Overview of Help-Pages

SNP Analysis

Introduction

SNP Analysis compares the potential effects of single nucleotide polymorphism (SNP) associated with your sequence.

SNPs located in regulatory regions (promoters, UTRs) may have a significant influence on the expression level of a gene. For each SNP allele the transcription factor binding sites that are either deleted or generated by the nucleotide exchange are calculated. The analysis is based on MatInspector and Genomatix' library of matrix descriptions for transcription factor binding sites. MatInspector is started using default parameters.
Note: Effects of SNPs on transcription factor binding sites are available up to ElDorado 04-2019. Starting with ElDorado 04-2020, effects of SNPs on TF binding sites are no longer pre-computed as the results are very large. Individual SNPs can still be analyzed with SNPInspector for newly generated or deleted transcription factor binding sites.

If the SNP is located within the coding sequence of an exon, additionally the influence on the corresponding amino acid is determined. The analysis refers to the ORFs annotated in the RefSeq mRNA sequences.

If the SNP Analysis is started from the general ElDorado result page, the user is provided with information about all SNPs located in the selected sequence fragment. Accessing the SNP Analysis through the link in the "Annotation / Analysis" column of the "Annotation & Analysis" table lists only the results for the selected SNP.

Output

For each SNP found in the selected sequence fragment there is a link to dbSNP at the NCBI, and a list of known alleles listed in the result file. A '-' instead of a nucleotide (A,C,G,T) indicates a deletion. The SNP is localized to either a promoter, exon, intron, or UTR.

For nucleotide exchanges affecting the protein sequence the accession number of the corresponding RefSeq sequence, the position of the affected amino acid and the modified peptide sequence are shown. For transcription factor binding sites either lost or generated due to the nucleotide exchange the start and end position of the binding site, the strand specificity and the core and the matrix similarity are shown.

In this example the substitution of a guanine (G) at position 22905 by a cytosine (C) results in the exchange of a non polar glycine (G) by a basic arginine (R) at position 12 of the human G6PD protein. The transcription factor binding sites CP2F, HEN1, and AREB detected in this region are destroyed by the G to C substitution. On the other hand a transcription factor binding site for the EBOX family and two HIF sites are generated.