel residue codon position aa position
rs114758821 9E-4 G -> A Pro 3 7
rs147297176 5E-4 C -> T Phe 3 58
rs147426902 3.2E-3 T -> C His 3 63
rs62625342 5E-4 C -> T Ser 3 76
rs148480830 - C -> G Ala 3 162
rs182920795 5E-4 T -> A Pro 3 253
rs201310322 - C -> T Pro 3 292
rs114038675 5E-4 G -> A Glu 3 298
rs148632352 - T -> C Val 3 315
rs35201683 6.4E-3 C -> T Tyr 3 342


SNPdbe

Comparison of databases

database last update version what information where from # entries homo sapiens # s SNPs # ns SNPs # disease causing SNPs # SNPs in UTR total
HGMD 2013 2013
dbSNP 26.06.2012 Build 137 192,678,553 10 41 10 162 213
SNPdbe

Mutation map

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_7:_Research_SNPs&oldid=32850"